Abteilung Aquatische Ökologie

Seit etwa 10 Jahren ist die Quaggamuschel nun in der Schweiz. Sie ist eine der einflussreichsten invasiven Arten in unseren Seen, und sie ist auch zunehmend in den Medien als wichtiges Thema präsent. Trotz der grossen Aufmerksamkeit bleiben viele Fragen zur Quaggamuschel bis heute offen und eine praktikable Methode, die Muschel wieder loszuwerden, ist nicht in Sicht. Verschiedene Schweizer Gewässer sind aber bis heute verschont geblieben. Diese Gewässer gilt es nun so lange wie möglich zu bewahren.

1. Stream ecosystem functioning and community structure are influenced by local and catchment land use. In mosaic landscapes, agricultural activities can also affect leaf breakdown and detritivore assemblages in downstream forest reaches.
2. We evaluated the combined effects of upstream deforestation and the input of a nonnative crop species on leaf breakdown and associated invertebrate assemblages within forest reaches. We incubated the leaves of banana trees (Musa spp.) and the native tree species Miconia chartacea in eight streams under both single-species and mixed-species treatments. The studied reaches were located upstream of the deforested areas in half of the streams and downstream of the deforested areas in the second half. We tested whether (i) crop leaves influence the leaf breakdown of native leaves and leaf colonisation by aquatic invertebrates and (ii) whether upstream deforestation exacerbates the effects of crop leaves on these processes.
3. In both reach types, M. chartacea monocultures had the highest breakdown rate, followed by M. chartacea exposed in mixtures, Musa spp. exposed in mixtures, and Musa spp. monocultures. All leaf treatments decomposed more slowly in downstream forest reaches, with mass losses 17.8%–8.7% lower than the mass loss of M. chartacea monocultures in upstream forest reaches. The invertebrate richness and density, shredder density, and scraper density did not differ among leaf treatments or reach types. The abundances of collector-gatherers were positively correlated with the mass loss of M. chartacea and Musa spp. In the downstream forest reaches, the calamoceratid shredder Phylloicus and the hydropsychid collector-filterer Smicridea were positively correlated with overall leaf mass loss.
4. Our study showed that upstream deforestation may cause alterations in the taxa distributions of invertebrate assemblages with consequences on leaf breakdown rates in forest reaches. These effects however strongly depend on the characteristics of the leaves and of the detritivores (i.e., their identity).

Aim: Variation in thermal tolerances along environmental gradients is assumed to follow similar patterns across different biological scales, including within and between species, and across communities. However, this assumption has yet to be tested using comprehensive datasets collected through standardised methodologies.
Location: Southern Asia.
Time period: 2017–2019.
Major taxa studied: Ants, beetles, grasshoppers, and spiders.
Methods: We quantified the associations between thermal tolerance traits and elevation or temperature at three biological scales (community, broad taxonomic group, and species) along two distinct elevational transects in Southern Asia. In total, we measured thermal tolerances of over 15,000 individuals from 114 arthropod species belonging to four invertebrate taxa (ants, beetles, grasshoppers, and spiders). We compared the relationships at each scale using mixed-effects models.
Results: At the community scale, across all individuals of all species, we found a consistent decline in the values of three thermal tolerance traits (upper tolerance, lower tolerance, and tolerance breadth) with elevation along the Himalayan transect but an increase in the values of upper and lower tolerance along the Sulaiman transect. The relationships of thermal tolerance traits and elevation/temperature varied among the groups and species between the Himalayan and Sulaiman transects. This suggests that factors beyond elevation, including vegetation composition, microclimate, landscape features, and local adaptation, drive observed variation in thermal tolerance traits among and within species.
Conclusion: Our study highlights the interplay between thermal physiology and the environment across different habitats and biological scales. Our findings indicate that predicting biodiversity responses to environmental change based on thermal tolerance–environment relationships requires careful consideration of group- and species-level variation. This is essential for improving the accuracy of climate change impact assessments on biodiversity.

The rise of anthelmintic-resistant strains in livestock threatens both animal and human health. Understanding the factors influencing anthelmintic resistance is crucial to mitigate the threat posed by these parasites. Due to difficulties in studying parasitic worms in the laboratory, the non-parasitic nematode Caenorhabditis elegans is used as a model organism to investigate anthelmintic resistance evolution. However, the suitability of this free-living nematode as a model for parasitic worms is debatable due to its rare androdioecious reproductive system, raising questions about the generalizability of findings from evolutionary experiments in C. elegans to other species. In this study, we developed a polygenic, population genetic model combined with pharmacodynamic approaches to investigate the effects of reproductive strategy and other aspects, such as dominance, mutational effects, the number of loci and population size, on determining the dynamics and outcome of evolutionary processes. We found that androdioecious populations showed both rapid initial adaptation typical for hermaphrodites and tolerance to high drug concentrations observed in dioecious populations. They also exhibited the highest diversity and shortest time for the fixation of the beneficial allele. These results suggest that androdioecious populations can harness the advantages of both selfing and outcrossing, optimizing their reproductive strategy in response to drug selection.

• Humans are driving biodiversity change, which also alters community functional traits. However, how changes in the functional traits of the community alter ecosystem functions—especially belowground—remains an important gap in our understanding of the consequences of biodiversity change.
• We test hypotheses for how the root traits of the root economics space (composed of the collaboration and conservation gradients) are associated with proxies for ecosystem functioning across grassland and forest ecosystems in both observational and experimental datasets from 810 plant communities. First, we assessed whether community-weighted means of the root economics space traits adhered to the same trade-offs as species-level root traits. Then, we examined the relationships between community-weighted mean root traits and aboveground biomass production, root standing biomass, soil fauna biomass, soil microbial biomass, decomposition of standard and plot-specific material, ammonification, nitrification, phosphatase activity, and drought resistance.
• We found evidence for a community collaboration gradient but not for a community conservation gradient. Yet, links between community root traits and ecosystem functions were more common than we expected, especially for aboveground biomass, microbial biomass, and decomposition.
• These findings suggest that changes in species composition, which alter root trait means, will in turn affect critical ecosystem functions.

Plant–animal interactions (PAIs) are critical in natural and agricultural ecosystems, mediating energy flow with both positive and negative interactions. Traditional methods of tracking PAIs, such as morphological identification and camera trapping, are limited in speed and scalability, posing challenges for comprehensive biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding has emerged as a promising technique for detecting species interactions non-destructively. This pilot study explores the application of eDNA metabarcoding to investigate frugivorous interactions involving 18 partially consumed and three intact fruits of each Carica papaya and Ananas comosus. Metabarcoding of mitochondrial COI gene fragments generated 796,234 paired-end reads representing 117 ASVs spanning diverse taxonomic groups, including Metazoans, Protozoans, Algae, Fungi, and Bacteria. After filtering for animal taxa, 41 ASVs were retained, dominated by Arthropoda (~97%). Major frugivores included Drosophila, Zaprionus, and Bactrocera species. Additional detections included beetles, ants, parasitoid wasps, and vertebrates such as Acridotheres javanicus, Callosciurus erythraeus, and Bandicota indica. Moreover, consumed fruits showed high insect (~90%–95%) and mammal (~4%–5%) DNA, while intact fruits were dominated by rotifers (~75%–80%). Distinct communities were found between pineapple and papaya, with 15 and 11 unique ASVs, respectively, and only one ASV was unique to intact fruits. Alpha and beta diversity analyses confirmed the differences in community structure between fruit types. Despite the limited sample size, our findings demonstrate the potential of fruit-surface eDNA to monitor frugivory and species interactions. Future studies should scale this approach across seasons and crop types to assess its potential in long-term biodiversity and pest management monitoring.

Der alpine Raum ist geprägt von oft komplexen geologischen und hydrogeologischen Verhältnissen, weist jedoch zugleich ein hohes geothermisches Potenzial auf, bedingt durch tektonische Strukturen und tiefreichende hydrothermale Strömungssysteme. Die Exploration geothermischer Ressourcen, insbesondere der Tiefengeothermie, ist jedoch mit zahlreichen Herausforderungen verbunden. Dazu zählen eine oft limitierte Datenverfügbarkeit, erhebliche Unsicherheiten hinsichtlich der geologischen Strukturen sowie der hydraulischen und thermischen Eigenschaften des Untergrunds ebenso wie administrative, ökologische und wirtschaftliche Risiken. Eine Bewertung geothermischer Potenziale (d. h. der Temperaturen und der Grundwasserfündigkeit) und der langfristigen Nachhaltigkeit beim Betrieb geothermischer Anlagen erfordert verlässliche Tools. Diese sollen insbesondere eine optimale Nutzung der wenigen verfügbaren Untergrunddaten über den tiefen Untergrund ermöglichen und die Integration der erzeugten Informationen in die Planung von Geothermieprojekten erleichtern. Der hier vorgestellte Modellierungsansatz für die hydrothermale Zirkulation im komplexen geologischen Untergrund des Oberwallis liefert grundlegende Informationen zu Grundwasserströmung (Fündigkeit) und Wärmetransport (Temperatur). Diese Ergebnisse stellen einen wichtigen Mehrwert für die Erstellung von Potenzialkarten dar, insbesondere im Rahmen von Play-Fairway-Analysen (PFA) und bei der Erarbeitung konsolidierter Planungsgrundlagen.

L'environnement alpin se caractérise par des conditions géologiques et hydrogéologiques souvent complexes, mais présente en même temps un potentiel géothermique élevé, en raison de la présence de structures tectoniques actives et de systèmes d'écoulement hydrothermal profonds. L'exploration des ressources géothermiques, en particulier en géothermie profonde, pose cependant de nombreux défis: une disponibilité souvent limitée des données, des incertitudes importantes concernant les structures géologiques, ainsi que leurs propriétés hydrauliques et thermiques du sous-sol, sans oublier les enjeux administratifs, environnementaux et économiques. L'évaluation du potentiel géothermique (c'està-dire des températures et de l'exploitabilité des eaux souterraines) ainsi que la détermination de la viabilité à long terme d'une centrale géothermique nécessitent des outils de modélisation fiables. Ceux ci doivent permettre une valorisation optimale des rares données disponibles du sous sol profond, tout en facilitant leur intégration dans la planification des projets géothermiques. La modélisation du flux hydrothermal à travers le sous-sol hétérogène du Haut-Valais présentée ici constitue une approche prometteuse pour fournir des informations de base précieuses sur l'écoulement des eaux souterraines (exploitabilité) et du transport de chaleur (température). Ces résultats constituent une valeur ajoutée importante pour l'établissement de cartes de potentiel, en particulier dans le cadre des analyses du type Play Fairway (PFA) et de l'élaboration de bases de planification consolidées.

Alpine landscapes are being rapidly transformed, being fueled by ongoing environmental change and glacial recession. Glacial recession has caused emergence of new stream channels as well as changes in the physico-chemistry of surface waters embedded in glaciated landscapes. Our research examined temporal changes in the physico-chemistry and macroinvertebrates during (1) the elongation of a glacial stream and (2) among different alpine lake networks (inlets, outlets, and downstream sites) over the last 24/25 years. The glacial stream study revealed rapid colonization of the emergent stream following deglaciation as well as colonization of previous sites by novel taxa (some from lower elevations). The water physico-chemical data revealed changes in the habitat template of sites over the study period, especially in respect to water temperature and turbidity. The lake network study also showed changes in macroinvertebrate assemblages over the observation period as well as differences on the basis of lake location and type. Here, lake outlet water temperatures increased more over time at northern than southern Alpine lakes. Further, kryal and rhithral lake outlets differed in response regarding water physico-chemistry and macroinvertebrate diversity. Both studies highlight the importance of monitoring alpine surface waters for better understanding of abiotic and biotic responses to landscape transformation resulting from ongoing and rapid environmental change, especially in relation to glacial recession.

Formally describing cryptic species is essential for conservation and protection purposes and to enable their use in environmental monitoring. The current scientific practice in many invertebrate groups requires assigning the original morphospecies name to a particular genetic lineage before formally describing the other lineages of the morphospecies and providing an exhaustive morphological characterization for each described lineage of the morphospecies. These practices considerably delay—and may even hinder—the scientific description of cryptic species. Furthermore, it may lead to confusion if the same name refers to both the entire morphospecies and a particular lineage. Here, we propose some recommendations to accelerate the description of cryptic species and avoid taxonomic confusion. They include assigning a new name to each lineage of the morphospecies without (necessarily) first obtaining DNA from the morphospecies holotype or paratype(s) or designating a neotype, providing a basic morphological diagnosis in the cryptic species descriptions, and systematically following the morphospecies names by 'sensu lato' or 'species group' when referring to the entire morphospecies and by 'sensu stricto' when referring to the original lineage. Our recommendations could contribute to rapidly increasing the proportion of scientifically described cryptic species and enhancing the consideration of cryptic species in ecological assessments and conservation/protection programmes.

In diesem Kapitel wird die Flora und Fauna der Gewässer auf der Seenplatte Macun besprochen, einschliesslich
Zooplankton, Kieselalgen, Makroinvertebraten und Fischen. Das Kapitel basiert auf der wissenschaftlichen
Beobachtung der Seen, Weiher, Tümpel und Bäche von Macun seit der Angliederung des Gebiets an den
Schweizerischen Nationalpark im Jahr 2000. Die präsentierten Daten sollen denjenigen, die sich für allgemeine
Ökologie interessieren, Hintergrundwissen über die Macun-Süsswasserorganismen bieten und hoffentlich
andere dazu inspirieren, sich eingehender mit bestimmten Gruppen und den Gruppen, die noch untersucht werden müssen, zu befassen.

In diesem Kapitel werden die wichtigsten Ergebnisse der Langzeitüberwachung der physikalischen und chemischen Eigenschaften von Oberflächengewässern (Seen, Weiher und Bäche) des Kars auf der Seenplatte Macun vorgestellt. Die Leser:innen sollten beachten, dass die Daten in den meisten Fällen aus Stichprobenmessungen stammen, die Ende Juli durchgeführt wurden, und dass die Aufzeichnungen relativ kurz sind, um langfristige klimabezogene Trends beurteilen zu können. Das bedeutet, dass Wetterbeziehungen in den präsentierten Daten am ausgeprägtesten sind. Es liegen kontinuierliche Aufzeichnungen der Wassertemperaturen von Flüssen respektive des Lai d'Immez in der Nähe der Mündung vor; Letztere wurden mittels einer sogenannten Exo-Sonde (Multiparameter-Wasserqualitätssonde) generiert. Die Ergebnisse zeigen die starken Beziehungen zwischen den Oberflächengewässern und Veränderungen der Landschaftseigenschaften auf der Seenplatte Macun. Sie liefern Hintergrunddaten für biotische Reaktionen, die in anderen Kapiteln des Buches erörtert werden.

1. As ecosystem engineers, Eurasian beavers (Castor fiber) modify aquatic and terrestrial ecosystems, which can benefit the biodiversity and community composition of plant and animal species. However, in contrast to aquatic taxa, beaver engineering impacts on terrestrial taxa, like bats, are so far largely overlooked. While it has been shown that bats prefer beaver-engineered ecosystems, the reason for this choice is poorly understood. We hypothesized that this preference may be associated with beaver-related changes in habitat characteristics and food availability.
2. To address this knowledge gap, we recorded bat species richness, activity and feeding activity in eight beaver-engineered ecosystems (pool) with paired control sites without beavers (control) along the same stream in Switzerland. In addition, we collected data on food availability (arthropods) with arthropod flight interception traps and characterized habitat suitability with deadwood volume and vegetation surveys, as well as assessing canopy heterogeneity based on different digital height models.
3. The nighly bat species richness increased from four to five species between control and pool sites. Bat activity increased 1.6 times and bat feeding activity 2.3 times in beaver-engineered systems compared to controls. These increases in richness and activity were explained by higher volumes of standing deadwood, higher canopy heterogeneity and higher arthropod abundance in beaver systems compared to controls.
4. Overall, the volume of standing deadwood, a critical resource for bat roosting and foraging, had a stronger effect on bat species richness than canopy heterogeneity or arthropod availability. Bat feeding guilds (short-, mid-, long-range echolocators) responded differently to beaver-engineered habitat changes, with edge-hunting mid-range species benefiting the most.
5. Our findings suggest that beaver engineering created structurally diverse habitats that supported a broader range of bat species. By modifying both habitat structure and prey abundance, beaver engineering affected bat activity, richness, and feeding activity directly and indirectly. These changes operated across aquatic–terrestrial boundaries, highlighting the cross-ecosystem influence and ecological complexity of ecosystem engineering.

Organismal abundance tends to decline with increasing body size. Metabolic theory links this size structure with energy use and productivity, postulating a size–abundance slope of −0.75 that is invariant across environments. We tested the robustness of this relationship across gradients of protist species richness (1–6 species), temperature (15°C–25°C) and time. Using replicated microcosms, we provide an empirical test of how temperature and biodiversity jointly shape the cross-community scaling relationship (CCSR). While our results support the expected slope of −0.75, we also found interactive effects showing the relationship is not invariant. Warming altered abundance scaling with size depending on richness; in high-richness communities, temperature favoured small protists, steepening the CCSR slope. These context-dependent responses emerged over time, suggesting a role of size-dependent species interactions in shaping responses to environmental change. Our findings demonstrate that cross-community size scaling is not fixed but shifts dynamically with ecological context.

Aim: Global change can impact the stability of biological communities by affecting species richness and synchrony. While most studies focus on terrestrial ecosystems, our research includes both terrestrial and aquatic realms. Previous works measure overall community synchrony as co-variation among co-occurring species, ignoring the tail dependence—when species fluctuate together at extreme abundance levels. We used community time-series data to test two hypotheses across realms: a positive relationship between diversity (richness) and stability, and a negative relationship between synchrony and stability. Additionally, we explored how tail-dependent synchrony contributes to variations in community stability.
Location: Global.
Time Period: 1923–2020.
Major Taxa Studied: 7 taxa across freshwater (fish, plants, invertebrates) and terrestrial (birds, plants, invertebrates, mammals) realms.
Methods: We synthesised 20+ years of species abundance/biomass data from 2668 communities across seven taxonomic groups. Using a variance-ratio approach and copula models, we measured overall and tail-dependent synchrony. Hierarchical linear mixed-effects models in a Bayesian framework were used to assess the effects of richness and both synchrony types on stability.
Results: We found a positive diversity–stability relationship in terrestrial but not in freshwater communities, with terrestrial stability being nearly three times higher. A negative synchrony –stability relationship was found in both realms. The best model explaining stability included realm differences, richness and both types of synchronies. For freshwater, only overall synchrony significantly impacted stability, while richness and both synchrony types were key predictors for terrestrial stability. Notably, the model overestimates terrestrial stability when tail-dependent synchrony is excluded.
Main Conclusions: Richness strongly enhanced terrestrial stability, offering the most extensive support for this relationship to date. In addition, tail-dependent synchrony provides key insights into stability differences across ecosystems. As extreme environmental events increase, incorporating tail-dependent synchrony in future stability studies is crucial.

Aquatic and terrestrial communities often co-occur at close distances, enabling biotic interactions across ecosystem boundaries. While such interactions in natural habitats contribute to complex, coupled food webs, their dynamics in engineered and fragmented urban habitats are hardly known. Using environmental DNA metabarcoding and a metaweb approach, we examined food web structure at 54 paired aquatic-terrestrial sites along an urbanisation gradient in Zurich, Switzerland. We found that urbanisation led to simpler, less connected, and more homogeneous food webs by replacing high-trophic-level predators with low-trophic-level basal consumers. This shift towards basal consumers, dependent on distinct aquatic or terrestrial basal resources, subsequently weakened the links between aquatic and terrestrial food webs. Conversely, enhancing habitat quantity and landscape connectivity bolstered predator diversity, promoting vertically diverse, connected, complex, and stable food webs. Our findings reveal that while urbanisation can disrupt aquatic-terrestrial food webs, careful urban habitat planning can enhance biodiversity and food web stability.

Robert Giacometti hat sich als Präsident der Gemeinde Lavin (1986–2000), als Vertreter für den Kreis Obtasna
im Grossen Rat des Kanton Graubünden (1997–2006), als Vize-Präsident (2001–2008) und als Präsident (2008–2015) der Eidgenössischen Nationalparkkommission stark für den Schweizerischen Nationalpark eingesetzt. Er ist in Lavin aufgewachsen und als Jäger und Fischer schon sein ganzes Leben auf der Seenplatte Macun unterwegs. Dieses Kapitel gibt mit Robert Giacomettis Erinnerungen einen kleinen Einblick in die Zeit, bevor Macun im Jahr 2000 in den Schweizerischen Nationalpark aufgenommen wurde. Robert Giacometti erzählt vom Drachen im Lai dal Dragun, von den menschlichen Aktivitäten auf Macun und der Eingliederung der Seenplatte in den Schweizerischen Nationalpark. Dieses Kapitel basiert auf Erinnerungen und Erzählungen von Robert Giacometti und wurde mit Unterstützung von Silvia Egler und Andres Grolimund geschrieben. Die Erzählform in der ersten Person Singular widerspiegelt Erinnerungen und Aussagen von Robert Giacometti.

Die Gründung des Schweizerischen Nationalparks im Jahr 1914 war eine Pionierleistung, deren Wichtigkeit nicht zu überschätzen ist. Er war der erste Nationalpark der Alpen und Mitteleuropas. Darauf darf die Schweiz stolz sein, auch wenn er bis heute leider der einzige Nationalpark des Landes geblieben ist. Von Anfang an diente er nicht nur dem konsequenten Schutz seiner einzigartigen Natur, sondern auch deren Erforschung. Diese wird von der Forschungskommission des Schweizerischen Nationalparks geleitet. Dank ihrer Ausrichtung auf langfristige
Beobachtungen liefert diese Forschung laufend wichtige Erkenntnisse, heutzutage besonders auch über die Auswirkungen des Klimawandels auf alpine Lebensräume und ihre Arten. [...]

Global demand for wood products is increasing forest harvest. One understudied consequence of logging is that it accelerates mobilization of dissolved organic matter (DOM) from soils to aquatic ecosystems where it is more easily rereleased to the atmosphere. Here, we tested how logging changed DOM in headwaters of hardwood-dominated catchments in northern Ontario, Canada. We applied a before-after-control-impact experiment across four catchments for 3 y and measured DOM monthly during ice-free seasons. DOM concentration in streams from logged catchments quadrupled, on average, only for the first 2 mo postharvest, but resulting changes to the molecular composition of DOM persisted for at least 2 y. Ultrahigh-resolution mass spectrometry revealed that DOM composition within logged streams became more available for microbial use and chemically diverse than in controls, with novel highly unsaturated polyphenols, carboxylic-rich alicyclic, and nitrogen-containing formulae. The molecular composition of stream DOM measured fortnightly postharvest was most similar to the DOM composition of surrounding soils, likely due to increased hydrological connectivity. Alongside carbon being more likely to be released into the atmosphere, we estimate that selective logging increased the total flux of dissolved organic carbon in streams by 6.4% of the carbon extracted as timber. Although these estimates are short-lived, they should affect the millions of hectares that are logged annually. Carbon accounting of forestry, including as a natural climate solution, must now consider the transport and fate of DOM from land into water.

Aim: Genetic diversity is key to the long-term maintenance and adaptability of species to changing environments. While for above-ground ecosystems, the monitoring and understanding of genetic diversity has advanced substantially, some less accessible ecosystems and their organisms have been largely overseen. This is particularly the case for groundwater organisms. It is not only difficult to collect sufficient genetic data to identify spatial patterns but they may also have been experiencing very different drivers to population size, occurrence, and genetic structure due to very limited dispersal capacity and persistence in areas extending glacial cycles.
Location: Switzerland.
Methods: Here, we use a unique and spatially highly resolved data set containing a representative collection of thousands of Niphargus amphipod individuals across Switzerland. We analysed the genetic structure of ~1300 individuals of five species within their contemporary distribution.
Results: We found a significantly higher diversity in karstic aquifers and a correlation between the genetic diversity of a species and the proportion of its distribution in the karst.
Main Conclusions: This identifies karstic ecosystems as specific targets for future conservation programmes but also indicates that these karstic areas could have been possible refugia of Pleistocene persistence. Being epicentres of genetic diversity, the protection of the karst is also central for the maintenance of groundwater organisms' adaptive potential to future climatic changes.

Indirect ecological interactions—where one species influences another via changes to a third species or the environment—are ubiquitous in natural communities but are rarely linked directly to rapid evolutionary change. Using large outdoor mesocosms, we show that terrestrial aphid herbivory on macrophytes (duckweed) cascades through species interaction networks to alter phytoplankton abundance and water chemistry, driving rapid adaptive evolution of the planktonic crustacean Daphnia magna. The aphid-herbivory-mediated changes in the aquatic community then benefited the aphids by enhancing their performance on duckweed. Our findings provide direct evidence that indirect ecological interactions in near-natural communities can drive rapid evolutionary changes and mediate ecoevolutionary interactions between seemingly independent organisms.

Environmental changes linked to urbanization influence wildlife health and may increase zoonotic risks. In this study, we examined the impact of urban stressors on the cellular immunity of two bat species, Nyctalus noctula and Eptesicus serotinus, along an urban-natural gradient in Eastern Ukraine. Using white blood cell (WBC) profiles as immunity markers, we found that N. noctula from urban and suburban habitats had significantly higher WBC counts, as well as lymphocyte and neutrophil proportions, compared to individuals from natural areas. Meanwhile, E. serotinus, a species more adapted to urban environments, exhibited lower neutrophil levels and a trend toward reduced neutrophil-to-lymphocyte ratios. These findings suggest species-specific immune responses to urban stressors, with potential implications for wildlife conservation and disease dynamics. Further research is needed to understand long-term physiological adaptations in urban-dwelling bats.

Freshwater ecosystems support a disproportionate share of global biodiversity. Freshwater macroinvertebrates are frequently used as bioindicators to assess the ecological status of streams and rivers. However, ongoing climate change is altering the compositions of these communities, highlighting the need for tools to detect climate-related shifts. We propose and evaluate an ecological index based on the SPEcies At Risk (SPEAR) approach to quantify the proportion of species that are sensitive to higher temperatures within Ephemeroptera, Plecoptera and Trichoptera communities. We calculated this index using six different data sources for thermal preferences: experimentally measured thermal tolerances, the mean temperature from global occurrence records (GBIF), preferred temperatures obtained from multivariate species distribution models (SDM), the central temperature tendency derived from Swiss monitoring data according to the KLIWA approach, and two different sources of expert knowledge from a curated trait database. For all sources, we designated the species comprising the lower 50th percentile of thermal preference values as sensitive and the upper half as insensitive to warmer temperatures. To evaluate the performance of the six versions of this SPEAR_temperature on a geographic scale, we leveraged data from two Swiss wide monitoring programs including samples from 570 sites for the period 2010–2022 and from 183 sites for 2018–2023. While all six versions recapitulated a declining proportion of sensitive species with increasing water temperature, the relation was strongest when using the KLIWA-based thermal preference classification. On average across all sites, we observed a significant decline of the SPEAR_temperature index over the 2010–2022 period, independent of the source for the classification. This is consistent with a signal of warming-related community turnover, or ‘thermophilisation’. These results indicate that the index is suitable to document temperature-associated variation in EPT communities over both time and space. The attempt to derive a similar SPEAR_temperature index for fish was not successful.

Motivation: Here, we make available a second version of the BioTIME database, which compiles records of abundance estimates for species in sample events of ecological assemblages through time. The updated version expands version 1.0 of the database by doubling the number of studies and includes substantial additional curation to the taxonomic accuracy of the records, as well as the metadata. Moreover, we now provide an R package (BioTIMEr) to facilitate use of the database. Main Types of Variables Included: The database is composed of one main data table containing the abundance records and 11 metadata tables. The data are organised in a hierarchy of scales where 11,989,233 records are nested in 1,603,067 sample events, from 553,253 sampling locations, which are nested in 708 studies. A study is defined as a sampling methodology applied to an assemblage for a minimum of 2 years. Spatial Location and Grain: Sampling locations in BioTIME are distributed across the planet, including marine, terrestrial and freshwater realms. Spatial grain size and extent vary across studies depending on sampling methodology. We recommend gridding of sampling locations into areas of consistent size. Time Period and Grain: The earliest time series in BioTIME start in 1874, and the most recent records are from 2023. Temporal grain and duration vary across studies. We recommend doing sample-level rarefaction to ensure consistent sampling effort through time before calculating any diversity metric. Major Taxa and Level of Measurement: The database includes any eukaryotic taxa, with a combined total of 56,400 taxa. Software Format: csv and. SQL.

Mountain building reorganizes drainage networks, influencing riverine biodiversity. Northern Italy offers a natural experiment in the impact of tectonic and geomorphic processes on aquatic species distribution. We combined geomorphic analysis with environmental DNA from rivers to assess the influence of tectonically driven drainage reorganization on genetic diversity, targeting an endemic fish species, Telestes muticellus (Risso et al., 1826, https://www.biodiversitylibrary.org/bibliography/58984). In the Northern Apennines, horizontal shortening and topographic advection in an orogenic wedge have been hypothesized as leading to river capture and drainage divide migration. In addition, slab rollback has produced a spatial transition from contraction to extension that is more pronounced from north to south, with normal faulting producing range-parallel drainage only in the southern regions. In contrast, the adjacent Ligurian Alps are a remnant of the Alpine orogen with little modern deformation. We found distinct zones of geomorphic characteristics from north to south, including divide asymmetry and frequency of range-parallel drainage. Analysis of DNA sequences shows cross-divide assemblage characteristics that correlate with the geomorphic zonation. In terms of directional measures of assemblage change, the Northern Apennines show higher values of overlap, gain, loss, turnover, and nestedness than those in the Ligurian Alps. Main drainage divide asymmetry correlates positively with genetic distance and gain, loss, and turnover of DNA sequences from Adriatic to Ligurian sites and negatively with overlap and nestedness. Since the species is confined to freshwater environments, tectonically driven drainage reorganization can explain its spatial genetic differentiation.

Genetic diversity is a fundamental aspect of biodiversity, yet it is rarely assessed and monitored in conservation practice. Unionid freshwater mussels exemplify the dramatic loss of biodiversity in freshwater ecosystems, yet genomic data for these ecologically important species remain scarce. Here, we conducted a high-resolution population genomics study of all Anodonta species in Switzerland, with a focus on two species with contrasting reproductive strategies. After generating draft genomes of the hermaphroditic Anodonta cygnea and the gonochoric Anodonta anatina, we performed whole-genome resequencing of 421 individuals collected in 31 localities. While A. anatina populations followed a metapopulation structure shaped by catchment areas, genetic diversity correlated positively with waterbody size, suggesting greater vulnerability in small ponds compared with large lakes. Inbreeding levels were low; however, effective population sizes were consistently below 100, indicating serious extinction risks. Strong divergence between A. anatina populations north and south of the Alps suggests a putative undescribed Anodonta species in the Ticino area. Furthermore, we detected hybridisation between A. cygnea and A. exulcerata, indicating genomic permeability between these species. In addition, genomic data suggested facultative selfing in A. cygnea, leading to a marked reduction in genetic diversity, increased population structure and inbreeding and a decline in effective population size compared to the outcrossing A. anatina. Our study underscores that reproductive strategy fundamentally shapes genetic indicators of biodiversity and influences extinction risk; conservation targets should therefore be adapted to the biology of the species of interest. To conclude, we advocate for integrating reproductive mode and genomic data into conservation planning to more accurately assess vulnerability and guide effective action.

Dreissena rostriformis bugensis and Dreissena polymorpha, collectively known as dreissenid mussels, were first documented in Lake Erie nearly 40 years ago and continue to strongly impact ecosystem structure and function. Recently, dreissenids have been recognized as the primary regulator of phosphorus dynamics in the Great Lakes, potentially reducing external phosphorus load management strategies. To evaluate the extent that dreissenids may modulate phosphorus dynamics and assess the effectiveness of external load management strategies, ecosystem models need to adequately represent spatial patterns of dreissenid biomass densities. Assessment of dreissenid populations in the Great Lakes are complicated by their vast size, as well as the heterogeneity and stochastic nature of critical physical variables that shape habitat suitability (e.g., depth, hypoxia, substrate type, and benthic shear stress). We used observations from a 2019 benthic survey and 10-fold cross validation to assess spatial prediction methods to create a spatially explicit data layer representing dreissenid biomass in Lake Erie, including inverse distance weighting, nearest neighbour, depth binned average, random forest, generalized linear, and general additive models. A random forest spatial prediction approach produced the best predictive surface for dreissenid biomass in Lake Erie. The estimated spatial pattern of dreissenid biomass may be used in nutrient modeling exercises across Lake Erie to improve estimates of dreissenid impacts on biogeochemistry and lower food web productivity. This work also provides insight for potential sampling design improvements for benthic surveys in future years that could help refine the predictive capacity of the developed spatial prediction framework.

Gewässerräume sind die Schnittstelle von Wasser und Land und von grosser ökologischer Bedeutung: als Lebensraum, Vernetzungskorridor und für Stoffkreisläufe verschiedenster Art. Doch nur wenn Gewässerräume gross genug, miteinander vernetzt und mit ausreichend Gehölzbestand bestückt sind, können sie ihr ökologisches Potenzial voll entfalten. Die gesetzlichen Vorgaben zur Ausgestaltung der Gewässerräume sind aus ökologischer Sicht als absolutes Minimum zu betrachten – umso wichtiger ist eine vollständige Umsetzung und Ausscheidung der Gewässerräume.

Anthropogenic land-cover changes are among the most pressing global threats to both aquatic and terrestrial ecosystems, jeopardizing biodiversity and the critical connections between these systems. Resource flows and trophic interactions intricately link aquatic and terrestrial ecosystems, with terrestrial-derived detritus playing a fundamental role in supporting aquatic food webs. These detrital inputs form essential cross-ecosystem linkages, underpinning key ecological processes and providing vital resources for aquatic communities. Yet, little research has focused on how land-cover changes cascade across this linkage. To better understand how land-cover changes in the watershed influence freshwater detrital food webs, we conducted a meta-analysis of field studies reporting the effects of vegetation changes on freshwater detrital consumers and organic matter decomposition. The results from 144 studies, reporting 1235 comparisons, showed that, overall, land-cover changes in the watershed vegetation, especially through harvest and land-use conversion, have negative effects on aquatic biodiversity and ecosystem processes. These vegetation changes reduced diversity, abundance, and biomass across multiple trophic levels in freshwater detrital food webs. Studies examining multiple organism groups most often observed negative responses across multiple trophic levels, suggesting that these land-cover changes negatively affected multiple detrital food-web components simultaneously. Our results also show that outcomes of restoration of watershed vegetation were context-dependent, and no clear trend of improvement was visible. Therefore, conservation of natural riparian and catchment vegetation is key to maintaining freshwater ecosystem processes and aquatic biodiversity worldwide, and more efficient and evidence-based restoration measures are urgently needed. As our global synthesis shows that direct human-induced alterations of vegetation in watersheds have significant negative effects on freshwater detrital food webs, there is a pressing need to consider cross-ecosystem consequences of land-cover changes in conservation and ecosystem management.

Freshwater biodiversity is critically affected by human modifications of terrestrial land use and land cover (LULC). Yet, knowledge of the spatial extent and magnitude of LULC-aquatic biodiversity linkages is still surprisingly limited, impeding the implementation of optimal management strategies. Here, we compiled fish diversity data using environmental DNA (eDNA) sampling across a 160,000-km² subtropical river catchment in Thailand characterized by exceptional biodiversity yet intense anthropogenic alterations, and attributed fish species richness and community composition to contemporary terrestrial LULC across the catchment. We estimated a spatial range of LULC effects extending up to about 20 km upstream from sampling sites, and explained nearly 60% of the variance in the observed species richness, associated with major LULC categories including croplands, forest, and urban areas. We find that integrating both the spatial range and magnitude of LULC effects is needed to accurately predict fish species richness. Further, projected LULC changes showcase future gains and losses of fish species richness across the river network and offer a scalable basis for riverine biodiversity conservation and land management, allowing for potential mitigation of biodiversity loss in highly diverse yet data-deficient tropical to sub-tropical riverine habitats.

Healthy ecosystems are critical for maintaining ecosystem services and water security; yet many freshwater ecosystems have been subject to environmental degradation. Impacts are often greatest in water-scarce and developing regions, including across much of Sub-Saharan Africa, where many people lack access to basic drinking water. However, environmental monitoring programmes to track ecosystem health are generally lacking across this region due to limited resources and funding. Recent advances in environmental DNA (eDNA) methods offer an increasingly cost-effective and information-rich solution. Here, we explore the potential of eDNA as a tool for ecological monitoring of freshwater ecosystems in Uganda, East Africa. We sampled eDNA to quantify the bacterial diversity of rivers, streams, and swamps across a gradient of human disturbance in and around Kibale National Park, using off-the-shelf sampling methods that require minimal pre-existing infrastructure. We found distinct bacterial communities between intact and degraded habitats, but the bacterial community in rivers converged when flowing through intact forest. We identified several taxa with differential abundances that might serve as potential bioindicators of degraded ecosystems, and showed that a machine learning tool trained on eDNA can accurately differentiate between intact and degraded habitats. Our proof-of-concept study demonstrates the potential of eDNA as a practical and cost-effective biomonitoring tool for freshwater ecosystems in resource-limited regions, including Sub-Saharan Africa. We also highlight the potential benefits of protected forest in modulating bacterial composition in freshwater ecosystems.

As natural ecosystems face unprecedented human-made degradation, it is urgent to provide quantitative forecasts of changes in biodiversity and identify relevant biotic and abiotic predictors. Forecasting natural ecosystems has proven challenging owing to their complexity, chaotic nonlinear nature and lack of adequate data. In this study, we investigate the predictability of lake plankton biodiversity using four years of daily data of environmental predictors and community metrics derived from state-dependent models. Our findings show that presence- and absence-based biodiversity metrics are more predictable than abundance-based metrics. For short-term forecasts, the most significant predictor of species richness is prior richness, while the key predictors for Jaccard dissimilarity are prior richness and prior Jaccard dissimilarity. In long-term forecasts of both metrics, water temperature emerges as the primary predictor, with community connectance (number of interactions) also contributing to improved predictions. We found that richness, connectance and water temperature can interact in nonlinear and synergistic ways depending on the forecast horizon, enhancing each other's effects on richness and Jaccard dissimilarity. These results underscore the challenges of forecasting biodiversity in natural ecosystems and highlight the importance of monitoring key community metrics and abiotic predictors to anticipate long-term changes.

Our knowledge of biogeographic patterns and processes in the deep sea has been limited by the lack of integrated datasets that cover its vast extent¹. Here we analyse a new global dataset of genomic DNA sequences, spanning an entire taxonomic class of benthic invertebrates (Ophiuroidea), to obtain a broad understanding of phylogenetic divergence and biotic movement across all oceans, from coastal margins down to the abyssal plains. We show that regional faunas on the continental shelf are phylogenetically divergent, particularly at temperate and tropical latitudes. By contrast, assemblages in the deep sea are much more connected. Many temperate deep-sea lineages have achieved distribution ranges across the planet, including over the Quaternary period. A close relationship exists between deep-sea faunas of the northern Atlantic and, on the opposite side of the globe, southern Australia. Bathymetric interchange is not only reliant on vertical migration through isothermal polar waters but also occurs across the thermal depth gradients of tropical regions. The connected nature of deep-sea life should be an important consideration in marine conservation assessments.

Deciphering dissolved organic matter (DOM) molecular complexity is crucial for understanding ecosystem function. Using the continental-scale Worldwide Hydrobiogeochemistry Observation Network for Dynamic Rivers Systems (WHONDRS) Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) dataset, we reveal fundamental scaling patterns of DOM chemodiversity with watershed characteristics. Analysis of 54 river sites shows local and regional watershed features significantly influence DOM chemodiversity (2500–8718 unique formulae), exhibiting consistent scaling patterns across compound classes and a novel latitudinal gradient (decreasing diversity with increasing latitude). Scaling relationships for DOM composition vary by compound class. Crucially, the scaling parameters (B, baseline chemodiversity; Z, sensitivity) are linearly interrelated. This B–Z relationship is most robust for potentially bio-labile carbohydrates (coefficient of determination R² ≈ 0.85), diminishing for recalcitrant, plant-derived molecules (such as lignin), and indicates (potential) biolability-dependent coupling between baseline diversity and environmental responsiveness. These quantitative scaling relationships, with scaling exponents ranging from − 2.1 to 2.2 across compound classes, enable prediction of DOM composition across watersheds, offering a framework to understand ecosystem responses to environmental change. This research bridges biogeochemistry and ecology, providing tools to anticipate molecular transformations across scales.

Parasitoids are important natural enemies of insects, imposing strong selection for the evolution of resistance. In aphids, the heritable endosymbiont Hamiltonella defensa is a key determinant of resistance, making symbiont-conferred defence a potential target for specific adaptation by parasitoids. We tested this hypothesis in the aphid parasitoid Lysiphlebus fabarum and four of its host species, Aphis fabae fabae, A. hederae, A. urticata, and A. ruborum. The parasitoids show host-associated genetic differentiation indicative of host specialization, and each of these aphid species harbours their own 1–3 distinct strains of H. defensa. We introduced eight H. defensa strains from all four aphid species into a common host background (a laboratory strain of symbiont-free A. fabae fabae) and then tested the ability of 35 field-collected L. fabarum lines from the same four hosts to parasitize the H. defensa-carrying aphids. The origin of symbionts affected parasitism success, with strains from A. fabae fabae and A. hederae conferring strong protection, and strains from A. urticata and A. ruborum providing virtually no protection. For one strain each from A. fabae fabae and A. hederae, we found a signature of specific adaptation by parasitoids, as parasitoids able to overcome their protection mostly came from the same hosts as the symbiont strains. Two other strains were so strongly protective that they permitted very little parasitism independent of where parasitoids came from. While not fully conclusive, these results are consistent with specialized parasitoids adapting to certain defensive symbionts of their host species, supporting the notion of symbiont-mediated coevolution.

Recent research has shown that climate change can both induce and modulate the expression of plastic traits but our understanding of the role of phenotypic plasticity as an adaptive response to climate change is limited. In this review, we dissect the mechanisms and impact of phenotypic plasticity as a response to accumulating climatic pressures on the individual, species and community levels. (i) We discuss how plasticity can affect individuals, populations and community dynamics and how climate change can alter the role of plasticity. We hypothesise that some pathways to phenotypic plasticity such as irreversible and anticipatory organismal responses will be reduced under increasing climate change. (ii) We then propose an integrated conceptual framework for studying phenotypic plasticity to advance our understanding of the feedbacks between the different levels of biological organisation. (iii) By formulating as yet unaddressed research questions within and across levels of biological organisation, we aim to instigate new research on phenotypic plasticity and its role in climate change responses.

The decomposition of leaf litter is a major ecological process in terrestrial and aquatic ecosystems worldwide. Leaf litter generally enters ecosystems in annual pulses and is subsequently decomposed across many seasons. Yet investigations into this process are rarely conducted in parallel in aquatic and terrestrial ecosystems and over the full year, limiting our understanding of its phenological context across the blue-green interface. Here, we assessed the decomposition of three litter species by microorganisms and macroinvertebrates in temperate streams and forests across a year using repeated litterbag assays at 6-week intervals. We observed higher decomposition rates in summer in most combinations of ecosystem, litter species, and decomposer type, indicating positive effects of higher temperatures and low standing crops of labile litter. Furthermore, forests showed lower decomposition rates than streams. Last, we found that the relative litter species effects on both microbial and invertebrate decomposition were consistent across environments, suggesting that the fast microbial activity decreased the quality of the remaining tissue mass for invertebrates. Overall, our work places known drivers of the decomposition of leaf litter into a phenological context, providing evidence that changes in the timing or strength of these drivers could drive temporal shifts of this central ecological process.

Inferring coexistence metrics, such as niche and fitness differences, in changing environments is key for understanding the mechanism behind species coexistence and predicting its likelihood. However, it first requires estimating the per capita interactions between organisms and their intrinsic growth rates-parameters that are typically measured by isolating organisms from their natural context. Here, we first use weighted multivariate regression on the per capita growth rates of populations to estimate these key ecological parameters directly from time-series data of species-rich communities. Second, we infer niche differences and species resistance, which are two important metrics for understanding species coexistence. Our approach allows these metrics to vary over time and under different environmental conditions. We validate our approach using synthetic data and apply it to both experimental and observational data as a proof of concept. Experimental results show an expected allocative trade-off between grazing resistance and rapid growth in algae. Moreover, coexistence likelihood decreases, and coexistence balance is disturbed under stressful environmental conditions. Observational data suggests variations in intrinsic growth rates and per capita interactions among autotrophic guilds with respect to seasonal patterns. In addition, interactions between cyanobacteria with green algae and chrysophytes might indicate a potential cause for bloom development. Our approach offers a powerful toolbox to gain insight into the mechanisms underlying ecological dynamics, species coexistence, and community structures under varying environments. Such an understanding will help us address important ecological and evolutionary questions, such as explaining biodiversity patterns and solving the problem of cyanobacteria bloom.

Green roofs are increasingly promoted to support urban biodiversity, potentially mitigating habitat loss from urban growth. Given their standardized design, however, green roofs are expected to differ ecologically from the ground-level habitats they are intended to substitute. Yet the extent of this divergence remains unclear, especially for taxa with varying dispersal abilities, including low-mobility invertebrates that are less often associated with green roofs. To quantify this divergence, we used environmental DNA metabarcoding to assess invertebrate diversity and identify environmental drivers affecting species with different dispersal abilities across 52 pairs of extensive green roof and ground-level sites in Zurich, Switzerland. We found that green roofs shared around 10 % of species with ground-level sites, regardless of how spatially isolated they were. Instead, green roofs harbored unique communities, albeit marginally poorer in number of species. However, this pattern varied by species mobility, with soil-dwelling species forming more heterogeneous communities, likely due to dispersal limitations between roofs. Additionally, green roof design choices, including substrate type and depth, as well as vegetation cover, emerged as key drivers of species richness, regardless of species dispersal abilities. Although green roofs do not structurally or ecologically replicate the ground-level habitats they would substitute, they provide complementary habitats that enhance urban biodiversity when designed with ecological considerations. While further research is required to evaluate the capacity of green roofs to sustain viable populations despite their spatial isolation, this study highlights practical design interventions, such as deepening the substrate, to improve their role as complementary habitats in cities.

Biotic interactions and environmental changes due to increasing water temperatures, nutrient enrichment, and other factors can affect species diversity, abundance, and distribution. Lake Superior is the deepest and one of the most oligotrophic lakes in the Laurentian Great Lakes system. While considered the least affected by cultural eutrophication, Lake Superior is among the world's fastest-warming freshwater bodies, having already exhibited resulting physical and ecological changes over the past three decades. We used data from current and historical surveys to identify spatial patterns and provide an assessment of the status and temporal trends of the Lake Superior benthic community over the last 50 years. Our study indicated that the dominance structure of the community remained quite stable, with the highest proportion of community comprised by the deepwater amphipod Diporeia hoyi, followed by Oligochaeta, Sphaeriidae, and Chironomidae. Benthic community structure differed spatially, with higher species diversity found in the shallow zone (≤30 m), the highest Diporeia densities at intermediate depth zones (30–50 and 50–90 m), and the lowest densities of all taxa in the deepest zone (>90 m). Lakewide benthos densities increased in the 1990s–2000s, most likely due to reduced fish predation, but are now stabilized. Although current benthos densities are still higher than in the 1970s, nearshore surveys indicated declines in Diporeia and other major taxa in the last decade. These changes may indicate a return to levels observed in the 1970s or reflect a long-term trend of decline in populations, reinforcing the importance of frequent monitoring that could foretell lakewide changes.

Understanding the robustness of ecological networks against sustained species losses is paramount to devising effective biodiversity conservation strategies. To explore the impacts of species losses on network robustness (the capacity of food webs to withstand primary extinctions), we used a trophic metaweb of 7808 vertebrates, invertebrates and plants and 281,023 interactions across Switzerland. We inferred twelve regional multi-habitat food webs and simulated non-random species extinction scenarios on these webs, focusing on broad habitat types and regional species abundances. Here, we show that targeted removal of species associated with specific habitat types, particularly wetlands, resulted in greater network fragmentation and accelerated network collapse compared to random species removals. Networks were more vulnerable to the initial loss of common rather than rare species. These findings underscore the critical need for integrated conservation strategies maintaining a diverse mosaic of habitats in a landscape to mitigate the cascading effects of species loss. (Figure presented.)

Understanding how species interact within ecological networks is essential for predicting the consequences of environmental change, from trophic cascades to broader changes in species distributions and ecosystem functioning across large spatial scales. To facilitate such explorations, we constructed trophiCH: a country-level trophic meta-food web (henceforth “metaweb”) that includes vertebrates, invertebrates, and vascular plants within Switzerland, based on literature published between 1862 and 2023. Our comprehensive dataset catalogues 1,112,073 trophic interactions involving 23,151 species and 125 feeding guilds (e.g., fungivores). Thirty percent of species-level interactions were empirically documented. Additional species-level interactions were inferred by resolving coarser taxonomic records (e.g., inferring links from “species A feeds on genus B”) based on habitat co-occurrences. While explorations of large-scale food webs have often relied on modelling approaches due to data gaps, this empirically based metaweb paves the way for data-driven studies of real-world food webs across space and time. By integrating the metaweb with local species assemblages knowledge, future studies can gain insights into broad patterns of food web structure across spatial scales.

1. Advancements have been made in the use of DNA-based methods for the detection of single species. However, the routine application of DNA-based methods to monitor whole communities using a metabarcoding approach and derive ecosystem status continues to be limited.
2. We undertook a structured experiment to assess factors influencing the precision and accuracy of molecular methods for freshwater macroinvertebrate community assessment. Macroinvertebrates were sorted, identified and counted from kick-net samples using standard morphometric protocols, then reconstituted. These bulk specimen samples were then homogenised. From each bulk sample, aliquots of the homogenate were distributed among seven laboratories across Europe for DNA extraction, PCR amplification, library preparation and sequencing. Additionally, each laboratory was provided with a DNA extract from the bulk homogenate to allow for amplification through to sequencing, in order to assess the influence of DNA extraction. Hierarchical nested analyses were used to identify sources of uncertainty in the data and explore factors influencing the returned community and metrics of ecosystem quality. Furthermore, comparison with morphological analysis enabled us to benchmark molecular to traditional processing approaches.
3. Metrics derived by morphological and DNA-based methods differed substantially. The strongest methodological influences on variance in metrics derived from DNA-based methods were attributed to sequencing (read count per sample) and laboratory (strong variation within samples). Furthermore, the performance of the DNA-based method varied among samples, most likely due to differences in the composition of the invertebrate community. Logistic regression indicated that detectability did not vary among taxa, but that taxa occurring in low abundance (less than five individuals in our samples) were more likely to be missed via metabarcoding.
4. Our findings highlight sources of uncertainty influencing DNA-based methods and, particularly, the variability of results generated from individual laboratories. Our findings underline the need for clear guidelines, standardisation and quality assurance schemes.

Feuchte und nasse Wälder sind einzigartige Lebensräume, die besondere und schützenswerte Artengemeinschaften beherbergen. Die Schweiz weist insgesamt 21 Waldgesellschaften der Feucht-, Moor- und Auenwälder auf. In den letzten Jahrhunderten wurden die Feuchtwälder jedoch zu grossen Teilen durch Entwässerung zu Gunsten der Forst- und Landwirtschaft verändert oder gerodet. Im Rahmen der Biodiversitätsstrategie strebt die Schweiz eine Umkehr des Habitat- und Artenverlustes der feuchten und nassen Wälder durch deren Erhalt, Aufwertung und Wiederherstellung an. Im vorliegenden Dokument werden die wissenschaftlichen Grundlagen zur Wiederherstellung feuchter Wälder sowie Erkenntnisse aus der Praxis in Form eines Leitfadens zusammengefasst. Der Leitfaden beinhaltet die wichtigsten Argumente, die für eine Wiedervernässung von Wäldern sprechen, eine Synthese des Wissens über die charakteristischen Standorte, Waldgesellschaften und jeweiligen Arten der feuchten Wälder, sowie Details zu möglichen Massnahmen zu deren Wiederherstellung und Förderung. Fallbeispiele aus der Schweiz geben Einblicke in die praktische Umsetzung. Zusätzlich werden rechtliche, administrative und planerische Aspekte behandelt. Die folgenden Kurzzusammenfassungen geben einen Überblick über die wichtigsten Inhalte dieses Leitfadens. [...]

Intensive agricultural practices, including neonicotinoid insecticides, and climate change are two potential drivers of global insect decline, contributing to biodiversity loss. However, ecologically realistic field experiments investigating these multiple stressor effects on emerging aquatic insects are scarce. To empirically test whether exposure to imidacloprid (1, 10 μg/L) and two different climate change scenarios (i) elevated temperatures (+4 °C vs. ambient temperatures) and (ii) reoccurring heatwaves (+0 to 8 °C) may cause a decline in insect emergence, we conducted an outdoor mesocosm study. Aquatic insect communities were exposed to single and combined stressors, while emergence was monitored during a 3-month period. We report significant losses in insect biomass and abundance under single and combined treatments. The high imidacloprid treatment and elevated temperatures combined caused a significant 47% decline in total insect biomass across the insect orders Diptera, Ephemeroptera, Coleoptera, Hymenoptera, Hemiptera, Odonata, and Trichoptera. Community structure and population dynamics were significantly affected, with Diptera and Ephemeroptera being most sensitive to the high and both imidacloprid treatments, respectively. Diptera dominated but was significantly reduced by the high imidacloprid and heatwave combination. Temperature-enhanced imidacloprid toxicity and the significant threat these stressors pose to aquatic insect communities highlight the need for effective climate change mitigation strategies to conserve aquatic insect biodiversity.

1. Although temporary streams are a common feature of fluvial networks, the prevalence of flow intermittency of perennial streams, especially in alpine landscapes, has increased with climate change. The fluvial network of the alpine Val Roseg catchment in eastern Switzerland experiences ca. 80% surface flow contraction over an annual cycle. Our aim was to determine how repeated dry phases of different durations and frequencies influence organic resources and macroinvertebrate assemblages in a perennial stream in this catchment.
2. We conducted a field experiment in which replicated mesocosms experienced varying dry-phase durations (1 or 9 days) and frequencies (every 3, 7 or 15 days, respectively) comprising six treatments and a control (continuous flow). A fine-meshed net was installed midway across the experimental reach to limit drift to a downstream section of mesocosms to determine the contribution made by drift to recolonisation when flows resumed. The upstream section contained other mesocosms in which drift was not limited by the drift net. At the end of the experiment, we measured coarse particulate organic matter (CPOM), periphyton biomass and taxonomic and functional metrics as well as compositional attributes of macroinvertebrates in each mesocosm.
3. CPOM (leaves and larch needles), periphyton chlorophyll-a and macroinvertebrate abundance and taxon richness decreased with increasing dry-phase duration and frequency, whereas Shannon's diversity and taxon evenness increased. Metrics of functional richness and diversity also decreased with increasing dry-phase duration and frequency. Most macroinvertebrate metrics, and functional measures in particular, were lower in the drift-limited downstream section. Lastly, assemblage composition differed in mesocosms in relation to increasing dry-phase frequency (15 days and controls) in both sections.
4. We conclude that dry-phase duration and especially frequency are strong drivers of organic resources and macroinvertebrate assemblages in intermittent alpine streams. Levels of CPOM and periphyton chlorophyll-a were reduced with dry phases. Macroinvertebrates had low resistance to dry phases but had resilience traits that enabled rapid recolonisation once flow resumed. This study provides a mechanistic explanation of the observed spatial patterns of macroinvertebrate assemblages in alpine fluvial networks exposed to intermittent drying.

First records of the harvestman Lacinius dentiger (C. L. Koch, 1847) for Switzerland (Opiliones: Phalangiidae). − Until recently, the harvestman Lacinius dentiger had never been observed in Switzerland. This report presents the first national records of this species. Observations are documented by distribution maps, and the habitat and phenology are presented. Based on the results, the absence of historical records for this species in Switzerland are discussed.

Die Weberknechtart Lacinius dentiger wurde bisher in der Schweiz nicht nachgewiesen. In diesem Bericht werden die ersten nationalen Nachweise dieser Art vorgestellt. Diese Beobachtungen werden mit Verbreitungskarten dokumentiert und das Habitat und die Phänologie charakterisiert. Auf Basis der Ergebnisse wird diskutiert, warum Nachweise dieser Art bis jetzt in der Schweiz fehlten.

Premières mentions de l'Opilion Lacinius dentiger (C. L. Koch, 1847) en Suisse (Opiliones: Phalangiidae). − L'Opilion Lacinius dentiger n'avait jusqu'à présent jamais été signalé en Suisse. Cette note présente les premières observations dans le pays, documentées à l'aide de cartes de répartition, et décrit l'habitat ainsi que la phénologie de l'espèce. Les raisons pour lesquelles cette espèce n'avait jamais été signalée jusqu'à présent en Suisse sont discutées.

Prime segnalazioni dell'opilione Lacinius dentiger (C. L. Koch, 1847) per la Svizzera (Opiliones: Phalangiidae). − Lacinius dentiger non era finora mai stato segnalato in Svizzera. Questo rapporto presenta le prime osservazioni della specie a livello nazionale, documentate con mappe di distribuzione, e presenta la caratterizzazione dell’habitat e della fenologia. Sulla base dei risultati, vengono discusse le ragioni della mancanza di segnalazioni di questa specie in Svizzera.

Lachmöwen gehören zu den auffälligsten Wintergästen der Schweiz. Dabei nutzt die Lachmöwe für die Überwinterung wie kaum eine andere Vogelart auch urbane Lebensräume. Dies und die geringe Scheu vor dem Menschen machte die Lachmöwe seit dem Beginn der regelmässigen Beobachtungen in Städten im 19. und frühen 20. Jahrhundert zu einem beliebten Studienobjekt. Die vorliegende Untersuchung knüpft an frühere Studien an, wobei wir weitere Aspekte des Verhaltens im Winterquartier und Veränderungen über die Zeit dokumentieren. Wir haben im Raum Basel und Morges während neun Wintern 1361 Lachmöwenringe von 224 Individuen aus 21 Ländern abgelesen. Nachweise aus Brutkolonien kamen aus 17 dieser Länder, meist nordöstlicher Herkunft, schwerpunktmässig aus Polen und Tschechien. Bis zu 19 % der Überwinterer waren Jungvögel, mehr als zu Beginn des 20. Jahrhunderts. Die bei uns überwinternden Lachmöwen zeigten eine teilweise jahrelange Treue zum Winterquartier und selbst zum Tagesstandort. Über eine Saison konnten 77 % der Lachmöwen (n = 56) nur in einem Gebiet beobachtet werden, weitere 18 % in zwei Gebieten. Über die Jahre (n = 59) wurden 46 % der Lachmöwen nur an einem Tagesstandort beobachtet, weitere 34 % an maximal zwei. Dies legt nahe, dass sich Lachmöwen im Winter auf einen Futterplatz spezialisieren und diesem über Jahre treu bleiben.

Adaptive radiation (AR), a process of rapid speciation and ecomorphological diversification, played an important role in generating past and contemporary global biodiversity. An unsolved question is what maintains high rates of speciation during AR, a phenomenon we call the "speciation paradox."One possible explanation for resolving this paradox is a sequential trait evolution, i.e., a series of ecological diversifications, which enables evolving lineages to fully and more effectively exploit the ecological space. We tested this hypothesis using the highly diverse subterranean amphipod genus Niphargus. Niphargus shows distinct signatures of adaptive radiation both at the genus level and at the level of four larger clades. Our analysis revealed the decoupled evolution of habitat-related traits and trophic-biology-related traits. Moreover, on a genus level, we found evidence that AR commences with a tight association between speciation rates and the dynamics of habitat-related traits. At a later stage, speciation dynamics become associated with the diversification of trophic-biology-related traits. This suggests that the dependence of macroevolutionary rates in this group switches among niche axes before saturation, resulting in prolonged high speciation rates during AR.

Freshwater biodiversity has been decreasing globally, with wetland habitats facing significant loss due to climate change and changes in land use. In Switzerland, over 90 % of low-elevation wetland habitats have been lost since 1850, mainly due to land transformation for agriculture. Recently, farmers started cultivating paddy rice in Switzerland to meet the increasing food demand and to support wetland biodiversity, particularly dragonflies. However, rice is often produced at high fertiliser levels, raising concerns about potentially harmful effects of high nutrient levels on dragonflies developing in rice paddies. Here, we assessed the impacts of nitrogen fertilisers on dragonflies from a conservation perspective. We exposed three dragonfly species to mineral and organic fertilisers at different concentrations in experimental mesocosms mimicking rice paddies. The effects of fertilisation on survival as well as development time and size at emergence were quantified. In total, 77 % of all dragonfly larvae survived until emergence, and survival was not significantly affected by either fertiliser type at concentrations that are used in Swiss rice paddies (ranging from 25 kg N/ha to 150 kg N/ha). Also, there were no negative impacts of any fertiliser type and concentration on emergence time and body size, which albeit differed significantly among the three dragonfly species. The study thus provides valuable and encouraging insights for conservation and management strategies aimed at promoting wetland biodiversity, particularly the diverse and vulnerable dragonflies, through paddy rice cultivation.

In the Afrotropical Region, Sphyracephala beccarii (Rondani) and S. munroi Curran are found, the former just extending into the Palaearctic Region. In the latter region, S. babadjanidesi Zaitzev occurs in the Balkan and Caucasus Regions and S. nigrimana Loew in Far Eastern Russia and North-Eastern China. The European stalk-eyed fly S. europaea Papp & Földvári is proposed as junior synonym of the Eurasian stalk-eyed fly S. babadjanidesi. In North America S. brevicornis (Say) and S. subbifasciata Fitch occur. The four true Holarctic Sphyracephala are shown to reach their northern limits between 45°30'N and 48°20'N. These species hibernate and show characteristic clustering behaviour in spring and autumn. The four Palaearctic and Afrotropical Sphyracephala are redescribed and extensively illustrated. A key is given to all nine Sphyracephala presently recognised. The subdivisions within the genus are discussed. A cladogram, based on morphological, molecular, wing morphometric and allometric considerations, is presented. It shows the two species groups recognised. Each species group is divided into two subtaxa. Geometric morphometric analysis supports the grouping in four subtaxa as well as the synonymy of S. babadjanidesi and S. europaea. In Sphyracephala, both sexual monomorphism and dimorphism with relation to eye span occur. The allometric lines for males and females of eight species are compared. A clear link is found between allometric slopes and the four subtaxa distinguished. In Sphyracephala, female-biased, balanced, and male-biased sex ratios are found. A remarkable case of female-biased sex ratio distortion is reported for Sphyracephala beccarii. In Continental Africa and the Arabian Peninsula, a balanced sex ratio was found, while in Madagascar a female-biased 2:1 ratio was found. This represents the first case of a female-biased sex-ratio in a geographically isolated population of a monomorphic diopsid.

The spatial distribution of genetic diversity within a species' range reflects its past demographic history, and its knowledge is essential to better understand the limits of species ranges and to predict range shifts in response to a changing environment. We present GenDivRange, a unified dataset of published geo-referenced estimates of genetic diversity for 1,109 species, each represented by at least five populations placed on their range maps estimated from Global Biodiversity Information Facility (GBIF) observations. A total of 19,173 populations across the globe and from most major taxa, covering terrestrial, freshwater, and marine organisms, are included. At least one of the three genetic diversity estimates is available for each study: expected heterozygosity, Nei's gene diversity, or allelic richness, mostly estimated from microsatellite markers. Additionally, the dataset contains the detailed taxonomy, biome, breeding, and adult habitat of each species.

Global health is threatened by the rise of antibiotic resistance. Bacteria of the Mycobacterium tuberculosis complex (Mtbc) are a major contributor to this antibiotic crisis, with about 450,000 new multidrug-resistant tuberculosis (MDR-TB) cases per year. This study investigates resistance evolution by defining the resistance mutant selection window (MSW) for the important MDR-TB treatment drugs moxifloxacin and bedaquiline. We employed a combination of long-term in vitro experiments supplemented with mathematical modeling that combined pharmacodynamics with population genetics. We assessed resistance selection at concentrations below the minimum inhibitory concentration (MIC), the MSW and fitness cost of eight mutant clones with different resistance-associated variants. Both computational and experimental results show that mutant clone populations are selected far below the MIC, leading to a major growth advantage of resistant populations under weak selection pressure. An eighth of the MIC was enough to enrich mutant clone populations in the short term (five bacterial passages or 20 generations), even in mutant clones with a major competitive fitness loss. In fact, gyrA, gyrB and most Rv0678 mutations have virtually no effect on the bacteria's competitive fitness in vitro. This work highlights the risk that ineffective drug delivery and dosing can lead to the emergence of resistance.

Zooplankton-associated microbiomes play an important role for host health, and contribute to ecosystem processes such as nutrient cycling. Yet, few studies have assessed how environmental gradients and biotic interactions, including parasitism and diet, may shape the microbiome composition of wild zooplankton. Here, we analyzed the microbiomes of water fleas from the Daphnia longispina species complex using 16S rRNA gene sequencing and a long-term field dataset spanning six sampling events over 13 years. Sampling coincided with outbreaks of the virulent eukaryotic gut parasite Caullerya mesnili. Additionally, we explored how microbiome structure varied in relation to water parameters, phytoplankton density (i.e., Daphnia diet), and zooplankton density and community structure. Daphnia microbiomes displayed strong temporal variation and comparatively small differences based on host infection status. Microbiome beta diversity correlated with phytoplankton density but not with its community composition, including green algae, protists, and cyanobacteria. Environmental conditions, including temperature, dissolved oxygen, and cyanobacterial abundance—previously found to drive Caullerya epidemics—were also associated with distinct microbiome structures. Importantly, microbiome beta diversity co-varied with infection prevalence, suggesting a link between microbiome shifts, epidemic size, and environmental conditions driving large epidemics. Dominant bacterial taxa correlated with Daphnia density, whereas the phylogenetic composition of rare taxa was associated with total zooplankton density. These findings demonstrate the dynamic nature of Daphnia microbiomes and suggest potential mechanisms by which they may mediate disease dynamics, particularly through associations with diet quantity, temperature, and host population density.

Different organismal functional feeding groups (FFGs) are key components of aquatic food webs and are important for sustaining ecosystem functioning in riverine ecosystems. Their distribution and diversity are tightly associated with the surrounding terrestrial landscape through land-water linkages. Nevertheless, knowledge about the spatial extent and magnitude of these cross-ecosystem linkages within major FFGs still remains unclear. Here, we conducted an airborne imaging spectroscopy campaign and a systematic environmental DNA (eDNA) field sampling of river water in a 740-km² mountainous catchment, combined with light detection and ranging (LiDAR) point clouds, to obtain the spectral and morphological diversity of the terrestrial landscape and the diversity of major FFGs in rivers. We identified the scale of these linkages, ranging from a few hundred meters to more than 10 km, with collectors and filterers, shredders, and small invertebrate predators having local-scale associations, while invertebrate-eating fish, grazers, and scrapers have more landscape-scale associations. Among all major FFGs, shredders, grazers, and scrapers in the streams had the strongest association with surrounding terrestrial vegetation. Our research reveals the reference spatial scales at which major FFGs are linked to the surrounding terrestrial landscape, providing spatially explicit evidence of the cross-ecosystem linkages needed for conservation design and management.

Polyploidization is an important evolutionary force. It drives sympatric speciation through reproductive isolation of different cytotypes, and often leads to loss of sexual reproduction in polyploid lineages. Polyploidization and asexuality can change how other species engage in ecological interactions with the polyploid lineage and may change coevolutionary dynamics. Here, we quantified the phenotypic divergence in the freshwater oligochaete worm Lumbriculus variegatus, the California blackworm, among its co-occurring sexual diploid (Lineage II) and asexual polyploid (Lineage I) lineages. We further investigated variation in parasite communities and infection prevalence among sympatric and allopatric diploid/polyploid populations. 10 out of 18 populations showed co-existence of both lineages, with 7 populations harbouring only the polyploid lineage. Both worm lineages hosted endoparasitic nematodes, an ectoparasitic rotifer, and one potentially symbiotic gut ciliate. The parasite community similarity and overlapping size range of diploid and polyploid worms points to the ecological similarity of the worm lineages, despite the substantial ploidy and reproductive strategy differentiation. Although parasite prevalence varied independently of worm lineage, the prevalence was associated with the frequency of local cytotypes. Specifically, the rotifer prevalence was highest on the rare local cytotype, and nematode prevalence was highest on the common local cytotype. These results suggest the presence of both positive and negative frequency-dependent parasitism, which may contribute to the co-existence in the L. variegatus species complex.

1. Species distribution models (SDMs) relate species observations to mapped environmental variables to estimate the realized niche of species and predict their distribution. SDMs are key tools for projecting the impact of climate change on species and have been used in many biodiversity assessments. However, when fitted within spatial extents that do not encompass the whole species range (i.e. subrange), the estimated realized environmental niche can be truncated, which can lead to wrong or inaccurate predictions.
2. A simple solution to this niche truncation consists in fitting SDMs at a spatial extent that encompasses the whole species range, but this often implies using a spatial resolution too coarse for local conservation assessments. To keep a fine resolution, a solution is to fit spatially nested SDMs (N-SDMs), where a whole range, coarse-grain SDM is combined with a subrange, fine-grain SDM. N-SDMs have demonstrated superior performance to subrange (truncated) SDMs in projecting species distributions under climate change and have accordingly regained considerable interest.
3. Here, we review developments, applications and effectiveness of N-SDMs. We present and discuss existing methods and tools to fit N-SDMs, and assess when N-SDMs are not needed. We highlight strengths and weaknesses of N-SDMs, underline their importance in reducing niche truncation, and identify remaining challenges and future perspectives. Our review highlights that subrange SDMs most often lead to niche truncation and thus to incorrect spatial projections, a problem that can be overcome by using N-SDMs. We show that the various N-SDM methods come with their strengths and weaknesses and should be selected depending on the intended goal of the study.
4. Synthesis. N-SDMs are key tools to develop untruncated regional climate change forecasts of species distributions at fine resolution over restricted extent. While several N-SDM approaches were proposed, there is currently no universal solution suggesting that further developments and testing are crucial if we are to derive robust future projections of species distributions, at least until SDMs can be applied for most species at high resolution over large geographic extents.

Rising temperatures and an increasing frequency of extreme events, such as heatwaves pose major threats to ecosystems, impacting ectothermic organisms including fish. Elevated water temperatures, coupled with reduced oxygen levels, intensify stress and mortality among fish fauna, necessitating urgent action to address the impacts of heatwaves on biodiversity. Here, we propose to combine sub-seasonal to seasonal (S2S) forecasting methodologies with ecological modeling integrated with physiological parameters. Specifically, we developed a sub-seasonal forecast model designed to assess fish stress during heatwaves in Swiss rivers. We first compiled from the literature physiological parameters related to fish thermal stress to construct a thermal stress index. The developed model integrates deep-learning forecasts of water temperature with fish physiological data and species distribution modelling to offer a process-driven prediction of heat-stress responses. To validate its efficacy, we retrospectively applied the model to the 2018 heatwave across 20 measurement stations on lowland Swiss rivers, comparing its results with assessments from experts and practitioners. We found that the model successfully forecast stress peaks 2–3 weeks in advance at two validated key sites, where high mortality was reported by practitioners. By classifying fish species based on their thermal sensitivity, we identified a high vulnerability of salmonids. Applications of our model intend to alleviate climate change impacts, resulting in targeted actions to reduce local fish mortality.

La biodiversité macroscopique (visible à l'oeil nu) du Léman, le plus grand lac d'Europe occidentale, est particulièrement riche. Le déclin irréversible des anodontes vient toutefois nous alerter sur la fragilité de la faune et de la flore de ce magnifique écosystème.

Vertebrate activity can significantly affect forensic investigations. Trauma interpretation is impaired when vertebrates scavenge on injuries and inflict damage, and scavengers can hinder the recovery of human remains through dispersal. However, forensic scavenging research is scarce in Europe and lacking for Switzerland. We conducted a 2-month baseline study followed by a 5-month experiment with six domestic pig (Sus scrofa domesticus) carcasses in a Swiss forest during summer through fall. We monitored each three caged and uncaged carcasses with camera traps and documented vertebrate activities and taphonomic signatures on the remains and calculated the scavenging rate. Rodents (Apodemus sylvaticus, A. flavicollis, and Myodes glareolus) and red fox (Vulpes vulpes) scavenged and dispersed the remains. All carcasses and ca. 4% of the recovered bones exhibited scavenging marks, including wet bone scavenging (rodents) mainly on small bones and protruding features, and scoring (red fox) on a rib. The presence of a carcass, decomposition stage, sun exposure, and use of cages significantly influenced the number of vertebrate visits at the plots. Rodents preferentially scavenged caged, skeletonized remains at tree-covered plots and modified perimortem wounds beyond recognition. The few carnivore sightings focused on uncaged specimens. The generally low scavenger participation was likely season-related, due to the rapid maggot infestation, or human presence. Future studies should evaluate the influence of these variables, including sun exposure. Our study informs forensic casework by highlighting the importance of rodents and to a lesser degree foxes as vertebrate scavengers and dispersal agents in central European temperate forests.

Die schweizerischen Gewässer werden insbesondere im Winter und zur Zugzeit von Lachmöwen genutzt; ihr Gesamtbestand ist in Mitteleuropa und auch in der Schweiz rückläufig. Da die Lachmöwe tagsüber auch abseits der Gewässer nach Nahrung sucht, dürfte der Schweizer Winterbestand anhand der Ergebnisse der winterlichen Wasservogelzählung unterschätzt werden. Dies erschwert die Beurteilung der Bedeutung der Schweiz als Rast- und Winterquartier für diese Art. Synchrone Zählungen an Schlafplätzen sind zur Erfassung des Winterbestands vermutlich besser geeignet. Daher führten wir im Winter 2021 die erste schweizweit koordinierte Lachmöwen-Schlafplatzzählung durch. Insgesamt wurden dabei rund 39 000 Individuen erfasst, deutlich mehr als bei der kurz zuvor durchgeführten Wasservogelzählung mit rund 32 000 gezählten Lachmöwen. Somit beherbergt die Schweiz im Winter rund 1,5 % der westeuropäischen Lachmöwenpopulation. Zusätzliche Erhebungen zeigten, dass die Bestände am grössten schweizerischen Lachmöwenschlafplatz in Basel Mitte Winter am höchsten waren, während die Zahlen in Zürich gegen Februar/März noch etwas anstiegen. Letzteres könnte auf den Zuzug von weiter südwestlich überwinternden Individuen zurückzuführen sein.

This study presents a comprehensive dataset from Lake Greifen, Switzerland, collected between April 2018 and June 2023, using high-frequency automated monitoring systems. The dataset integrates meteorological data, nutrient chemistry, water column profiles for water physics, and plankton underwater imaging, offering insights into the lake's physical and biological processes. A dual-magnification dark field underwater microscope captured hourly plankton dynamics at 3 m depth, providing size, shape, and taxonomic information. A profiler with a multiparametric probe monitored water temperature, oxygen, and other key parameters from 1 to 17 m depth, while weekly nutrient sampling complemented the measurements. Data processing involved rigorous cleaning protocols to remove technical artefacts, ensuring data quality. Our dataset showcases the utility of integrating different approaches for high-frequency monitoring to detect lake temporal processes, from phytoplankton blooms to zooplankton vertical migration and seasonal shifts in water column stability. This dataset provides a unique resource for studying limnology and plankton community ecology. All data and related processing codes are publicly available for further research, supporting interdisciplinary studies.

The degradation of climate and biodiversity are two major crises humans are facing and for which rapid action is needed. Both crises are partially linked and susceptible to threaten nature's contribution to peoples (NCPs). Hence, it is essential to find efficient strategies for protecting key areas for both biodiversity and NCPs for a sustainable future. Studies at various scales have already used species distributions and NCP maps to identify the most optimal areas for safeguarding both components. Yet, an evaluation of how changes in species distributions could affect NCPs was still lacking. Here, based on a recently established table of relationships between more than 2,000 native vertebrate and tracheophyte species and 17 NCPs, we propose and illustrate a novel approach to predict the spatial distribution of NCPs from individual species predictions for the current period and four future time-scenarios in the Western Swiss Alps. Predictions of the different NCPs and their categories show varying degrees of spatial correlation, with some NCPs revealing very distinct patterns across time-scenarios. An overall decrease of NCP value is predicted for each future time-scenario. According to our results, NCPs would not increase at higher elevations in the subalpine and alpine belts and would remain high at mid-elevations in the montane belt along river valleys. Our study highlights the potential to predict NCPs directly from species predictions in biodiversity assessments, allowing a better understanding and a better anticipation of the way species contribute to NCP and human well-being. The species-based NCP prediction approach we propose constitutes a major new asset to improve spatial conservation planning, but the development of such species-NCP tables should continue, and larger databases be compiled.

The use of biodegradable plastics as an alternative to conventional non-degradable synthetic polymers is gaining market to reduce plastic pollution, however, their biodegradability is not unconditional. In this study, we hypothesized that planktonic protists (nanoflagellates and ciliates) increase the degradation of the biodegradable PLGA (poly(lactic-co-glycolic) acid) due to particle uptake. We conducted uptake and degradation experiments using PLGA microspheres of 4.9 ± 2.8 μm diameter and the microbial planktonic community from the Baltic Sea. We found that planktonic protists ingested PLGA of different sizes, with ciliates displaying higher clearance rates and ingesting larger particles compared to nanoflagellates. In addition, we observed a more pronounced decrease in PLGA concentration and particle size over time in the presence of seawater containing microbial plankton compared to a control with only ultrapure water, suggesting that the presence of these organisms increases the rate of degradation of PLGA in marine ecosystems. Altogether, these results indicate that microbial plankton enhances the degradation of biodegradable microplastics like PLGA, specifically through rapid uptake by planktonic protists. These findings highlight the role of particle ingestion by planktonic protists in the fate of the so-called biodegradable plastics when they enter aquatic ecosystems.

Heatwaves and increasing average temperatures associated with climate change pose severe stress on nature, including freshwater ecosystems. As these thermal stressors do not act in isolation over temporal or spatial scales, interactions with other stressors, like pesticides, may lead to unpredictable combined effects. Empirical studies investigating multiple stressor effects across different trophic levels are scarce and often lack environmental realism. Here, we performed a multiple stressor experiment using outdoor freshwater mesocosms and realistic pond assemblages including microbes, phytoplankton, macrophytes, and invertebrates. The effects of the pesticide imidacloprid at three dosings (0, 1, 10 μg/L) were examined in combination with three temperature scenarios comprising natural ambient, elevated temperatures (+4 °C), and repeated heatwaves (+8 °C). Our results reveal fast imidacloprid dissipation for all temperature treatments with the lowest average dissipation half-lives (DT₅₀: 6 days) in the heatwave treatment. Imidacloprid induced a series of significant effects on the macroinvertebrate community at 10 μg/L across the temperature treatments. Significant declines in abundance appeared throughout the experiment for the most sensitive taxa Cloeon dipterum, Caenis sp., Chironomini, and Dero sp., whereas significant imidacloprid effects on Tanytarsini, Chironomus, and Gammarus pulex occurred only after each dosing. Only Zygoptera showed an imidacloprid-related increase in abundance, whereas significantly adverse time-cumulative effects on abundance occurred for Asellus aquaticus. The zooplankton community showed imidacloprid tolerance (10 μg/L) with increasing abundances of Chydorus sphaericus, Acroperus harpae, and Ascomorpha. Heatwaves induced significantly meliorating effects on Dero sp. and adverse effects on Caenis sp., Tanytarsini, G. pulex, and A. harpae. The macroinvertebrate community demonstrated faster post-exposure recovery dynamics in the highest imidacloprid treatment when previously exposed to heatwaves and elevated temperatures compared to ambient conditions. Overall, heatwaves amplified the effects of imidacloprid on the invertebrate community, manifesting in manifold effects that adversely impacted multiple trophic levels.

Urban blue and green spaces, like ponds and parks, can mitigate the negative effects of urbanization on biodiversity by providing diverse, connected habitats and enabling resource flows between ecosystems. While studies have evaluated these spaces for terrestrial and aquatic communities individually, few have examined shared factors influencing both communities simultaneously. Consequently, it is unclear how these spaces should be conceived and maintained to support the diversity of both aquatic and terrestrial species, as well as their interactions. Here, we use environmental DNA (eDNA) metabarcoding to identify shared drivers and assess if and how aquatic and terrestrial invertebrate communities are coupled across 54 paired aquatic and terrestrial habitats along an urbanization gradient in the city of Zurich, Switzerland. Contrary to general expectations, we find no significant correlation in aquatic and terrestrial community structure, which we attribute to distinct drivers identified for both communities. Aquatic communities were primarily influenced by local factors related to habitat quality, while terrestrial communities were associated to landscape drivers pertaining to habitat quantity, suggesting that different processes at different spatial scales need to be considered to support both communities. Furthermore, with increasing urbanization, aquatic and terrestrial communities exhibited signs of decoupling driven by the filtering of organisms straddling ecosystem boundaries. We conclude that increasing levels of urbanization weaken resource flow between aquatic and terrestrial environments. By employing eDNA across ecosystem boundaries, our study highlights the critical importance of both the quality and quantity of urban habitats in conserving aquatic and terrestrial communities, as well as their linkages.

Material fluxes are ubiquitous in nature within and across ecosystems, connecting habitats with vastly different characteristics, like forests to rivers and lakes.^1,2,3 Although individual fluxes and their cascading effects are well known,^4,5,6 very few studies address the intra-annual phenology of ecosystem processes, despite the pronounced seasonality of fluxes. Here, we empirically quantified and resolved fluxes of recalcitrant and labile types of leaf litter in temperate riparian forests and streams across a year, representing one of the most emblematic examples of seasonal systems. We quantified intra-annual variation in litter inputs from terrestrial plants to forest floors and streams and estimated aquatic and terrestrial decomposition rates across the year at 6-week intervals. Our data show that the autumn pulse of leaf litter is complemented by smaller magnitude but more constant-through-the-year lateral flows to the stream ecosystems. Decomposition of labile litter fluctuated seasonally, on a different phenology, with generally higher rates in summer, but rates of recalcitrant litter decomposition remained largely constant. Microorganisms were the main contributors to the decomposition process in both forests and streams. Overall, our work highlights the asynchronous and seasonally variable changes in decomposition rates between recalcitrant and labile detritus despite their initial synchronized availability and suggests that the dominating presence of recalcitrant litter buffers ecosystem responses to the concentrated temporal distribution of litter resources.^7,8 Investigating such ecological processes both across ecosystem borders and at fine intra-annual resolutions is imperative to understand complex system responses in the context of species’ shifts in phenologies and resource quality.^9,10,11

The late Smithian and Smithian-Spathian boundary (SSB) witnessed significant conodont extinction approximately 2.7 million years after the major Permian-Triassic boundary extinction. This study offers a detailed examination of the Smithian-Spathian transition at the Guryul Ravine section in the Srinagar district, Kashmir, focusing on conodonts and δ¹³C_carb values. The section features an unprecedented conodont taxonomic richness, with 53 species from 17 genera, including three newly formalized species: Neospathodus aristatus n. sp., Neospathodus guryulensis n. sp. and Borinella? prima n. sp. Additionally, Borinella ex gr. buurensis and Scythogondolella ex gr. milleri are subdivided into multiple morphotypes, facilitating a refined biochronological scheme.
A high-resolution δ¹³C_carb record spanning the Early Triassic captures global carbon isotope excursions. The integration of δ¹³C_carb with conodont biostratigraphy enhances global correlation of the Smithian-Spathian transition. The late Smithian conodont extinction aligns with a globally observed positive δ¹³C_carb excursion, reaching an exceptional value of + 12 ‰, likely of diagenetic origin.
This study proposes a new conodont biochronological framework based on the Unitary Association Method (UAM). Placing the SSB between the extinction climax and re-diversification onset, the framework relies on a rich conodont collection from Guryul Ravine, Kashmir, and a comprehensive reassessment of conodont data from 19 other sections along the northern Gondwana margin. The resulting 16 Unitary Association Zones (UAZs) are cross-referenced with lithological, chemostratigraphical (δ¹³C_carb), and ammonoid markers, establishing an unprecedentedly robust basis for defining the SSB. The proposed boundary is within UAZ₈ but allows for future refinements.

Aquatic and terrestrial ecosystems are linked through the reciprocal exchange of materials and organisms. Aquatic-to-terrestrial subsidies are relatively small in most terrestrial ecosystems, but they can provide high contents of limiting resources that increase consumer fitness and ecosystem production. However, they also may carry significant contaminant loads, particularly in anthropogenically impacted watersheds. Global change processes, including land use change, climate change and biodiversity declines, are altering the quantity and quality of aquatic subsidies, potentially shifting the balance of costs and benefits of aquatic subsidies for terrestrial consumers. Many global change processes interact and impact both the bright and dark sides of aquatic subsidies simultaneously, highlighting the need for future integrative research that bridges ecosystem as well as disciplinary boundaries. We identify key research priorities, including increased quantification of the spatiotemporal variability in aquatic subsidies across a range of ecosystems, greater understanding of the landscape-scale extent of aquatic subsidy impacts and deeper exploration of the relative costs and benefits of aquatic subsidies for consumers.

Global efforts aimed at safeguarding and restoring biodiversity require methods to monitor progress towards conservation objectives. Such methods should provide a systematic and robust assessment of biodiversity for the lowest cost. River environmental DNA (eDNA) metabarcoding has been successfully applied to measure biodiversity in dendritic riverine habitats and is increasingly used to describe communities of terrestrial vertebrates in ecosystems that are challenging to survey using traditional methods. However, interpreting eDNA surveys in riverine habitats requires an understanding of the influence of eDNA transport, decay, and production on the distribution of eDNA. To this end, the hydrology-based eDITH (eDNA Integrating Transport and Hydrology) model incorporates such factors and can recover reliable spatial biodiversity patterns for aquatic taxa, but its potential to successfully model terrestrial taxa is so far unexplored. Here, we applied eDITH to eDNA metabarcoding data for terrestrial mammals collected over two mountainous catchments (575 and 745 km²) in British Columbia, Canada. We assessed prediction transferability between neighboring catchments and compared model predictions with observations from camera trapping. We found that for 9 out of 15 taxa detected by both eDNA and camera traps, predicted distributions predominantly matched observations from camera trap surveys, illustrating that eDITH can uncover patterns of mammal distribution in mountainous catchments. While lacking knowledge of actual taxon density prevents us from determining whether discrepancies stem from data limitations or complex eDNA production-density relationships, good transferability of predictions to the neighboring catchments suggests that eDNA distribution of some terrestrial and semi-aquatic mammals is partly determined by habitat preference and hydrology. Downstream sampling can recover most biodiversity across the catchment, but the inclusion of upstream samples can aid in detecting elusive species. This study underscores the broader applications of river eDNA beyond aquatic species and illustrates its potential use in addressing terrestrial mammal biodiversity monitoring objectives with tailored sampling approaches.

Human activities drive a wide range of environmental pressures, including habitat change, pollution and climate change, resulting in unprecedented effects on biodiversity^1,2. However, despite decades of research, generalizations on the dimensions and extent of human impacts on biodiversity remain ambiguous. Mixed views persist on the trajectory of biodiversity at the local scale³ and even more so on the biotic homogenization of biodiversity across space^4,5. We compiled 2,133 publications covering 97,783 impacted and reference sites, creating an unparallelled dataset of 3,667 independent comparisons of biodiversity impacts across all main organismal groups, habitats and the five most predominant human pressures^1,6. For all comparisons, we quantified three key measures of biodiversity to assess how these human pressures drive homogenization and shifts in composition of biological communities across space and changes in local diversity, respectively. We show that human pressures distinctly shift community composition and decrease local diversity across terrestrial, freshwater and marine ecosystems. Yet, contrary to long-standing expectations, there is no clear general homogenization of communities. Critically, the direction and magnitude of biodiversity changes vary across pressures, organisms and scales at which they are studied. Our exhaustive global analysis reveals the general impact and key mediating factors of human pressures on biodiversity and can benchmark conservation strategies.

Spatial environmental heterogeneity is an important driver of aquatic biodiversity. Ecological and evolutionary theory often consider spatial heterogeneity as being driven by exogenous factors, yet heterogeneity can also be generated and modified by organisms. Here we used a mesocosm experiment to investigate if consumers influence the build-up of spatial heterogeneity. We expected that consumer effects on heterogeneity would depend on consumer composition and differ among response variables. We constructed metacommunities consisting of three mesocosms and manipulated the presence and composition of consumers, using four treatment levels: (1) no consumers, (2) two genotypes of Daphnia galeata, (3) D. galeata and Daphnia longispina, and (4) D. galeata and a hybrid of D. galeata × D. longispina. We then continuously increased heterogeneity among the three patches of each metacommunity by adding nutrients and dissolved organic carbon (DOC), respectively, to two of the three mesocosms. We found that consumers affected the build-up of heterogeneity, but the direction and magnitude of this effect differed among consumer compositions. Metacommunities with only D. galeata had increased heterogeneity in phytoplankton biomass, whereas metacommunities with D. longispina or the hybrid had low phytoplankton heterogeneity. The differential effects of Daphnia taxa on phytoplankton heterogeneity cascaded down to the abiotic environment and resulted in taxon-specific effects on heterogeneity in light extinction, dissolved inorganic nitrogen, and total inorganic carbon. Our results imply that changes in consumer species (e.g., due to environmental change or invasion) might affect not only the local environment but could also impact heterogeneity among environments, with important consequences for aquatic biodiversity.

Biodiversity underpins the functional integrity of ecosystems. At present, our understanding of the relationship between biodiversity and ecosystem functioning (BEF) is essentially based on manipulative experiments. Compelling data at large spatial scales are scarce, especially for river networks. BEF patterns across landscapes are complex because they unfold in the context of environmental gradients and compositional turnover of natural communities. Leaf litter decomposition, a pivotal ecosystem process in streams, is no exception to this context dependency. The dendritic structure of river networks plus the unidirectional water flow shape both environmental conditions and the distribution of leaf resources and consumers. However, it is difficult to predict how spatial gradients of resource and consumer composition can overlap across a river network, and thus govern spatial patterns of decomposition. Here, we investigated the capacity of macroinvertebrate biodiversity to control decomposition rates of heterogeneous leaf resources at the river-network scale. We deployed five litterbags containing either one of four single leaf species or a mixture of all species at 51 sites across the Thur River network (Switzerland). We measured litter decomposition rates, variation of decomposition among leaf resources, and the effect of leaf litter diversity on decomposition. We found that decomposition rates decreased from headwaters to downstream reaches mainly due to the parallel decrease in the abundance of key shredder taxa (namely, Amphinemura, Nemoura, Leuctra, Habroleptoides, and Stenophylacini). Macroinvertebrate diversity had a minor, negative effect on decomposition rates. However, high functional macroinvertebrate diversity at the reach scale reduced the variation of decomposition among leaf resources, thus alleviating nutritional constraints exerted by nutrient-poor leaf resources. Furthermore, litter mixtures were preferably decomposed by communities with low evenness and dominated by a few taxa. These findings point to a critical role of macroinvertebrates in controlling litter decomposition at the network scale beyond environmental effects. While shredder abundance and community composition are key to determining decomposition rates across the river network, functional diversity is important in decreasing the variation of decomposition rates among leaf resources. Our results stress the importance of biodiversity controlling ecosystem functioning not only at the local but also at the river network scale.

Leaf litter decomposition (LLD) is a key ecosystem function where invertebrate shredders produce large amounts of fine particulate organic matter (FPOM) that serves as a substrate for microbial assemblages. Here, we explore the shredder-produced FPOM composition and activity of FPOM-associated microbial communities in response to different leaf species and their conditioning. In a laboratory experiment, we fed leaves of different elemental compositions (alder, beech and maple), conditioned under oxic or anoxic conditions, to caddisfly larvae (Sericostoma sp.). We hypothesized differences in FPOM elemental and fatty acid composition and FPOM-associated microbial activity among the leaf species, conditioning, and two types of shredder-produced FPOM, i.e. shredded leaves and faecal pellets. Our results suggest that leaf conditioning and shredder activity play pivotal roles in shaping FPOM composition and FPOM-associated microbial activity. We observed lower C/N ratios with high-C/N litter (beech and maple leaves) after conditioning and no change in the elemental composition of the faecal pellets compared to the leaves. However, we observed differences in microbial fatty acid proportions and composition on leaves and faecal pellets with significantly higher fractions of bacterial fatty acids on faecal pellets than on leaves. We also noted a significant impact of leaf conditioning on the microbial activity of shredded leaves and faecal pellets, with a higher microbial growth efficiency observed on faecal pellets compared to ingested leaves. These findings highlight the crucial influence of leaf species and conditioning on the activity of shredder-produced FPOM, emphasizing the complex interplay between leaf properties and fate and microbial processes in streams.

Ongoing anthropogenic eutrophication and warming temperatures are expected to increase the extent and severity of hypoxia globally. Monitoring hypoxia has traditionally relied on costly surveys or sensor networks. While benthic macroinvertebrates are valuable indicators of hypoxia, community analysis is limited by small spatial scales of traditional grab sampling and labor-intensive processing. To address this, we combined benthic grab samples with underwater video to detect hypoxic habitats in two productive embayments of the Laurentian Great Lakes: Saginaw Bay, Lake Huron with periodic short-term hypoxia, and Hamilton Harbour, Lake Ontario with prolonged hypoxia. Using supervised classification, we identified significant grouping of in situ video data with cluster analysis, and then aligned video groups with environmental and biological datasets. These video groups were supported by cluster analysis of measured environmental variables, with clusters differing in duration of low near-bottom dissolved oxygen concentration and by depth. Independent cluster analysis confirmed significant separation of benthic communities among the selected video groups, with hypoxic habitats showing reduced species diversity and a higher proportion of tubificids. The gradient of conditions sampled in our study revealed assemblages of benthic invertebrates sensitive to and tolerant of hypoxia. The agreement among video, biological, and environmental data confirmed that video analysis can provide a novel, quick and reliable method to detect benthic habitats affected by hypoxia and determine their spatial extent once a baseline is established.

Reconstructions of past changes in algal community composition provide important context for future alterations in biogeochemical cycling. However, many existing phytoplankton proxies are indicative of individual algal groups and are not fully representative of the whole community. Here, we evaluated hydrogen isotope ratios of algal lipids (δ²H_Lipid) as a potential proxy for phytoplankton community composition. We sampled the water column of Rotsee, a small eutrophic lake in Switzerland, every second week from January 2019 to February 2020 and analyzed distributions and the relative offsets between δ²H_Lipid values (δ²H_{Lipid1/Lipid2}) from short-chain fatty acids, phytosterols and phytol. Comparing these data with phytoplankton cell counts, we found that δ²H_{C16:0 Acid/Sterol} and δ²H_{Sterol/Phytol} values reflect shifts within the eukaryotic algal community. To assess whether the selected phytoplankton groups were the main sources of the selected lipids, we further modeled algal δ²H_{Lipid1/Lipid2} values based on δ²H_{C16:0 Acid}, δ²H_Sterol and δ²H_Phytol values from batch cultures of individual algal groups and their biovolume in Rotsee and evaluated the role of heterotrophy on δ²H_{Lipid1/Lipid2} values using a model incorporating δ²H_{C16:0 Acid} and δ²H_Sterol values from microzooplankton. Annually-integrated and amount-weighted δ²H_{Lipid1/Lipid2} values measured in Rotsee were within 2 to 20 ‰ of the mean of modeled algal δ²H_{Lipid1/Lipid2} values, demonstrating a strong link with the phytoplankton community composition, while δ²H_{Lipid1/Lipid2} values including microzooplankton lipids had a larger offset. Additionally, cyanobacterial biovolume was positively correlated with the ratio of phytol and phytosterols (phytol:sterol ratio) as well as the ratio of unsaturated C18 and C16:0 fatty acids (C18:C16 ratio). Our results support the application of sedimentary δ²H_{Lipid1/Lipid2} values in eutrophic lakes as a proxy for past phytoplankton community assemblages. Moreover, the calculation of sedimentary phytol:sterol and C18:C16 ratios provides an additional proxy for reconstructing cyanobacterial blooms.

As the urgency to evaluate the impacts of climate change on marine ecosystems increases, there is a need to develop robust projections and improve the uptake of ecosystem model outputs in policy and planning. Standardizing input and output data is a crucial step in evaluating and communicating results, but can be challenging when using models with diverse structures, assumptions, and outputs that address region-specific issues. We developed an implementation framework and workflow to standardize the climate and fishing forcings used by regional models contributing to the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) and to facilitate comparative analyses across models and a wide range of regions, in line with the FishMIP 3a protocol. We applied our workflow to three case study areas-models: the Baltic Sea Mizer, Hawai'i-based Longline fisheries therMizer, and the southern Benguela ecosystem Atlantis marine ecosystem models. We then selected the most challenging steps of the workflow and illustrated their implementation in different model types and regions. Our workflow is adaptable across a wide range of regional models, from non-spatially explicit to spatially explicit and fully-depth resolved models and models that include one or several fishing fleets. This workflow will facilitate the development of regional marine ecosystem model ensembles and enhance future research on marine ecosystem model development and applications, model evaluation and benchmarking, and global-to-regional model comparisons.

The interplay between abiotic (resource supply, temperature) and biotic (grazing) factors determines growth and loss processes in phytoplankton through resource competition and trophic interactions, which are mediated by morphological traits like size. Here, we study the relative importance of grazers, water physics, and chemistry on the daily net accumulation rates (ARs) of individual phytoplankton from natural communities, grouped into six size classes from circa 10 to 500 μm. Using a Random Forest modelling approach and 4 years of daily data from a lake, we find that water temperature is generally a pivotal control of all phytoplankton ARs. At the same time, nutrients and light are important for the smallest and the largest classes. Mesozooplankton abundance is a key predictor of the AR for small phytoplankton, with microzooplankton being important for the middle-size range. In our data, large and small phytoplankton have different (seasonal) blooming patterns: small forms are favoured by low temperature and grazing, and high phosphorus levels. Larger forms show positive ARs at high temperatures and low phosphorus (being relatively insensitive to zooplankton grazing). These results help us understand the opportunities and limitations of using size to explain and model phytoplankton responses to biotic and abiotic environmental change.

Invaders can have devastating impacts on freshwater ecosystems, but these impacts can subside over time as ecosystems "adapt" to the invasion of new species. We analyzed changes in species composition and density of molluscs in Oneida Lake (New York, USA), one of the best studied North American lakes based on detailed surveys conducted in 1915–17, 1967–68, 1992–95, 2012, and 2022–23, and on annual benthic surveys from 2009 through 2023. Eutrophication and habitat alteration after 1920 resulted in a 25% decline in species richness and a 95% decline in the density of native gastropods by 1967, while species richness of unionids did not change. The arrival of zebra mussels in 1991 and quagga mussels in 2005 was associated with an increase in species richness and density of native gastropods and an extirpation of unionids by 1995. However, an invasion by the round goby in 2013 led to a significant decline across all gastropod families, disproportionately impacting soft-shelled and shallow-dwelling species, while other species, including invasive dreissenids, partially recovered 3–7 years after the goby invasion. This mollusc recovery was depth-related and was limited to deeper areas. Altogether, molluscan communities were sensitive to ecosystem change and invasives species, with some invaders offsetting the impacts of eutrophication and habitat alterations. While individual stressors have taxon-specific and sometimes positive impacts, eutrophication and species invasions have collectively decimated the native mollusc community over the past century.

We report the results of the first survey of bdelloid rotifers, microscopic aquatic animals, in continental Norway, collected from coastal ponds in the Southern part of the country in Autumn 2021, using a morphological approach in species identification. Out of 25 ponds, 19 bdelloid species were found, ten in water samples and another nine in limno-terrestrial habitats just above the waterline of the ponds. Seven of the species are new records for mainland Norway. Three species could be identified to genus level only and may be novel taxa, not only for Norway but for science: further studies are needed on these animals to clarify their taxonomic identity. We also obtained COI sequences from 194 animals of eight of the species to compare them with what is known in GenBank in a phylogenetic context and confirm the reliability of morphological identification. This data contributes to our understanding of the taxonomic and biogeographic diversity of bdelloid rotifers in Norway. In addition, the newly available sequences increase the coverage of the reference library of bdelloid rotifers for future studies employing DNA metabarcoding.

As a key life-history trait, growth rates are often used to measure individual performance and to inform parameters in demographic models. Furthermore, intraspecific trait variation generates diversity in nature. Therefore, partitioning out and understanding drivers of spatiotemporal variation in growth rate is of fundamental interest in ecology and evolution. However, this has rarely been attempted owing to the amount of individual-level data required through both time and space, and issues with missing data in important covariates. Here, we implemented a Bayesian state-space model using individual-level data from 20 populations of Arctic charr (Salvelinus alpinus) across 15 capture occasions, which allowed us to: (i) integrate over the uncertainty of missing recapture records; (ii) robustly estimate size-dependence; and (iii) include a covariate (water temperature) that contained missing data. Interestingly, although there was substantial spatial, temporal and spatiotemporal variation in growth rate, this was only weakly associated with variation in water temperature and almost entirely independent of size, suggesting that spatiotemporal variation in other environmental conditions affected individuals across sizes similarly. This fine-scale spatiotemporal variation emphasizes the importance of local conditions and highlights the potential for spatiotemporal variation in a size-dependent life-history trait, even when environmental conditions are apparently very similar.

The recent advances in both theoretical and modeling approaches (species distribution models) and molecular techniques (environmental DNA) offer new opportunities to advance the assessment of biodiversity. This is particularly the case for riverine environments, whose biodiversity is disproportionately under peril, but also whose dendritic connectivity allows a spatial interpretation of eDNA samples, which reflect a biodiversity signal averaged over a certain upstream area. Conversely, traditional, direct observation surveys provide localized information on taxon density. Here, I propose a framework to leverage both data types to improve estimates of a taxon's spatial distribution. Specifically, I expand the eDITH model (which allows estimating the spatial distribution of taxa based on spatially replicated stream eDNA data) to include direct observations, and upgrade the eDITH R-package to allow a broad implementation of such method. Moreover, I propose optimized sampling strategies for both eDNA and direct sampling, with algorithms (included in the upgraded eDITH package) that mathematically translate rule-of-thumb criteria to maximize the spatial coverage of sites’ arrangement in a riverscape based on the peculiar features of each data type. Finally, I test such framework by means of an in-silico experiment, whereby I show that optimized sampling strategies outperform random-based strategies in the ability to reconstruct a taxon's spatial distribution. When eDNA and direct sampling sites are spatially arranged in an optimized fashion, the highest prediction skill for a fixed total number of sampling sites deployed is reached when both data types are included in the model fitting. The optimal trade-off between eDNA and direct sampling observations depends on both characteristics of the investigated taxon (e.g., the spatial heterogeneity in its distribution) and the level of uncertainty in the observed data. These results will contribute to designing efficient strategies for integrated biomonitoring in river networks.

Ecosystem ecology needs a framework that explicitly considers the roles of organic compounds. The ecology of molecules integrates compound identity, diversity, and interactions to understand ecosystem processes, such as nutrient and carbon cycling. This approach leverages advances in analytical chemistry and molecular biology to unravel the complex chemical interplay within ecosystems.

1. Cryptic species are an important part of freshwater biodiversity, yet it remains unclear how these species integrate into communities from local to regional geographic scales. To protect biodiversity, particularly overlooked cryptic species, an accurate understanding of the underlying processes and adequate level of protection is needed.
2. We analysed patterns of syntopies (local co-occurrences) and sympatries (regional range overlap) to explore how the phylogenetic origin of cryptic species shapes biodiversity patterns. We hypothesised (i) that syntopies were more common among distantly than closely related cryptic species, and (ii) that the existing sympatries were an outcome of phylogenetic relatedness and dispersal.
3. The hypotheses were tested on a polyphyletic species complex of subterranean amphipod species (Niphargus rhenorhodanensis complex) by deploying molecular species delimitation, time-calibrated phylogenies, and co-occurrence analyses with probabilistic and generalised linear models (GLM).
4. The studied complex comprised 37–48 molecular operational taxonomic units (MOTUs) from nine different clades, with syntopies occurring at random or less frequently than expected. GLM indicated age of divergence did not predict species sympatries, although they emerged more frequently among MOTUs from different clades. Sympatries, however, emerged through dispersal, in MOTUs with large geographic ranges. These mostly overlapped at the foothills of the Alps, the Jura and the Central Massif.
5. We conclude that the observed spatial patterns are mainly driven by dispersal and presumably reflect the geographic circumstances of speciation. While species richness on a local scale may be an outcome of competition and dispersal, regional biodiversity patterns presumably arise through a clade-level cascade of historical events, including orogeny and climatic shifts.

Temperate streams are subsidized by inputs of leaf litter peaking in fall. Yet, stream communities decompose dead leaves and integrate their energy into the aquatic food web throughout the whole year. Most studies investigating stream decomposition largely overlook long-term trajectories, which must be understood for an appropriate temporal upscaling of ecosystem processes. Using mesocosms, we quantified changes in carbon, nitrogen, and phosphorus content of three leaf species during decomposition at weekly to multi-month intervals for up to a year; then, we tested how decomposition duration affected the subsequent consumption by a keystone amphipod macroinvertebrate. Over a year, nitrogen and phosphorus percentage increased across all leaf species, but only the recalcitrant species maintained initial levels of absolute nitrogen and phosphorus. Prolonged decomposition barely affected or impaired amphipod consumption of labile leaf species, whereas it enhanced feeding on the recalcitrant species. Overall, we demonstrate that recalcitrant leaves might serve as longer stored potential resources for when labile species have already been consumed and that their increasing palatability observed over multi-month intervals of sustained decomposition may stabilize fluctuations in the rates of leaf litter integration into aquatic food webs. This yearlong perspective highlights the relevancy of slow-decomposing leaves for aquatic detrital communities.

In aquatic ecosystems facing climate change, higher temperatures often co-occur with alterations in resource availability. The metabolic theory of ecology uses activation energy to assess the sensitivity of biological processes to temperature, but neglects how resource availability might modify temperature sensitivities. To understand the impacts of resource limitation on temperature sensitivities, we performed experiments manipulating temperature and three key resources (nitrogen, phosphorus, and light) in six species of freshwater phytoplankton. We measured activation energies of population growth rates and how they were modulated by resource limitation. We find that the interaction of temperature and resource limitation is dependent on the resource type. Phosphorus limitation did not modify the temperature sensitivity of growth rates, light limitation reduced the sensitivity of growth rates to temperature in all species, and nitrogen limitation had species-dependent effects. We explore how stoichiometry and cell physiology may explain the complex responses of phytoplankton to multiple environmental changes.

Biodiversity–ecosystem functioning experiments have established generally positive species richness-productivity relationships in plots of single ecosystem types, typically grassland or forest. However, it remains unclear whether these findings apply in real-world landscapes that resemble a heterogeneous mosaic of different ecosystem and plant types that interact through biotic and abiotic processes. Here, we show that landscape-level diversity, measured as number of land-cover types (different ecosystems) per 250×250 m, is positively related to landscape-wide remotely-sensed primary production across all of North America, covering 16 of 18 ecoregions of Earth. At higher landscape diversity, productivity was temporally more stable, and 20-year greening trends were accelerated. These effects occurred independent of local species diversity, suggesting emergent mechanisms at hitherto neglected levels of biological organization. Specifically, mechanisms related to interactions among land-cover types unfold at the scale of entire landscapes, similar to, but not necessarily resulting from, interactions between species within single ecosystems.

Phytoplankton play a key role in biogeochemical cycles, impacting atmospheric and aquatic chemistry, food webs, and water quality. However, it remains challenging to reconstruct changes in algal community composition throughout the geologic past, as existing proxies are suitable only for a subset of taxa and/or influenced by degradation. Here, we investigate if compound-specific hydrogen isotope ratios (δ²H values) of common algal lipids can serve as (paleo)ecological indicators. First, we grew 20 species of algae – representing cyanobacteria, diatoms, dinoflagellates, green algae, and cryptomonads – in batch cultures under identical conditions and measured δ²H values of their lipids. Despite identical source water δ²H values, lipid δ²H values ranged from −455 ‰ to −52 ‰, incorporating variability associated with chemical compound classes and taxonomic groups. In particular, green algae synthesized fatty acids with higher δ²H values than other taxa, cyanobacteria synthesized phytol with relatively low δ²H values, and diatoms synthesized sterols with higher δ²H values than other eukaryotes. Second, we assessed how changes in algal community composition can affect net δ²H values of common algal lipids in 20 experimental outdoor ponds, which were manipulated via nutrient loading, and the addition of macrophytes and mussels. High algal biomass in the ponds, which was mainly caused by cyanobacterial and green algal blooms, was associated with higher δ²H values for generic fatty acids, relatively stable δ²H values for phytol and the dinoflagellate biomarker dinostanol, and lower δ²H values for the more cosmopolitan sterol stigmasterol. These results are consistent with expectations from our culture-based analyses, with both datasets indicating large taxon-specific changes that are unlikely to be driven by bacterial heterotrophy. This suggests that measuring δ²H values of multiple lipids from sediment and calculating ²H-offsets between them can resolve changes in algal community composition from changes in source water isotopes. With an appropriate availability of sedimentary lipids, this approach could permit the reconstruction of both taxonomic variability and hydroclimate from diverse sedimentary systems.

Phytoplankton is an essential resource in aquatic ecosystems, situated at the base of aquatic food webs. Plastic pollution can impact these organisms, potentially affecting the functioning of aquatic ecosystems. The interaction between plastics and phytoplankton is multifaceted: while microplastics can exert toxic effects on phytoplankton, plastics can also act as a substrate for colonisation. By reviewing the existing literature, this study aims to address pivotal questions concerning the intricate interplay among plastics and phytoplankton/phytobenthos and analyse impacts on fundamental ecosystem processes (e.g. primary production, nutrient cycling). This investigation spans both marine and freshwater ecosystems, examining diverse organisational levels from subcellular processes to entire ecosystems. The diverse chemical composition of plastics, along with their variable properties and role in forming the "plastisphere", underscores the complexity of their influences on aquatic environments. Morphological changes, alterations in metabolic processes, defence and stress responses, including homoaggregation and extracellular polysaccharide biosynthesis, represent adaptive strategies employed by phytoplankton to cope with plastic-induced stress. Plastics also serve as potential habitats for harmful algae and invasive species, thereby influencing biodiversity and environmental conditions. Processes affected by phytoplankton–plastic interaction can have cascading effects throughout the aquatic food web via altered bottom-up and top-down processes. This review emphasises that our understanding of how these multiple interactions compare in impact on natural processes is far from complete, and uncertainty persists regarding whether they drive significant alterations in ecological variables. A lack of comprehensive investigation poses a risk of overlooking fundamental aspects in addressing the environmental challenges associated with widespread plastic pollution.

The adaptation of marine fish to freshwater environments includes prodigious examples of rapid evolution.Given the scarcity of ω-3 long-chain polyunsaturated fatty acids (LC-PUFA) in freshwater, we expect selection to be strong on fish transitioning to freshwater habitats and yet the underlying ecological causes of genomic and phenotypic differentiation are poorly understood for traits associated with lipid content and composition. Threespine stickleback Gasterosteus aculeatus have repeatedly colonized, and adapted to, freshwater habitats across the Northern Hemisphere. These freshwater populations often show elevated copy number of the fatty acid desaturase 2 gene (FADS2), which increases the biosynthetic capacity of LC-PUFA. The starkly lower content of LC-PUFA in freshwater compared to marine prey, especially docosahexaenoic acid (DHA), likely imposes strong positive selection on freshwater fish for either increased biosynthesis or greater dietary acquisition of LC-PUFA. The recently colonized and relatively undisturbed threespine stickleback populations in postglacial coastal lakes of southern Greenland offer an exceptional opportunity to study how variation in the copy number of FADS2 is related to abiotic and biotic conditions of lakes and their morphometry. As expected, given its position on the stickleback X chromosome, we found strong sexual dimorphism in FADS2 copy number in all populations (19 freshwater, 1 marine and 1 brackish), and an increased dimorphism in some freshwater populations. We also found that FADS2 copy number was negatively correlated, for both males and females, with the abundance of copepods, which are a DHA-rich food source in the zooplankton community. Overall, our results suggest that the prey community context of lakes might influence the process of metabolic adaptation of marine fish colonizing freshwater ecosystems.

Rivers exhibit hierarchical spatial structures of habitat and physical attributes, providing directed pathways for biological population and community dynamics and thus shaping the meta-ecosystems therein. While the River Continuum Concept has generalized the spatial patterns of abiotic and biotic components along rivers, a mechanistic understanding of how river networks' shape may constrain the attributes of riverine meta-ecosystems remains lacking. Here, we address this gap with an in silico study. We integrate the Optimal Channel Network concept (and the well-established scaling of river geomorphological and hydrological attributes) with a meta-ecosystem model (with trait-based food-web dynamics and spatial dynamics of species and inorganic resources) to explore how distinct river network shapes (elongated vs. compact) may drive the spatial patterns of biodiversity and community trophic structure. We analyse metrics of biomass distribution, trophic structure and composition of locally realized food webs and show that elongated and compact networks foster very different upstream-downstream biological patterns, and even more contrasting patterns are often observed between the long and short paths of elongated networks. Overall, we observe a transition from prevailing detritus-based to nutrient-based trophic channels moving downstream, leading to peaks in alpha diversity at intermediate river size, where both channels are more balanced. Higher spatial heterogeneity in community composition and lower biomass levels are observed in elongated than in compact networks, driven by higher variability in nutrient input loads and higher water volumes, respectively. Together, our findings associate river shapes to the emergent riverine meta-ecosystems properties and help reveal the underpinning physical attributes-driven mechanisms.

Marine heatwaves (MHWs) are episodes of anomalous warming in the ocean that can last from a few days to years. MHWs have different characteristics in terms of intensity, duration and frequency and generate thermal stress in marine ecosystems. In reef ecosystems, they are one of the main causes of the decreased presence and abundance of corals, invertebrates and fish. The deleterious capacity of thermal stress often depends on biotic factors, such as the trophic control of predators on prey. Despite the evidence of thermal stress and biotic factors affecting individual species, the combined effects of both stressors on entire reef ecosystems are much less studied. Here, using a food web modelling approach, we estimated the rate of change in species' biomass due to different MHW characteristics. Specifically, we modelled the mechanistic link between species' consumption rate and seawater temperature (thermal stressor), simulating species' biomass dynamics for different MHW characteristics under different trophic control assumptions (top-down, mixed trophic control and bottom-up). We find that total reef ecosystem biomass declined by 10% ± 5% under MHWs with severe intensity and a top-down control assumption. The bottom-up control assumption moderates the total ecosystem biomass reduction by 5% ± 5%. Irrespective of the MHW characteristics and the trophic control assumption, the most substantial biomass changes occur among top, mesopredators and corals (5% to 20% ± 10%). We show that reef ecosystems where predators exert top-down control on prey are prone to suffer species abundance declines under strong MHW events. We identify food web trophic control as a crucial driver that modulates the impacts of MHWs. Overall, our results provide a unified understanding of the interplay between abiotic stressors and biotic factors in reef ecosystems under extreme thermal events, offering insights into present baselines and future ecological states for reef ecosystems.

Spatial truncation in species distribution models (SDMs) might cause niche truncation and model transferability issues, particularly when extrapolating models to non-analog environmental conditions. While broad calibration extents reduce truncation issues, they usually overlook local ecological factors driving species distributions at finer resolution. Spatially-nested hierarchical SDMs (HSDMs) address truncation by merging (a) a global model calibrated with broadly extended, yet typically low-resolution, basic, and imprecise data; and (b) a regional model calibrated with spatially restricted but more precise and reliable data. This study aimed to examine HSDMs' efficacy to overcome spatial truncation in national-scale studies. We compared two hierarchical strategies (‘covariate', which uses the global model output as a covariate for the regional model, and ‘multiply', which calculates the geometric mean of the global and regional models) and a non-hierarchical strategy. The three strategies were compared in terms of niche truncation, environmental extrapolation, model performance, species' predicted distributions and shifts, and trends in species richness. We examined the consistency of the results over two study areas (Spain and Switzerland), 108 tree species, and four future climate scenarios. Only the non-hierarchical strategy was susceptible to niche truncation, and environmental extrapolation issues. Hierarchical strategies, particularly the ‘covariate' one, presented greater model accuracy than non-hierarchical strategies. The non-hierarchical strategy predicted the highest overall values and the lowest decreases over time in species distribution ranges and richness. Differences between strategies were more evident in Switzerland, which was more affected by niche truncation issues. Spain was more negatively affected by climate change and environmental extrapolation. The ‘covariate' strategy exhibited higher model performance than the ‘multiply' one. However, uncertainties regarding model temporal transferability advocate for adopting and further examining multiple hierarchical approaches. This research underscores the importance of adopting spatially-nested hierarchical SDMs given the compromised reliability of non-hierarchical approaches due to niche truncation and extrapolation issues.

Des moules quagga ont été détectées pour la première fois à Bâle en 2014 grâce à l'ADN environnemental (ADNe) (De Ventura et al. 2017). En 2016, des spécimens de moules quagga ont été découverts pour la première fois dans le lac de Constance. Dès 2021, des initiatives d'information et de sensibilisation à grande échelle ont été lancées en Suisse. Cependant, entre-temps, plusieurs grands lacs ont été envahis par cette espèce. Bien que la dynamique de propagation laisse présager un risque élevé de colonisation supplémentaire en Suisse, nous estimons que chaque année de retard dans l'arrivée des moules quagga dans un lac constitue un gain précieux. Sur le plan financier, cela permet de réaliser des économies, de disposer de plus de temps pour adapter les infrastructures, et de préserver l'état naturel des lacs aussi longtemps que possible. C'est pourquoi nous recommandons vivement que les mesures de protection et de surveillance des eaux décrites dans ce rapport soient mises en œuvre dans les plus brefs délais réalisables par tous les acteurs concernés. Ce rapport a pour objectif de faciliter cette démarche. Plus l'action sera rapide, plus ses effets seront bénéfiques. [...]

Quaggamuscheln wurden 2014 zum ersten Mal in Basel mittels Umwelt DNA (eDNA) nachgewiesen (De Ventura et al. 2017). Im Jahr 2016 wurden das erste Mal Exemplare der Quaggamuschel im Bodensee gefunden. Ab 2021 wurden in der Schweiz grossflächig Informations- und Sensibilisierungs- Massnahmen ergriffen. In der Zwischenzeit sind einige grosse Seen von Quaggamuscheln befallen. Auch wenn die Risiken für eine weitere Ausbreitung in der Schweiz gross sind, wie die Ausbreitungsdynamik zeigt, sind wir der Meinung, dass jedes Jahr, in dem die Quaggamuschel später in einen See kommt, ein gewonnenes Jahr ist. Es werden monetär gesehen Kosten eingespart, es bleibt mehr Zeit Infrastrukturanlagen entsprechend vorzubereiten und der natürliche Zustand der Seen bleibt so lange wie möglich erhalten. Wir empfehlen darum dringend, dass die in diesem Bericht beschriebenen Massnahmen zum Schutz und zum Monitoring von Gewässern von allen betroffenen Akteuren möglichst schnell umgesetzt werden. Der vorliegende Bericht soll hierfür eine Hilfestellung bieten. Je früher gehandelt wird, desto besser. [...]

Aquatic and terrestrial ecosystems are deeply coupled and inherently connected through spatial flows of organisms and resources, modulating the flow or exchange of organisms thereby the land-water linkage of biodiversity at local to global scales. Although there is a plethora of studies about aquatic-terrestrial cross-ecosystem linkages, these researches normally only focus on a few taxa and in a few local catchments. This lack of a systematic and comprehensive understanding of the spatial scale and magnitude of linkages is partly due to the laborious and costly field sampling especially in aquatic ecosystems, impeding effective aquatic biodiversity protection strategy.

Recent advances in environmental DNA (eDNA) metabarcoding and remote sensing (RS) have made large-scale sampling possible in a time- and cost-efficient manner, with abundant and booming amount of biodiversity data available. RS is advantageous in monitoring terrestrial ecosystems, while eDNA is especially effective in assessment of aquatic biodiversity. When combined together, they can provide a holistic view of biodiversity at the landscape level.

Based on these two technologies, this thesis studies the land-water linkage of biodiversity at regional to global scales. Briefly, two dimensions—spatial range and magnitude—were adopted to depict such linkages within drainage catchments, which were the basic spatial unit for analysis. Specifically, I combined satellite remote sensing imagery and eDNA extraction from river water across a temperate mountainous catchment and identified a characteristic spatial land-water fingerprint, attesting that biodiversity patterns in the river can be linked to the functional diversity of surrounding terrestrial ecosystems. The spatial scale of this linkage was measured to be 2.0 km upstream from sampling sites with a peaking signal at a 400 m distance. Further analysis using high-resolution airborne imaging spectroscopy and light detection and ranging (LiDAR) point clouds showed a variation in spatial scales of the land-water linkage across major aquatic functional feeding groups (FFGs). I detected the scale of the linkage ranging from a few hundred meters to more than 10 km, with collectors and filterers, shredders, and small invertebrate predators having local-scale association, while invertebrate eating fish, grazers and scrapers having more regional-scale associations. [...]

Heatwaves (HWs) are predicted to increase in frequency and severity due to climate change. Yet, there is limited information about how ecological resilience of aquatic communities is going to be impacted by recurrent HWs. Here, we used data from an outdoor freshwater mesocosm experiment where a semi-natural phytoplankton community was exposed to three subsequent HWs. The data were used to test two different hypotheses regarding community and ecosystem responses to recurrent perturbations: critical slowing down and rescue. Slowing down would determine a reduction in resilience and eventually a community or ecosystem collapse, whereas rescue would increase community or ecosystem resilience and maintain stable community and ecosystem properties. The results of our experiment showed evidence for critical slowing down, but not for community or ecosystem rescue. The recovery capacity of phytoplankton biomass and dissolved oxygen gradually decreased after the first two HWs and sharply declined after the third one. The decline in these community and ecosystem properties were linked to a significant compositional turnover in the phytoplankton community. Although we did not find evidence for a transition into an alternative stable state, our results provide insights into how the overall resilience of a phytoplankton community may decline in the presence of recurrent heatwaves. Thus, we highlight the importance of monitoring the slowing down of recovery of aquatic communities experiencing repeated exposure to severe perturbations.

Ecosystem size and spatial resource flows are key factors driving species diversity and ecosystem function. However, the question of whether and how these drivers interact has been largely overlooked. Here, we investigated how ecosystem size asymmetry affects species diversity and function of two-patch meta-ecosystems connected through flows of nonliving resources. We conducted a microcosm experiment, mimicking resource flows between ecosystems of different sizes yet otherwise identical properties or between ecosystems of the same size. Meta-ecosystems with asymmetric ecosystem sizes displayed higher α-diversity but lower β-diversity and ecosystem function (total biomass) than their unconnected counterparts. At the same time, such an effect was not found for meta-ecosystems of identical patch sizes. Our work demonstrates how the size of ecosystems, interconnected via resource flows, can modulate cross-ecosystem dynamics, having implications for species diversity and function across scales.

Modern plankton high-throughput monitoring relies on deep learning classifiers for species recognition in water ecosystems. Despite satisfactory nominal performances, a significant challenge arises from dataset shift, which causes performances to drop during deployment. In our study, we integrate the ZooLake dataset, which consists of dark-field images of lake plankton (Kyathanahally et al. 2021a), with manually annotated images from 10 independent days of deployment, serving as test cells to benchmark out-of-dataset (OOD) performances. Our analysis reveals instances where classifiers, initially performing well in in-dataset conditions, encounter notable failures in practical scenarios. For example, a MobileNet with a 92% nominal test accuracy shows a 77% OOD accuracy. We systematically investigate conditions leading to OOD performance drops and propose a preemptive assessment method to identify potential pitfalls when classifying new data, and pinpoint features in OOD images that adversely impact classification. We present a three-step pipeline: (i) identifying OOD degradation compared to nominal test performance, (ii) conducting a diagnostic analysis of degradation causes, and (iii) providing solutions. We find that ensembles of BEiT vision transformers, with targeted augmentations addressing OOD robustness, geometric ensembling, and rotation-based test-time augmentation, constitute the most robust model, which we call BEsT. It achieves an 83% OOD accuracy, with errors concentrated on container classes. Moreover, it exhibits lower sensitivity to dataset shift, and reproduces well the plankton abundances. Our proposed pipeline is applicable to generic plankton classifiers, contingent on the availability of suitable test cells. By identifying critical shortcomings and offering practical procedures to fortify models against dataset shift, our study contributes to the development of more reliable plankton classification technologies.

Ökologische Gemeinschaften in Flüssen und Seen reagieren ähnlich auf den Klimawandel wie Gemeinschaften an Land. Das zeigt der erste umfassende Vergleich von Süsswasser- und Landökosystemen weltweit unter der Leitung von Eawag und WSL. Steigen die Temperaturen, profitieren vor allem wärmeliebende Arten. Eine überraschende Ausnahme könnte das Plankton sein.

Les communautés écologiques des lacs et rivières réagissent aux changements climatiques à peu près comme les communautés terrestres. C’est ce que montre la première comparaison des écosystèmes limniques et terrestres, réalisée à l’échelle de la planète sous la houlette de l’Eawag et du WSL. L’augmentation des températures profite surtout aux espèces thermophiles. Le plancton pourrait être une exception surprenante.

Nonliving resources frequently flow across ecosystem boundaries, which can yield networks of spatially coupled ecosystems. Yet the significance of resource flows for ecosystem function has predominantly been understood by studying two or a few coupled ecosystems, overlooking the broader resource flow network and its spatial structure. Here, we investigate how the spatial structure of larger resource flow networks influences ecosystem function at metaecosystem scales by analyzing metaecosystem models with homogeneously versus heterogeneously distributed resource flow networks but otherwise identical characteristics. We show that metaecosystem function can differ strongly between metaecosystems with contrasting resource flow networks. Differences in function generally arise through the scaling up of nonlinear local processes interacting with spatial variation in local dynamics, the latter of which is influenced by network structure. However, we find that neither network structure guarantees the greatest metaecosystem function. Rather, biotic (organism traits) and abiotic (resource flow rates) properties interact with network structure to determine which yields greater metaecosystem function. Our findings suggest that the spatial structure of resource flow networks coupling ecosystems can be a driver of ecosystem function at landscape scales. Furthermore, our study demonstrates how modifications to the structural, biotic, or abiotic properties of metaecosystem networks can have nontrivial large-scale effects on ecosystem function.

Host–bacterial communities (microbiomes) are influenced by a wide range of factors including host genotype and parasite exposure. However, few studies disentangle temporal and host-genotype-specific variation in microbiome response to infection across several host tissues. We experimentally exposed the freshwater crustacean Daphnia magna to its fungal parasite Metschnikowia bicuspidata and characterized changes in host–bacterial communities associated with the parasite's development within the host. We used 16S rRNA gene sequencing to assess bacterial communities of the host (a) 24 h ('initial parasite exposure') and (b) 10 days ('successful infection') after exposure to a standard dose of M. bicuspidata spores, in host guts, body tissue (excluding guts) and whole individuals. We also investigated whether bacterial community responses to parasite exposure varied by host genotype.
Parasite exposure did not immediately alter host gut bacterial communities, but drove host-genotype-specific changes in the bacterial community composition of whole individuals. We validated that these changes were not driven by shifts in bacterial communities of the culturing medium, due to the addition of the parasite spore solution. Successful infection (i.e. the proliferation of M. bicuspidata spores in the host body) reduced alpha diversity and shifted abundance of dominant bacterial orders in the gut. Moreover, it induced a host-genotype-specific changes in body bacterial community composition. Overall, bacterial community responses to parasite exposure and subsequent infection are complex: they occur in a host-genotype-dependent manner, differentially at distinct timepoints after parasite exposure, and in specific host tissue.

Climate projections for continental Europe indicate drier summers, increased annual precipitation, and less snowy winters, which are expected to cause shifts in species' distributions. Yet, most regions/countries currently lack comprehensive climate-driven biodiversity projections across taxonomic groups, challenging effective conservation efforts. To address this gap, our study evaluated the potential effects of climate change on the biodiversity of an alpine country of Europe, Switzerland. We used a state-of-the art species distribution modeling approach and species occurrence data that covered the climatic conditions encountered across the full species' ranges to help limiting niche truncation. We quantified the relationship between baseline climate and the spatial distribution of 7291 species from 12 main taxonomic groups and projected future climate suitability for three 30-year periods and two greenhouse gas concentration scenarios (RCP4.5 and 8.5). Our results indicated important effects of projected climate changes on species' climate suitability, with responses varying by the taxonomic and conservation status group. The percentage of species facing major changes in climate suitability was higher under RCP8.5 (68%) compared to RCP4.5 (66%). By the end of the century, decreases in climate suitability were projected for 3000 species under RCP8.5 and 1758 species under RCP4.5. The most affected groups under RCP8.5 were molluscs, algae, and amphibians, while it was molluscs, birds, and vascular plants under RCP4.5. Spatially, by 2070–2099, we projected an overall decrease in climate suitability for 39% of the cells in the study area under RCP8.5 and 10% under RCP4.5, while projecting an increase for 50% of the cells under RCP8.5 and 73% under RCP4.5. The most consistent geographical shifts were upward, southward, and eastward. We found that the coverage of high climate suitability cells by protected areas was expected to increase. Our models and maps provide guidance for spatial conservation planning by pointing out future climate-suitable areas for biodiversity.

While it is commonly accepted that ecosystem dynamics are nonlinear, what is often not acknowledged is that nonlinearity implies scale-dependence. With the increasing availability of high-resolution ecological time series, there is a growing need to understand how scale and resolution in the data affect the construction and interpretation of causal networks—specifically, networks mapping how changes in one variable drive changes in others as part of a shared dynamic system ("dynamic causation"). We use Convergent Cross Mapping (CCM), a method specifically designed to measure dynamic causation, to study the effects of varying temporal and taxonomic/functional resolution in data when constructing ecological causal networks. As the system is viewed at different scales relationships will appear and disappear. The relationship between data resolution and interaction presence is not random: the temporal scale at which a relationship is uncovered identifies a biologically relevant scale that drives changes in population abundance. Further, causal relationships between taxonomic aggregates (low-resolution) are shown to be influenced by the number of interactions between their component species (high-resolution). Because no single level of resolution captures all the causal links in a system, a more complete understanding requires multiple levels when constructing causal networks.

Parasites spend at least a part of their lives in or on host organisms from which they obtain resources. Many parasites have complex life cycles, requiring transmission through multiple host species to mature and reproduce. In order to increase the likelihood of successful transmission between hosts via predation events, some parasites alter the phenotype of the host. Fishes are common hosts in the aquatic environment and are often the targets of manipulation. Diplostomid eye flukes and the tapeworm Schistocephalus solidus have been well studied for their ability to alter fish phenotypes, increasing transmission via predation.

Die Erhaltung der Biodiversität ist eine gesellschaftliche Herausforderung. Die gesetzten Schutzziele werden bisher oft nur unvollständig oder nicht erreicht. Kann ein stärkerer Wissenstransfer zwischen Forschung und Praxis dazu beitragen, Antworten auf Fragen aus der Naturschutzpraxis zu finden? Das Synthesezentrum Biodiversität probiert es aus.

The processing of organic matter is a central ecosystem function in freshwater ecosystems that allows the integration of terrestrial plant material into aquatic heterotrophic food webs. From an energetic perspective, many temperate aquatic systems fundamentally depend on such allochthonous inputs. Current research established that this central ecosystem function may be linked to population density of few yet dominant invertebrate detritivores, showing a negative density-dependent relationship. Here, we extended the current knowledge and experimentally assessed the processing of leaf litter by freshwater amphipods, using broad density gradients, interspecific competition, and laboratory and field experiments. We used two species of dominant amphipods, namely the native Gammarus fossarum and the non-native Gammarus roeselii, varying their density by two orders of magnitude, both in single-species and two-species treatments. Results from 252 mesocosms in the lab and 97 mesocosms in a natural stream show that per capita leaf litter processing rates are strongly negatively dependant on population density in monocultures. Interspecific competition in two-species treatments corroborated the negative density-dependent ecosystem function and highlighted the functional redundancy of the two detritivore species. We identified a flattening in the processing rates at previously unreported but well-defined breakpoints. These breakpoints may reflect minimal metabolic requirements at which survival takes precedence over any other process, such as interference competition. The breakpoints were consistent across both species, indicating that they must process leaf litter equalling one fifth to one fourth of their dry body weight per day as a minimal nutritional threshold. Our results suggest the need for integrating nonlinear density-dependencies and breakpoint population densities in key ecosystem functions in aquatic ecosystem modelling alongside classical biodiversity–ecosystem functioning relationships. Depending on the population density the corresponding ecosystem functioning could differ significantly. This corroborates the need to better understand biodiversity–abundance relationships when protecting aquatic ecosystems.

1. Global environmental change will cause shifts in species communities, with non-native species likely replacing native ones at an unprecedented rate. This will have consequences for biodiversity and ecosystem services, in addition to the ecological and economic damage caused by those non-native species that are invasive. Understanding general patterns driving distributions of native and non-native species is therefore vital, but no study has compared yet whether environmental variables that correlate with a species' presence differ between the two groups other than at local scale and often with very limited sample size.
2. In this study, we focus on 141 native and non-native congeneric plant species pairs at the scale of Switzerland. In the framework of correlative species distribution models, we used newly developed methods for efficient automated selection of a parsimonious number of predictor environmental variables to determine which ones, out of a large candidate set in eight classes, have the strongest explanatory power for both species groups.
3. Our results indicated that variables influence the two groups in significantly different ways. Climate was by far the strongest determinant of both native and non-native species distributions, although it had significantly more explanatory power in native species models.
4. Models for non-native species were significantly more influenced by anthropogenic factors, land use variables and forest cover. The presence of non-native species was also associated with habitats with a significantly lower mean naturality value than native species.
5. These findings provide novel empirical evidence for the different environmental factors driving native and non-native plants' distributions and guidance for non-native species management.
6. Practical implications: species distribution models are an increasingly frequently advised tool for conservation management and our results provide guidelines on which covariates should be specifically considered to assess the habitat suitability of non-native versus native species. The distributions of the former group of species are particularly important to research, as, in time, they may turn invasive. In addition, areas close to infrastructure should be scanned regularly for incipient colonizations by non-native species, especially in as yet uninvaded areas, such as high mountains.

Terrestrial and aquatic ecosystems are tightly linked, with direct implications for applied resource management and conservation. It is well known that human land use change and intensification of terrestrial systems can have large impacts on surface freshwater ecosystems. Contrastingly, the study and understanding of such land use impacts on groundwater communities is lagging behind. Both the impact strength of land use on groundwater communities and the spatial extents at which such interlinkages are operating are largely unknown, despite our reliance on groundwater for drinking water extraction as a key ecosystem service. Here, we analyzed groundwater amphipod occurrence from several hundred shallow groundwater aquifers used for drinking water extraction across a region of varying agricultural intensity and human population density in Switzerland. Despite drinking water extraction sites being generally built at locations with expected minimal aboveground impacts on water quality, we found a direct correlation between land use type and intensity within the surrounding catchment area and the locally measured nitrate concentrations, which is a direct proxy for drinking water quality. Furthermore, groundwater amphipods were more likely to be found at sites with higher forest coverage than at sites with higher crop and intensive pasture coverages, clearly indicating a tight connection between aboveground land use and groundwater biodiversity. Our results indicate that land use type effects on groundwater communities are most relevant and pronounced to spatial scales of about 400–1000 m around the groundwater sampling site. Importantly, the here identified spatial scale is 1.2- to 3-fold exceeding the average extent of currently defined groundwater protection zones. We postulate that incorporating an ecosystem perspective into groundwater management strategies is needed for effective protection of groundwater quality and biodiversity.

Implementing and optimizing biodiversity monitoring is crucial given the current, worldwide biodiversity decline. Compared to other ecosystems, monitoring of biodiversity is lagging behind in groundwater ecosystems, both because of sparse taxonomic knowledge and methodological constraints. We here assessed temporal variation in the occurrence and abundance of macroinvertebrates collected systematically from shallow groundwater aquifers of Switzerland to establish general principles on seasonality and repeatability of assessment outcomes. We found no seasonal abundance pattern for obligate groundwater amphipods and isopods, indicating temporal consistency. In contrast, other macroinvertebrates (predominantly stygophiles and stygoxenes) showed pronounced seasonality in their detection rate. However, we found variability in detection rates across groundwater amphipod species and especially across sampling sites. For groundwater communities, characterized by narrowly-distributed and rare species, our results highlight the need for tailored and extensive sampling strategies. When setting up monitoring programs on groundwater fauna, detection probability, temporal autocorrelation, and standardization of sampling effort should be carefully considered. Applying novel, systematic approaches, can offer promising methodologies for understanding and conserving groundwater ecosystems.

Human land-use intensification threatens arthropod (for example, insect and spider) biodiversity across aquatic and terrestrial ecosystems. Insects and spiders play critical roles in ecosystems by accumulating and synthesizing organic nutrients such as polyunsaturated fatty acids (PUFAs). However, links between biodiversity and nutrient content of insect and spider communities have yet to be quantified. We relate insect and spider richness to biomass and PUFA-mass from stream and terrestrial communities encompassing nine land uses. PUFA-mass and biomass relate positively to biodiversity across ecosystems. In terrestrial systems, human-dominated areas have lower biomass and PUFA-mass than more natural areas, even at equivalent levels of richness. Aquatic ecosystems have consistently higher PUFA-mass than terrestrial ecosystems. Our findings reinforce the importance of conserving biodiversity and highlight the distinctive benefits of aquatic biodiversity.

Der Übergangsbereich zwischen Wasser und Land beherbergt vielfältige Lebensräume und zahlreiche Arten: Die dort vorhandene Biodiversität ist besonders hoch und über die blaugrüne Grenze hinweg laufen zahlreiche ökologische Prozesse ab und Stoffe werden ausgetauscht. Der Mensch hat die blaugrünen Lebensräume schon immer genutzt, ja manche verdanken ihre Entstehung dem Menschen. Auch in Zukunft wird der Mensch blaugrüne Landschaftselemente vielfältig nutzen, aber auch vonihnen abhängig sein, sei dies zur Wasserrückhaltung unter dem Klimawandel oder für die Erholung.

Aim: Seagrass meadows represent a key marine ecosystem owing to the significant biodiversity they host. Protection actions are often implemented without considering connectivity between habitats. In this article, we project and prioritise Mediterranean seagrass habitats (Posidonia oceanica and Cymodocea nodosa) based on their potential as sources/retention and stepping stones for dispersal propagules of the associated biotic communities. We use this information to identify gaps in the protection of highly ranked habitats.
Location: Mediterranean Sea.
Methods: We related seagrass observations with marine environmental predictors to run species distribution models and infer the distribution of Mediterranean seagrasses. We then used a network-based approach (CONEFOR) to rank patches of seagrass suitable areas based on their contribution to the seascape in terms of patch area, potential as source/retention of propagules and stepping stone. Finally, by overlaying our ranking with the spatial distribution of marine protected areas (MPAs), we identified potential gaps in the protection of important seagrass habitats across the Mediterranean and its basins.
Results: Most of the identified patches of seagrass suitable areas are not included in MPAs, only reaching a maximum protection coverage of ~50% in the Northwestern Mediterranean. Relatively few patches contribute disproportionately to connectivity, but top-ranked habitat patches are not included within the existing MPAs network, both at the Mediterranean scale and for most basins. The largest gaps for the source/sink role are in the Aegean and Ionian Sea, and largest gaps for the stepping stone role are in the Adriatic, Ionian and Tyrrhenian Sea.
Main Conclusions: Our results suggest that the current MPAs network fails to protect highly relevant patches of seagrass suitable areas in most of the Mediterranean basins. However, this gap could be filled by a few well-placed MPAs. Overall, we provide novel insights for the identification of key habitats and planning novel coastal MPAs in the region.

Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we used inhibitors to disrupt the gut microbiota of juvenile Epibolus pulchripes (tropical, CH₄-emitting) and Glomeris connexa (temperate, non-CH₄-emitting) and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, with Bacteroidota dominant in E. pulchripes and Pseudomonadota in G. connexa. Sodium-2-bromoethanesulfonate treatment halted CH₄ emissions in E. pulchripes, but it resumed after returning to normal feeding. Employing ¹³C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipede’s nutrition.

Biodiversity loss is increasing worldwide, necessitating effective approaches to counteract negative trends. Here, we assessed aquatic macroinvertebrate biodiversity in two river catchments in Switzerland; one significantly degraded and associated with urbanisation and instream barriers, and one in a near-natural condition. Contrary to our expectations, environmental heterogeneity was lower in the near-natural stream, with enhanced productivity in the degraded system resulting in a greater range of environmental conditions. At face value, commonly employed alpha, beta and gamma biodiversity metrics suggested both catchments constituted healthy systems, with greater richness or comparable values recorded in the degraded system relative to the near-natural one. Further, functional metrics considered to be early indicators for anthropogenic disturbance, demonstrated no anticipated differences between degraded and near-natural catchments. However, investigating the identity of the taxa unique to each river system showed that anthropogenic degradation led to replacement of specialist, sensitive species indicative of pristine rivers, by generalist, pollution tolerant species. These replacements reflect a major alteration in community composition in the degraded system compared with the near-natural system. Total nitrogen and fine sediment were important in distinguishing the respective communities. We urge caution in biodiversity studies that employ numerical biodiversity metrics alone. Assessing just one aspect of diversity, such as richness, is not sufficient to track biodiversity changes associated with environmental stress. We advocate that biodiversity monitoring for conservation and management purposes must go beyond traditional richness biodiversity metrics, to include indices that incorporate detailed nuances of biotic communities that relates to taxon identity.

Introgressive hybridization is a pivotal force influencing genetic diversity and adaptive potential of invasive species, however to date has received less attention for even the most globally destructive species. Golden apple snails (Pomacea spp.), one of the world’s worst invasive species, were first introduced during the 1980s into Taiwan for commerce and have since emerged as a significant threat to regional biodiversity. Two of the most destructive invasive species of Pomacea, P. canaliculata and P. maculata, have been reported to hybridize in its native and non-native range, the latter of which has been posited to facilitate an adaptive advantage for increasing invasiveness. Thus, our study combined mitochondrial COI (Cytochrome c oxidase subunit I) barcoding and nuclear EF1-α (elongation factor 1-alpha) gene analysis to identify putative hybridization among 254 samples collected across 14 cities/counties in Taiwan. Our investigation confirmed hybridization within the sympatric but heterogeneous distribution of P. canaliculata and P. maculata in Taiwan. The results indicated that 18.9% of the total sampled population consists of hybrids, whereas 81.1% of the samples demonstrated pure P. canaliculata genetics. Remarkably, no pure P. maculata were detected across the island, and all P. maculata mtDNA samples appeared to be genetically introgressed. The dearth of pure P. maculata populations, despite the prevalence of canaliculata-maculata hybrids, invites speculation about introduction mechanisms, genetic drift and maybe the nuanced influence of environmental factors on distribution dynamics, all of which required further investigation. These findings contribute significant scientific insights into the invasive dynamics of Pomacea in Taiwan, and the results underline findings applicable for devising targeted and effective conservation strategies in regions grappling with the challenges posed by invasive species.

Als Folge des Klimawandels etablieren sich immer mehr wärmeliebende Arten in Schweizer Gewässern. Da wirbellose Kleinlebewesen als Bioindikatoren für die Qualität von Fliessgewässern dienen, könnte diese Entwicklung die biologische Gewässerbeurteilung verfälschen. Simulationen zeigen, dass die Vielfalt der Wirbellosen tatsächlich zunehmen wird, jedoch auf Kosten kälteliebender Arten. Soweit sich das beurteilen lässt, sind die verwendeten Indizes aber robust genug, um ihre Aussagekraft zur Gewässerqualität für die nächsten Jahrzehnte zu behalten.

Plant–insect trophic systems should be particularly sensitive to processes altering species spatial co-occurrences, as impacts on one level can cascade effectively through the strong trophic reliance to the other level. Here, we predicted the biogeography of Lepidoptera–plant communities under global-change scenarios, exploiting spatially resolved data on 423 Lepidoptera species and their 848 food plants across the German state of Baden-Württemberg (ca. 36,000 km²). We performed simulations of plant extinction and Lepidoptera expansion, and respectively assessed their cascading consequences—namely secondary extinction of Lepidoptera and change in functional distance of plants—on the interaction networks. Importantly, the simulations were spatially explicit, as we accounted for realistic landscape contexts of both processes: Plant extinctions were simulated as "regional" (a species goes extinct in the whole region at once) vs. "isolation-driven" (a species gradually goes extinct from the peripheral or isolated localities according to its real regional distribution); Lepidoptera expansions were simulated with random, northward, and upward directions according to real topography. The consequences were assessed based on empirical community composition and trophic relationships. When evaluated by regional richness, the robustness of Lepidoptera assemblages against secondary extinctions was higher under isolation-driven plant extinctions than regional plant extinction; however, this relationship was reversed when evaluated by averaged local richness. Also, with isolation-driven plant extinctions, Lepidoptera at the central sub-region of Baden-Württemberg appeared to be especially vulnerable. With Lepidoptera expansions, plants' functional distances in local communities dropped, indicating a possible increase of competition among plants, yet to a lesser extent particularly with upward movements. Together, our results suggested that the communities' composition context at the landscape scale (i.e., how communities, with respective species composition, are arranged within the landscape) matters when assessing global-change influences on interaction systems; spatially explicit consideration of such context can reveal localised consequences that are not necessarily captured via a spatially implicit, regional perspective.

Der Bau von Weihern hat sich als wirksame Massnahme erwiesen, um die Bestände von Amphibien zu fördern und ihre Bestände zu stabilisieren. Im Kanton Aargau zeigen Ergebnisse aus zwei Jahrzehnten Weiherbau und begleitendem Monitoring, was eine funktionierende ökologische Infrastruktur für Amphibien ausmacht: Es braucht gut vernetzte Amphibienlaichgebiete aus mehreren Weihern mit grosser Wasserfläche.

L'aménagement d'étangs s'est révélé efficace pour promouvoir et stabiliser les populations de batraciens. Dans le canton d'Argovie, les résultats de deux décennies d'aménagement et de suivi d'étangs montrent ce qu'est une infrastructure écologique pour batraciens fonctionnelle: il faut que les sites de reproduction soient interconnectés et comprennent plusieurs étangs dotés d'une importante surface aquatique.

Widely used methods to assess population genetic structure and differentiation rely on independence of marker loci. Following the assumption, the common metrics, for example FST, evaluate genetic structure by averaging across loci. Common metrics do not use information in the associations among loci at the individual level and are often criticized for failing to measure true differentiation even when loci segregate independently. We introduce a new concept to measure β-variation (Effective Number of Different Populations, ENDP). It requires the following steps: (a) calculation of a proper dissimilarity between genetic profiles of all individuals; (b) calculation of suitable pairwise distances between the samples based on the dissimilarities between individuals; (c) calculation of diversity (in terms of Hill numbers) and dispersion of samples based on the pairwise distances between samples; (d) ENDP is then estimated by combining the diversity and dispersion. ENDP estimates β-variation independently of estimates of within-sample α-variation, although β-and α-estimates could statistically correlate to some extent. This new concept differs from the existing standard where β-diversity is estimated based on the “partition of variation” scheme (beta = gamma − alpha or beta = gamma∕alpha), so that estimates of β-diversity directly depend on the corresponding values of α-diversity. ENDP estimates are obtained by evaluating information in the available genetic profiles of individuals including association of loci. Therefore, ENDP can be used even in an absence of panmixia. We illustrate the use of this concept by analyzing the population genetic structure of a sexual species (a trematode parasite) occupying connected populations across a broad geographic area. The analysis is complicated by geographically coexisting cryptic species and the potential mixed-mating system of this hermaphroditic parasite. Analyses with subsampled data demonstrated that ENDP estimates are robust. Number of loci used for genotyping has much stronger effect on variation of point ENDP estimates than sample size.

A central goal in evolutionary biology is to understand how different evolutionary processes cause trait change in wild populations. However, quantifying evolutionary change in the wild requires linking trait change to shifts in allele frequencies at causal loci. Nevertheless, datasets that allow for such tests are extremely rare and existing theoretical approaches poorly account for the evolutionary dynamics that likely occur in ecological settings. Using a decade-long integrative phenome-to-genome time-series dataset on wild threespine stickleback (Gasterosteus aculeatus), we identified how different modes of selection (directional, episodic, and balancing) drive microevolutionary change in correlated traits over time. Most strikingly, we show that feeding traits changed by as much 25% across 10 generations which was driven by changes in the genetic architecture (i.e., in both genomic breeding values and allele frequencies at genetic loci for feeding traits). Importantly, allele frequencies at genetic loci related to feeding traits changed at a rate greater than expected under drift, suggesting that the observed change was a result of directional selection. Allele frequency dynamics of loci related to swimming traits appeared to be under fluctuating selection evident in periodic population crashes in this system. Our results show that microevolutionary change in a wild population is characterized by different modes of selection acting simultaneously on different traits, which likely has important consequences for the evolution of correlated traits. Our study provides one of the most thorough descriptions to date of how microevolutionary processes result in trait change in a natural population.

DNA methylation (DNAm) is a mechanism for rapid acclimation to environmental conditions. In natural systems, small effect sizes relative to noise necessitates large sampling efforts to detect differences. Large numbers of individually sequenced libraries are costly. Pooling DNA prior to library preparation may be an efficient way to reduce costs and increase sample size, yet there are to date no recommendations in ecological epigenetics research. We test whether pooled and individual libraries yield comparable DNAm signals in a natural system exposed to different pollution levels by generating whole-epigenome data from two invasive molluscs (Corbicula fluminea, Dreissena polymorpha) collected from polluted and unpolluted localities (Italy). DNA of the same individuals were used for pooled and individual epigenomic libraries and sequenced with equivalent resources per individual. We found that pooling effectively captures similar genome-wide and global methylation signals as individual libraries, highlighting that pooled libraries are representative of the global population signal. However, pooled libraries yielded orders of magnitude more data than individual libraries, which was a consequence of higher coverage. We would therefore recommend aiming for a high initial coverage of individual libraries (15×) in future studies. Consequently, we detected many more differentially methylated regions (DMRs) with the pooled libraries and a significantly lower statistical power for regions from individual libraries. Computationally pooled data from the individual libraries produced fewer DMRs and the overlap with wet-lab pooled DMRs was relatively low. We discuss possible causes for discrepancies, list benefits and drawbacks of pooling, and provide recommendations for future epigenomic studies.

Amphibien sind aus vielen Gründen stark gefährdet, sowohl global, national als auch lokal: Lebensräume gehen verloren und verlieren an Qualität, standortfremde Fische fressen Amphibienlarven, Pestizide beeinträchtigen die Populationen, auf der Wanderung zu den Laichgebieten stellen Straßen eine Gefahr dar, neue Krankheitserreger machen den Tieren zu schaffen, und das sich ändernde Klima führt zu Trockenheit - die Liste könnte noch erweitert werden. Trotz dieser negativen Faktoren ist wirkungsvoller Amphibienschutz möglich, wie die Ergebnisse des Weiherbauprogramms des Schweizer Kantons Aargau zeigen.

Anthropogene Einflüsse auf die Umwelt wirken sich auf das Plankton und seine Rolle im See aus und beeinträchtigen so Nahrungsnetze, Ökosystemleistungen und Wasserqualität. In der Schweiz wird das traditionelle Planktonmonitoring durch taxonomische Fachpersonen mittels Mikroskopie aufgrund von Ressourcen- und Personalmangel zunehmend eingeschränkt. Diese Studie untersucht das Potenzial automatisierter Bildgebungsverfahren wie dem Aquascope und zeigt die Defizite und Chancen für zukünftige Entwicklungen auf.

Host–parasite interactions are influenced by present and past eco-evolutionary interactions and the local environment. An ecological community defines the potential host range of each parasite and the potential parasite diversity of each host species. Past and present processes translate potential to realised interaction niches of parasite and host species. Host–parasite interactions are antagonistic, which may slow the saturation of their interaction niches. Intervality, a property of bipartite networks, measures saturation of interaction niches. Intervality of a community increases as the interaction niches of species of one guild (e.g. hosts) become saturated for their interactions with another guild (e.g. parasites). Characteristics driving intervality in host and parasite communities are largely unknown, as well as the effect of environmental change on intervality of these communities. In our study, we assess if the characteristics 'phylogenetic relatedness' and 'overlap in ecological interactions' explain intervality of rodent host–helminth parasite communities. In addition, we contrast intervality of these communities from habitats that differ in their history of human-driven modification. We performed the analyses for the interaction niches of both parasites and hosts, independently. Our results indicated that host and parasite communities were non-interval or significantly less interval than expected by chance. Phylogenetic relatedness and overlap in ecological interactions did not explain the maximum values of intervality. We speculate that antagonistic coevolution in host–parasite communities may hinder communities to reach saturation, which would explain why it is difficult to find the characteristics that explain intervality of a community. Interestingly, intervality of the interaction niche of parasites (host range) increased with habitat modification (i.e. saturation increased), whereas intervality of the interaction niche of hosts (parasite diversity) decreased as habitat modification increased. These opposite trends suggest that interaction niches of parasites and hosts respond differently to habitat modification.

1. Freshwater and terrestrial biodiversity are linked through spatial resource flows. Key examples are detrital subsidies from the riparian vegetation that form the base of food webs in small streams. Despite the central role of detritivores in these food webs, the consequences of altered riparian vegetation type and resource availability on their trophic strategies are less known.
2. Therefore, we experimentally tested direct and indirect effects of riparian vegetation type (i.e. riparian forests present vs. absent) on trophic interactions and dietary imbalances of aquatic detritivores. To characterise trophic strategies, we used stoichiometric and isotopic differences between consumers and resources as functional measures of trophic link strength in leaf litter bags naturally colonised by stream decomposers and detritivores.
3. Our results show that an absence of riparian forests affected stoichiometric and isotopic properties in stream detrital food webs. Where local riparian forests were absent, leaf litter showed lower C:N ratios, which only trichopteran detritivores mirrored, whereas plecopteran and crustacean detritivores showed differences in their isotopic signatures. Diverging patterns between resources and consumers could lead to a rewiring of energy flow paths and weaken the coupling between aquatic detritivores and terrestrial detritus.
4. Consequently, our findings demonstrate that riparian forests are essential for aquatic food webs by not only influencing organisms themselves but also their trophic interactions and energy flow paths. Aquatic detritivores depending on terrestrial subsidies can be highly sensitive to local changes in their resource environment. Therefore, functionally divergent patterns between resources and consumers in recipient systems highlight how habitat properties of the donor system can affect food webs connected across ecosystem boundaries. Read the free Plain Language Summary for this article on the Journal blog.

More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes.

Cyanobacterial blooms require monitoring, as they pose a threat to ecosystems and human health, especially by the release of toxins. Along with widely reported microcystins, cyanobacteria coproduce other bioactive metabolites; however, information about their dynamics in surface waters is sparse. We investigated dynamics across full bloom successions throughout a five-year lake monitoring campaign (Greifensee, Switzerland) spanning 150 sampling dates. We conducted extensive suspect screening of cyanobacterial metabolites using the database CyanoMetDB. Across all 850 samples, 35 metabolites regularly co-occurred. Microcystins were present in 70% of samples, with [d-Asp³,(E)-Dhb⁷]MC-RR reaching concentrations of 70 ng/L. Anabaenopeptins, meanwhile, were detected in 95% of all samples with concentrations of Oscillamide Y up to 100-fold higher than microcystins. Based on LC-MS response and frequency, we identified indicator metabolites exclusively produced by one of three cyanobacteria isolated from the lake, these being [d-Asp³,(E)-Dhb⁷]MC-RR from Planktothrix sp. G2020, Microginin 761B from Microcystis sp. G2011, and Ferintoic acid B from Microcystis sp. G2020. These indicators showed distinct temporal trends and peaking seasons that reflect the variance in either the abundance of the producing cyanobacteria or their toxin production dynamics. Our approach demonstrates that selecting high LC-MS response and frequent and species-specific indicator metabolites can be advantageous for cyanobacterial monitoring.

Rivers are biodiverse ecosystems that play an essential role in the processing of organic matter from headwaters to the lower reaches. The biodiversity within these spatially complex ecosystems is often subject to huge seasonal variation, particularly in temperate regions, for example seasonal peaks in emergence of aquatic insects or migration of fish through the river network. However, these ecosystems are also subject to strong anthropogenic pressures that affect not only the biodiversity within this system, but the functions this biodiversity provides to key ecosystem processes. Therefore, spatial and temporally dynamics must be considered to effectively assess and understand the biodiversity and functioning within an ecosystem. Here, we assessed ecosystem function at a high spatial and temporal resolution across a large river network, specifically focussing on standardised organic–matter decomposition. Our results show—even when correcting for temperature—significant effects of both season and water chemistry parameters on microbial decomposition. However, we found no effect of space (i.e., site location within the network) on ecosystem function, contrary to expectations. We also found no imprint of the microbial community richness assessed in the water column (α–diversity and Shannon Index) on the patterns of organic–matter decomposition, however, this may be due to our focus on potential colonising microbes rather than benthic communities. Our study highlights the need to include functional indicators for the assessment of ecosystems.

Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves, or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.

Crop protection from algal grazers is a key area of concern, as grazing zooplankton and flagellates can decimate microalgae crops and impede economic viability of cultivation for biofuels and bioproducts. Inhibition of grazing by chemical and physical interference is one promising solution; however, there have been few empirical tests of this approach that use defense traits innate to algal crop species. Botryococcus braunii is of particular interest because a) it excretes high levels of hydrocarbons and exopolysaccharides and b) forms colonies and possesses chemical defenses. Here we conduct a controlled laboratory experiment to test whether B. braunii can mitigate losses to grazing by two distinct grazers, Daphnia magna and Poterioochromonas malhamensis, due to both chemical inhibition and physical interference linked to large/inedible colonies. We show that chemical and physical defenses interactively reduce the total effect of grazing, thus significantly increasing the biomass and growth rates of cultures of B. braunii and Nannochloropsis limnetica when either grazer is present. We also find that B. braunii medium enhances the growth of N. limnetica. Our study demonstrates how community engineering can identify synergies arising from algal co-cultivation (e.g., by using industrially relevant strains for crop protection). While our lab study serves as a proof-of-concept, future research should test this strategy at pilot scale; if successful, such ecological discoveries may help to reduce the costs of large-scale deployment of algal cultivation for sustainable foods, fuels, bioproducts (e.g., bioplastics), and carbon capture.

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self-compatible hermaphrodites, the mating system (e.g., self-fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (N_e). This can potentially accelerate genetic drift, particularly in small populations where self-fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (N_e) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within-population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and N_e estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within-population genetic diversity.

Environmental DNA (eDNA) has revolutionized ecological research, particularly for biodiversity assessment in various environments, most notably aquatic media. Environmental DNA analysis allows for non-invasive and rapid species detection across multiple taxonomic groups within a single sample, making it especially useful for identifying rare or invasive species. Due to dynamic hydrological processes, eDNA samples from running waters may represent biodiversity from broad contributing areas, which is convenient from a biomonitoring perspective but also challenging, as hydrological knowledge is required for meaningful biological interpretation. Hydrologists could also benefit from eDNA to address unsolved questions, particularly concerning water movement through catchments. While naturally occurring abiotic tracers have advanced our understanding of water age distribution in catchments, for example, current geochemical tracers cannot fully elucidate the timing and flow paths of water through landscapes. Conversely, biological tracers, owing to their immense diversity and interactions with the environment, could offer more detailed information on the sources and flow paths of water to the stream. The informational capacity of eDNA as a tracer, however, is determined by the ability to interpret the complex biological heterogeneity at a study site, which arguably requires both biological and hydrological expertise. As eDNA data has become increasingly available as part of biomonitoring campaigns, we argue that accompanying eDNA surveys with hydrological observations could enhance our understanding of both biological and hydrological processes; we identify opportunities, challenges, and needs for further interdisciplinary collaboration; and we highlight eDNA's potential as a bridge between hydrology and biology, which could foster both domains.

The loss of biodiversity in freshwater environments is becoming an increasing problem globally. As a result, many tools have been developed and improved to reduce this decline. However, there is still a need for the identification and evaluation of precise restoration measures to improve habitats and preserve sentinel freshwater species, such as brown trout. This paper provides an up-to-date viewpoint about the life history, habitat characteristics, suitability conditions, and metapopulation dynamic modelling of brown trout, aiming to identify and discuss gaps and propose possible improvements based on collating and reinterpreting literature data. Results suggest that habitat suitability curves for environmental and hydraulic variables possess some degree of universality, for spawning habitat, fry, juvenile and adult trout. Further, an improved method to estimate the amount of suitable area by including the role of stream obstacles (i.e., macro-roughness with characteristic size in the order of the mean water depth) is proposed and discussed. This approach can be integrated into advanced metapopulation models and will allow experts to evaluate the best measures towards restoring and preserving freshwater riverine environments.

Aquatische und terrestrische Lebensräume sind eng miteinander verknüpft. Zahlreiche Pflanzen- und Tierarten nutzen während ihres Lebens beide Lebensräume: zwischen «Wasser» und «Land» herrscht ein reger Austausch von Stoffen und Organismen. Auch die menschliche Nutzung und Gestaltung der Landschaft wird vom Wechselspiel zwischen aquatischen und terrestrischen Lebensräumen geprägt. Das vorliegende Buch lädt dazu ein, auf acht Exkursionen die Funktionsweise dieser Lebensräume und ihre Biodiversität aktiv zu erkunden.

Alpine landscapes are notable regarding their sensitivity to environmental change. Surface waters are especially sensitive as many are influenced by glacial meltwaters that are diminishing with the retreat of glaciers worldwide. The Macun Lakes region, Swiss National Park, is an alpine cirque landscape housing a number of lakes interconnected by streams. The area has been non-glaciated for decades, although rock glaciers are still present in the south basin. Surface waters, 10 stream sites in the present study, have been monitored in mid-summer since the year 2001 for physico-chemistry, periphyton and macroinvertebrates (including 74 species of chironomids). Water physico-chemistry revealed that the two main basins in the catchment differed, reflecting the inputs of rock glacier waters in the south basin. However, trends suggest that waters are becoming more similar as rock glacier inputs diminish over time along with a general decrease in nitrogen levels in all waters. Periphyton biomass showed some spatial differences among sites and a general decrease after 2010. Macroinvertebrate assemblages, including chironomids, clearly differed among basins and spatially along the stream network in each basin. Notably, no significant temporal trend was observed in the long-term data for macroinvertebrates, including chironomids, at the monitored sites. The results suggest that lotic macroinvertebrates may be buffered by the interconnectedness of streams and lakes in the landscape, which mitigates major response patterns of running waters to environmental change.

Aim: groundwater ecosystems harbour a unique biodiversity, but remain poorly studied, mainly due to difficulties in accessibility and imperfect species detection. Consequently, knowledge on the state and change of groundwater biodiversity remains highly deficient. In the context of global warming and excessive groundwater extraction, understanding groundwater from an ecosystem-perspective, including organism diversity and distribution, is essential. This study presents the largest ever systematic assessment of groundwater amphipods, which are a key component of European groundwater biodiversity.
Location: Switzerland (41,285 km²), including data from 906 sampling sites.
Taxon: groundwater amphipods, genera Niphargus and Crangonyx (Crustacea, Amphipoda).
Methods: we applied a highly standardized citizen science approach to collect repeated groundwater fauna samples in collaboration with municipal drinking water providers. Using detection–nondetection data of the genetically identified groundwater amphipod species, we assessed the overall species diversity of both rare and common species. The distribution of commonly found species was predicted using multispecies occupancy modelling.
Results: we retrieved 3882 samples from 906 sites, yielding 2350 groundwater amphipod individuals. We identified a remarkable species diversity, comprising few commonly and many rarely found species. Considering commonly found species, we identified distinct distribution ranges, low local species richness and a predominance of negative co-occurrences. In contrast, a major portion of species were found rarely (generally at just one or two sites each), distributed uniformly throughout the study area and unrelated to common species' recognized hotspots. Many of these rarely found species are not yet formally described.
Main conclusions: Our results give robust emphasis on the rare occurrence and narrow distribution of many groundwater dwellers. Our systematic and standardized sampling data of groundwater amphipods suggest that rarity is particularly prominent and inherent to groundwater organisms. We emphasize the need of systematic data to integrate rare groundwater species in biodiversity assessments, especially in times of global change.

The collection of environmental DNA (eDNA) and subsequent metabarcoding are useful tools for assessing marine fish biodiversity noninvasively. It is of particular importance to evaluate biodiversity in regions that are hard to access and thus less well studied. Sampling and preservation methods tailored to the specific circumstances are required. Aquatic eDNA is often captured on filters made of different materials and pore sizes, and subsequently stored under divergent conditions for varying periods of time. Previous studies on multispecies detection in marine systems have primarily focused on capture and extraction effects. Our study, in contrast, examined the effects of filter type, storage method, and storage time on DNA yield, alpha (i.e., ZOTU richness) and beta diversity (i.e., ZOTU composition) recovered from a marine ecosystem in Shark Bay, Western Australia. We compared two different filter types (cellulose-nitrate filters with pore sizes of 0.45 μm; glass-fiber filters with pore sizes of 0.1 μm), two storage methods (preservation in Longmire's solution and drying, respectively), various storage times (30–68 days) on two metabarcoding assays using different fish-specific primers. Our results showed that storage time decreased DNA yield and affected alpha and beta diversity estimates. Cellulose-nitrate filters stored in Longmire's solution proved to be the best combination with the smallest decrease in DNA yield, no effect on alpha diversity and consistent community compositions. Storing glass-fiber filters in Longmire's solution led to a decrease in eDNA yield and alpha diversity estimates with increasing storage time. Furthermore, the largest change in beta diversity for each metabarcode was found for glass-fiber filters regardless of storage method. Our results highlight the importance of considering storage time and interactions between storage method and filter when analyzing eDNA results, especially when storing samples for an extended time period or comparison of samples stored for different durations.

1. Global change drives multiple facets of biodiversity including interaction diversity, which is fundamental for ecosystem functioning. However, studying trophic interactions is challenging in meta-ecosystems, that is ecosystems connected by spatial flows of energy, materials and organisms across ecosystem boundaries. While analytical methods based on abundances of polyunsaturated fatty acids (PUFAs) and stable isotopes of amino acids (AAs) are being increasingly used, it has never been explored if both approaches could be: (i) combined in mixing models to enhance precision in dietary inference (ii) compared to disentangle transfers of various PUFAs and proteins in food webs in the wild.
2. We explore the utility of analytical approaches based on PUFA abundances and AA isotopes to resolve resource transfers in a natural riparian food web. We focus on spiders and their potential prey from blue, green and brown sources to address three important and persisting methodological issues in food-web ecology, namely whether (i) essential AA carbon isotopes can resolve protein origin from blue, green and brown resources, (ii) PUFA relative abundance and AA isotopes can be combined in a mixing model to provide higher precision estimates (i.e. narrower intervals) and (iii) combining the two approaches can unveil the coupling of protein and PUFA transfers in food webs. 3. Our research demonstrates the power of AA isotopes and PUFAs to distinguish blue, green, and brown sources and their transfer up to consumers. We show that combining PUFA relative abundance and AA isotopes in a mixing model provides overall estimates similar to the individual estimates but significantly increases precision. In addition, we showcase how combining approaches unveil the coupling of protein and PUFA transfers. For instance, we show that most PUFAs are less concentrated from prey to predators, relative to proteins, highlighting uncoupling of PUFAs and protein transfer along food chains.
4. We show for the first time the effectiveness of combining AA isotopes and PUFA abundances, particularly relevant for complex trophic interactions in a meta-ecosystem context. Our study illustrates the trophic uncoupling of proteins and PUFAs, highlighting the necessity in combining both approaches.

The monitoring and management of aquatic ecosystems depend on precise estimates of biodiversity. Metabarcoding analyses of environmental nucleic acids (eNAs), including environmental DNA (eDNA) and environmental RNA (eRNA), have garnered attention for their cost-effective and non-invasive biomonitoring capabilities. However, the accuracy of biodiversity estimates obtained through eNAs can vary among different organismal groups. Here we evaluate the performance of eDNA and eRNA metabarcoding across nine organismal groups, ranging from bacteria to terrestrial vertebrates, in three cross-sections of the Yangtze River, China. We observe robust complementarity between eDNA and eRNA data. The relative detectability of eNAs was notably influenced by major taxonomic groups and organismal sizes, with eDNA providing more robust signals for larger organisms. Both eDNA and eRNA exhibited similar cross-sectional and longitudinal patterns. However, the detectability of larger organisms declined in eRNA metabarcoding, possibly due to differential RNA release and decay among different organismal groups or sizes. While underscoring the potential of eDNA and eRNA in large river biomonitoring, we emphasize the need for differential interpretation of eDNA versus eRNA data. This highlights the importance of careful method selection and interpretation in biomonitoring studies.

The Anthropocene has driven a transformative era where human activities exert unprecedented influence on Earth's biosphere. Consequently, synanthropic organisms, adept at thriving in human-modified environments, have emerged. While well studied in terrestrial ecosystems, the presence and ecological importance of synanthropic species in aquatic ecosystems, specifically among cyanobacteria, are less understood. Cyanobacteria blooms, notorious for their detrimental effects on ecosystems and human health, are increasing in frequency and intensity globally. In this perspective, we explore the evidence supporting this rise of cyanobacteria blooms, emphasizing the roles of human-induced eutrophication and climate change on select cyanobacteria genera. Cyanobacteria are not a monolith, with certain genera showing an observable increase within anthropogenically modified environments. We propose the establishment of a new sub-branch of phycology that explicitly investigates the ecology and physiology of synanthropic cyanobacteria. Understanding the intricate interactions between synanthropic species and human populations is imperative for managing human-altered ecosystems and conserving freshwater resources, particularly in the face of increasing global water insecurity.

Practitioner Points:
• The rise in cyanobacteria blooms is driven by a small subset of human-adapted genera—synanthropic cyanobacteria.
• Research is needed to characterize synanthropic cyanobacteria, which will aid in developing tailored management approaches.
• A paradigm shift from domesticating to "rewilding" landscapes and modifying behaviors to facilitate cohabitation are solutions to reducing risks.

Ongoing global climate change will shift nature towards Anthropocene's unprecedented conditions by increasing average temperatures and the frequency and severity of extreme events, such as heatwaves. While such climatic changes pose an increased threat for freshwater ecosystems, other stressors like pesticides may interact with warming and lead to unpredictable effects. Studies that examine the underpinned mechanisms of multiple stressor effects are scarce and often lack environmental realism. Here, we conducted a multiple stressors experiment using outdoor freshwater mesocosms with natural assemblages of macroinvertebrates, zooplankton, phytoplankton, macrophytes, and microbes. The effects of the neonicotinoid insecticide imidacloprid (1 µg/L) were investigated in combination with three temperature scenarios representing ambient, elevated temperatures (+4 °C), and heatwaves (+0 to 8 °C), the latter two having similar energy input. We found similar imidacloprid dissipation patterns for all temperature treatments with lowest average dissipation half-lives under both warming scenarios (DT₅₀: 3 days) and highest under ambient temperatures (DT₅₀: 4 days) throughout the experiment. Amongst all communities, only the zooplankton community was significantly affected by the combined treatments. This community demonstrated low chemical sensitivity with lagged and significant negative imidacloprid effects only for cyclopoids. Heatwaves caused early and long-lasting significant effects on the zooplankton community as compared to elevated temperatures, with Polyarthra, Daphnia longispina, Lecanidae, and cyclopoids being the most negatively affected taxa, whereas Ceriodaphnia and nauplii showed positive responses to temperature. Community recovery from imidacloprid stress was slower under heatwaves, suggesting temperature-enhanced toxicity. Finally, microbial and macrofauna litter degradation were significantly enhanced by temperature, whereas the latter was also negatively affected by imidacloprid. A structural equation model depicted cascading food web effects of both stressors with stronger relationships and significant negative stressor effects at higher than at lower trophic levels. Our study highlights the threat of a series of heatwaves compared to elevated temperatures for imidacloprid-stressed freshwaters.

Understanding spatial patterns of biodiversity within the context of long-term climatic shifts is of high importance, particularly in the face of contemporary climate change. In comparison to aboveground taxa, subterranean organisms respond to changing climates with generally much lower dispersal and recolonization potential, yet possible persistence in refugial groundwater habitats under ice-shields. However, knowledge on general and geographically large-scale effects of glaciation on contemporary groundwater biodiversity patterns is still very limited. Here, we tested how Late Pleistocene glaciation influenced the diversity and distribution of 36 groundwater amphipod species in Alpine and peri-Alpine regions, characterized by extensive glaciation cycles, and how its legacy explains contemporary diversity patterns. We based our analysis on an unprecedented density of ~ 1000 systematic sampling sites across Switzerland. Using presence–absence data, we assessed biodiversity and species' ranges, and calculated for each site within-catchment distance to the Last Glacial Maximum (LGM) glacier extent. We then applied a sliding window approach along the obtained distance gradient from LGM ice-covered to ice-free sites to compute biodiversity indices reflecting local richness, regional richness, and differentiation, respectively. We found a strong signal of the LGM ice extent on the present-day distribution of groundwater amphipods. Our findings revealed pronounced species turnover and spatial envelopes of individual species' occurrences in formerly ice-covered, ice-free, or transitional zones, respectively. While local richness remained constant and low along the LGM distance gradient, groundwater communities in LGM ice-covered areas were more similar to each other and had lower gamma diversities and decreased occurrence probabilities per sliding window compared to communities in Pleistocene ice-free areas. These results highlight the significant impact of Pleistocene glaciation on shaping biodiversity patterns of subterranean communities and imprinting contemporary distribution of groundwater organisms.

The genus Niphargus is the most diverse subterranean amphipod genus in the western Palearctic region but, owing to the presence of cryptic species and homoplasy, its taxonomy and biogeographic scenarios are complex, making molecular methods essential to understand its evolution. We conducted a study combining dna-based taxonomy with traditional morphotaxonomy to investigate Niphargus bihorensis Schellenberg, 1940, known from the Western Alps and Carpathians. We redescribed the type material of N. bihorensis from Bihor County, Romania, and revealed the presence of a cryptic species, N. absconditus n. sp., in the same karstic area (Pădurea Craiului Mountains). Additionally, the Alpine populations previously attributed to N. bihorensis turned out to belong to a new, not so closely related species, N. tizianoi n. sp. Phylogenetic analyses based on a concatenated dataset of one mitochondrial and two nuclear markers suggest that the N. bihorensis species complex belongs to a strongly supported clade, together with several species distributed from Switzerland to Iran.

Freshwater macroinvertebrates are a diverse group and play key ecological roles, including accelerating nutrient cycling, filtering water, controlling primary producers, and providing food for predators. Their differences in tolerances and short generation times manifest in rapid community responses to change. Macroinvertebrate community composition is an indicator of water quality. In Europe, efforts to improve water quality following environmental legislation, primarily starting in the 1980s, may have driven a recovery of macroinvertebrate communities. Towards understanding temporal and spatial variation of these organisms, we compiled the TREAM dataset (Time seRies of European freshwAter Macroinvertebrates), consisting of macroinvertebrate community time series from 1,816 river and stream sites (mean length of 19.2 years and 14.9 sampling years) of 22 European countries sampled between 1968 and 2020. In total, the data include >93 million sampled individuals of 2,648 taxa from 959 genera and 212 families. These data can be used to test questions ranging from identifying drivers of the population dynamics of specific taxa to assessing the success of legislative and management restoration efforts.

Rivers and streams contribute to global carbon cycling by decomposing immense quantities of terrestrial plant matter. However, decomposition rates are highly variable and large-scale patterns and drivers of this process remain poorly understood. Using a cellulose-based assay to reflect the primary constituent of plant detritus, we generated a predictive model (81% variance explained) for cellulose decomposition rates across 514 globally distributed streams. A large number of variables were important for predicting decomposition, highlighting the complexity of this process at the global scale. Predicted cellulose decomposition rates, when combined with genus-level litter quality attributes, explain published leaf litter decomposition rates with high accuracy (70% variance explained). Our global map provides estimates of rates across vast understudied areas of Earth and reveals rapid decomposition across continental-scale areas dominated by human activities.

Insects are frequently infected with heritable bacterial endosymbionts. Some of them confer resistance to parasitoids. Such defensive symbionts are sensitive to variation in temperature. Drawing predominantly from the literature on aphids and flies, we show that temperature can affect the reliability of maternal transmission and the strength of protection provided by defensive symbionts. Costs of infection with defensive symbionts can also be temperature-dependent and may even turn into benefits under extreme temperatures, for example, when defensive symbionts increase heat tolerance. Alone or in combination, these mechanisms can drive temperature-associated (latitudinal) clines of infection prevalence with defensive symbionts. This has important consequences for host–parasitoid coevolution, as the relative importance of host-encoded vs. symbiont-provided defenses will shift along such clines.

The rapid loss of biodiversity in freshwater systems asks for a robust and spatially explicit understanding of species' occurrences. As two complementing approaches, habitat suitability models provide information about species' potential occurrence, while environmental DNA (eDNA) based assessments provide indication of species' actual occurrence. Individually, both approaches are used in ecological studies to characterize biodiversity, yet they are rarely combined. Here, we integrated high-resolution habitat suitability models with eDNA-based assessments of aquatic invertebrates in riverine networks to understand their individual and combined capacity to inform on species' occurrence. We used eDNA sampling data from 172 river sites and combined the detection of taxa from three insect orders (Ephemeroptera, Plecoptera, Trichoptera; hereafter EPT) with suitable habitat predictions at a subcatchment level (2 km²). Overall, we find congruence of habitat suitability and eDNA-based detections. Yet, the models predicted suitable habitats beyond the number of detections by eDNA sampling, congruent with the suitable niche being larger than the realized niche. For local mismatches, where eDNA detected a species but the habitat was not predicted suitable, we calculated the minimal distance to upstream suitable habitat patches, indicating possible sources of eDNA signals from upstream sites subsequently being transported along the water flow. We estimated a median distance of 1.06 km (range 0.2–42 km) of DNA transport based on upstream habitat suitability, and this distance was significantly smaller than expected by null model predictions. This estimated transport distance is in the range of previously reported values and allows extrapolations of transport distances across many taxa and riverine systems. Together, the combination of eDNA and habitat suitability models allows larger scale and spatially integrative inferences about biodiversity, ultimately needed for the management and protection of biodiversity.

Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20–35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change.

Freshwater habitats are frequently contaminated by diverse chemicals of anthropogenic origin, collectively referred to as micropollutants, that can have detrimental effects on aquatic life. The animals' tolerance to micropollutants may be mediated by their microbiome. If polluted aquatic environments select for contaminant-degrading microbes, the acquisition of such microbes by the host may increase its tolerance to pollution. Here we tested for the potential effects of the host microbiome on the growth and survival of juvenile Asellus aquaticus, a widespread freshwater crustacean. Using faecal microbiome transplants, we provided newly hatched juveniles with the microbiome isolated from donor adults reared in either clean or micropollutant-contaminated water and, after transplantation, recipient juveniles were reared in water with and without micropollutants. The experiment revealed a significant negative effect of the micropollutants on the survival of juvenile isopods regardless of the received faecal microbiome. The micropollutants had altered the composition of the bacterial component of the donors' microbiome, which in turn influenced the microbiome of juvenile recipients. Hence, we show that relatively high environmental concentrations of micropollutants reduce survival and alter the microbiome composition of juvenile A. aquaticus, but we have no evidence that tolerance to micropollutants is modulated by their microbiome.

Different host plants represent ecologically dissimilar environments for phytophagous insects. The resulting divergent selection can promote the evolution of specialized host races, provided that gene flow is reduced between populations feeding on different plants. In black bean aphids belonging to the Aphis fabae complex, several morphologically cryptic taxa have been described based on their distinct host plant preferences. However, host choice and mate choice are largely decoupled in these insects: they are host-alternating and migrate between specific summer host plants and shared winter hosts, with mating occurring on the shared hosts. This provides a yearly opportunity for gene flow among aphids using different summer hosts, and raises the question if and to what extent the ecologically defined taxa are reproductively isolated. Here, we analyzed a geographically and temporally structured dataset of microsatellite genotypes from A. fabae that were mostly collected from their main winter host Euonymus europaeus, and additionally from another winter host and fourteen summer hosts. The data reveals multiple, strongly differentiated genetic clusters, which differ in their association with different summer and winter hosts. The clusters also differ in the frequency of infection with two heritable, facultative endosymbionts, separately hinting at reproductive isolation and divergent ecological selection. Furthermore, we found evidence for occasional hybridization among genetic clusters, with putative hybrids collected more frequently in spring than in autumn. This suggests that similar to host races in other phytophagous insects, both prezygotic and postzygotic barriers including selection against hybrids maintain genetic differentiation among A. fabae taxa, despite a common mating habitat.

Aquatic macroinvertebrates, including many aquatic insect orders, are a diverse and ecologically relevant organismal group yet they are strongly affected by anthropogenic activities. As many of these taxa are highly sensitive to environmental change, they offer a particularly good early warning system for human-induced change, thus leading to their intense monitoring. In aquatic ecosystems there is a plethora of biotic monitoring or biomonitoring approaches, with more than 300 assessment methods reported for freshwater taxa alone. Ultimately, monitoring of aquatic macroinvertebrates is used to calculate ecological indices describing the state of aquatic systems. Many of the methods and indices used are not only hard to compare, but especially difficult to scale in time and space. Novel DNA-based approaches to measure the state and change of aquatic environments now offer unprecedented opportunities, also for possible integration towards commonly applicable indices. Here, we first give a perspective on DNA-based approaches in the monitoring of aquatic organisms, with a focus on aquatic insects, and how to move beyond traditional point-based biotic indices. Second, we demonstrate a proof-of-concept for spatially upscaling ecological indices based on environmental DNA, demonstrating how integration of these novel molecular approaches with hydrological models allows an accurate evaluation at the catchment scale. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Biodiversity generally increases productivity in ecosystems; however, this is mediated by the specific functional traits that come with biodiversity loss or gain and how these traits interact with environmental conditions. Most biodiversity studies evaluate the effects of species richness alone, despite our increasing understanding that intraspecific diversity can have equally strong impacts. Here, we manipulate both species richness and intraspecific richness (i.e., number of distinct strains) in marine diatom communities to explicitly test the relative importance of species and strain richness for biomass and trait diversity in six distinct temperature/nutrient environments. We show that species and strain richness both have significant effects on biomass and growth rates, but more importantly, they interact with each other, indicating that cross-species diversity effects depend on within-species diversity and vice versa. This intertwined relationship thus calls for more integrative approaches quantifying the relative importance of distinct biodiversity components and environmental context on ecosystem functioning.

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.

The success of ponds constructed to restore ecological infrastructure for pond-breeding amphibians and benefit aquatic biodiversity depends on where and how they are built. We studied effects of pond and landscape characteristics, including connectivity, on metapopulation dynamics of 12 amphibian species in Switzerland. To understand the determinants of long-term occupancy (here summarized as incidence), environmental effects on both colonization and persistence should be considered. We fitted dynamic occupancy models to 20 years of monitoring data on a pond construction program to quantify effects of pond and landscape characteristics and different connectivity metrics on colonization and persistence probabilities in constructed ponds. Connectivity to existing populations explained dynamics better than structural connectivity metrics, and simple metrics (distance to the nearest neighbor population, population density) were useful surrogates for dispersal kernel-weighted metrics commonly used in metapopulation theory. Population connectivity mediated the persistence of conservation target species in new ponds, suggesting source–sink dynamics in newly established populations. Population density captured this effect well and could be used by practitioners for site selection. Ponds created where there were 2–4 occupied ponds within a radius of ∼0.5 km had >3.5 times higher incidence of target species (median) than isolated ponds. Species had individual preferences regarding pond characteristics, but breeding sites with larger (≥100 m²) total water surface area, that temporarily dried, and that were in surroundings with maximally 50% forest benefitted multiple target species. Pond diversity will foster amphibian diversity at the landscape scale.

Changes in climate and land use represent significant risks of biodiversity loss globally, affect ecological stability, impact nature's contributions to people (NCP, i.e. ecosystem services) and compromise human livelihood. As framings of conservation evolve to consider the interdependence between species and human needs, there is a growing recognition of the importance of NCP and biodiversity in conservation actions. However, knowledge on the interactions and spatial repartition of NCP and biodiversity remains limited. Here we show a comprehensive spatial assessment for 15 NCP and one biodiversity – distribution of threatened species – indicators in Switzerland. Indicators values were computed using a panel of mapping and modelling methods extracted from the literature, or specifically developed for this study. Through the analysis of their relationships, we reveal significant trade-offs and synergies in the spatial repartition of these indicators. Results from a spatial bundle analysis performed on the 16 indicators revealed the existence of four bundles showing a heterogeneous repartition over the Swiss landscape. Furthermore, we identified that topography (slope), climate (temperature and precipitations), and habitat (forest and meadows) were among the most influential factors to explain the spatial distribution of the four bundles. We conclude that various significant relationships exist between NCP and biodiversity indicators in Switzerland, emphasizing the importance of informed conservation approaches considering both NCP and biodiversity supply. This work helps fill the gap in our understanding of the links among different NCP, between NCP and biodiversity, and highlight their relationship to climate and land use, providing key insights for optimizing conservation efforts.

Blue-green infrastructure (BGI), combining semi-natural and engineered elements, offers multifaceted benefits like stormwater management, water purification, heat mitigation, and habitat provision. However, current BGI designs prioritize engineering goals, overlooking its ecological potential. Here we advocate for integrating engineering and ecological objectives into BGI design to enhance performance and biodiversity. Through an interdisciplinary literature review, we emphasize the importance of species diversity, abundance, and ecological processes, to improve engineering performance and resilience, and lower management costs. We emphasize the importance of interdisciplinary collaboration to navigate trade-offs between engineering and ecological objectives, ultimately enabling us to engineer both for and with biodiversity.

Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.

The impacts of global change—from shifts in climate to overfishing to land use change—can depend heavily on local abiotic context. Building an understanding of how to downscale global change scenarios to local impacts is often difficult, however, and requires historical data across large gradients of variability. Such data are often not available—particularly in peer reviewed or gray literature. However, these data can sometimes be gleaned from casual records of natural history—field notebooks, data sheet marginalia, course notes, and more. Here, we provide an example of one such approach for the Gulf of Maine, as we seek to understand how environmental context can influence local outcomes of region-wide shifts in subtidal community structure. We explore a decade of hand-drawn algal cover maps around Appledore Island made by Dr. Art Borror while teaching at the Shoals Marine Lab. Appledore's steep wave exposure gradient—from exposed to the open ocean to fully protected—provides a living laboratory to test interactions between global change and local conditions. We then recreate Borror's methods two and a half decades later. We show that overfishing-driven urchin outbreaks in the 1980s were slowed or stopped by wave exposure and benthic topography. Similarly, local variation appears to have curtailed current invasions by filamentous red algae. Last, some formerly dominant kelps have disappeared over the past 40 years—an observation verified by subtidal surveys. Global change is altering life in the seas around us. While underutilized, solid natural history observations stand as a key resource for us to begin to understand how global change will translate to the heterogeneous mosaic of life in a future Gulf of Maine and other ecosystems around the world.

Patella caerulea (Linnaeus, 1758) is a mollusc limpet species of the class Gastropoda. Endemic to the Mediterranean Sea, it is considered a keystone species due to its primary role in structuring and regulating the ecological balance of tidal and subtidal habitats. It is currently being used as a bioindicator to assess the environmental quality of coastal marine waters and as a model species to understand adaptation to ocean acidification. Here, we provide a high-quality reference genome assembly and annotation for P. caerulea. We generated ∼30 Gb of Pacific Biosciences high-fidelity data from a single individual and provide a final 749.8 Mb assembly containing 62 contigs, including the mitochondrial genome (14,938 bp). With an N50 of 48.8 Mb and 98% of the assembly contained in the 18 largest contigs, this assembly is near chromosome-scale. Benchmarking Universal Single-Copy Orthologs scores were high (Mollusca, 87.8% complete; Metazoa, 97.2% complete) and similar to metrics observed for other chromosome-level Patella genomes, highlighting a possible bias in the Mollusca database for Patellids. We generated transcriptomic Illumina data from a second individual collected at the same locality and used it together with protein evidence to annotate the genome. A total of 23,938 protein-coding gene models were found. By comparing this annotation with other published Patella annotations, we found that the distribution and median values of exon and gene lengths was comparable with other Patella species despite different annotation approaches. The present high-quality P. caerulea reference genome, available on GenBank (BioProject: PRJNA1045377; assembly: GCA_036850965.1), is an important resource for future ecological and evolutionary studies.

1. Ecological and ecosystem monitoring is rapidly shifting towards using environmental DNA (eDNA) data, particularly in aquatic systems. This approach enables a combined coverage of biodiversity across all major organismal groups and the assessment of ecological indices. Yet, most current approaches are not exploiting the full potential of eDNA data, largely interpreting results in a localized perspective. In riverine networks, by explicitly modelling hydrological transport and associated DNA decay, hydrology-based models enable upscaling eDNA-based diversity information, providing spatially integrated inference. To capitalize on these unprecedented biodiversity data and translate it into space-filling biodiversity projections, a streamlined implementation is needed.
2. Here, we introduce the eDITH R-package, implementing the eDITH model to project biodiversity across riverine networks with minimal prior information. eDITH couples a species distribution model relating a local taxon's eDNA shedding rate in streamwater to environmental covariates, a mass balance expressing the eDNA concentration at a river's cross-section as a weighted sum of upstream contributions, and an observational model accounting for uncertainties in eDNA measurements. By leveraging on spatially replicated eDNA measurements and minimal hydro-morphological data, eDITH enables disentangling the various upstream eDNA sources, and produces space-filling maps of a taxon's spatial distribution at any chosen resolution. eDITH is applicable to both eDNA concentration and metabarcoding data, and to any taxon whose DNA can be retrieved in streamwater.
3. The eDITH package provides user-friendly functions for single-run execution and fitting of eDITH to eDNA data with both Bayesian methods (via the BayesianTools package) and non-linear optimization. An interface to the DHARMa package allows model validation via posterior predictive checks. Necessary preliminary steps such as watershed delineation and hydrological characterization are implemented via the rivnet package. We illustrate eDITH's workflow and functionalities with two case studies from published fish eDNA data.
4. The eDITH package provides a user-friendly implementation of eDITH, specifically intended for ecologists and conservation biologists. It can be used without previous modelling knowledge but also allows customization for experienced users. Ultimately, eDITH allows upscaling eDNA biodiversity data for any river globally, transforming how state and change in biodiversity in riverine systems can be tracked at high resolution in a highly versatile manner.

The synthesis of a large body of evidence from field experiments suggests more diverse plant communities are more productive as well as more resistant to the effects of climatic extremes like drought. However, this view is strongly based on data from grasslands due to the limited empirical evidence from tree diversity experiments. Here we report on the relationship between tree diversity and productivity over 10 years in a field experiment established in 2005 that was then affected by the 2018 mega-drought in central Europe. Across a number of years, tree species diversity and productivity were significantly positively related; however, the slope switched to negative in the year of the drought. Net diversity effects increased through time, with complementarity effects making greater contributions to the net diversity effect than selection effects. Complementarity effects were clearly positive in three- and five-species mixtures before the drought (2012–2016) but were found to decrease in the year of the drought. Selection effects were clearly positive in 2016 and remained positive in the drought year 2018 in two-, three-, and five-species mixtures. The survival of Norway spruce (Picea abies) plummeted in response to the drought, and a negative relationship between species diversity and spruce survival was found. Taken together, our findings suggest that tree diversity per se may not buffer communities against the impacts of extreme drought and that tree species composition and the drought tolerance of tree species (i.e., species identity) will be important determinants of community productivity as the prevalence of drought increases.

99 Schweizer Bäche wurden anhand der beiden Bioindikatoren Fische und Makrozoobenthos untersucht. Die Mehrzahl der Bäche zeigt wesentliche Defizite beim ökologischen Zustand. So fehlen beispielsweise in über 70% der Gewässer ein Teil der pestizidempfindlichen Insektenlarven und andere Kleinlebewesen. Statistische Auswertungen deuten darauf hin, dass sich eine beeinträchtigte Ökomorphologie sowie ein grosser Anteil Ackerland, Obstkulturen und Reben im Einzugsgebiet besonders negativ auf das Vorkommen dieser empfindlichen Kleinlebewesen auswirken.

Invasive species are pervasive around the world and have profound impacts on the ecosystem they invade. Invasive species, however, can also have impacts beyond the ecosystem they invade by altering the flow of non-living materials (for example, nutrients or chemicals) or movement of organisms across the boundaries of the invaded ecosystem. Cross-ecosystem interactions via spatial flows are ubiquitous in nature, for example, connecting forests and lakes, grasslands and rivers, and coral reefs and the deep ocean. Yet, we have a limited understanding of the cross-ecosystem impacts invasive species have relative to their local effects. By synthesizing emerging evidence, here we demonstrate the cross-ecosystem impacts of invasive species as a ubiquitous phenomenon that influences biodiversity and ecosystem functioning around the world. We identify three primary ways by which invasive species have cross-ecosystem effects: first, by altering the magnitude of spatial flows across ecosystem boundaries; second, by altering the quality of spatial flows; and third, by introducing novel spatial flows. Ultimately, the strong impacts invasive species can drive across ecosystem boundaries suggests the need for a paradigm shift in how we study and manage invasive species around the world, expanding from a local to a cross-ecosystem perspective.

Moths and other insects are attracted by artificial light sources. This flight-to-light behaviour disrupts their general activity focused on finding resources, such as mating partners, and increases predation risk. It thus has substantial fitness costs. In illuminated urban areas, spindle ermine moths Yponomeuta cagnagella were reported to have evolved a reduced flight-to-light response. Yet, the specific mechanism remained unknown, and was hypothesized to involve either changes in visual perception or general flight ability or overall mobility traits. Here, we test whether spindle ermine moths from urban and rural populations—with known differences in flight-to-light responses—differ in flight-related morphological traits. Urban individuals were found to have on average smaller wings than rural moths, which in turn correlated with a lower probability of being attracted to an artificial light source. Our finding supports the reduced mobility hypothesis, which states that reduced mobility in urban areas is associated with specific morphological changes in the flight apparatus.

How barriers to gene flow arise and are maintained are key questions in evolutionary biology. Speciation research has mainly focused on barriers that occur either before mating or after zygote formation. In comparison, postmating prezygotic (PMPZ) isolation—a barrier that acts after gamete release but before zygote formation—is less frequently investigated but may hold a unique role in generating biodiversity. Here we discuss the distinctive features of PMPZ isolation, including the primary drivers and molecular mechanisms underpinning PMPZ isolation. We then present the first comprehensive survey of PMPZ isolation research, revealing that it is a widespread form of prezygotic isolation across eukaryotes. The survey also exposes obstacles in studying PMPZ isolation, in part attributable to the challenges involved in directly measuring PMPZ isolation and uncovering its causal mechanisms. Finally, we identify outstanding knowledge gaps and provide recommendations for improving future research on PMPZ isolation. This will allow us to better understand the nature of this often-neglected reproductive barrier and its contribution to speciation.

Plant diversity effects on community productivity often increase over time. Whether the strengthening of diversity effects is caused by temporal shifts in species-level overyielding (i.e., higher species-level productivity in diverse communities compared with monocultures) remains unclear. Here, using data from 65 grassland and forest biodiversity experiments, we show that the temporal strength of diversity effects at the community scale is underpinned by temporal changes in the species that yield. These temporal trends of species-level overyielding are shaped by plant ecological strategies, which can be quantitatively delimited by functional traits. In grasslands, the temporal strengthening of biodiversity effects on community productivity was associated with increasing biomass overyielding of resource-conservative species increasing over time, and with overyielding of species characterized by fast resource acquisition either decreasing or increasing. In forests, temporal trends in species overyielding differ when considering above- versus belowground resource acquisition strategies. Overyielding in stem growth decreased for species with high light capture capacity but increased for those with high soil resource acquisition capacity. Our results imply that a diversity of species with different, and potentially complementary, ecological strategies is beneficial for maintaining community productivity over time in both grassland and forest ecosystems.

Although the general impacts of zooplankton grazing on phytoplankton communities are clear, we know comparatively less about how specific grazing strategies interact with environmental conditions to shape the size structure of phytoplankton communities. Here, we present a new data-driven, size-based model that describes changes in the size composition of lake phytoplankton under various environmental constraints. The model includes an ecological trade-off emerging from observed allometric relationships between (1) phytoplankton cell size and phytoplankton growth and (2) phytoplankton cell size and zooplankton grazing. In our model, phytoplankton growth is nutrient-dependent and zooplankton grazing varies according to specific grazing strategies, namely, specialists (targeting a narrow range of the size-feeding spectrum) vs. generalists (targeting a wide range of the size-feeding spectrum). Our results indicate that grazing strategies shape the size composition of the phytoplankton community in nutrient-rich conditions, whereas inorganic nutrient concentrations govern phytoplankton biomass. Under oligotrophic regimes, the phytoplankton community is dominated by small cell sizes and the grazers have little to no impact. Under eutrophic regimes, dominating specialist grazers push phytoplankton towards small cells, whereas dominating generalist grazers push phytoplankton towards large cells. Our work highlights that trait-based modeling, based on realistic eco-physiological trade-offs, represents a valuable tool for disentangling the interactive roles played by nutrient regimes and grazing strategies in determining the size compositions of lake phytoplankton. Ultimately, our study offers a quantitative basis for understanding how communities of lake phytoplankton may reorganize in the future in response to changes in nutrient levels and zooplankton grazing strategies.

How does diversity in nature come about? One factor contributing to this diversity are species interactions; diversity on one trophic level can shape diversity on lower or higher trophic levels. For example, parasite diversity enhances host immune diversity. Insect protective symbionts mediate host resistance and are, therefore, also engaged in reciprocal selection with their host's parasites. Here, we applied experimental evolution in a well-known symbiont-aphid-parasitoid system to study whether parasitoid diversity contributes to maintaining symbiont genetic diversity. We used caged populations of black bean aphids (Aphis fabae), containing uninfected individuals and individuals infected with different strains of the bacterial endosymbiont Hamiltonella defensa, which protects aphids against parasitoids. Over multiple generations, these populations were exposed to three different species of parasitoid wasps (Aphidius colemani, Binodoxys acalephae or Lysiphlebus fabarum), simultaneous or sequential mixtures of these species or no wasps. Surprisingly, we observed little selection for H. defensa in most treatments, even when it clearly provided protection against a fatal parasitoid infection. This seemed to be caused by high induced costs of resistance: aphids surviving parasitoid attacks suffered an extreme reduction in fitness. In marked contrast to previous studies looking at the effect of different genotypes of a single parasitoid species, we found little evidence for a diversifying effect of multiple parasitoid species on symbiont diversity in hosts.

Die noch wenig bekannte Grundwasserfauna ist ein bedeutender Bestandteil der Biodiversität und trägt zum Funktionieren der Grundwasserökosysteme bei. Mittels Proben aus der ganzen Schweiz wurde erstmals ein Überblick über die Vielfalt und Biomasse von Makroinvertebraten in Grundwasserökosystemen der Schweiz erarbeitet. Eine hohe Diversität an ober- und unterirdischen Makroinvertebraten im Grundwasser weist auf die Wechselwirkungen zwischen Oberfläche und Grundwasser hin.

Die Quaggamuschel wurde 2015 erstmalig im Genfersee nachgewiesen. Seitdem hat sich
diese ursprünglich aus dem Dnepr stammende invasive Art in den voralpinen Seen rasant ausgebreitet. Was bedeutet das für die Ökosysteme und die regionale Wasserversorgung?

Rising temperatures are leading to increased prevalence of warm-affinity species in ecosystems, known as thermophilisation. However, factors influencing variation in thermophilisation rates among taxa and ecosystems, particularly freshwater communities with high diversity and high population decline, remain unclear. We analysed compositional change over time in 7123 freshwater and 6201 terrestrial, mostly temperate communities from multiple taxonomic groups. Overall, temperature change was positively linked to thermophilisation in both realms. Extirpated species had lower thermal affinities in terrestrial communities but higher affinities in freshwater communities compared to those persisting over time. Temperature change’s impact on thermophilisation varied with community body size, thermal niche breadth, species richness and baseline temperature; these interactive effects were idiosyncratic in the direction and magnitude of their impacts on thermophilisation, both across realms and taxonomic groups. While our findings emphasise the challenges in predicting the consequences of temperature change across communities, conservation strategies should consider these variable responses when attempting to mitigate climate-induced biodiversity loss.

Facing climate change and biodiversity loss, it is critical that ecology advances so that processes, such as species interactions and dynamics, can be correctly estimated and skillfully forecasted. As different processes occur on different time scales, the sampling frequency used to record them should intuitively match these scales. Yet, the effect of data sampling frequency on ecological forecasting accuracy is understudied. Using a simple simulated dataset as a baseline and a more complex high-frequency plankton dataset, we tested how different sampling frequencies impacted abundance forecasts of different plankton classes and the estimation of their interactions. We then investigated whether plankton growth rates and body sizes could be used to select the most appropriate sampling frequency. The simple simulated dataset showed that the optimal sampling frequency scaled positively with growth rate. This finding was not repeated in the analyses of the plankton time series, however. There, we found that a reduction in sampling frequency worsened forecasts and led us to both over- and underestimate plankton interactions. This suggests that forecasting can be used to determine the ideal sampling frequency in scientific and monitoring programs. A better study design will improve theoretical understanding of ecology and advance policy measures dealing with current global challenges.

Aim: Climate is a major driver of large-scale variability in biodiversity, as a likely result of more intense biotic interactions under warmer conditions. This idea fuelled decades of research on plant-herbivore interactions, but much less is known about higher-level trophic interactions. We addressed this research gap by characterizing both bird diversity and avian predation along a climatic gradient at the European scale.
Location: Europe.
Taxon: Insectivorous birds and pedunculate oaks. Methods: We deployed plasticine caterpillars in 138 oak trees in 47 sites along a 19° latitudinal gradient in Europe to quantify bird insectivory through predation attempts. In addition, we used passive acoustic monitoring to (i) characterize the acoustic diversity of surrounding soundscapes; (ii) approximate bird abundance and activity through passive acoustic recordings; and (iii) infer both taxonomic and functional diversity of insectivorous birds from recordings.
Results: The functional diversity of insectivorous birds increased with warmer climates. Bird predation increased with forest cover and bird acoustic activity but decreased with mean annual temperature and functional richness of insectivorous birds. Contrary to our predictions, climatic clines in bird predation attempts were not directly mediated by changes in insectivorous bird diversity or acoustic activity, but climate and habitat still had independent effects on predation attempts.
Main Conclusions: Our study supports the hypothesis of an increase in the diversity of insectivorous birds towards warmer climates but refutes the idea that an increase in diversity would lead to more predation and advocates for better accounting for activity and abundance of insectivorous birds when studying the large-scale variation in insect-tree interactions.

Rivers are an important component of the global carbon cycle and contribute to atmospheric carbon exchange disproportionately to their total surface area. Largely, this is because rivers efficiently mobilize, transport and metabolize terrigenous organic matter (OM). Notably, our knowledge about the magnitude of globally relevant carbon fluxes strongly contrasts with our lack of understanding of the underlying processes that transform OM. Ultimately, OM processing en route to the oceans results from a diverse assemblage of consumers interacting with an equally diverse pool of resources in a spatially complex network of heterogeneous riverine habitats. To understand this interaction between consumers and OM, we must therefore account for spatial configuration, connectivity, and landscape context at scales ranging from local ecosystems to entire networks. Building such a spatially explicit framework of fluvial OM processing across scales may also help us to better predict poorly understood anthropogenic impacts on fluvial carbon cycling, for instance human-induced fragmentation and changes to flow regimes, including intermittence. Moreover, this framework must also account for the current unprecedented human-driven loss of biodiversity. This loss is at least partly due to mechanisms operating across spatial scales, such as interference with migration and habitat homogenization, and comes with largely unknown functional consequences. We advocate here for a comprehensive framework for fluvial networks connecting two spatially aware but disparate lines of research on (i) riverine metacommunities and biodiversity, and (ii) the biogeochemistry of rivers and their contribution to the global carbon cycle. We argue for a research agenda focusing on the regional scale—that is, of the entire river network—to enable a deeper mechanistic understanding of naturally arising biodiversity–ecosystem functioning coupling as a major driver of biogeochemically relevant riverine carbon fluxes.

Differentiation of foraging traits among predator populations may help explain observed variation in the structure of prey communities. However, few studies have investigated the phenotypic effects of predators on their prey in natural communities. Here, we use a comparative analysis of 78 Greenlandic lakes to examine how foraging trait variation among threespine stickleback populations can help explain variation in zooplankton community composition among lakes. We find that landscape-scale variation in zooplankton composition was jointly explained by lake properties, such as size and water chemistry, and the presence and absence of both stickleback and arctic char. Additional variation in zooplankton community structure can be explained by stickleback jaw protrusion, a trait with known utility for foraging on zooplankton, but only in lakes where stickleback co-occur with arctic char. Overall, our results illustrate how trait variation of predators, alongside other ecosystem properties, can influence the composition of prey communities in nature.

Increasing temperatures caused by anthropogenic climate change are leading to changes in the composition of local communities across biomes. This has implications for ecological assessment methods that rely on macroinvertebrates as bioindicators of water quality. To investigate the influence of changing water temperature on these assessment methods, we analysed macroinvertebrate data from Swiss national monitoring programs. We used a species distribution model to simulate temperature change effects on macroinvertebrate communities and estimated the resulting changes on three biological indices commonly used in Switzerland, namely the species richness of Ephemeroptera, Plecoptera and Trichoptera (EPT), the Swiss biological (IBCH) index along with its components, as well as the species at risk pesticides (SPEAR_pesticides) index. While results vary by temperature scenario and index, our model results for the most realistic water temperature increase scenario of + 2 °C across most sites in Switzerland suggest no, or only a minor, influence of temperature (not accounting for other hydrological changes). Our model projection predicted only a small increase in the probability of occurrence for 70 % of the studied families. The sensitivity to temperature as captured in our model is generally not very high and varies among the biological indices: on average across all sites, a + 2 °C increase in temperature resulted in a 7 % increase in EPT species richness, a 4 % increase in the IBCH index, and a less than 1 % increase in the SPEAR_pesticides index. Our study suggests the robustness of these biological indices to moderate warming and points towards the usefulness of these biological indices for the next few decades as tools for water quality assessment. Despite some limitations of statistical species distribution models (e.g., not accounting for dispersal limitation or biotic interactions, predictive performance varying by taxon), the study provides valuable insights into the complex relationships between environmental factors and macroinvertebrate communities, and the potential impacts of future temperature change. These findings can inform conservation and management efforts for these important ecological systems.

Humans impact terrestrial, marine and freshwater ecosystems, yet many broad-scale studies have found no systematic, negative biodiversity changes (for example, decreasing abundance or taxon richness). Here we show that mixed biodiversity responses may arise because community metrics show variable responses to anthropogenic impacts across broad spatial scales. We first quantified temporal trends in anthropogenic impacts for 1,365 riverine invertebrate communities from 23 European countries, based on similarity to least-impacted reference communities. Reference comparisons provide necessary, but often missing, baselines for evaluating whether communities are negatively impacted or have improved (less or more similar, respectively). We then determined whether changing impacts were consistently reflected in metrics of community abundance, taxon richness, evenness and composition. Invertebrate communities improved, that is, became more similar to reference conditions, from 1992 until the 2010s, after which improvements plateaued. Improvements were generally reflected by higher taxon richness, providing evidence that certain community metrics can broadly indicate anthropogenic impacts. However, richness responses were highly variable among sites, and we found no consistent responses in community abundance, evenness or composition. These findings suggest that, without sufficient data and careful metric selection, many common community metrics cannot reliably reflect anthropogenic impacts, helping explain the prevalence of mixed biodiversity trends.

The EU Nature Restoration Law represents an important opportunity for freshwater habitat restoration and, consequently, freshwater biodiversity protection. However, a number of challenges must be anticipated in its implementation, which may compromise its success. Some aspects, particularly those relating to freshwater ecosystems, require more clarification. We use riverine ecosystems to illustrate existing ambiguities in the proposed legislation and the potential consequences of leaving these aspects open to interpretation during the implementation process. We also discuss potential solutions to these problems which could help ensure that the law's objectives are met. We argue that river network structure and connectivity dimensions, which result into river meta-ecosystems, must be explicitly considered. For that purpose, we ask for clear definitions of the critical terms "free-flowing rivers," "barriers," and "reference areas." In addition, we recommend developing methods for integrated assessment of connectivity across river networks. As a key property of river ecosystems, this must be used to prioritize actions to increase the length and number of free-flowing rivers. Adequate restoration planning at larger spatial scales will benefit from a meta-ecosystem perspective and accurate representation of aquatic-terrestrial linkages, which will significantly improve the efficacy of restoration efforts. Furthermore, stakeholder and citizen engagement offer important opportunities at local, national, and European scales, and should be fostered to ensure inclusive decision-making. The conservation challenges outlined here are particularly important for rivers, but they also have implications for other ecosystems. These considerations are useful for policymakers, conservationists, and other stakeholders involved in the Nature Restoration Law and related policy initiatives.

Host–parasite coevolution is mediated by genetic interactions between the antagonists and may lead to reciprocal adaptation. In the black bean aphid, Aphis fabae fabae, resistance to parasitoids can be conferred by the heritable bacterial endosymbiont Hamiltonella defensa. H. defensa has been shown to be variably protective against different parasitoid species, and different genotypes of the black bean aphid's main parasitoid Lysiphlebus fabarum. However, these results were obtained using haphazard combinations of laboratory-reared insect lines with different origins, making it unclear how representative they are of natural, locally (co)adapted communities. We therefore comprehensively sampled the parasitoids of a natural A. f. fabae population and measured the ability of the five most abundant species to parasitize aphids carrying the locally prevalent H. defensa haplotypes. H. defensa provided resistance only against the dominant parasitoid L. fabarum (70% of all parasitoids), but not against less abundant parasitoids, and resistance to L. fabarum acted in a genotype-specific manner (G × G interactions between H. defensa and L. fabarum). These results confirm that strong species- and genotype-specificity of symbiont-conferred resistance is indeed a hallmark of wild A. f. fabae populations, and they are consistent with symbiont-mediated adaptation of aphids to the parasitoids posing the highest risk.

Subterranean ecosystems (comprising terrestrial, semi-aquatic, and aquatic components) are increasingly threatened by human activities; however, the current network of surface-protected areas is inadequate to safeguard subterranean biodiversity. Establishing protected areas for subterranean ecosystems is challenging. First, there are technical obstacles in mapping three-dimensional ecosystems with uncertain boundaries. Second, the rarity and endemism of subterranean organisms, combined with a scarcity of taxonomists, delays the accumulation of essential biodiversity knowledge. Third, establishing agreements to preserve subterranean ecosystems requires collaboration among multiple actors with often competing interests. This perspective addresses the challenges of preserving subterranean biodiversity through protected areas. Even in the face of uncertainties, we suggest it is both timely and critical to assess general criteria for subterranean biodiversity protection and implement them based on precautionary principles. To this end, we examine the current status of European protected areas and discuss solutions to improve their coverage of subterranean ecosystems.

Standard and easily accessible cross-thematic spatial databases are key resources in ecological research. In Switzerland, as in many other countries, available data are scattered across computer servers of research institutions and are rarely provided in standard formats (e.g., different extents or projections systems, inconsistent naming conventions). Consequently, their joint use can require heavy data management and geomatic operations. Here, we introduce SWECO25, a Swiss-wide raster database at 25-meter resolution gathering 5,265 layers. The 10 environmental categories included in SWECO25 are: geologic, topographic, bioclimatic, hydrologic, edaphic, land use and cover, population, transportation, vegetation, and remote sensing. SWECO25 layers were standardized to a common grid sharing the same resolution, extent, and geographic coordinate system. SWECO25 includes the standardized source data and newly calculated layers, such as those obtained by computing focal or distance statistics. SWECO25 layers were validated by a data integrity check, and we verified that the standardization procedure had a negligible effect on the output values. SWECO25 is available on Zenodo and is intended to be updated and extended regularly.

Aim: The spatial-structural patterns of plant-insect interaction networks, particularly their associations with landscape-scale environmental factors, remain poorly understood. We apply data-driven network constructions that integrate biogeographic and trophic interaction knowledge to uncover how Lepidoptera-plant networks vary across environmental gradients in a real-world landscape.
Location: The 36,000 km² German state Baden-Württemberg, Central Europe. Taxon: Lepidoptera insects and angiosperm plants.
Materials and Methods: We integrated extensive data of Lepidoptera-plant occurrences and interactions to infer local interaction networks across Baden-Württemberg, encompassing 3148 plant and 980 Lepidoptera species, covering butterflies, Noctuoid moths, Geometrid moths, and Bombycoid moths. We quantified clade- and life-stage-specific network structures and related them to GIS-informed environmental conditions, thereby revealing the spatial (environmental) patterns and potential drivers of network variations. Results: Spanning shared environmental gradients, Lepidoptera clades and life stages formed various interaction structures with plants and exhibit distinct spatial-structural patterns. For all Lepidoptera groups, except Geometrid moths, potential diet across life stages broadened toward low-elevation farmlands. The larval and adult networks of butterflies became less modular with farmland coverage; the same for adult Noctuoid moths, but the inverse for adult Geometrid moths. With increasing elevation, the larval and adult networks of Noctuoid moths became less and more modular, respectively, whereas Geometrid adult networks became more modular. While the adult dietary niche of butterflies overlapped more at low elevation, those of Noctuoid and Geometrid moths further associated with land cover and overlapped more toward low- and high-elevation farmlands, respectively.
Main Conclusions: The spatial-structural patterns of Lepidoptera-plant networks vary along geo-climate and land-cover gradients in ways depending on the Lepidoptera's clade and life stage. The driving mechanisms likely include both evolutionary (e.g., resource-consumer [co-]evolution) and ecological (e.g., competitive exclusion) processes, and differentially affect Lepidoptera across clades and life stages. These findings pinpoint conservation implications at both species and community levels, with potential trade-offs for managing different Lepidoptera-plant communities under environmental changes.

The logistic growth model is one of the most frequently used formalizations of density dependence affecting population growth, persistence and evolution. Ecological and evolutionary theory, and applications to understand population change over time often include this model. However, the assumptions and limitations of this popular model are often not well appreciated. Here, we briefly review past use of the logistic growth model and highlight limitations by deriving population growth models from underlying consumer–resource dynamics. We show that the logistic equation likely is not applicable to many biological systems. Rather, density-regulation functions are usually non-linear and may exhibit convex or concave curvatures depending on the biology of resources and consumers. In simple cases, the dynamics can be fully described by the Schoener model. More complex consumer dynamics show similarities to a Maynard Smith–Slatkin model. We show how population-level parameters, such as intrinsic rates of increase and equilibrium population densities are not independent, as often assumed. Rather, they are functions of the same underlying parameters. The commonly assumed positive relationship between equilibrium population density and competitive ability is typically invalid. We propose simple relationships between intrinsic rates of increase and equilibrium population densities that capture the essence of different consumer–resource systems. Relating population level models to underlying mechanisms allows us to discuss applications to evolutionary outcomes and how these models depend on environmental conditions, like temperature via metabolic scaling. Finally, we use time-series from microbial food chains to fit population growth models as a test case for our theoretical predictions. Our results show that density-regulation functions need to be chosen carefully as their shapes will depend on the study system's biology. Importantly, we provide a mechanistic understanding of relationships between model parameters, which has implications for theory and for formulating biologically sound and empirically testable predictions.

In times of rapid environmental changes, baseline biodiversity data are crucial for management. In freshwaters, fish inventories are commonly based on the capture and morphological identification of specimens. The sampling of environmental DNA (eDNA) provides an alternative to assess diversity across large catchments. Here, we used extensive historic data of fish communities collected across 89 river sites in all major catchments of Switzerland and compared their diversity and community composition to a single campaign of eDNA and electrofishing, respectively. Locally, we found that eDNA provided diversity estimates similar to the integrated historic richness, while the electrofishing campaign captured a significantly lower local richness. Fish species locally recorded by electrofishing were nested (Jaccard's dissimilarity index) within the respective eDNA community for most sites. Finally, eDNA sequence reads positively correlated with the overall electrofishing biomass. Despite the congruences, the eDNA data did not correlate well with the electrofishing water quality index. Overall, eDNA was more accurately assessing overall diversity than a simultaneous electrofishing campaign, but yet cannot be directly used to calculate fish-based water quality indices.

Numerous biodiversity–ecosystem functioning (BEF) experiments have shown that plant community productivity typically increases with species diversity. In these studies, diversity is generally quantified using metrics of taxonomic, phylogenetic, or functional differences among community members. Research has also shown that the relationships between species diversity and functioning depends on the spatial scale considered, primarily because larger areas may contain different ecosystem types and span gradients in environmental conditions, which result in a turnover of the species set present locally. A fact that has received little attention, however, is that ecological systems are hierarchically structured, from genes to individuals to communities to entire landscapes, and that additional biological variation occurs at levels of organization above and below those typically considered in BEF research. Here, we present cases of diversity effects at different hierarchical levels of organization and compare these to the species-diversity effects traditionally studied. We argue that when this evidence is combined across levels, a general framework emerges that allows the transfer of insights and concepts between traditionally disparate disciplines. Such a framework presents an important step towards a better understanding of the functional importance of diversity in complex, real-world systems.

Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change.

Human activities have facilitated the invasion of freshwater ecosystems by various organisms. Especially, invasive bivalves such as the quagga mussels, Dreissena bugensis, have the potential to alter ecosystem function as they heavily affect the food web. Quagga mussels occur in high abundance, have a high filtration rate, quickly spread within and between waterbodies via pelagic larvae, and colonize various substrates. They have invaded various waterbodies across the Northern Hemisphere. In Central Europe, they have invaded multiple large and deep perialpine lakes with first recordings in Lake Geneva in 2015 and 2016 in Lake Constance. In the deep perialpine lakes, quagga mussels quickly colonized the littoral zone but are also abundant deeper (>80 m), where they are often thinner and brighter shelled. We analysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights into the genetic population structure of quagga mussels across Central European lakes and across various sites and depth habitats in Lake Constance. We revealed substantial genetic differentiation amongst quagga mussel populations from three unconnected lakes, and all populations showed high genetic diversity and effective population size. In Lake Constance, we detected no genetic differentiation amongst quagga mussels sampled across different sites and depth habitats. We also did not identify any convincing candidate loci evidential for adaptation along a depth gradient and a transplant experiment showed no indications of local adaptation to living in the deep based on investigating growth and survival. Hence, the shallow-water and the deep-water morphotypes seem to be a result of phenotypic plasticity rather than local adaptation to depth. In conclusion, our ddRAD approach revealed insight into the establishment of genetically distinct quagga mussel populations in three perialpine lakes and suggests that phenotypic plasticity and life history traits (broadcast spawner with high fecundity and dispersing pelagic larvae) facilitate the fast spread and colonization of various depth habitats by the quagga mussel.

Biodiversity loss in river ecosystems is much faster and more severe than in terrestrial systems, and spatial conservation and restoration plans are needed to halt this erosion. Reliable and highly resolved data on the state of and change in biodiversity and species distributions are critical for effective measures. However, high-resolution maps of fish distribution remain limited for large riverine systems. Coupling data from global satellite sensors with broad-scale environmental DNA (eDNA) and machine learning could enable rapid and precise mapping of the distribution of river organisms. Here, we investigated the potential for combining these methods using a fish eDNA dataset from 110 sites sampled along the full length of the Rhone River in Switzerland and France. Using Sentinel 2 and Landsat 8 images, we generated a set of ecological variables describing both the aquatic and the terrestrial habitats surrounding the river corridor. We combined these variables with eDNA-based presence and absence data on 29 fish species and used three machine-learning models to assess environmental suitability for these species. Most models showed good performance, indicating that ecological variables derived from remote sensing can approximate the ecological determinants of fish species distributions, but water-derived variables had stronger associations than the terrestrial variables surrounding the river. The species range mapping indicated a significant transition in the species occupancy along the Rhone, from its source in the Swiss Alps to outlet into the Mediterranean Sea in southern France. Our study demonstrates the feasibility of combining remote sensing and eDNA to map species distributions in a large river. This method can be expanded to any large river to support conservation schemes.

Catchment urbanisation results in urban streams being exposed to a multitude of stressors. Notably, stressors originating from diffuse sources have received less attention than stressors originating from point sources. Here, advances related to diffuse urban stressors and their consequences for stream benthic communities are summarised by reviewing 92 articles. Based on the search criteria, the number of articles dealing with diffuse urban stressors in streams has been increasing, and most of them focused on North America, Europe, and China. Land use was the most common measure used to characterize diffuse stressor sources in urban streams (70.7 % of the articles characterised land use), and chemical stressors (inorganic nutrients, xenobiotics, metals, and water properties, including pH and conductivity) were more frequently reported than physical or biological stressors. A total of 53.3 % of the articles addressed the impact of urban stressors on macroinvertebrates, while 35.9 % focused on bacteria, 9.8 % on fungi, and 8.7 % on algae. Regarding ecosystem functions, almost half of the articles (43.5 %) addressed changes in community dynamics, 40.3 % addressed organic matter decomposition, and 33.9 % addressed nutrient cycling. When comparing urban and non-urban streams, the reviewed studies suggest that urbanisation negatively impacts the diversity of benthic organisms, leading to shifts in community composition. These changes imply functional degradation of streams. The results of the present review summarise the knowledge gained to date and identify its main gaps to help improve our understanding of urban streams.

La urbanización de las cuencas expone a los arroyos urbanos a multitud de factores de estrés. Destacan aquellos que tienen su origen en fuentes difusas, los cuales han recibido menos atención que aquellos estresores procedentes de fuentes puntuales. Este estudio resume los avances relacionados con los estresores urbanos difusos y sus consecuencias para las comunidades bentónicas fluviales, a partir de la revisión de 92 artículos. En base a los criterios de búsqueda, el número de artículos que tratan sobre estresores urbanos difusos en arroyos ha ido en aumento, la mayoría de ellos centrados en América del Norte, Europa y China. Los usos del suelo fueron la variable más utilizada para caracterizar las fuentes difusas de estrés (el 70.7 % de los artículos caracterizó los usos del suelo), y los factores de estrés químico (nutrientes inorgánicos o propiedades del agua, como pH o conductividad) se mencionaron con más frecuencia que los factores de estrés físico o biológico. El 53.3 % de los trabajos abordaron el impacto de los estresores urbanos difusos sobre los macroinvertebrados, mientras que el 35.9 % se centraron en bacterias, el 9.8 % en hongos y el 8.7 % en algas. En cuanto al funcionamiento de los ecosistemas, prácticamente la mitad de los trabajos (43.5 %) analizó cambios en la dinámica de las comunidades, el 40.3 % en la descomposición de materia orgánica y el 33.9 % en los ciclos de los nutrientes. Al comparar los arroyos urbanos y no urbanos, los trabajos revisados sugieren que la urbanización afecta negativamente a la diversidad de organismos bentónicos, provocando cambios en la composición de la comunidad. Estos cambios implican la degradación funcional de los arroyos. Los resultados de la presente revisión resumen los conocimientos adquiridos hasta hoy e identifican sus principales carencias a fin de ayudar a mejorar nuestra comprensión de los arroyos urbanos.

Multiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly, and invasive capture and examination of host species, and require specialized expertise for every host and pathogen of interest. Environmental DNA could provide simultaneous occurrence data for multiple pathogens across different host taxa, valuable for using parasite diversity as, for example, a bioindicator of ecosystem disturbance. Here, we tested the potential for simultaneous detection of four wildlife pathogens in water samples from 280, mainly riverine, sites across Switzerland. We targeted the crayfish pathogen Aphanomyces astaci, the amphibian pathogen Batrachochytrium dendrobatidis, and the fish pathogens Saprolegnia parasitica and Tetracapsuloides bryosalmonae. The eDNA detection showed a widespread distribution of A. astaci, S. parasitica, and T. bryosalmonae, although A. astaci and T. bryosalmonae were not detected in some alpine river catchments. B. dendrobatidis was detected only rarely, which was expected since the sampling did not target amphibian breeding sites. Co-detection rates were higher in rivers than in lakes, likely reflecting the habitat preferences and distributions of the host species. We discuss the advantages and limitations of eDNA-based pathogen monitoring and list a set of recommendations for managers. Our study illustrates how eDNA-based techniques can monitor several pathogen species concurrently, thus facilitating more comprehensive disease monitoring schemes. Combined with metabarcoding approaches in the future, eDNA-based sampling and detection can facilitate the incorporation of parasite and pathogen occurrence and diversity as an indicator for aquatic ecosystem health, and for revealing the hidden biodiversity and structure of parasite communities.

Predicting contemporary and future species distributions is relevant for science and decision making, yet the development of high-resolution spatial predictions for numerous taxonomic groups and regions is limited by the scalability of available modelling tools. Uniting species distribution modelling (SDM) techniques into one high-performance computing (HPC) pipeline, we developed N-SDM, an SDM platform aimed at delivering reproducible outputs for standard biodiversity assessments. N-SDM was built around a spatially-nested framework, intended at facilitating the combined use of species occurrence data retrieved from multiple sources and at various spatial scales. N-SDM allows combining two models fitted with species and covariate data retrieved from global to regional scales, which is useful for addressing the issue of spatial niche truncation. The set of state-of-the-art SDM features embodied in N-SDM includes a newly devised covariate selection procedure, five modelling algorithms, an algorithm-specific hyperparameter grid search, and the ensemble of small-models approach. N-SDM is designed to be run on HPC environments, allowing the parallel processing of thousands of species at the same time. All the information required for installing and running N-SDM is openly available on the GitHub repository https://github.com/N-SDM/N-SDM.

1. Selecting the best subset of covariates out of a panel of many candidates is a key and highly influential stage of the species distribution modelling process. Yet, there is currently no commonly accepted and widely adopted standard approach by which to perform this selection.
2. We introduce a two-step "embedded" covariate selection procedure aimed at optimizing the predictive ability and parsimony of species distribution models fitted in a context of high-dimensional candidate covariate space. The procedure combines a collinearity-filtering algorithm (Step A) with three model-specific embedded regularization techniques (Step B), including generalized linear model with elastic net regularization, generalized additive model with null-space penalization, and guided regularized random forest.
3. We evaluated the embedded covariate selection procedure through an example application aimed at modelling the habitat suitability of 50 species in Switzerland from a suite of 123 candidate covariates. We demonstrated the ability of the embedded covariate selection procedure to provide significantly more accurate species distribution models as compared to models obtained with alternative procedures. Model performance was independent of the characteristics of the species data, such as the number of occurrence records or their spatial distribution across the study area.
4. We implemented and streamlined our embedded covariate selection procedure in the covsel R package, paving the way for a ready-to-use, automated, covariate selection tool that was missing in the field of species distribution modelling. All the information required for installing and running the covsel R package is openly available on the GitHub repository https://github.com/N-SDM/covsel.

Während fünfeinhalb Jahren untersuchten Forschende aus den drei Bodenseeländern den Einfluss und die Wechselwirkung verschiedener Stressfaktoren wie Nährstoffänderungen, invasive Arten und Klimawandel auf das Ökosystem des Sees. Der aktuelle Wandel ist tiefgreifend und mit voraussichtlich weitreichenden Folgen für das komplexe Ökosystemgefüge und die Gewässernutzenden. Am 13. und 14. Juni 2023 schliesst das Projekt mit einem wissenschaftlichen Symposium und einer Informationsveranstaltung für die Praxis ab.

Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems and informing policy and decision-making, especially in an era of massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at the forefront of technological advances in biodiversity monitoring, and the last few years have seen major progress and solutions to technical challenges from the laboratory to bioinformatics. Water eDNA has been shown to allow the fast and efficient recovery of biodiversity signals, but the rapid pace of technological development has meant that some important principles regarding sampling design, which are well established in traditional biodiversity inventories, have been neglected. Using a spatially explicit river flow model, we illustrate how sampling must be adjusted to the size of the watercourse to increase the quality of the biodiversity signal recovered. We additionally investigate the effect of sampling parameters (volume, number of sites, sequencing depth) on detection probability in an empirical data set. Based on traditional sampling principles, we propose that aquatic eDNA sampling replication and volume must be scaled to match the organisms' and ecosystems' properties to provide reliable biodiversity estimates. We present a generalizable conceptual equation describing sampling features as a function of the size of the ecosystem monitored, the abundance of target organisms, and the properties of the sequencing procedure. The aim of this formalization is to enhance the standardization of critical steps in the design of biodiversity inventory studies using eDNA. More robust sampling standards will generate more comparable biodiversity data from eDNA, which is necessary for the method's long-term plausibility and comparability.

Amphipods are among the most abundant macroinvertebrates in freshwater ecosystems of the Palaearctic and crucial for ecosystem functioning. Furthermore, their high sensitivity to environmental change and pollutants makes them widely used model organisms in environmental sciences and ecotoxicology. In field studies and surveys across Eurasia, species of the genus Gammarus are commonly used, yet laboratory-based studies and ecotoxicological tests are often restricted to the in most parts of the world non-native Hyalella azteca, as Gammarus is much harder to breed and maintain under laboratory conditions. However, for direct comparisons and extrapolations of results of field- vs. laboratory-based studies, the use of the same species would be desirable. Here, we investigated different settings with respect to feeding, shelter and day length to successfully increase survival, juvenile production and their respective growth and survival, and ultimately multi-generation breeding of the amphipod Gammarus fossarum. Amphipod populations persisted and reproduced successfully under optimized husbandry conditions for 12 months and were partially maintained for another year in populations up to a few hundred individuals. Specifically, supplementing diet with protein-rich food sources as well as the provisioning of shelters improved survival rate of G. fossarum significantly. However, we found no significant effect of different day length treatments on the overall relative reproductive activity or on the total amphipod abundance maintained. We conclude that G. fossarum can be kept and reared under standardized conditions. Despite the longer generation times of G. fossarum and higher effort required for maintenance compared to H. azteca, direct ecological relevance and comparability of results to natural systems may justify its future use and development as a study organism for environmental sciences and ecotoxicology.

Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTU) approach of our raw reads and assigned it taxonomically (i) in combination with publicly available reference sequences (open databases) or (ii) with an OSU (Operational Sequence Units) database approach, using a curated database of reference sequences generated from specimen barcoding (closed database). We show both approaches gave comparable results for common species. However, the commonalities between the approaches decreased with read abundance and were thus less reliable and not comparable for rare species. The success of the zOTU approach depended on the suitability, rather than the size, of a reference database. Contrastingly, the OSU approach used reliable DNA sequences and thus often enabled species-level identifications, yet this resolution decreased with the recent phylogenetic age of the species. We show the need to include target group coverage, outgroups and full taxonomic annotation in reference databases to avoid misleading annotations that can occur when using short amplicon sizes as commonly used in eDNA metabarcoding studies. Finally, we make general suggestions to improve the construction and use of reference databases for metabarcoding studies in the future.

South America is home to the highest freshwater fish biodiversity on Earth, and the hotspot of species richness is located in the western Amazon basin. The location of this hotspot is enigmatic, as it is inconsistent with the pattern observed in river systems across the world of increasing species richness towards a river’s mouth. Here we investigate the role of river capture events caused by Andean mountain building and repeated episodes of flooding in western Amazonia in shaping the modern-day richness pattern of freshwater fishes in South America, and in Amazonia in particular. To this end, we combine a reconstruction of river networks since 80 Ma with a mechanistic model simulating dispersal, allopatric speciation and extinction over the dynamic landscape of rivers and lakes. We show that Andean mountain building and consequent numerous small river capture events in western Amazonia caused freshwater habitats to be highly dynamic, leading to high diversification rates and exceptional richness. The history of marine incursions and lakes, including the Miocene Pebas mega-wetland system in western Amazonia, played a secondary role.

1. Fragmentation of habitat, for example by intensive agricultural practices, can be detrimental to local biodiversity. However, it often remains unclear whether such biodiversity declines are caused by loss of habitat area or increased fragmentation, and how habitat quality factors into it. In our study system, vegetated vineyards are typically small, and isolated from one another, potentially limiting the distribution and dispersal of organisms.
2. In a full-factorial experiment of a priori selected vegetated vineyard patches of differing size and fragmentation, we aimed to disentangle the effects of habitat area (area of vegetated vineyards), habitat fragmentation (number of vegetated vineyards per 100 ha) and field-scale ground vegetation density on ground beetle, leafhopper and wild bee communities using a combined framework of multiscale and multispecies modelling (Hierarchical Model of Species Communities).
3. We demonstrate variable effects of habitat area, fragmentation and local ground vegetation density on the three insect groups: Increased habitat area at fine scales favours higher species richness of leafhoppers, while local vegetation density boosts species richness of both leafhoppers and ground beetles, whereas no community-level responses were detected for wild bees.
4. We conclude that increased ground vegetation density at both field and landscape scales (i.e. higher habitat area) favours more diverse and abundant insect communities, while fragmentation effects are highly variable and species specific. In addition, our results highlight that mainly ground beetles and leafhoppers will benefit from simple ground greening measures in vineyards, while for wild bees environmental factors other than the ones tested here may drive community structure.
5. We recommend increasing the number and area of vegetated vineyards (even at small spatial scales) requiring more nature-friendly farming practices especially regarding a reduction or renunciation from herbicide applications, while the within-field vegetation density should optimally be intermediate or high to favour a diverse insect community.

Reliable biodiversity data are crucial for environmental research and management. Unfortunately, data paucity prevails for many regions and organismal groups such as aquatic invertebrates. High-throughput DNA-based identification, in particular DNA metabarcoding, has accelerated biodiversity data generation. However, in the process of metabarcoding, specimens are usually destroyed, precluding later specimen-based analyses. Metabarcoding of DNA released into the preservative ethanol has been proposed as a non-destructive alternative, but proof-of-principle studies have yielded ambiguous results, reporting variance in detection probability for various taxa and methodological biases. In this study, we tested the performance of preservative-based metabarcoding of aquatic invertebrates in comparison to a standard morpho-taxonomic assessment based on samples from one of Europe’s last free-flowing rivers, the Vjosa. Multi-habitat samples were collected at 43 sites in two seasons and stored in ethanol, after fixation in formaldehyde for morpho-taxonomic analyses. Preservative-based DNA metabarcoding detected three times more taxa but failed to detect other taxa found using the standard method. In addition to incomplete reference data and primer bias that likely precluded the detection of specific taxa, preservative-based DNA metabarcoding cannot provide accurate abundance estimates. However, the metabarcoding data revealed distinct small-scale and large-scale community patterns in the Vjosa river network, which were also recovered by quantitative data of the standard approach. Overall, our results indicate that preservative-based metabarcoding provides important biodiversity data, which could be further improved by quantitative validation. The method is robust and reliable, even though samples were taken under harsh field-conditions and stored without cooling. Further, our results emphasise the need for reliable DNA barcoding reference libraries. Building those may be supported by preservative-based metabarcoding that maintains intact vouchers for subsequent specimen-based analyses.

Variation in food resources can result in dramatic fluctuations in the body condition of animals dependent on those resources. Decreases in body mass can disrupt patterns of energy allocation and impose stress, thereby altering immune function. In this study, we investigated links between changes in body mass of captive cane toads (Rhinella marina), their circulating white blood cell populations, and their performance in immune assays. Captive toads that lost weight over a three-month period had increased levels of monocytes and heterophils and reduced levels of eosinophils. Basophil and lymphocyte levels were unrelated to changes in mass. Because individuals that lost mass had higher heterophil levels but stable lymphocyte levels, the ratio of these cell types was also higher, partially consistent with a stress response. Phagocytic ability of whole blood was higher in toads that lost mass, owing to increased circulating levels of phagocytic cells. Other measures of immune performance were unrelated to mass change. These results highlight the challenges faced by invasive species as they expand their range into novel environments which may impose substantial seasonal changes in food availability that were not present in the native range. Individuals facing energy restrictions may shift their immune function towards more economical and general avenues of combating pathogens.

Global change assessments have typically ignored synthetic chemical pollution, despite the rapid increase of pharmaceuticals, pesticides and industrial chemicals in the environment. Part of the problem reflects the multifarious origins of these micropollutants, which can derive from urban and agricultural sources. Understanding how micropollutants harm ecosystems is a major scientific challenge due to asymmetries of stress across trophic levels and ecological surprises generated by multiple drivers interacting in human-impacted landscapes. We used field assays above and below municipal wastewater treatment plants (WWTPs) in 60 sampling locations across 20 Swiss streams to test how micropollutants and nutrients originating from WWTPs affect two trophic levels (microbes and detritivores) and their role in leaf litter processing. Wastewater impacts were asymmetric across trophic levels, with the detritivore contribution declining relative to microbial-driven decomposition. The strength of negative impacts were context dependent, peaking at sites with the highest upstream abundances of detritivorous invertebrates. Diffuse pollution from intensive agriculture and wastewater-born micropollutants contributed to reduced litter processing rates, including indirect effects apparently mediated through negative influences of insecticides on detritivores. Asymmetries in stress responses across trophic levels can introduce quantitative changes in consumer–resource dynamics and leaf litter processing. This means functional redundancies at different trophic levels are insufficient to compensate for biodiversity losses, causing environmental stressors such as chemical pollutants to have pervasive ecosystem-level impacts.

The ever-increasing threats to riverine ecosystems call for novel approaches for highly resolved biodiversity assessments across taxonomic groups and spatio-temporal scales. Recent advances in the joint use of environmental DNA (eDNA) data and eDNA transport models in rivers (e.g., eDITH) allow uncovering the full structure of riverine biodiversity, hence elucidating ecosystem processes and supporting conservation measures. We applied eDITH to a metabarcoding dataset covering three taxonomic groups (fish, invertebrates, bacteria) and three seasons for a catchment sampled for eDNA at 73 sites. We upscaled eDNA-based biodiversity predictions to approximately 1900 reaches, and assessed α- and β-diversity patterns across seasons and taxonomic groups over the whole network. Genus richness predicted by eDITH was generally higher than values from direct eDNA analysis. Both predicted α- and β-diversity varied depending on season and taxonomic group. Predicted fish α-diversity increased downstream in all seasons, while invertebrate and bacteria α-diversity either decreased downstream or were unrelated to network position. Spatial β-diversity mostly decreased downstream, especially for bacteria. The eDITH model yielded a more refined assessment of freshwater biodiversity as compared to raw eDNA data, both in terms of spatial coverage, diversity patterns and effect of covariates, thus providing a more complete picture of freshwater biodiversity.

Spatially explicit mathematical models are key to a mechanistic understanding of environmental processes in rivers. Such models necessitate extended information on networks' morphology, which is often retrieved from geographic information system (GIS) software, thus hindering the establishment of replicable script-based workflows. Here I present rivnet, an R package for GIS-free extraction and analysis of river networks based on digital elevation models (DEMs). The package exploits TauDEM's flow direction algorithm in user-provided or online accessible DEMs, and allows for computing covariate values and assigning hydraulic variables across any network node. The package is designed so as to require minimal user input while allowing for customization for experienced users. It is specifically intended for application in models of ecohydrological, ecological or biogeochemical processes in rivers. As such, rivnet aims to make river network analysis accessible to users unfamiliar with GIS-based and geomorphological methods and therefore enhance the use of spatially explicit models in rivers.

Global ecosystems are facing a deepening biodiversity crisis, necessitating robust approaches to quantifying species extinction risk. The lower limit of the macroecological relationship between species range and body size has long been hypothesized as an estimate of the relationship between the minimum viable range size (MVRS) needed for species persistence and the organismal traits that affect space and resource requirements. Here, we perform the first explicit test of this assumption by confronting the MVRS predicted by the range-body size relationship with an independent estimate based on the scale of synchrony in abundance among spatially separated populations of riverine fish. We provide clear evidence of a positive relationship between the scale of synchrony and species body size, and strong support for the MVRS set by the lower limit of the range-body size macroecological relationship. This MVRS may help prioritize first evaluations for unassessed or data-deficient taxa in global conservation assessments.

Biological assemblages are the result of dynamic processes that have explicit temporal and spatial dimensions. Although biodiversity patterns can be directly inferred from the structure of these assemblages, an assessment of changes through time and space is needed to understand how organisms initially assembled and how they are responding to local environmental and biotic factors. Small freshwater streams are particularly affected by contemporary anthropogenic activities and biological invasions, yet they are commonly less studied, as studies often focus on lakes and large streams. Here, we conducted a spatially explicit analysis of keystone shredder assemblages across eight years in 12 replicated small tributary streams. In each stream, we monitored multiple sites per kilometer of stream length. By assessing temporal beta diversity dynamics, defined by the gain or loss of species or abundance per species at individual sites, we show that changes in amphipod assemblages occur within the context of the surrounding terrestrial matrix and reflect recent amphipod colonization history. While amphipod composition was mostly constant in streams located in forested catchments, streams embedded in catchments with more extensive agricultural land use displayed more pronounced temporal changes, either driven by colonization of unoccupied upstream locations or by more pronounced but undirected fluctuations in gains and losses of species or abundance per species. Our study thus suggests that agricultural landscapes might destabilize aquatic amphipod assemblages, causing higher temporal changes in community structures and highlighting the vulnerability of aquatic ecosystems to terrestrial land use drivers.

Disturbance can strongly influence ecosystems, yet much remains unknown about the relative importance of key processes (selection, drift, and dispersal) in the recovery of ecological communities following disturbance. We combined field surveys with a field experiment to elucidate mechanisms governing the recovery of aquatic macroinvertebrates in habitats of an alluvial floodplain following flood disturbance. We monitored macroinvertebrates in 24 natural parafluvial habitats over 60 days after a major flood, as well as the colonization of 24 newly-built ponds by macroinvertebrates over 45 days in the same floodplain. We examined the sources of environmental variation and their relative effects on aquatic assemblages using a combination of null models and Mantel tests. We also used a joint species distribution model to investigate the importance of primary metacommunity structuring processes during recovery: selection, dispersal, and drift. Contrary to expectations, we found that beta diversity actually decreased among natural habitats over time after the flood or the creation of the ponds, instead of increasing. This result was despite environmental predictors showing contrasting patterns for explaining community variation over time in the natural habitats compared with the experimental ponds. Flood heterogeneity across the floodplain and spatial scale differences between the experimental ponds and the natural habitats seemingly constrained the balance between deterministic and stochastic processes driving the ecological convergence of assemblages over time. While environmental selection was the dominant structuring process in both groups, biotic interactions also had a prominent influence on community assembly. These findings have profound implications towards understanding metacommunity structuring in riverscapes that includes common linkages between disturbance heterogeneity, spatial scale properties, and community composition.

1. Flow regime is a major determinant of the structure and functioning of aquatic ecosystems. Under climate change, flow intermittency is becoming more prevalent in glaciated alpine catchments, but the effects of increasing dryness on aquatic biodiversity remain largely unknown.
2. We characterised flow intermittency patterns in 30 streams of a glaciated alpine catchment over 15 months and separated these streams into four intermittency categories: perennial streams, winter-drying streams, moderately intermittent streams with occasional drying in summer, and periodically intermittent streams with extensive dry periods throughout the year.
We then examined how these drying patterns affected structural and functional properties of benthic macroinvertebrate communities, and whether these changes were primarily deterministic or stochastic.
3. At the taxonomic level, we observed a response at the highest intermittency levels, with α diversity lower and β diversity higher in periodically intermittent streams than in other stream types. This result suggested that local biota were well adapted to intermediate intermittency levels (mostly during winter) but not to high intermittency during summer. In contrast, functional diversity indices at the α and β levels (based on trait abundances) did not differ across intermittency categories. Considering the moderate level of functional redundancy, we interpreted this as an indication that changes in taxonomic diversity may have resulted primarily from stochastic processes.
4. Analysis of community and trait composition indicated that deterministic selection may indeed have occurred with increased intermittency, but this process was likely to be minor in comparison to stochastic extinctions. Notably, community evenness was highest in periodically intermittent streams and lowest in perennial streams, suggesting that frequent drying prevented competitive exclusion.
5. Our results suggested that most macroinvertebrate populations are resilient to intermediate intermittency levels but are filtered at high intermittency, irrespective of their resilience capacities. However, more research is needed to clarify the specific roles of different facets of flow regimes, specifically frequency, duration, and timing of intermittency. Understanding the consequences of responses in diversity and community evenness with increasing intermittency on the functional properties of communities will allow better prediction of the future ecological status of alpine stream networks to ongoing environmental change.

The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large-scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.

Flow regulation of montane and alpine headwater streams can fundamentally alter food web structure and energy flows through changes in productivity, resource availability, and community assembly. Dam flow-release schemes can be used to mitigate the environmental impacts of flow regulation via environmental flows, which can increase discharge variability and other ecologically important hydrological properties. In particular, managed floods can reintroduce disturbance to the system and stimulate the reactivation of physical habitat dynamics. However, how managed floods might restore ecosystem processes is virtually unknown. In this study, we examined patterns in potential energy fluxes before, during and after a long-term experimental flood program on the river Spöl, a regulated alpine River in southeast Switzerland. We used benthic samples collected during long-term monitoring and stable isotope analysis (δ¹³C and δ¹⁵N) of macroinvertebrates and their potential food sources to reconstruct secondary production, and potential energy fluxes, over a 20-year study period. The experimental floods did not alter the relative importance of basal resources but resulted in a considerable decline in secondary production, which remained low after the discontinuation of the floods. Our data suggest that a lack of recolonization by mosses following the discontinuation of the experimental flood program on the river Spöl may have driven patterns in energy fluxes by limiting macroinvertebrates using mosses for habitat. The effects of environmental flows on energy flows in this system thus depend on flood disturbance and the environmental context following the discontinuation of floods.

Despite being the most important source of liquid freshwater on the planet, groundwater is severely threatened by climate change, agriculture, or industrial mining. It is thus extensively monitored for pollutants and declines in quantity. The organisms living in groundwater, however, are rarely the target of surveillance programmes and little is known about the fauna inhabiting underground habitats. The difficulties accessing groundwater, the lack of expertise, and the apparent scarcity of these organisms challenge sampling and prohibit adequate knowledge on groundwater fauna. Environmental DNA (eDNA) metabarcoding provides an approach to overcome these limitations but is largely unexplored. Here, we sampled water in 20 communal spring catchment boxes used for drinking water provisioning in Switzerland, with a high level of replication at both filtration and amplification steps. We sequenced a portion of the COI mitochondrial gene, which resulted in 4917 ASVs, yet only 3% of the reads could be assigned to a species, genus, or family with more than 90% identity. Careful evaluation of the unassigned reads corroborated that these sequences were true COI sequences belonging mostly to diverse eukaryotic groups, not present in the reference databases. Principal component analyses showed a strong correlation of the community composition with the surface land-use (agriculture vs. forest) and geology (fissured rock vs. unconsolidated sediment). While incomplete reference databases limit the assignment of taxa in groundwater eDNA metabarcoding, we showed that taxonomy-free approaches can reveal large hidden diversity and couple it with major land-use drivers, revealing their imprint on chemical and biological properties of groundwater.

Groundwater is the physically largest freshwater ecosystem, yet one of the least explored habitats on earth, both because of accessing difficulties and the scarcity of the organisms inhabiting it. Here, we demonstrate how a two-fold approach provides complementary information on the occurrence and diversity of groundwater amphipods. Firstly, we used a citizen science approach in collaboration with municipal water providers who sampled groundwater organisms in their spring catchment boxes over multiple weeks, followed by DNA barcoding. Secondly, we collected four 10 L water samples at each site, in one sampling event, for environmental DNA (eDNA) metabarcoding. We found that citizen science was very effective in describing the distribution and abundance of groundwater amphipods. Although the single time-point of eDNA sampling did not detect as many amphipods, it allowed the assessment of the entire groundwater community, including microorganisms. By combining both methods, we found different amphipod species co-occurring with distinct sequences from the eDNA-metabarcoding dataset, representing mainly micro-eukaryotic species. We also found a distinct correlation between the diversity of amphipods and the overall biodiversity of groundwater organisms detected by eDNA at each site. We thus suggest that these approaches can be used to get a better understanding of subterranean biodiversity.

Molecular techniques using DNA retrieved from community or environmental samples, in particular environmental DNA (eDNA), are becoming increasingly popular for detecting individual species, assessing biodiversity, and quantifying ecological indices. More recently, eDNA has also been proposed as a template for population genetics, and several studies have already tested the feasibility of this approach, mostly looking at vertebrate species. Their results along with general opportunities offered by these types of "community-based" samples, such as the possibility to target multiple species at the same time, have generated great enthusiasm and expectations for using eDNA in population genetics. However, not every aspect of population genetics can be addressed by eDNA-based data and some inherent limitations may challenge its conclusions. Here, we firstly review the state of current knowledge of DNA retrieved from environmental and community samples for population genetics. Then, focusing on eDNA, we summarize the opportunities but also detail four main limitations of its use for population-level inferences, namely, (1) the difficulty to retrieve a species-specific dataset, (2) the potential lack of correlation between observed and true allelic frequencies, (3) the loss of individual information in multi-locus genotyping and linkage between loci, and (4) the uncertainty about the individuals contributing to the sampled DNA pool (e.g., number, life-stage, or sex). Some of these limitations might be overcome with the development of new technologies or models that account for the specificities of eDNA. Others, however, are inherent, and their effect on the inferences must be thoroughly evaluated. The possibility of gaining insights into genetic diversity and population structure from DNA retrieved from community and environmental samples is appealing for scientists, conservation managers, and other practitioners. Yet, to avoid false expectations and incorrect inferences, it is imperative that these limitations are known and considered alongside the opportunities and advantages.

Choosing to mate with an infected partner has several potential fitness costs, including disease transmission and infection-induced reductions in fecundity and parental care. By instead choosing a mate with no, or few, parasites, animals avoid these costs and may also obtain resistance genes for offspring. Within a population, then, the quality of sexually selected ornaments on which mate choice is based should correlate negatively with the number of parasites with which a host is infected ("parasite load"). However, the hundreds of tests of this prediction yield positive, negative, or no correlation between parasite load and ornament quality. Here, we use phylogenetically controlled meta-analysis of 424 correlations from 142 studies on a wide range of host and parasite taxa to evaluate explanations for this ambiguity. We found that ornament quality is weakly negatively correlated with parasite load overall, but the relationship is more strongly negative among ornaments that can dynamically change in quality, such as behavioral displays and skin pigmentation, and thus can accurately reflect current parasite load. The relationship was also more strongly negative among parasites that can transmit during sex. Thus, the direct benefit of avoiding parasite transmission may be a key driver of parasite-mediated sexual selection. No other moderators, including methodological details and whether males exhibit parental care, explained the substantial heterogeneity in our data set. We hope to stimulate research that more inclusively considers the many and varied ways in which parasites, sexual selection, and epidemiology intersect.

1. Parasite species that use two or more host species during their life cycle depend on successful transmission between these species. These successive host species may have different habitat requirements. For example, one host species may be aquatic while the other is terrestrial. To overcome this complicating factor in transmission, a wide diversity of parasite species have adaptations that alter the habitat preference in one host species to facilitate transmission to the next host species.
2. Two common trematode parasites in New Zealand, Atriophallophorus winterbourni and Notocotylus spp., both have a life cycle with two host species. The aquatic snail Potamopyrgus antipodarum is the intermediate host, from which the parasites require transmission to dabbling ducks or other waterfowl. Of these parasites, A. winterbourni is most frequently found in snails from the shallow-water margin. This may indicate parasite-induced movement of infected snails into the foraging habitat of dabbling ducks.
3. To test whether the parasites manipulate the snails to move into shallow water, we stretched tubular mesh cages across depth-specific ecological habitat zones in a lake. Both infected and healthy snails were released into the cages. After 11 days, significantly higher infection frequencies of A. winterbourni were retrieved from the shallowest end of the cages, while Notocotylus spp. frequencies did not vary with depth.
4. The hypothesis that A. winterbourni induces its snail host to move into the shallow-water habitat cannot be rejected based on the experimental results. Although further research is needed to address alternative explanations, the depth preference of infected snails may be due to a parasite adaptation that facilitates trophic transmission of parasites to dabbling ducks.

To understand mating-system evolution in self-compatible hermaphrodites, variation in selfing rates is highly relevant. Empirical studies are rarely designed to capture variation between individuals, instead often comparing species and populations. Yet, evolution primarily occurs within populations, rendering among-individual variation essential. Observed individual selfing rates depend on the environment (e.g. differences in mate availability) and individuals' propensity for selfing. We quantified individual variation in selfing propensity in the snail Radix balthica by conducting laboratory mating trials that manipulated mate availability (low versus moderate) and estimating selfing rates from progeny arrays. We also measured female lifetime fitness. We found substantial among-individual variation in selfing propensity, including pure selfers (32%), pure outcrossers (31%) and mixed-mating individuals that selfed and outcrossed (37%). Experimental levels of mate availability did not significantly affect selfing rates. Selfers had reduced female liftetime fitness. Our results show that the propensity for selfing can differ considerably among individuals, with similar proportions of selfers, outcrossers and mixed maters. As mate availability did not affect selfing, our ‘moderate’ experimental level of mate availability might still have been too low to prompt selfers to outcross. This and the observed fitness differences also cautiously suggest that investigating the heritability of selfing propensities might be worthwhile in this population.

Defensive symbiosis describes the interaction between two species where one species protects the other from dangers, in exchange for another benefit. Protagonist of this thesis is Hamiltonella defensa, a vertically transmitted bacterial endosymbiont of aphids. H. defensa can defend its aphid host against parasitoid wasps and in return profits from nutrients and shelter inside the aphid body. In wild aphid populations, H. defensa often occurs at intermediate prevalence, that is, some aphid individuals carry the bacteria, but others do not. This might be explained by balancing selection, as carrying H. defensa has not only benefits but also costs for the aphid. The tripartite interaction between aphids, H. defensa and aphid parasitoids is considered a model system for symbiont-driven hostparasite coevolution and has been studied from various angles during the past twenty years. However, there is still a lack of data on the role of defensive symbiosis in the ecology and evolution of natural communities. With my PhD work, I sought to improve on that by studying patterns and dynamics of H. defensa-conferred resistance in the field. [...]

Symbiose beschreibt das enge Zusammenleben zweier unterschiedlicher Organismen. In sogenannten defensiven Symbiosen bietet eine Art der anderen Schutz oder Resistenz gegen Feinde oder Gefahren. Protagonist der vorliegenden Arbeit ist Hamiltonella defensa, ein endosymbiotisches Bakterium, das im Körper von Blattläusen lebt und von einer zur nächsten Blattlausgeneration vererbt wird. H. defensa kann Blattläusen Resistenz gegen parasitische Schlupfwespen verleihen, welche wichtige natürliche Feinde der Läuse sind. H. defensa ist also ein defensiver Symbiont von Blattläusen. Im Gegenzug profitiert H. defensa von 'Kost und Logis' im Innern der Blattlaus. In natürlichen Blattlauspopulationen leben meist einige Individuen mit, andere ohne symbiotische H. defensa. Das wird damit erklärt, dass H. defensa für die Läuse nicht nur Vorteile bringt, sondern auch Kosten. Diese Kosten kommen besonders dann zur Geltung, wenn keine Schlupfwespen die Blattläuse bedrohen, weil die Resistenz gegen solche dann nichts bringt, H. defensa aber weiterhin von den Blattlausressourcen zehrt. Je nach Situation sind also Blattläuse mit oder solche ohne H. defensa fitter. [...]

Parasite-mediated selection can rapidly drive up resistance levels in host populations, but fixation of resistance traits may be prevented by costs of resistance. Black bean aphids (Aphis fabae) benefit from increased resistance to parasitoids when carrying the defensive bacterial endosymbiont Hamiltonella defensa. However, due to fitness costs that come with symbiont infection, symbiont-conferred resistance may result in either a net benefit or a net cost to the aphid host, depending on parasitoid presence as well as on the general ecological context. Balancing selection may therefore explain why in natural aphid populations, H. defensa is often found at intermediate frequencies. Here we present a 2-year field study where we set out to look for signatures of balancing selection in natural aphid populations. We collected temporally well-resolved data on the prevalence of H. defensa in A. f. fabae and estimated the risk imposed by parasitoids using sentinel hosts. Despite a marked and consistent early-summer peak in parasitism risk, and significant changes in symbiont prevalence over time, we found just a weak correlation between parasitism risk and H. defensa frequency dynamics. H. defensa prevalence in the populations under study was, in fact, better explained by the number of heat days that previous aphid generations were exposed to. Our study grants an unprecedentedly well-resolved insight into the dynamics of endosymbiont and parasitoid communities of A. f. fabae populations, and it adds to a growing body of empirical evidence suggesting that not only parasitism risk, but rather multifarious selection is shaping H. defensa prevalence in the wild.

Motivation: Aquatic insects comprise 64% of freshwater animal diversity and are widely used as bioindicators to assess water quality impairment and freshwater ecosystem health, as well as to test ecological hypotheses. Despite their importance, a comprehensive, global database of aquatic insect occurrences for mapping freshwater biodiversity in macroecological studies and applied freshwater research is missing. We aim to fill this gap and present the Global EPTO Database, which includes worldwide geo-referenced aquatic insect occurrence records for four major taxa groups: Ephemeroptera, Plecoptera, Trichoptera and Odonata (EPTO).
Main type of variables contained: A total of 8,368,467 occurrence records globally, of which 8,319,689 (99%) are publicly available. The records are attributed to the corresponding drainage basin and sub-catchment based on the Hydrography90m dataset and are accompanied by the elevation value, the freshwater ecoregion and the protection status of their location.
Spatial location and grain: The database covers the global extent, with 86% of the observation records having coordinates with at least four decimal digits (11.1 m precision at the equator) in the World Geodetic System 1984 (WGS84) coordinate reference system.
Time period and grain: Sampling years span from 1951 to 2021. Ninety-nine percent of the records have information on the year of the observation, 95% on the year and month, while 94% have a complete date. In the case of seven sub-datasets, exact dates can be retrieved upon communication with the data contributors.
Major taxa and level of measurement: Ephemeroptera, Plecoptera, Trichoptera and Odonata, standardized at the genus taxonomic level. We provide species names for 7,727,980 (93%) records without further taxonomic verification.
Software format: The entire tab-separated value (.csv) database can be downloaded and visualized at https://glowabio.org/project/epto_database/. Fifty individual datasets are also available at https://fred.igb-berlin.de, while six datasets have restricted access. For the latter, we share metadata and the contact details of the authors.

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.

Invasive species have far-reaching consequences for whole ecosystems. The two dreissenids zebra and quagga mussels are two of the most successful invaders in aquatic systems. Quagga mussels can colonize deeper parts of a lake while zebra mussels prefer shallow areas. Both species show large variability in shell morphology, but only quagga mussels show a shallow and deep-water morphotype. The aim of this study is to investigate the depth adaptation of quagga mussels and the potential filtration advantage of the quagga mussel compared to the zebra mussel. We conducted common garden experiments, where we measured filtration rates at different temperatures of quagga mussels collected from different water depths and compared them to zebra mussel from 1m depth. We found filtration rates to be strongly temperature dependent, and in particular, lower at 4 °C. Overall, zebra mussels fed less than quaggas. Quagga mussels collected from 1 m depth fed more at higher temperature than quaggas from 30 and 60 m. We hypothesize that deep-water quagga mussels are less sensitive to lower temperature and/or constrained to modify filtration rates at higher temperatures.

The integration of ecosystem processes over large spatial extents is critical to predicting whether and how local and global changes may impact biodiversity and ecosystem functions. Yet, there remains an important gap in meta-ecosystem models to predict multiple functions (e.g. carbon sequestration, elemental cycling, trophic efficiency) across ecosystem types (e.g. terrestrial-aquatic, benthic-pelagic). We derive a flexible meta-ecosystem model to predict ecosystem functions at landscape extents by integrating the spatial dimension of natural systems as spatial networks of different habitat types connected by cross-ecosystem flows of materials and organisms. We partition the physical connectedness of ecosystems from the spatial flow rates of materials and organisms, allowing the representation of all types of connectivity across ecosystem boundaries. Through simulating a forest-lake-stream meta-ecosystem, our model illustrates that even if spatial flows induced significant local losses of nutrients, differences in local ecosystem efficiencies could lead to increased secondary production at regional scale. This emergent result, which we dub the 'cross-ecosystem efficiency hypothesis', emphasizes the importance of integrating ecosystem diversity and complementarity in meta-ecosystem models to generate empirically testable hypotheses for ecosystem functions.

Parasitoids in the genus Lysiphlebus specialize on ant-tended aphids and have previously been reported to mimic the cuticular hydrocarbon (CHC) profiles of their aphid hosts to avoid detection by ants. However, the precise mechanisms that mediate reduced ant aggression toward Lysiphlebus spp. are not known, nor is it clear whether such mechanisms are broadly effective or specialized on particular aphid hosts. Here we explore the effects of wasp genotype and host environment on Lysiphlebus CHC profiles and ant aggression. Rearing asexual Lysiphlebus lines in different host aphid environments revealed effects of both wasp line and aphid host on wasp CHCs. However, variation in genotype and host affected different features of the CHC profile, with wasp genotype explaining most variation in linear and long-chain methyl alkanes, while aphid host environment primarily influenced short-chain methyl alkanes. Subsequent behavioural experiments revealed no effects of host environment on ant aggression, but strong evidence for genotypic effects. The influence of genotypic variation on experienced ant aggression and relevant chemical traits is particularly relevant in light of recent evidence for genetic divergence among Lysiphlebus parasitoids collected from different aphid hosts.

Introduction: Understanding how species are distributed in space and how they interact with each other is central for scientific and conservation purposes. Species' distributions and interactions result from a complex interplay of local trophic dynamics, dispersal processes, resource availability, and abiotic factors governed by the landscape matrix, which also determines the spatial connectivity for organisms' dispersal and resource fluxes. River networks not only exhibit universal spatial structures, but their dendritic landscape structure is tightly linked to species and metacommunity processes therein.
Methods: Here, using a mechanistic model of spatially connected food webs integrating both essential biological and hydrological aspects, we investigate how food-web properties vary in space, and how these patterns are influenced by key model parameters. We then contrast our predictions with a suite of null models, where different aspects (such as spatial structure or trophic interactions) of the spatial food-web model are alternatively relaxed.
Results: We find that species richness is highest in areas where local nutrient load is maximal (lowland headwaters, according to our default assumption). Overall, species richness is positively associated with link density, modularity and omnivory, and negatively related to connectance, nestedness, and niche overlap. However, for metrics such as connectance and omnivory, stochasticity of trophic interactions is a much stronger predictor than spatial variables such as distance to outlet and drainage area. Remarkably, relationships between species richness and food-web metrics do not generally hold in null models, and are hence the outcome of coupled biological and physical (i.e., hydrological) processes characteristic to river networks.
Discussion: Our model generates realistic patterns of species richness and food-web properties, shows that no universal food-web patterns emerge as a result of the riverine landscape structure, and paves the way for future applications aimed at disentangling metacommunity dynamics in river networks.

Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi-natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild-caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population expansion into unoccupied habitats and accelerate invasion success.

In recent years, unexplained declines in lake total phosphorus (TP) concentrations have been observed at northern latitudes (> 42°N latitude) where most of the world's lakes are found. We compiled data from 389 lakes in Fennoscandia and eastern North America to investigate the effects of climate on lake TP concentrations. Synchrony in year-to-year variability is an indicator of climatic influences on lake TP, because other major influences on nutrients (e.g., land use change) are not likely to affect all lakes in the same year. We identified significant synchrony in lake TP both within and among different geographic regions. Using a bootstrapped random forest analysis, we identified winter temperature as the most important factor controlling annual TP, followed by summer precipitation. In Fennoscandia, TP was negatively correlated with the winter East Atlantic Pattern, which is associated with regionally warmer winters. Our results suggest that, in the absence of other overriding factors, lake TP and productivity may decline with continued winter warming in northern lakes.

Riverine exports of silicon (Si) influence global carbon cycling through the growth of marine diatoms, which account for ∼25% of global primary production. Climate change will likely alter river Si exports in biome-specific ways due to interacting shifts in chemical weathering rates, hydrologic connectivity, and metabolic processes in aquatic and terrestrial systems. Nonetheless, factors driving long-term changes in Si exports remain unexplored at local, regional, and global scales. We evaluated how concentrations and yields of dissolved Si (DSi) changed over the last several decades of rapid climate warming using long-term data sets from 60 rivers and streams spanning the globe (e.g., Antarctic, tropical, temperate, boreal, alpine, Arctic systems). We show that widespread changes in river DSi concentration and yield have occurred, with the most substantial shifts occurring in alpine and polar regions. The magnitude and direction of trends varied within and among biomes, were most strongly associated with differences in land cover, and were often independent of changes in river discharge. These findings indicate that there are likely diverse mechanisms driving change in river Si biogeochemistry that span the land-water interface, which may include glacial melt, changes in terrestrial vegetation, and river productivity. Finally, trends were often stronger in months outside of the growing season, particularly in temperate and boreal systems, demonstrating a potentially important role of shifting seasonality for the flux of Si from rivers. Our results have implications for the timing and magnitude of silica processing in rivers and its delivery to global oceans.

The current advances of environmental DNA (eDNA) bring profound changes to ecological monitoring and provide unique insights on the biological diversity of ecosystems. The very nature of eDNA data is challenging yet also revolutionizing how biological monitoring information is analysed. In particular, new metrics and approaches should take full advantage of the extent and detail of molecular data produced by genetic methods. In this perspective, machine learning algorithms are particularly promising as they can capture complex relationships between the multiple environmental pressures and the diversity of biological communities. We investigated the potential of a new generation of biomonitoring tools that implement machine-learning techniques to fully exploit eDNA datasets. We trained a machine learning model to discriminate between reference and impacted communities of freshwater macroinvertebrates and assessed its performances using a large eDNA dataset collected at 64 standard federal monitoring sites across Switzerland. We show that a model trained on eDNA is significantly better than a naive model and performs similarly to a model trained on traditional data. Our proof-of-concept shows that such a combination of eDNA and machine learning approaches has the potential to complement or even replace traditional environmental monitoring, and could be scaled along temporal or spatial dimensions.

DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be—and often has been—done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.

Evaluating the impact of future changes in land-use and climate on species communities, especially species richness, is one of the most important challenges of current research in ecology and conservation. The impact of environmental changes on species richness depends on its sensitivity (i.e., how strongly a given level of change influences the ecological community) and its exposure (i.e., the amount of change that occurs). To examine the sensitivity, exposure, and potential impact of future environmental conditions on bird communities, we compiled data on bird species richness for Pakistan-a neglected region in macro- or country-scale studies. Since bird species richness strongly varies across seasons due to the seasonal occurrence of migratory species in winter, we compared both wintering (migratory plus resident species) and breeding (resident species only) bird richness. We found breeding and wintering species richness to be sensitive to temperature, precipitation and rainfed cropland by being positively related to these factors. Exposure varied regionally, with projected temperature changes being most profound in northern regions while the strongest projected precipitation changes occurred in central and southern regions. The projected impact of future environmental change were highly heterogeneous across the country and differed between the wintering and breeding communities. Overall, the most negatively impacted region was projected to be the Khyber Pakhtunkha province in the North of Pakistan, due to reductions in precipitation and rainfed cropland, resulting in a projected negative impact, especially on wintering species richness. By highlighting the regional and seasonal bird communities most at risk, our findings provide useful information for policy makers to help devise new policies for mitigating negative impacts of future environmental changes on birds within Pakistan.

1. Understanding the role of thermal tolerances in determining species distributions is important for assessing species responses to climate change. Two hypotheses linking physiology with species distributions have been put forward—the climatic variability hypothesis and the climatic extreme hypothesis. The climatic variability hypothesis predicts the selection of individuals with broad thermal tolerance in more variable climatic conditions and the climatic extreme hypothesis predicts the selection of individuals with extreme thermal tolerance values under extreme climatic conditions. However, no study has tested the predictions of these hypotheses simultaneously for several taxonomic groups along elevational gradients.
2. Here, we related experimentally measured critical thermal maxima, critical thermal minima and thermal tolerance breadths for 15,187 individuals belonging to 116 species of ants, beetles, grasshoppers, and spiders from mountain ranges in central and northern Pakistan to the limits and breadths of their geographic and temperature range.
3 Across all species and taxonomic groups, we found strong relationships between thermal traits and elevational distributions both in terms of geography and temperature. The relationships were robust when repeating the analyses for ants, grasshoppers, and spiders but not for beetles. These results indicate a strong role of physiology in determining elevational distributions of arthropods in Southern Asia.
4. Overall, we found strong support for the climatic variability hypothesis and the climatic extreme hypothesis. A close association between species' distributional limits and their thermal tolerances suggest that in case of a failure to adapt or acclimate to novel climatic conditions, species may be under pressure to track their preferred climatic conditions, potentially facing serious consequences under current and future climate change.

In river systems worldwide, land cover changes have been identified as major drivers of biodiversity change. Quantifying how terrestrial land cover impacts riverine diversity requires local biodiversity assessments. In this study, we investigated the association of terrestrial land cover and the corresponding riverine fish species communities using eDNA-metabarcoding in the Chinese Shaying River basin. This basin is home to about 37 million people and is largely dominated by a mix of intense agriculture and urban areas, creating a relatively homogeneous, intensely used landscape. We investigated whether the homogeneous landscape is mirrored in the composition and structure of fish communities in the river network. We sampled eDNA in spring and fall of 2018, amplified it with a primer designed for local fish species and used operational taxonomic units (OTU) assigned to fish as proxy for diversity. Furthermore, we used redundancy analysis, general linear models, and distance decay curves to assess the effects of land cover on fish communities. We found that the Shaying River showed relatively high basin-wide richness (63 OTU) and seasonal differences in local richness, but limited community differentiation. Variations in alpha- and beta-diversity, measured as local OTU richness and pairwise distance-decay across the basin were low. Redundancy analysis showed only a weak association between observed aquatic communities and their terrestrial surroundings in a 10 km buffer upstream. The lack of community differentiation assessed by eDNA metabarcoding reflects the homogeneous and intense land-use in this basin.

Subterranean fauna is an important contributor to the global fauna, but it is still understudied and a large part of its taxonomy is not yet resolved. One species complex with unresolved taxonomy is the groundwater amphipod Niphargus ruffoi, endemic to the Alpine chain. Here, we used new samples from across the Alpine arc to review the taxonomic status of the entire clade, including the species N. ruffoi and Niphargus arolaensis. We sequenced four genetic markers from the collected specimens, assessed the phylogenetic position of N. ruffoi within the genus, and studied the structure of this species complex using four molecular species delimitation methods. We tested for recombination using the alignments of the concatenated nuclear rDNA genes. The phylogenetic analyses revealed high support for the monophyly of the studied species complex, defining two lineages (i.e., N. arolaensis and N. ruffoi) within the clade. Molecular species delimitation methods suggested that N. arolaensis is a single species, while N. ruffoi should be considered as a species complex of three (using ITS) to eight (using COI) putative species. Moreover, we found a discrepancy between the different nuclear ribosomal DNA markers, indicating a possible recombination with fragments of 28S DNA of N. ruffoi s. lat. present in the genome of N. arolaensis. For the above-mentioned reasons, the internal phylogenetic structure of N. ruffoi s. lat. could not be fully resolved. Moreover, no clear morphological evidence supported the molecular species delimitation. Consequently, no taxonomic changes were proposed. We postulate that this complex scenario was influenced by Pleistocene climate oscillations with subsequent fragmentation events and secondary contacts, making this an interesting study system to investigate the evolution and biogeography of Alpine clades.

Diatom species identification with DNA metabarcoding is an economical, fast and reliable alternative to identification via light microscopy for river quality monitoring. Using a short DNA sequence of the rbcL gene and 'Diat.barcode', a reference barcode library, enables the identification of more than 90% of the environmental sequences to species level in French rivers. But the completeness of this library is much lower in other regions, such as the tropical French overseas departments. A barcode library completion method using high-throughput sequencing data combined with microscopy count data from natural samples (Rimet et al. Citation2018) was applied and tested in rivers of Martinique and Guadeloupe (West Indies), for which only 45% of the environmental sequences could be identified to species level using Diat.barcode v9. Assigning barcodes to the most abundant species in the islands by this method is illustrated with Ulnaria goulardii and two new species belonging to Nupela and Epithemia, which are also described in this paper. The more complex situation of morphologically similar species is illustrated by reference to Gomphonema designatum and G. bourbonense. Using a combination of molecular and morphological data, their conspecificity, as G. bourbonense, is demonstrated with their reference barcodes. However, when several morphologically similar species and several environmental sequences belonging to the same clade are present, it is not possible to relate the barcodes to corresponding morphological species.
Applying this method enabled the Diat.barcode library (v.10) to be updated, with 84% of the environmental sequences from the West Indies now identifiable at the species level. However, many morphological species still lack barcodes. In these cases, more classical methods, such as cell isolation, Sanger sequencing and morphological observations of cultures, must be applied.

Lignocellulose biomass has recently been considered a cost-effective and renewable energy source within circular economy management. Cellulases are important key enzymes for simple, fast, and clean biomass decomposition. The intestinal tract of millipedes is the environment which can provide promising microbial strains with cellulolytic potential. In the present study, we used the tropical millipede Telodeinopus aoutii as an experimental organism. Within a feeding test in which millipedes were fed with oak and maple leaf litter, we focused on isolating culturable cellulolytic microbiota from the millipede gut. Several growth media selecting for actinobacteria, bacteria, and fungi have been used to cultivate microbial strains with cellulolytic activities. Our results showed that oak-fed millipedes provided a higher number of culturable bacteria and a more diversified microbial community than maple-fed ones. The screening for cellulolytic activity using Congo red revealed that about 30% of bacterial and fungal phylotypes isolated from the gut content of T. aoutii, produced active cellulases in vitro. Actinobacteria Streptomyces and Kitasatospora were the most active cellulolytic genera on Congo red test. In contrast, fungi Aspergillus, Penicillium, Cheatomium, Clonostachys, and Trichoderma showed the highest protein-specific cellulase activity quantified by 4-Methylumbelliferyl β-d-cellobioside (4‐MUC). Our findings provide a basis for future research on the enzyme activities of microbes isolated from the digestive tracts of invertebrates and their biocatalytic role in biomass degradation.

Freshwater systems have undergone drastic alterations during the last century, potentially affecting cross-boundary resource transfers between aquatic and terrestrial ecosystems. One important connection is the export of biomass by emergent aquatic insects containing omega-3 polyunsaturated fatty acids (PUFAs), especially eicosapentaenoic acid (EPA), that is scarce in terrestrial systems. Because of taxon-specific differences in PUFA content and functional traits, the contribution of different insect groups should be considered, in addition to total biomass export. In this context, one important trait is the emergence mode. Stoneflies, in contrast to other aquatic insects, crawl to land to emerge instead of flying directly from the water surface, making them accessible to ground-dwelling predators. Because stoneflies are especially susceptible to environmental change, stream degradation might cause a mismatch of available and required nutrients, particularly for ground-dwelling predators. In this study, we estimated emergent biomass and EPA export along two streams with different levels of habitat degradation. The EPA content in aquatic insects did not differ with different degrees of habitat degradation and total biomass export in spring was with 7.9 ± 9.6 mg m^-2 day^-1 in the degraded and 7.3 ± 8.5 mg m^-2 day^-1 in the natural system, also unaffected. However, habitat degradation substantially altered the contribution of crawling emergence to the total export in spring, with no biomass export by stoneflies at the most degraded sites. The EPA content in ground-dwelling spiders was correlated with emergent stonefly biomass, making up only 16.0 ± 6.2 % of total fatty acids at sites with no stonefly emergence, but 27.3 ± 3.0 % at sites with highest stonefly emergence. Because immune function in ground-dwelling spiders has been connected to EPA levels, reduced crawling emergence might impact spider fitness. Functional traits, like emergence mode as well as nutritional quality, should be considered when assessing the effects of stream degradation on adjacent terrestrial ecosystems.

Quagga mussels have expanded their range across the northern hemisphere in recent decades owing to their dispersal abilities, prolific reproduction rates, and broad ecological tolerances. Their remarkable capacity to filter particulates from the water column has had profound effects on inland aquatic ecosystems. In the North American Great Lakes, quagga mussel populations have increased inexorably since the late 1980's, but it remains unclear whether quagga mussels will follow a similar trajectory in Europe where they have appeared more recently. Here we apply knowledge from a long-term quagga population monitoring effort in the North American lakes to predict future quagga populations in deep European lakes, where quaggas are quickly becoming a conspicuous part of the underwater landscape. We predict that quagga mussel biomass in Lakes Biel, Constance, and Geneva may increase by a factor of 9-20 by 2045. Like in North America, this increase may be characterized by a shift to larger individuals and deeper depths as the population matures. If realized, this rapid expansion of quagga mussels would likely drive the largest aquatic ecosystem change in deep European lakes since the eutrophication period of the mid-20th century.

Human activity is a major driver of ecological and evolutionary change in wild populations and can have diverse effects on eukaryotic organisms as well as on environmental and host-associated microbial communities. Although host–microbiome interactions can be a major determinant of host fitness, few studies consider the joint responses of hosts and their microbiomes to anthropogenic changes. In freshwater ecosystems, wastewater is a widespread anthropogenic stressor that represents a multifarious environmental perturbation. Here, we experimentally tested the impact of treated wastewater on a keystone host (the freshwater isopod Asellus aquaticus) and its gut microbiome. We used a semi-natural flume experiment, in combination with 16S rRNA amplicon sequencing, to assess how different concentrations (0%, 30%, and 80%) of nonfiltered wastewater (i.e. with chemical toxicants, nutrients, organic particles, and microbes) versus ultrafiltered wastewater (i.e. only dissolved pollutants and nutrients) affected host survival, growth, and food consumption as well as mid- and hindgut bacterial community composition and diversity. Our results show that while host survival was not affected by the treatments, host growth increased and host feeding rate decreased with nonfiltered wastewater – potentially indicating that A. aquaticus fed on organic matter and microbes available in nonfiltered wastewater. Furthermore, even though the midgut microbiome (diversity and composition) was not affected by any of our treatments, nonfiltered wastewater influenced bacterial composition (but not diversity) in the hindgut. Ultrafiltered wastewater, on the other hand, affected both community composition and bacterial diversity in the hindgut, an effect that in our system differed between sexes. While the functional consequences of microbiome changes and their sex specificity are yet to be tested, our results indicate that different components of multifactorial stressors (i.e. different constituents of wastewater) can affect hosts and their microbiome in distinct (even opposing) manners and have a substantial impact on eco-evolutionary responses to anthropogenic stressors.

Immune defence is an important determinant of organismal fitness. While theoretical models based on tradeoffs in resource allocation predict quantitative immune traits to be subject to stabilizing selection due to associated energetic costs and self-harm, empirical studies report mainly positive directional selection. This discrepancy may arise from multiple ecological factors that vary in nature and could influence selection. We examined if selection on immune activity varies depending on immune challenge/infection risk, between immune traits and among populations in the freshwater snail Lymnaea stagnalis. We assessed selection on the phenoloxidase-like and antibacterial activity of snail haemolymph while manipulating the level of immune challenge imposed by environmental microbes. We did this using snails from multiple populations and also quantified within-population family-level variation (i.e. evolutionary potential) in the snails' immune activity. We found that the strength of immune challenge and the examined immune trait determined selection on the snails' immune function. Thus, variation in infection risk can be an important factor in maintaining genetic variation in defence traits. Additionally, immune traits showed low among-population differentiation but high within-population genetic variation. This pattern could arise if natural snail populations are exposed to higher temporal than spatial variation in infection risk.

Human-driven environmental stressors are increasingly threatening species survival and diversity of river systems worldwide. However, it remains unclear how the stressors affect the stability changes across aquatic multiple communities. Here, we used environmental DNA (eDNA) data sets from a human-dominated river in China over 3 years and analyzed the stability changes in multiple communities under persistent anthropogenic stressors, including land use and pollutants. First, we found that persistent stressors significantly reduced multifaceted species diversity (e.g., species richness, Shannon’s diversity, and Simpson’s diversity) and species stability but increased species synchrony across multiple communities. Second, the structures of interaction networks inferred from an empirical meta-food web were significantly changed under persistent stressors, for example, resulting in decreased network modularity and negative/positive cohesion. Third, piecewise structural equation modeling proved that the persistent stress-induced decline in the stability of multiple communities mainly depended upon diversity-mediated pathways rather than the direct effects of stress per se; specifically, the increase of species synchrony and the decline of interaction network modularity were the main biotic drivers of stability variation. Overall, our study highlights the destabilizing effects of persistent stressors on multiple communities as well as the mechanistic dependencies, mainly through reducing species diversity, increasing species synchrony, and changing interaction networks.

The freshwater isopod Asellus aquaticus is an important decomposer of leaf detritus, and its diverse gut microbiome has been depicted as key contributors in lignocellulose degradation as of terrestrial isopods. However, it is not clear whether the individual-level microbiome profiles in the isopod digestive system across different habitats match the implied robust digestion function of the microbiome. Here, we described the bacterial diversity and abundance in the digestive system (hindgut and caeca) of multiple A. aquaticus individuals from two contrasting freshwater habitats. Individuals from a lake and a stream harboured distinct microbiomes, indicating a strong link between the host-associated microbiome and microbes inhabiting the environments. While faeces likely reflected the variations in environmental microbial communities included in the diet, the microbial communities also substantially differed in the hindgut and caeca. Microbes closely related to lignocellulose degradation are found consistently more enriched in the hindgut in each individual. Caeca often associated with taxa implicated in endosymbiotic/parasitic roles (Mycoplasmatales and Rickettsiales), highlighting a complex host–parasite–microbiome interaction. The results highlight the lability of the A. aquaticus microbiome supporting the different functions of the two digestive organs, which may confer particular advantages in freshwater environments characterized by seasonally fluctuating and spatially disparate resource availability.

Bipartite network analysis is a powerful tool to study the processes structuring interactions in ecological communities. In applying the method, it is assumed that the sampled interactions provide an accurate representation of the actual community. However, acquiring a representative sample may be difficult as not all species are equally abundant or easily identifiable. Two potential sampling issues can compromise the conclusions of bipartite network analyses: failure to capture the full range of interactions (sampling completeness) and use of a taxonomic level higher than species to evaluate the network (taxonomic resolution). We asked how commonly used descriptors of bipartite antagonistic communities (modularity, nestedness, connectance, and specialization [H₂′]) are affected by reduced host sampling completeness, parasite taxonomic resolution, and their crossed effect, as they are likely to co-occur. We used a quantitative niche model to generate weighted bipartite networks that resembled natural host–parasite communities. The descriptors were more sensitive to uncertainty in parasite taxonomic resolution than to host sampling completeness. When only 10% of parasite taxonomic resolution was retained, modularity and specialization decreased by ~76% and ~12%, respectively, and nestedness and connectance increased by ~114% and ~345% respectively. The loss of taxonomic resolution led to a wide range of possible communities, which made it difficult to predict its effects on a given network. With regards to host sampling completeness, standardized nestedness, connectance, and specialization were robust, whereas modularity was sensitive (~30% decrease). The combination of both sampling issues had an additive effect on modularity. In communities with low effort for both sampling issues (50%–10% of sampling completeness and taxonomic resolution), estimators of modularity, and nestedness could not be distinguished from those of random assemblages. Thus, the categorical description of communities with low sampling effort (e.g., if a community is modular or not) should be done with caution. We recommend evaluating both sampling completeness and taxonomic certainty when conducting bipartite network analyses. Care should also be exercised when using nonrobust descriptors (the four descriptors for parasite taxonomic resolution; modularity for host sampling completeness) when sampling issues are likely to affect a dataset.

Microbes often exist in spatially structured environments and many of their interactions are mediated through diffusible metabolites. How does such a context affect microbial coexistence? To address this question, we use a model in which the spatial distributions of species and diffusible interaction mediators are explicitly included. We simulate the enrichment process, examining how microbial species spatially reorganize and how eventually a subset of them coexist. In our model, we find that slower motility of cells promotes coexistence by allowing species to co-localize with their facilitators and avoid their inhibitors. We additionally find that a spatially structured environment is more influential when species mostly facilitate each other, rather than when they are mostly competing. More coexistence is observed when species produce many mediators and consume some (not many or few) mediators, and when overall consumption and production rates are balanced. Interestingly, coexistence appears to be disfavored when mediators are diffusing slowly because that leads to weaker interaction strengths. Overall, our results offer new insights into how production, consumption, motility, and diffusion intersect to determine microbial coexistence in a spatially structured environment.

Dispersal is a central life history trait that affects the ecological and evolutionary dynamics of populations and communities. The recent use of experimental evolution for the study of dispersal is a promising avenue for demonstrating valuable proofs of concept, bringing insight into alternative dispersal strategies and trade-offs, and testing the repeatability of evolutionary outcomes. Practical constraints restrict experimental evolution studies of dispersal to a set of typically small, short-lived organisms reared in artificial laboratory conditions. Here, we argue that despite these restrictions, inferences from these studies can reinforce links between theoretical predictions and empirical observations and advance our understanding of the eco-evolutionary consequences of dispersal. We illustrate how applying an integrative framework of theory, experimental evolution and natural systems can improve our understanding of dispersal evolution under more complex and realistic biological scenarios, such as the role of biotic interactions and complex dispersal syndromes.

1. Estimating phenotypic distributions of populations and communities is central to many questions in ecology and evolution. These distributions can be characterized by their moments (mean, variance, skewness and kurtosis) or diversity metrics (e.g. functional richness). Typically, such moments and metrics are calculated using community-weighted approaches (e.g. abundance-weighted mean). We propose an alternative bootstrapping approach that allows flexibility in trait sampling and explicit incorporation of intraspecific variation, and show that this approach significantly improves estimation while allowing us to quantify uncertainty.
2. We assess the performance of different approaches for estimating the moments of trait distributions across various sampling scenarios, taxa and datasets by comparing estimates derived from simulated samples with the true values calculated from full datasets. Simulations differ in sampling intensity (individuals per species), sampling biases (abundance, size), trait data source (local vs. global) and estimation method (two types of community-weighting, two types of bootstrapping).
3. We introduce the traitstrap R package, which contains a modular and extensible set of bootstrapping and weighted-averaging functions that use community composition and trait data to estimate the moments of community trait distributions with their uncertainty. Importantly, the first function in the workflow, trait_fill, allows the user to specify hierarchical structures (e.g. plot within site, experiment vs. control, species within genus) to assign trait values to each taxon in each community sample.
4. Across all taxa, simulations and metrics, bootstrapping approaches were more accurate and less biased than community-weighted approaches. With bootstrapping, a sample size of 9 or more measurements per species per trait generally included the true mean within the 95% CI. It reduced average percent errors by 26%–74% relative to community-weighting. Random sampling across all species outperformed both size- and abundance-biased sampling.
5. Our results suggest randomly sampling ~9 individuals per sampling unit and species, covering all species in the community and analysing the data using nonparametric bootstrapping generally enable reliable inference on trait distributions, including the central moments, of communities. By providing better estimates of community trait distributions, bootstrapping approaches can improve our ability to link traits to both the processes that generate them and their effects on ecosystems.

Haplotaxis Hoffmeister, 1843 is a poorly known genus: it is rarely collected because it usually inhabits groundwater, and many species are only known from immature specimens. Even the type species, Haplotaxis gordioides (Hartmann in Oken, 1819) remains poorly defined because of the absence of reference types. Most of the Haplotaxis species have been placed in synonymy with H. gordioides since the end of the 19^th century, a situation that has remained essentially unchanged until now. As a result, the species is supposedly present on all continents, except Antarctica. This observation is all the more questionable as the aquatic subterranean environment is nowadays well known to harbour many species with restricted distribution, due to the strong hydrogeographic isolation and the low dispersal abilities of its inhabitants.
In this study we assessed the hypothesis of H. gordioides as a single species with wide distribution versus a complex of cryptic species with narrow distribution. We used a DNA-barcoding approach based on the COI mitochondrial marker of 46 Haplotaxis specimens collected in Switzerland, mostly as part of a countrywide sampling campaign to study groundwater macroinvertebrates.
Preliminary results suggested that H. gordioides is a complex of at least 6 cryptic species in Switzerland, which has important implications both for the knowledge of the exact identity of the type species and for the synonymy of most of the species described in the 19^th century. However, as it is based on a single-locus approach, this study should be seen as the first step in an integrative taxonomic process that should include additional biological material, the study of complementary markers (especially nuclear), and the morphological study of specimens.

1. The mayfly Prosopistoma pennigerum (Müller, 1785) (Insecta: Ephemeroptera) once occurred in many European river networks. However, observations decreased in the last decades and the species can be considered largely extinct throughout Europe due to river alterations.
2. Only three extant populations are known from Cabriel (southern Spain), Volga (Russia) and Vjosa (Albania) rivers.
3. We recorded the species along a 150 km stretch in the Vjosa River in three sampling seasons (spring 2018, fall 2018 and fall 2019), counting up to 302 P. pennigerum per m², the highest recorded abundance for the species to date. Moreover, we detected traces of environmental DNA in a newly designed targeted eDNA assay.
4. In our modelling approach we define the species' niche in a theoretically available niche space given by the Vjosa River network and predict a high probability of presence (θ) in downstream located sections of this river. Expected abundances (λ) could be related to a set of environmental variables, importantly to higher discharge and increased sediment dynamics.
5. Simultaneous occurrence of larvae of different sizes at individual sites suggests an asynchronous life cycle, which may be advantageous to cope with the highly dynamic river hydrology.
6. The P. pennigerum population in the Vjosa is of key importance for the species' global survival.

Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with greater effects projected into the future. Evidence suggests human impacts may differ substantially between terrestrial and freshwater ecosystems, but the reasons for these differences are poorly understood. We propose an integrative approach to explain these differences by linking impacts to four fundamental processes that structure communities: dispersal, speciation, species-level selection and ecological drift. Our goal is to provide process-based insights into why human impacts, and responses to impacts, may differ across ecosystem types using a mechanistic, eco-evolutionary comparative framework. To enable these insights, we review and synthesise (i) how the four processes influence diversity and dynamics in terrestrial versus freshwater communities, specifically whether the relative importance of each process differs among ecosystems, and (ii) the pathways by which human impacts can produce divergent responses across ecosystems, due to differences in the strength of processes among ecosystems we identify. Finally, we highlight research gaps and next steps, and discuss how this approach can provide new insights for conservation. By focusing on the processes that shape diversity in communities, we aim to mechanistically link human impacts to ongoing and future changes in ecosystems.

Fast-growing and reproducing sun corals have successfully invaded rocky reefs around the Atlantic Ocean, markedly reducing the diversity of fouling invertebrates and macroalgae, and profoundly changing the composition of reef-associated mobile invertebrates. Here, we address sun-coral rubble depositions and report, for the first time, the effects of sun corals on near-reef soft-bottom invertebrate assemblages. Abundance, richness and diversity were higher at rubble habitats compared to bare sandy grounds, which could be a positive effect of substrate complexity. All those parameters were also higher at rubble patches dominated by sun-coral fragments compared to rubble patches dominated by pebbles or shell fragments, also suggesting possible additive effects of coral-borne chemical attraction (sun-coral specific, as inputs of other coral species were virtually absent). Different epifaunal groups were exclusive of rubble habitats and a subset of those exclusive of sun-coral rubble, explaining the incremental richness across habitats. The relative abundance of the two dominant groups – polychaetes (p) and amphipods (a) – contributed the most to the observed contrasts on community structure, as their proportion (p:a) changed from 10:1 in bare sand to nearly co-dominance in coral rubble. While previous research suggested that spreading sun corals reduce prey supply for fish foraging on reef walls, our results suggest they may increase prey abundance and diversity at the adjacent non-consolidated habitat, possibly reshaping trophic pathways connecting the benthic and the pelagic environment.

Understanding structural and functional changes in plankton communities is essential to predict cascading effects of environmental change on aquatic biodiversity and ecosystem services (e.g., carbon storage and water quality) (Chapter I). External abiotic (environment) and internal biotic processes (taxa interactions) have been suggested to drive plankton community dynamics. Limitations in available data and analytical methods to infer interactions between taxa have made studying the relative importance of biotic and abiotic processes in shaping natural plankton communities difficult. Recent advances in plankton monitoring and equation-free modeling deliver promising tools to investigate natural communities in-situ and eventually make accurate predictions of changes in plankton communities. [...]

Das Verständnis struktureller und funktioneller Veränderungen in Planktongemeinschaften ist unerlässlich für die Vorhersage von kaskadeartigen Auswirkungen von Umweltveränderungen auf die aquatische Artenvielfalt und Ökosystemleistungen (z. B. Kohlenstoffspeicherung und Wasserqualität) (Kapitel I). Es wird vermutet, dass externe abiotische (Umweltfaktoren) und interne biotische Prozesse (Interaktionen zwischen Arten) die Dynamik von Planktongemeinschaften bestimmen. Aufgrund der begrenzten Verfügbarkeit von Daten und Analysemethoden zur Ermittlung von Interaktionen zwischen Arten ist die Untersuchung der relativen Wichtigkeit von biotischen und abiotischen Prozessen bei der Zusammensetzung von natürlichen Planktongemeinschaften schwierig. Jüngste Fortschritte in der Planktonüberwachung und gleichungsfreie Modellierungsverfahren liefern vielversprechende Mittel, um natürliche Gemeinschaften in-situ zu untersuchen und schliesslich genaue Vorhersagen über Veränderungen in Planktongemeinschaften zu ermöglichen. [...]

Climate change interacts with local processes to threaten biodiversity by disrupting the complex network of ecological interactions. While changes in network interactions drastically affect ecosystems, how ecological networks respond to climate change, in particular warming and nutrient supply fluctuations, is largely unknown. Here, using an equation-free modelling approach on monthly plankton community data in ten Swiss lakes, we show that the number and strength of plankton community interactions fluctuate and respond nonlinearly to water temperature and phosphorus. While lakes show system-specific responses, warming generally reduces network interactions, particularly under high phosphate levels. This network reorganization shifts trophic control of food webs, leading to consumers being controlled by resources. Small grazers and cyanobacteria emerge as sensitive indicators of changes in plankton networks. By exposing the outcomes of a complex interplay between environmental drivers, our results provide tools for studying and advancing our understanding of how climate change impacts entire ecological communities.

Im «Wasserschloss» Schweiz fühlten sich Amphibien wohl. In unseren heutigen trockengelegten Landschaen haben sie jedoch einen schweren Stand. Viele Arten sind gefährdet. Der Kanton Aargau hat vorgemacht, was im Amphibienschutz möglich ist. In den letzten 20 Jahren hat er grossflächig neue Weiher gebaut und das mit Erfolg: Die Anzahl der Populationen fast aller Amphibienarten hat sich stabilisiert oder in einer Trendwende sogar zugenommen.

Lineages with independent evolutionary histories often differ in both their morphology and diet. Experimental work has improved our understanding of the links between the biomechanics of morphological traits and foraging performance (trait utility). However, because the expression of foraging-relevant traits and their utility can be highly context-specific, it is often unclear how dietary divergence arises from evolved phenotypic differences. Here, we explore the phenotypic causes of dietary divergence between two genetically and phenotypically divergent lineages of threespine stickleback (Gasterosteus aculeatus) with independent evolutionary histories of freshwater colonization and adaptation. First, using individuals from a line-cross breeding design, we conducted 150 common-garden foraging trials with a community of multiple prey species and performed morphological and behavioral analyses to test for prey-specific trait utility. Second, we tested if the traits that explain variation in foraging performance among all individuals could also explain the dietary divergence between the lineages. Overall, we found evidence for the utility of several foraging traits, but these traits did not explain the observed dietary divergence between the lineages in a common garden. This work suggests that evolved dietary divergence results not only from differences in morphology but also from divergence in behaviors that underlie prey capture success in species-rich prey communities.

Headwater streams harbor diverse macroinvertebrate communities and are hotspots for leaf litter breakdown. The process of leaf litter breakdown mediated by macroinvertebrates forms an important link between terrestrial and aquatic ecosystems. Yet, how the vegetation type in the local riparian zone influences leaf-associated macroinvertebrate assemblages and leaf litter breakdown rates is still not resolved. We investigated how leaf-associated macroinvertebrate assemblages and leaf litter fragmentation rates differ between forested and non-forested sites using experimental leaf litter bags in sixteen sites paired across eight headwater streams in Switzerland. Our results show that sensitive taxa of the invertebrate orders Ephemeroptera, Plecoptera and Trichoptera (EPT) and the functional group of shredders were strongly associated with forested sites with overall higher values of abundance, diversity, and biomass of EPTs in forested compared to non-forested sites. However, the importance of riparian vegetation differed between study regions, especially for shredders. Fragmentation rates, which are primarily the result of macroinvertebrate shredding, were on average three times higher in forested compared to non-forested sites. Our results demonstrate that not only the composition of the aquatic fauna but also the functioning of an essential ecosystem process depend on the vegetation type in the local riparian zone.

Background: MacArthur and Wilson's theory of island biogeography has been a foundation for obtaining testable predictions from models of community assembly and for developing models that integrate across scales and disciplines. Historically, however, these developments have focused on integration across ecological and macroevolutionary scales and on predicting patterns of species richness, abundance distributions, trait data and/or phylogenies. The distribution of genetic variation across species within a community is an emerging pattern that contains signatures of past population histories, which might provide an historical lens for the study of contemporary communities. As intraspecific genetic diversity data become increasingly available at the scale of entire communities, there is an opportunity to integrate microevolutionary processes into our models, moving towards development of a genetic theory of island biogeography.
Motivation/goal: We aim to promote the development of process-based biodiversity models that predict community genetic diversity patterns together with other community-scale patterns. To this end, we review models of ecological, microevolutionary and macroevolutionary processes that are best suited to the creation of unified models, and the patterns that these predict. We then discuss ongoing and potential future efforts to unify models operating at different organizational levels, with the goal of predicting multidimensional community-scale data including a genetic component.
Main conclusions: Our review of the literature shows that despite recent efforts, further methodological developments are needed, not only to incorporate the genetic component into existing island biogeography models, but also to unify processes across scales of biological organization. To catalyse these developments, we outline two potential ways forward, adopting either a top-down or a bottom-up approach. Finally, we highlight key ecological and evolutionary questions that might be addressed by unified models including a genetic component and establish hypotheses about how processes across scales might impact patterns of community genetic diversity.

Migration is ubiquitous and can strongly shape food webs and ecosystems. Less familiar, however, is that the majority of life cycle, seasonal and diel migrations in nature are partial migrations: only a fraction of the population migrates while the other individuals remain in their resident ecosystem. Here, we demonstrate different impacts of partial migration rendering it fundamental to our understanding of the significance of migration for food web and ecosystem dynamics. First, partial migration affects the spatiotemporal distribution of individuals and the food web and ecosystem-level processes they drive differently than expected under full migration. Second, whether an individual migrates or not is regularly correlated with morphological, physiological, and/or behavioural traits that shape its food-web and ecosystem-level impacts. Third, food web and ecosystem dynamics can drive the fraction of the population migrating, enabling the potential for feedbacks between the causes and consequences of migration within and across ecosystems. These impacts, individually and in combination, can yield unintuitive effects of migration and drive the dynamics, diversity and functions of ecosystems. By presenting the first full integration of partial migration and trophic (meta-)community and (meta-)ecosystem ecology, we provide a roadmap for studying how migration affects and is affected by ecosystem dynamics in a changing world.

This paper describes a new diatom species (Orthoseira helvetica sp. nov.) found in the Swiss Alps at an elevation over 2600 m a.s.l. The diatom was recorded at the Macun plateau, Swiss National Park, from samples of terrestrial and wet semi-terrestrial mosses near the stream splash zone. The diatom has a unique set of features and is easily recognized under light and scanning electron microscopy. The most distinctive feature is the presence of a prominent silica collar in a 'rose flower' shape rounding each carinoportulae and an additional silica collar on the areolae (first 3-4 rows) bordering the hyaline area. The valve diameter of O. helvetica sp. nov. is 7.5-26.5 µm and possesses 2-3 (usually 3) carinoportulae. Linking spines at the valve face/mantle junction are present, having a simple basis and being triangular in shape.

Uncovering the demographic basis of population fluctuations is a central goal of population biology. This is particularly challenging for spatially structured populations, which require disentangling synchrony in demographic rates from coupling via movement between locations. In this study, we fit a stage-structured metapopulation model to a 29-year time series of threespine stickleback abundance in the heterogeneous and productive Lake Mývatn, Iceland. The lake comprises two basins (North and South) connected by a channel through which the stickleback disperse. The model includes time-varying demographic rates, allowing us to assess the potential contributions of recruitment and survival, spatial coupling via movement, and demographic transience to the population's large fluctuations in abundance. Our analyses indicate that recruitment was only modestly synchronized between the two basins, whereas survival probabilities of adults were more strongly synchronized, contributing to cyclic fluctuations in the lake-wide population size with a period of approximately 6 years. The analyses further show that the two basins were coupled through movement, with the North Basin subsidizing the South Basin and playing a dominant role in driving the lake-wide dynamics. Our results show that cyclic fluctuations of a metapopulation can be explained in terms of the combined effects of synchronized demographic rates and spatial coupling.

1. Species performance depends on the concerted interplay of their functional traits. Natural selection acts on the performance of the species and influences entire suits of interdependent functional traits, thereby driving the evolution of functional diversity (FD) within a clade.
2. In a given habitat, interdependent functional traits are expected to integrate into only a few adaptive combinations. When a clade diversifies in different habitats, the FD within habitats (herein called α-FD) diversifies in response to local selections, while between the habitats, alternative adaptive combinations of interdependent traits that are specific to the habitat emerge. This multivariate selection leads to two hypotheses. First, realized α-FD within one habitat represents only a small fraction of the variation of functional traits, and second, realized FDs across habitats (hereafter called β-FD) are equal to or greater than would be in the absence of the interdependence of functional traits.
3. We tested these hypotheses using 185 species of the highly diverse subterranean amphipod genus Niphargus living in three habitats: river interstitial, cave lakes, and cave streams. We (i) explored integration of functional traits related to locomotion and feeding biology and tested (ii) if realized α-FD within each habitat is lower than it would be without trait interdependence, and (iii) if realized β-FD in pairwise comparisons of habitats is higher than it would be without trait interdependence.
4. In all three habitats, the length of the appendages as a proxy of the locomotion speed was positively correlated with the trophic position of the species. On the contrary, the body shape correlations were habitat dependent: species in high trophic positions were slender, stout or invariant in shape in interstitial, cave streams and cave lakes, respectively.
5. Using null models, we show that only a fraction of functional trait combinations was realized in each habitat, whereas β-FD between habitats was equal to or greater than the null expectations.
6. The results indicate preserved potential for diversification in species within and between habitats. This potential can be realized through hybridization and can drive diversification in adaptive radiations. Moreover, this perspective on the evolution of FD is compatible with several central ecological and evolutionary concepts, such as adaptive landscape or ecological niche theory. Read the free Plain Language Summary for this article on the Journal blog.

Host genotype may shape host-associated bacterial communities (commonly referred to as microbiomes). We sought to determine (a) whether bacterial communities vary among host genotypes in the water flea Daphnia galeata and (b) if this difference is driven by the genetic distance between host genotypes, by using D. galeata genotypes hatched from sediments of different time periods. We used 16S amplicon sequencing to profile the gut and body bacterial communities of eight D. galeata genotypes hatched from resting eggs; these were isolated from two distinct sediment layers (dating to 1989 and 2009) of a single sediment core of the lake Greifensee, and maintained in a common garden in laboratory cultures for 5 years. In general, bacterial community composition varied in both the Daphnia guts and bodies; but not between genotypes from different sediment layers. Specifically, genetic distances between host genotypes did not correlate with beta diversity of bacterial communities in Daphnia guts and bodies. Our results indicate that Daphnia bacterial community structure is to some extent determined by a host genetic component, but that genetic distances between hosts do not correlate with diverging bacterial communities.

Host microbiomes play an important role in host-parasite interaction, but few studies integrate hostparasite-microbiome tripartite interactions in the wild. In this thesis, I combine field and laboratory experiments using the water flea Daphnia to investigate the role of host microbiomes in host-parasite interactions. In Chapter I, I surveyed with my co-authors the bacterial communities of eight Daphnia galeata genotypes isolated from Lake Greifensee and found host genotype-specific variation. We additionally found no correlation between host genetic distances based on whole genome sequencing of the hosts, and bacterial community composition, suggesting that host genetic distances do not predict divergence in bacterial communities. In Chapter II, we compared the bacterial communities of Daphnia sp. in Lake Greifensee between hosts infected or not infected with the virulent, eukaryotic gut parasite Caullerya mesnili. We found that infection associates with reduced alpha diversity in the gut (the site of infection) and altered community composition in both the gut and body. In Chapter III we tested longterm dynamics of host-parasite-bacterial community associations between Daphnia and Caullerya in Lake Greifensee. For this, we compared infected and uninfected Daphnia across six natural epidemics spanning 13 years. Here we found that Daphnia bacterial community composition showed substantial temporal variation in both dominant bacterial taxa as well as rare taxa, but that infection by Caullerya only altered the composition of rare taxa. Host bacterial community composition also correlated with parasite infection prevalence, i.e. years with larger epidemics had distinct host bacterial communities than those with smaller epidemics. We further found that the environmental abiotic conditions temperature, dissolved oxygen content and cyanobacterial abundance in lake water, all previously known to drive epidemics all associated with distinct host bacterial community compositions. In Chapter IV, we tested the directionality of infection and host microbiome interaction in a laboratory experiment with Daphnia magna and the fungal parasite Metschnikowia bicuspidata. We found that initial parasite exposure drives host genotype specific changes in bacterial community compositions that correlate with the parasite's life stage. We also found that successful infection drives a loss of bacterial community diversity and abundance shifts in dominant bacterial taxa in the host gut. Overall, the results of this thesis indicate that Daphnia bacterial communities play a significant role in host-parasite interaction.

Wirtsmikrobiome spielen eine wichtige Rolle bei der Interaktion zwischen Wirt und Parasit, aber nur wenige Studien integrieren dreigliedrige Interaktionen zwischen Wirt, Parasit und Mikrobiom in freier Wildbahn. In dieser Arbeit kombinieren wir Feld- und Laborexperimente mit dem Wasserfloh Daphnia, um die Rolle von Wirtsmikrobiomen in Wirt-Parasit-Interaktionen zu untersuchen. In Kapitel I untersuchten wir die Bakteriengemeinschaften von acht Daphnia galeata-Genotypen, die aus dem Greifensee isoliert wurden, und fanden wirtsgenotypspezifische Variationen. Darüber hinaus fanden wir keine Korrelation zwischen den genetischen Distanzen der Wirte, die auf der Gesamtgenomsequenzierung der Wirte basieren, und der Zusammensetzung der Bakteriengemeinschaften, was darauf hindeutet, dass die genetischen Distanzen der Wirte keine Divergenz in den Bakteriengemeinschaften vorhersagen. In Kapitel II verglichen wir die Bakteriengemeinschaften von Daphnia sp. im Greifensee zwischen Wirten, die mit dem virulenten, eukaryotischen Darmparasiten Caullerya mesnili infiziert waren und solchen, die nicht infiziert waren. Wir haben festgestellt, dass eine Infektion mit einer geringeren Alpha-Diversität im Darm (dem Ort der Infektion) und einer veränderten Zusammensetzung der Gemeinschaft sowohl im Darm als auch im Körper einhergeht. In Kapitel III untersuchten wir die Langzeitdynamik von Beziehungen zwischen Wirt, Parasit und Bakteriengemeinschaften zwischen Daphnien und Caullerya im Greifensee. Zu diesem Zweck verglichen wir infizierte und nicht infizierte Daphnien in sechs natürlichen Epidemien über einen Zeitraum von 13 Jahren hinweg. Dabei stellten wir fest, dass die Zusammensetzung der Daphnia-Bakteriengemeinschaft sowohl bei den dominanten Bakterientaxa als auch bei den seltenen Taxa erhebliche zeitliche Schwankungen aufwies, während eine Infektion mit Caullerya nur die Zusammensetzung der seltenen Taxa veränderte. Die Zusammensetzung der Wirtsbakteriengemeinschaft korrelierte auch mit der Prävalenz von Parasiteninfektionen, d. h. Jahre mit größeren Epidemien wiesen andere Wirtsbakteriengemeinschaften auf als solche mit kleineren Epidemien. Wir fanden ferner heraus, dass die abiotischen Umweltbedingungen Temperatur, Gehalt an gelöstem Sauerstoff und Cyanobakterienhäufigkeit im Seewasser, von denen bereits bekannt war, dass sie Epidemien fördern, alle mit unterschiedlichen Zusammensetzungen der Wirtsbakteriengemeinschaft verbunden sind. In Kapitel IV haben wir die Richtungsabhängigkeit der Interaktion zwischen Infektion und Wirtsmikrobiom in einem Laborexperiment mit Daphnia magna und dem Pilzparasiten Metschnikowia bicuspidata getestet. Wir fanden heraus, dass die anfängliche Exposition gegenüber dem Parasiten zu wirtsgenotypspezifischen Veränderungen in der Zusammensetzung der Bakteriengemeinschaft führt, die mit dem Lebensstadium des Parasiten korrelieren. Wir fanden auch heraus, dass eine erfolgreiche Infektion zu einem Verlust der Diversität der Bakteriengemeinschaft und zu Abundanzverschiebungen bei den dominanten Bakterientaxa im Wirtsdarm führt. Insgesamt deuten die Ergebnisse dieser Arbeit darauf hin, dass Daphnien-Bakteriengemeinschaften eine bedeutende Rolle in der Wirt-Parasit-Interaktion spielen.

Predicting the spread of populations across fragmented habitats is vital if we are to manage their persistence in the long term. We applied network theory with a model and an experiment to show that spread rate is jointly defined by the configuration of habitat networks (i.e., the arrangement and length of connections between habitat fragments) and the movement behavior of individuals. We found that population spread rate in the model was well predicted by algebraic connectivity of the habitat network. A multigeneration experiment with the microarthropod Folsomia candida validated this model prediction. The realized habitat connectivity and spread rate were determined by the interaction between dispersal behavior and habitat configuration, such that the network configurations that facilitated the fastest spread changed depending on the shape of the species' dispersal kernel. Predicting the spread rate of populations in fragmented landscapes requires combining knowledge of species-specific dispersal kernels and the spatial configuration of habitat networks. This information can be used to design landscapes to manage the spread and persistence of species in fragmented habitats.

Monitoring of terrestrial and aquatic species assemblages at large spatial scales based on environmental DNA (eDNA) has the potential to enable evidence-based environmental policymaking. The spatial coverage of eDNA-based studies varies substantially, and the ability of eDNA metabarcoding to capture regional biodiversity remains to be assessed; thus, questions about best practices in the sampling design of entire landscapes remain open. We tested the extent to which eDNA sampling can capture the diversity of a region with highly heterogeneous habitat patches across a wide elevation gradient for five days through multiple hydrological catchments of the Swiss Alps. Using peristaltic pumps, we filtered 60 L of water at five sites per catchment for a total volume of 1800 L. Using an eDNA metabarcoding approach focusing on vertebrates and plants, we detected 86 vertebrate taxa spanning 41 families and 263 plant taxa spanning 79 families across ten catchments. For mammals, fishes, amphibians and plants, the detected taxa covered some of the most common species in the region according to long-term records while including a few more rare taxa. We found marked turnover among samples from distinct elevational classes indicating that the biological signal in alpine rivers remains relatively localised and is not aggregated downstream. Accordingly, species compositions differed between catchments and correlated with catchment-level forest and grassland cover. Biomonitoring schemes based on capturing eDNA across rivers within biologically integrated catchments may pave the way toward a spatially comprehensive estimation of biodiversity.

Die drei Felchenarten des Bodensees sind die «Brotfische» der dortigen Berufsfischerei. Sie sind sich äusserlich ähnlich und genetisch nahe verwandt, unterscheiden sich aber stark in ihrer Lebensweise. Gegenüber Veränderungen ihres Lebensraums sind sie empfindlich. Das Projekt «See-Wandel: Leben im Bodensee – gestern, heute und morgen» untersuchte die Bodenseefelchen genetisch und auf Populationsebene. Im Fokus der angewandten Forschung stand der Zusammenhang zwischen dem Auftreten neuer Wirkfaktoren und dem aktuellen Rückgang der Felchenbestände.

Die Bodenseefische waren in den vergangenen 60 Jahren starken Nährstoffschwankungen des Sees unterworfen und sind seit etwas über zehn Jahren auch invasiv ausbreitenden Neozoen und Klimaänderungen wie kontinuierlich ansteigenden Wassertemperaturen ausgesetzt. Diese Faktoren haben das gesamte aquatische Ökosystem Bodensee verändert und mit ihm auch die Fischbestände. «SeeWandel» hat die komplexen Zusammenhänge dieser Entwicklung untersucht und aktuelle Daten zu den Fischbeständen des Bodensees geliefert.

Invasive predatory species may alter population dynamic processes of their prey and impact biological communities and ecosystem processes. Revealing biotic interactions, however, including the relationship between predator and prey, is a difficult task, in particular for species that are hard to monitor. Here, we present a case study that documents the utility of environmental DNA analysis (eDNA) to assess predator–prey interactions between two invasive fishes (Lepomis gibbosus, Pseudorasbora parva) and two potential amphibian prey species, (Triturus cristatus, Pelobates fuscus). We used species-specific TaqMan assays for quantitative assessment of eDNA concentrations from water samples collected from 89 sites across 31 ponds during three consecutive months from a local amphibian hotspot in Germany. We found a negative relationship between eDNA concentrations of the predators (fishes) and prey (amphibians) using Monte-Carlo tests. Our study highlights the potential of eDNA application to reveal predator–prey interactions and confirms the hypothesis that the observed local declines of amphibian species may be at least partly caused by recently introduced invasive fishes. Our findings have important consequences for local conservation management and highlight the usefulness of eDNA approaches to assess ecological interactions and guide targeted conservation action.

Die Erhaltung der Biodiversität ist eine gesellschaftliche Herausforderung. Die gesetzten Schutzziele werden heute oft nur unvollständig oder nicht erreicht. Ein stärkerer Wissenstransfer zwischen Forschung und Praxis soll dazu beitragen, Antworten auf Fragen aus der Naturschutzpraxis zu finden. Dies erfordert, dass relevante wissenschaftliche Erkenntnisse für die Praxis besser zugänglich gemacht und mit dem Wissen aus der Praxis für die Umsetzung aufbereitet werden.
La préservation de la biodiversité est un défi sociétal et les objectifs de protection ne sont souvent pas atteints. Un transfert de connaissances plus efficace entre la recherche et la pratique peut contribuer à fournir des solutions aux questions de la pratique en matière de conservation de la nature. Cela nécessite que les connaissances scientifiques pertinentes soient rendues plus accessibles pour la pratique et préparées avec les connaissances issues de la pratique en vue de leur mise en oeuvre.

Artificial high flows attempt to simulate natural flood pulses in flow-regulated rivers with the intent to improve their ecological integrity. The long-term use of such high flow events have shown beneficial ecological effects on various rivers globally. However, such responses are often non-linear and characterized by underlying feedback mechanisms among ecosystem components. The question arises as to what happens when such high flow releases are disrupted or even discontinued. Here, we used the long-term (22 years) monitoring dataset from the river Spöl to examine whether discontinuation (2016–2021) of the flood program (annual artificial high flows from 2000 to 2016) resulted in the ecological degradation of the river. We used monitoring data of physico-chemistry, periphyton, benthic organic matter, macroinvertebrates and fish (brown trout, Salmo trutta fario L.) in the analysis. The flood program had no long-term effect on water physico-chemistry with most parameters showing typical variations associated with season and inter-annual weather patterns. The floods were effective at mobilizing bed sediments that reduced periphyton biomass and benthic organic matter following each flood. Increases in periphyton biomass and benthic organic matter occurred between floods, but both parameters showed no significant increase with discontinuation of the flood program. Floods reduced macroinvertebrate densities, but with density increases occurring between floods. The pulsed disturbances, and the progressive change in the habitat template, resulted in shifts in community assembly by reducing densities of Gammarus fossarum, a dominant crustacean, which allowed other taxa to colonize the system. Macroinvertebrate densities remained low after discontinuation of the floods, although G. fossarum densities have increased substantially while other taxa, especially some stoneflies, remained low in abundance. Notably, community assembly returned to a pre-flood composition with discontinuation of the floods. The abundance of brown trout increased substantially during the flood program but returned to low pre-flood numbers with discontinuation of the floods. We conclude that the flood program was beneficial to the ecology of the river Spöl and discontinuation of the floods resulted in degradation of the system after a relatively short lag period. However, the system showed high resilience to an earlier perturbation, a sediment spill in 2013, suggesting a rapid positive response by biota with resumption of the flood program.

Human-mediated dispersal is a major contributor of biological invasions. To reduce impacts induced by the introduction and spread of exotic species, biosecurity interventions are put into place. These interventions often rely on risk-assessment procedures, whereby biosecurity practitioners (which includes researchers, stakeholders such as national park managers, and all other decision makers who determine when and how to protect biodiversity) attempt to preemptively identify and predict which exotic species could potentially become a threat to natural ecosystems. In theory, extensive field and experimental studies would be required to accurately and precisely determine the risks of biological invasion of a species or group of species. However, due to a lack of resources or knowledge, such critical studies are limited. As a result, biosecurity practitioners rarely have a full picture of the extent to which the exotic species has and will spread at the time of decision making. Hence, they instead opt for preventive measures such as identifying and managing potential target exotic species which are likely to be invasive or dispersal pathways through which exotic species are likely to be introduced and spread. As most of the uncertainties pertaining to biosecurity interventions lie in the resolution of data made available to practitioners at the time of decision making, we first present some of the different types of information which are readily available during the risk-assessment procedure. We then highlight how one could exploit these different resolutions of data during the risk-assessment procedure using network analysis to better understand human-mediated dispersal of exotic species. By doing so, our paper puts forward what network analysis has to offer practitioners in the context of biosecurity interventions.

Among a multitude of stressors to which wildlife is exposed, environmental pollution is a pervasive one that poses a serious threat. The permeable skin of amphibians is likely to increase direct contact of the body with pollutants, making them a group worth studying to access environmental quality. Consequently, finding reliable and complementary biomarkers that will present detectable and predictable changes in response to pollutants is essential to identify pollution sublethal effects on amphibians and to investigate whether these are in part responsible for population declines. The glucocorticoid hormone corticosterone (CORT), involved in many metabolic functions, is often used to measure the physiological stress response to environmental stressors in amphibians. In this study, we evaluated whether water-borne CORT can serve as a non-invasive biomarker for nitrate pollution stress in the European common frog (Rana temporaria) by comparing the effect of nitrate exposure on hormone release rates and on other physiological downstream biomarkers, i.e., ultimate physiological effects of the stressor. Specifically, we investigated the effect of different nitrate concentrations (0, 10, 50, and 100 mg/L) on water-borne CORT release rates, age, size, and body condition. Exposure to nitrate pollution significantly increased age at metamorphosis and water-borne CORT release rates, and led to reduced mass and body condition, but only at higher nitrate concentrations (i.e., 50 and 100 mg/L). Considering this similar sensitivity to other acknowledged biomarkers, water-borne CORT was a reliable biomarker of physiological stress in R. temporaria exposed to nitrate pollution stress in a controlled single-stressor laboratory approach. Thus, water-borne CORT is a promising method to be included in more holistic approaches. We recommend that such approaches keep testing multiple biomarker combinations, as species are exposed to several stressors likely to interact and produce varied outcomes in different biomarkers in their natural habitats.

Groundwater is a vast ecosystem harboring a high diversity of specialized taxa. Despite its diversity, groundwater is a still relatively unexplored and threatened ecosystem. Especially the linkage of groundwater with other ecosystems remains largely unknown from the perspective of groundwater fauna. Here, we used citizen science data to get a first baseline knowledge of the occurrence, diversity, and biomass of major macroinvertebrate groups found in shallow groundwater systems of Switzerland. We investigated all organisms collected from the groundwater in 346 spring catchment boxes of municipal drinking water providers. We morphologically identified the organisms on a broad taxonomic level and estimated their biomass and pigmentation using automated image processing. Crustaceans, particularly Niphargus and groundwater isopods, were the most common taxa of obligate groundwater organisms. We also found a surprisingly high number of macroinvertebrates associated with surface and subsurface ecosystems. These taxa might be accidentally entering the groundwater or use it as temporary habitat. In both cases they possibly contribute essential allochthonous energy imports from the surface. We found a positive relationship between the estimated biomass of macroinvertebrates in the samples and the occurrence and abundance of Niphargus. Owing to the widespread occurrences of surface and subsurface macroinvertebrates in our groundwater samples, our study provides evidence for common interactions between groundwater, soil, and surface ecosystems.

Ecoimmunological research on molluscs and other invertebrates frequently quantifies phenoloxidase (PO) activity to estimate the strength of the immune function. PO enzymes form different families whose relative roles in oxidative reactions are typically unknown. Understanding this could allow enzyme-specific assays with higher accuracy than in commonly used nonspecific assays. We tested the contribution of different PO enzyme families to haemolymph PO-like activity in Lymnaea stagnalis snails using substrates specific to enzymes detected in L. stagnalis transcriptome data (p-phenylenediamine, specific to laccases; L-tyrosine, specific to tyrosinases) and compared the reactions to those with a nonspecific substrate (L-dopa). We found laccase-like but no tyrosinase-like activity. However, reactions with L-dopa were the strongest, possibly due to other oxidative enzymes in snail haemolymph. Laccase-like activity is common in molluscs, and we propose the use of enzyme-specific assays in future ecoimmunological studies of this taxon. The lack of tyrosinase-like activity in L. stagnalis contradicts earlier transcriptome data, which calls for investigating the expression of PO enzymes in L. stagnalis at the proteome level.

As alien invasive species are a key driver of biodiversity loss, understanding patterns of rapidly changing global species compositions depends upon knowledge of invasive species population dynamics and trends at large scales. Within this context, the Ponto-Caspian region is among the most notable donor regions for aquatic invasive species in Europe. Using macroinvertebrate time series collected over 52 years (1968–2020) at 265 sites across 11 central and western European countries, we examined the occurrences, invasion rates, and abundances of freshwater Ponto-Caspian fauna. We examined whether: (i) successive Ponto-Caspian invasions follow a consistent pattern of composition pioneered by the same species, and (ii) Ponto-Caspian invasion accelerates subsequent invasion rates. In our dataset, Ponto-Caspian macroinvertebrates increased from two species in 1972 to 29 species in 2012. This trend was parallelled by a non-significant increasing trend in the abundances of Ponto-Caspian taxa. Trends in Ponto-Caspian invader richness increased significantly over time. We found a relatively uniform distribution of Ponto-Caspian macroinvertebrates across Europe without any relation to the distance to their native region. The Ponto-Caspian species that arrived first were often bivalves (46.5% of cases), particularly Dreissena polymorpha, followed secondarily by amphipods (83.8%; primarily Chelicorophium curvispinum and Dikerogammarus villosus). The time between consecutive invasions decreased significantly at our coarse regional scale, suggesting that previous alien establishments may facilitate invasions of subsequent taxa. Should alien species continue to translocate from the Ponto-Caspian region, our results suggest a high potential for their future invasion success highly connected central and western European waters. However, each species' population may decline after an initial 'boom' phase or after the arrival of new invasive species, resulting in different alien species dominating over time.

Aim: Invasive alien species are a growing problem worldwide due to their ecological, economic and human health impacts. The “killer shrimp” Dikerogammarus villosus is a notorious invasive alien amphipod from the Ponto-Caspian region that has invaded many fresh and brackish waters across Europe. Understandings of large-scale population dynamics of highly impactful invaders such as D. villosus are lacking, inhibiting predictions of impact and efficient timing of management strategies. Hence, our aim was to assess trends and dynamics of D. villosus as well as its impacts in freshwater rivers and streams.
Location: Europe.
Methods: We analysed 96 European time series between 1994 and 2019 and identified trends in the relative abundance (i.e. dominance %) of D. villosus in invaded time series, as well as a set of site-specific characteristics to identify drivers and determinants of population changes and invasion dynamics using meta-regression modelling. We also looked at the spread over space and time to estimate the invasion speed (km/year) of D. villosus in Europe. We investigated the impact of D. villosus abundance on recipient community metrics (i.e. abundance, taxa richness, temporal turnover, Shannon diversity and Pielou evenness) using generalized linear models.
Results: Population trends varied across the time series. Nevertheless, community dominance of D. villosus increased over time across all time series. The frequency of occurrences (used as a proxy for invader spread) was well described by a Pareto distribution, whereby we estimated a lag phase (i.e. the time between introduction and spatial expansion) of approximately 28 years, followed by a gradual increase before new occurrences declined rapidly in the long term. D. villosus population change was associated with decreased taxa richness, community turnover and Shannon diversity.
Main Conclusion: Our results show that D. villosus is well-established in European waters and its abundance significantly alters ecological communities. However, the multidecadal lag phase prior to observed spatial expansion suggests that initial introductions by D. villosus are cryptic, thus signalling the need for more effective early detection methods.

Vorfahren des Dreistacheligen Stichlings haben nach der letzten Eiszeit von Atlantik und Ostsee aus die mitteleuropäischen Binnengewässer besiedelt. In einige Schweizer Gewässer konnten sie nur mithilfe des Menschen gelangen. Auch im Bodensee verbreiten sie sich erst seit den 1950er-Jahren. Um 2012 haben dort Stichlinge invasionsartig das Freiwasser besiedelt, fressen überwiegend Zooplankton und konkurrieren so mit den dort lebenden Felchen um dieselbe Nahrungsressource.

In nur fünf Jahren hat die Quaggamuschel den Boden- und den Genfersee vollständig besiedelt, in sechs weiteren Seen wurde sie bereits nachgewiesen. In Wassertiefen von 10 bis 30 Metern findet man mittlerweile bis zu 25 000 Muscheln pro Quadratmeter. Auch an den tiefsten Stellen der Seen gibt es bereits Vorkommen. Die Muscheln verstopfen die Infrastrukturanlagen von Trinkwasserbetrieben und thermischen Nutzungen, was Schäden in Millionenhöhe verursacht. Da das Ausbreitungsmuster der Schweizer Seen vergleichbar mit dem der Grossen Seen in Nordamerika ist, muss mit gravierenden Folgen gerechnet werden.

Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here, we integrate whole-genome sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome wide divergence, yet multiple traits (body size, gill raker structure and defence traits) were divergent along known ecological gradients (temperature, predatory bird densities and water depth). SNP based heritability of all measured traits was high (h² = 0.42–0.65), indicating adaptive potential for all traits. Environment-association analyses further identified thousands of loci putatively involved in selection, related to genes linked to, for instance, neuron development and protein phosphorylation. Finally, we found that loci linked to water depth were concurrently associated with pelvic spine length variation - supporting the conclusion that divergence in pelvic spine length occurred in the face of gene flow. Our results suggest that whilst there is substantial genetic variation in the traits measured, phenotypic divergence of Mývatn stickleback is mostly weakly associated with environmental gradients, potentially as a result of substantial gene flow. Our study illustrates the value of integrative studies that combine genomic assays of multivariate trait variation with landscape genomics.

The sustainability of marine communities is critical for supporting many biophysical processes that provide ecosystem services that promote human well-being. It is expected that anthropogenic disturbances such as climate change and human activities will tend to create less energetically-efficient ecosystems that support less biomass per unit energy flow. It is debated, however, whether this expected development should translate into bottom-heavy (with small basal species being the most abundant) or top-heavy communities (where more biomass is supported at higher trophic levels with species having larger body sizes). Here, we combine ecological theory and empirical data to demonstrate that full marine protection promotes shifts towards top-heavy energetically-efficient structures in marine communities. First, we use metabolic scaling theory to show that protected communities are expected to display stronger top-heavy structures than disturbed communities. Similarly, we show theoretically that communities with high energy transfer efficiency display stronger top-heavy structures than communities with low transfer efficiency. Next, we use empirical structures observed within fully protected marine areas compared to disturbed areas that vary in stress from thermal events and adjacent human activity. Using a nonparametric causal-inference analysis, we find a strong, positive, causal effect between full marine protection and stronger top-heavy structures. Our work corroborates ecological theory on community development and provides a quantitative framework to study the potential restorative effects of different candidate strategies on protected areas.

Contaminating organisms (grazers, pathogens, competitors) and self-inhibition by algae-produced allelopathic chemicals are two issues that may limit the productivity of algal cultivation for bioproducts. One potential solution is to identify algal strains that are not affected by allelopathic inhibition even while undesirable organisms are suppressed. Here we used two experiments to test how sensitivity to allelopathy varies across algae. In the first experiment, we tested the sensitivity of five biofuel candidate green algae strains to two allelopathic compounds (i.e., free fatty acids) and found that the degree of inhibition depends strongly on both the species and specific compound. In the second experiment, we exposed one alga (Chlorella) to the sterile-filtered medium of each species, and found that the concentration of free fatty acids released into the media predicted Chlorella's growth response. This provides a better understanding of how the production of, and sensitivity to, allelopathic compounds determines algal productivity.

Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.

Global urbanization trends have led to the widespread increasing occurrence of contaminants of emerging concern (CECs) such as pharmaceuticals, personal care products, pesticides, and micro- and nano-plastics in aquatic systems. Even at low concentrations, these contaminants pose a threat to aquatic ecosystems. To better understand the effects of CECs on aquatic ecosystems, it is important to measure concentrations of these contaminants present in these systems. Currently, there is an imbalance in CEC monitoring, with more attention to some categories of CECs, and a lack of data about environmental concentrations of other types of CECs. Citizen science is a potential tool for improving CEC monitoring and to establish their environmental concentrations. However, incorporating citizen participation in the monitoring of CECs poses some challenges and questions. In this literature review, we explore the landscape of citizen science and community science projects which monitor different groups of CECs in freshwater and marine ecosystems. We also identify the benefits and drawbacks of using citizen science to monitor CECs to provide recommendations for sampling and analytical methods. Our results highlight an existing disparity in frequency of monitoring different groups of CECs with implementing citizen science. Specifically, volunteer participation in microplastic monitoring programs is higher than volunteer participation in pharmaceutical, pesticide, and personal care product programs. These differences, however, do not necessarily imply that fewer sampling and analytical methods are available. Finally, our proposed roadmap provides guidance on which methods can be used to improve monitoring of all groups of CECs through citizen science.

The Research Topic on the 16^th Deep Sea Biology Symposium compiles a range of articles presented during the conference that was held in Brest (France) in September 2021 and hosted by the Institut Français de Recherche pour l’Exploitation de la Mer (Ifremer). This triannual event is the central meeting for deep-sea research, where scientists from all over the world gather together to showcase and discuss the latest advances in their field. For the first time in 2021, this event was held in a hybrid mode with participants attending on site and online. Puccinelli et al. showed that, while meetings organized by the Deep-Sea Biology Society had typically less than 400 participants, the use of a hybrid format increased participation by 33% (581 attendees), 73% of whom joined online.
The 26 articles of this Research Topic span research conducted by 138 authors across all ocean basins, encompassing a range of topics that we classified in four sections: 1) zoology and systematics, 2) biodiversity, 3) ecology and 4) conservation and policy. These works investigated most trophic levels from phytoplankton to benthos, fish and whales, across diverse deep-sea environments such as mesopelagic to abyssal environments, vents, seeps and seamounts. This Research Topic provides novel insights on the largest biome of the planet, while advancing our understanding of the complex interactions between organisms and their physical environment, and how such equilibrium is affected by human-induced activities and climate change.

Bacterial assemblages on amphibian skin may play an important role in protecting hosts against infection. In hosts that occur over a range of environments, geographic variation in composition of bacterial assemblages might be due to direct effects of local factors and/or to evolved characteristics of the host. Invasive cane toads (Rhinella marina) are an ideal candidate to evaluate environmental and genetic mechanisms, because toads have evolved major shifts in physiology, morphology, and behavior during their brief history in Australia. We used samples from free-ranging toads to quantify site-level differences in bacterial assemblages and a common-garden experiment to see if those differences disappeared when toads were raised under standardised conditions at one site. The large differences in bacterial communities on toads from different regions were not seen in offspring raised in a common environment. Relaxing bacterial clustering to operational taxonomic units in place of amplicon sequence variants likewise revealed high similarity among bacterial assemblages on toads in the common-garden study, and with free-ranging toads captured nearby. Thus, the marked geographic divergence in bacterial assemblages on wild-caught cane toads across their Australian invasion appears to result primarily from local environmental effects rather than evolved shifts in the host.

Alpine river biodiversity around the world is under threat from glacier retreat driven by rapid warming, yet our ability to predict the future distributions of specialist cold-water species is currently limited. Here we link future glacier projections, hydrological routing methods and species distribution models to quantify the changing influence of glaciers on population distributions of 15 alpine river invertebrate species across the entire European Alps, from 2020 to 2100. Glacial influence on rivers is projected to decrease steadily, with river networks expanding into higher elevations at a rate of 1% per decade. Species are projected to undergo upstream distribution shifts where glaciers persist but become functionally extinct where glaciers disappear completely. Several alpine catchments are predicted to offer climate refugia for cold-water specialists. However, present-day protected area networks provide relatively poor coverage of these future refugia, suggesting that alpine conservation strategies must change to accommodate the future effects of global warming.

Aquatic and terrestrial ecosystems are tightly connected via spatial flows of organisms and resources. Such land-water linkages integrate biodiversity across ecosystems and suggest a spatial association of aquatic and terrestrial biodiversity. However, knowledge about the extent of this spatial association is limited. By combining satellite remote sensing (RS) and environmental DNA (eDNA) extraction from river water across a 740-km² mountainous catchment, we identify a characteristic spatial land-water fingerprint. Specifically, we find a spatial association of riverine eDNA diversity with RS spectral diversity of terrestrial ecosystems upstream, peaking at a 400 m distance yet still detectable up to a 2.0 km radius. Our findings show that biodiversity patterns in rivers can be linked to the functional diversity of surrounding terrestrial ecosystems and provide a dominant scale at which these linkages are strongest. Such spatially explicit information is necessary for a functional understanding of land-water linkages.

The world's largest rivers are home to diverse, endemic, and threatened fish species. However, their sheer sizes make large-scale biomonitoring challenging. While environmental DNA (eDNA) metabarcoding has become an established monitoring approach in smaller freshwater ecosystems, its suitability for large rivers may be challenged by the sheer extent of their cross sections (>1 km wide and tens of meters deep). Here, we sampled fish eDNA from multiple vertical layers and horizontal locations from two cross sections of the lower reach of the Yangtze River in China. Over half of the ASVs (amplicon sequence variants) were detected in only a single combination of the vertical layers and horizontal locations, with ∼7% across all combinations. We estimated the need to sample >100 L of water across the cross-sectional profiles to achieve ASV richness saturation, which translates to ∼60 L of water at the species level. No consistent pattern emerged for prioritizing certain depth and horizontal samples, yet we underline the importance of sampling and integrating different layers and locations simultaneously. Our study highlights the significance of spatially stratified sampling and sampling volumes when using eDNA approaches. Specifically, we developed and tested a scalable and broadly applicable strategy that advances the monitoring and conservation of large rivers.

Quagga and zebra mussels (Dreissena bugensis and D. polymorpha) are spreading across lakes in Europe and North America. In particular, quagga mussels colonize lakes to great depths (>200 m). To better understand the colonization pattern of quagga mussels in deep lakes, we studied the settlement of quagga mussels along a depth gradient on colonization plates at multiple depths (1–140 m) in the pelagic zone of two recently invaded perialpine lakes, Lake Constance and Lake Geneva. We measured colonization rates every three months over one year on colonization plates deployed in both lakes at defined depths. We also assessed long-term population dynamics from abundance and size distribution using repeated photogrammetry of colonization plates. Highest colonization rates and largest mussel sizes occurred above 8 m depth, and almost no zebra mussels were found. Colonization rates decreased to almost zero below 30 m. Colonization rates on plates were associated with variation in environmental conditions as well as veliger densities in the plankton across season and depth. Temperature was the most important environmental parameter that influenced colonization. Our results will help to better understand the seasonal colonization patterns of invasive quagga mussels in deep lakes.

Global change encompasses many co-occurring anthropogenic drivers, which can act synergistically or antagonistically on ecological systems. Predicting how different global change drivers simultaneously contribute to observed biodiversity change is a key challenge for ecology and conservation. However, we lack the mechanistic understanding of how multiple global change drivers influence the vital rates of multiple interacting species. We propose that reaction norms, the relationships between a driver and vital rates like growth, mortality, and consumption, provide insights to the underlying mechanisms of community responses to multiple drivers. Understanding how multiple drivers interact to affect demographic rates using a reaction-norm perspective can improve our ability to make predictions of interactions at higher levels of organization - that is, community and food web. Building on the framework of consumer–resource interactions and widely studied thermal performance curves, we illustrate how joint driver impacts can be scaled up from the population to the community level. A simple proof-of-concept model demonstrates how reaction norms of vital rates predict the prevalence of driver interactions at the community level. A literature search suggests that our proposed approach is not yet used in multiple driver research. We outline how realistic response surfaces (i.e., multidimensional reaction norms) can be inferred by parametric and nonparametric approaches. Response surfaces have the potential to strengthen our understanding of how multiple drivers affect communities as well as improve our ability to predict when interactive effects emerge, two of the major challenges of ecology today.

Biodiversity is under enormous pressure from multiple threats including climate change, land use change, habitat alterations and hunting pressure. One way to ease this pressure on biodiversity and to mitigate the effects of above-mentioned threats, is to establish protected areas. Importance of protected increases many folds in regions that are considered as biodiversity poor regions i.e. deserts. Protected areas have long been a major pillar of biodiversity conservation strategies; the Houbara Protected Area (HPA) is one of the 13 terrestrial protected areas in Abu Dhabi Emirate officially declared in 2017. However, no information regarding the status of biodiversity in the HPA has been communicated to the research fraternity. During the present study, surveys were conducted to fill this gap. The survey area was divided in to 50 grids of 5 × 5 km² and monitoring surveys were undertaken from January to December 2016. A total of 14 bi-monthly to monthly surveys were conducted within HPA and 196 species of different taxonomical groups were recorded. A year-long survey yielded highly diversified fauna and flora from 19 different habitat types (H) 1.32, (E) 2.28, Shannon Diversity Index). We looked at the influence of habitat breadth and temperature on the species richness and abundance, results shows that in desert setup heterogeneity of habitat is not an important factor in maintaining the biodiversity as total number of individuals as well as species were similar in the grids that have different number of habitat types (df = 34.3, t = -0.472, P = 0.640). However, we did find a positive impact of mean monthly temperature on species richness (df = 154, t = 2.53, P = 0.012). Our study highlights the importance of temperature in driving species abundance and richness in protected area. Abundance and species richness are similar in protected areas indicating that protection is allowing species to explore the heterogenous habitats. Overall, we can conclude that protection is beneficial for species.

À ce jour, dix espèces exotiques ont pu s’établir en Suisse, dont cinq sont considérées comme envahissantes. Certaines de ces espèces ont, en partie, un régime alimentaire de prédateur ou se nourrissent en filtrant l’eau; leurs populations peuvent atteindre des densités très élevées. Jusqu’à présent, les espèces exotiques ne sont toutefois apparues que dans de grand lacs et cours et plans d’eau.

Until now, ten alien amphipod species have become established in Switzerland, of which five are considered invasive. These species are partly predatory or are filter-feeding and can reach very high densities. Until now they have only been found in larger bodies of water, however.

In der Schweiz konnten sich bislang zehn gebietsfremde Arten etablieren. Von diesen zählen fünf zu den invasiven Arten. Einige dieser Arten ernähren sich teilweise räuberisch oder leben filtrierend und können sehr hohe Dichten erreichen. Allerdings sind die gebietsfremden Arten bisher nur in grösseren Gewässern aufgetreten.

The structure and functioning of Arctic ecosystems have been drastically modified by global warming, with fish species potentially performing habitat shifts such as the northern expansion of generalist and warm-adapted species. The freshwater fish species Arctic charr (Salvelinus alpinus, hereafter charr) plays a key role in Arctic lake food webs, but sticklebacks (Gasterosteus aculeatus) may impact the trophic position (TP) of charr by affecting their habitat choice and food resources. In the present study, we used multiple regression analyses to examine the role of lake morphology (i.e., depth and area) and the influence of sticklebacks on the TP of charr (estimated from δ¹⁵N and δ¹³C) sampled in nine Arctic lakes in Western Greenland between 2011 and 2013. Results showed that charr populations exhibited larger TP values when co-occurring with sticklebacks. Specifically, for larger and deeper lakes, a significant positive effect on TP values was observed for medium-sized (25 to 35 cm) charr. Moreover, the TP of sticklebacks had a null effect on the TP values of the largest charr (> 40 cm), suggesting that the largest-sized charr individuals did not prey on sticklebacks. We conclude that charr undergoes flexible ontogenetic trophic trajectories depending on the species composition of the Arctic fish community structure (here presence or absence of sticklebacks) and abiotic lake features.

Maternal effects have the potential to alter early developmental processes of offspring and contribute to adaptive diversification. Egg size is a major contributor to offspring phenotype, which can influence developmental trajectories and potential resource use. However, to what extent intraspecific variation in egg size facilitates evolution of resource polymorphism is poorly understood. We studied multiple resource morphs of Icelandic Arctic charr, ranging from an anadromous morph—with a phenotype similar to the proposed ancestral phenotype—to sympatric morphs that vary in their degree of phenotypic divergence from the ancestral anadromous morph. We characterized variation in egg size and tested whether egg size influenced offspring phenotype at early life stages (i.e., timing of- and size at- hatching and first feeding [FF]). We predicted that egg size would differ among morphs and be less variable as morphs diverge away from the ancestral anadromous phenotype. We also predicted that egg size would correlate with offspring size and developmental timing. We found morphs had different egg size, developmental timing, and size at hatching and FF. Egg size increased as phenotypic proximity to the ancestral anadromous phenotype decreased, with larger eggs generally giving rise to larger offspring, especially at FF, but egg size had no effect on developmental rate. The interaction between egg size and the environment may have a profound impact on offspring fitness, where the resulting differences in early life-history traits may act to initiate and/or maintain resource morphs diversification.

Regular monitoring of ecosystems can be used for the early detection of invasive alien species (IAS), and provide information for management and preventing them from becoming established or advancing into new areas. Current methods of monitoring freshwater systems for IAS can be both financially costly and time-consuming, with routine monitoring often carried out at low intensity and at only a small number of sites. In this study, we evaluate how environmental DNA (eDNA) metabarcoding for monitoring freshwater macroinvertebrate IAS compares to traditional kick-net sampling as part of a national (Switzerland) and a catchment monitoring programme. Kick-net sampling was more fruitful for the detection of several well-known target macroinvertebrate IAS. However, eDNA samples proved complementary for the detection of IAS that belong to species often being unnoticed by traditional sampling due to methodological or taxonomic reasons. Specifically, the invasive jellyfish Craspedacusta sowerbii, hardly detectable using classic kick-net sampling, was found to be widespread in both the national and the catchment-scale monitoring with the eDNA method only. Our study shows that IAS detection using eDNA is easily implemented in both national- and catchment-scale monitoring campaigns. However, successful detection of target IAS is still highly dependent on primer choice, species' biology, and availability of adequate markers. Specifically, multiple markers should be considered for detecting IAS from several different taxonomic groups, such as those under the 'freshwater macroinvertebrate' umbrella term. While eDNA is still developing in terms of these fundamental methodological requirements, surveillance for both target and non-target IAS using eDNA is likely to increase efficiency in early detection of IAS in freshwater systems.

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups. Local richness showed statistically significant, season-dependent increases and decreases towards downstream location within the catchment for fish and bacteria, respectively. Meanwhile, invertebrate richness remained spatially unchanged but varied across seasons. The structure of local food webs, such as link density and nestedness, also varied across space and time. However, these patterns did not necessarily mirror those observed for biodiversity and functional feeding characteristics. Our results suggest that biodiversity patterns and food-web dynamics are not directly scalable to each other even at the same spatial and temporal scales. In order to conserve species diversity as well as the functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied.

Aim: Groundwater harbours an exceptional fauna and provides invaluable ecosystem services, yet is among the least explored and consequently least protected ecosystems. Successful protection of its biodiversity depends on complete species inventories, knowledge of species spatial distribution, and quantification of biodiversity patterns, as well as disentanglement of the processes that shaped biodiversity patterns. We studied the hyper-speciose amphipod genus Niphargus as a model system within a global subterranean biodiversity hotspot. We linked the biodiversity patterns with possible underlying processes and discuss the needs to include information on different origins of biodiversity into conservation approaches.
Location: Europe, Western Balkans.
Methods: We analysed biodiversity patterns of Niphargus using two biodiversity metrics, species richness and phylogenetic diversity, on a grid-based approach. To account for high cryptic diversity, we replaced nominal species with taxonomic units identified in unilocus delimitations (MOTUs). We built a time-calibrated multilocus phylogeny of 512 Niphargus MOTUs from within and outside the study area, and calculated Faith's phylogenetic diversity, standardized effect sizes of phylogenetic diversity, and residual of phylogenetic diversity regressed onto species richness.
Results: Within the study area, we recognized 245 MOTUs, belonging to different Niphargus clades. Species richness is highest in a north-western hotspot, although some species-rich cells were detected also in the south-east. High phylogenetic diversity coincides with high species richness in the north-west, while in the south-east it is lower than expected.
Main conclusions: We have shown that species richness does not predictably correlate with phylogenetic diversity. This difference suggests that different processes have led to the formation of species-rich areas in the Western Balkans: through a combination of dispersal and speciation in the north-west, and local radiation in the south-east, respectively. This calls for caution in conservation strategies relying solely on number of species and may change the view on conservation priorities within this region.

Ramon Margalef was a pioneering scientist who introduced an interdisciplinary approach to ecological studies. His studies were among the first to incorporate various concepts in the literature of aquatic ecology, covering topics such as organisms, ecosystem interactions and evolution. To bring Margalef's approach into current scientific studies, in this review we explore his vision of aquatic ecology within four interrelated fields of study: ecological theory, microbial di-versity, biogeochemical cycles and global environmental changes. Taking inspiration from his studies, we analyse current scientific challenges and propose an integrated approach, considering the unifying concept of Margalef's Mandala with the aim of improving future studies on aquatic microbial ecology.

Macroinvertebrates serve as key indicators in ecological assessments of aquatic ecosystems, where the composition and richness of their communities are indicative of environmental and anthropogenic change. Established monitoring of macroinvertebrates is expensive and time-consuming, and relies on expert taxonomic knowledge. In contrast, biomonitoring based on molecular tools can support faster characterization of aquatic communities but needs validation for the target taxonomic groups and the study region. Here, we used data from a biomonitoring program covering a large biogeographic gradient to compare the routine kick-net method with eDNA metabarcoding. We used two primer pairs targeting COI, one targeting a broad metazoan spectrum (mICOIintF/jgHCO2198) and another more recently developed primer pair optimized for the detection of freshwater invertebrates (fwhF2/EPTDr2n). We used the data of the macroinvertebrate monitoring with a focus on the orders of Ephemeroptera, Plecoptera, and Trichoptera across 92 rivers in Switzerland, covering four continental drainage basins and an elevational range from 198 to 1650 m a.s.l. Across all sample sites, the kick-net detected more distinct taxa than either of the metabarcoding approaches. At a site level, however, both primer pairs detected on average more species. Comparing both primer pairs, the fwhF2/EPTDr2n primer pair captured more species assigned to the indicator groups Ephemeroptera, Plecoptera, and Trichoptera, and showed a significantly larger overlap with the kick-net method. However, the community composition still varied significantly among the different metabarcoding approaches. Fewer Trichoptera species were recovered by eDNA, whereas the fwhF2/EPTDr2n primer pair detected more Plecopterans than the other two approaches. This study highlights the importance of the optimization and validation of novel molecular approaches under consideration of the target organismal group and the study area.

Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.

1. Freshwater is vital to much life on Earth and is an essential resource for humans. Climate change, however, dramatically changes freshwater systems and reduces water quality, poses a risk to drinking water availability and has severe impacts on aquatic ecosystems and their biodiversity.
2. The direct effects of climate change, such as increased temperatures and higher frequency of extreme meteorological events, interact with human responses to climate change, which we refer to here as 'indirect effects'. The latter possibly have even greater impact than the direct effects of climate change. Specifically, changes in land-use practices as responses to climate change, such as adjusted cropping regimes or a shift to renewable hydroelectricity to mitigate climate change, can very strongly affect freshwater ecosystems.
3. Hitherto, these indirect effects and the possibility of idiosyncratic outcomes are under-recognized. Here, we synthesize knowledge and identify threats to freshwater environments in alpine and pre-alpine regions, which are particularly affected by climate change.
4. We focus on the effects of adapted agriculture and hydropower production on freshwater quality and ecological status, as these examples have strong indirect effects that interact with direct effects of climate change (e.g., water temperature, droughts, isolation of populations).
5. We outline how failure to effectively account for indirect effects associated with human responses to climate change may exacerbate direct climate change impacts on aquatic ecosystems. If managed properly, however, human responses to indirect effects offer potential for rapid and implementable leverage to mitigate some of the direct climate change effects on aquatic ecosystems. To better address looming risks, policy- and decisionmakers must account for indirect effects and incorporate them into restoration planning and the respective sectorial policies.

1. Global warming challenges the persistence of local populations, not only through heat-induced stress, but also through indirect biotic changes. We study the interactive effects of temperature, competition and parasitism in the water flea Daphnia magna.
2. We carried out a common garden experiment monitoring the dynamics of Daphnia populations along a temperature gradient. Halfway through the experiment, all populations became infected with the ectoparasite Amoebidium parasiticum, enabling us to study the interactive effects of temperature and parasite dynamics. We combined Integral Projection Models with epidemiological models, parameterized using the experimental data on the performance of individuals within dynamic populations. This enabled us to quantify the contribution of different vital rates and epidemiological parameters to population fitness across temperatures and Daphnia clones originating from two latitudes.
3. Interactions between temperature and parasitism shaped competition, where Belgian clones performed better under infection than Norwegian clones. Infected Daphnia populations performed better at higher than at lower temperatures, mainly due to an increased host capability of reducing parasite loads. Temperature strongly affected individual vital rates, but effects largely cancelled out on a population-level. In contrast, parasitism strongly reduced fitness through consistent negative effects on all vital rates. As a result, temperature-mediated parasitism was more important than the direct effects of temperature in shaping population dynamics. Both the outcome of the competition treatments and the observed extinction patterns support our modelling results.
4. Our study highlights that shifts in biotic interactions can be equally or more important for responses to warming than direct physiological effects of warming, emphasizing that we need to include such interactions in our studies to predict the competitive ability of natural populations experiencing global warming. A free Plain Language Summary can be found within the Supporting Information of this article.

Der Greifensee ist ausserhalb des Kantons Zürichs nicht so vielen Leuten bekannt, doch weil das Wasserforschungsinstitut Eawag seit 1970 in Dübendorf den Hauptsitz hat, ist er sehr gut erforscht. Für gewisse Themen, zum Beispiel die Einführung einer einheitlichen Beprobung von kleinen Zuflüssen aus landwirtschaftlich genutzten Einzugsgebieten, kommt ihm für die ganze Schweiz Modellcharakter zu. Zusammen mit anderen Forschungspartnern - wie Empa oder ETH Zürich - sowie mit kantonalen Stellen forscht und entwickelt die Eawag aktuell moderne, automatisierte Untersuchungsmethoden, welche helfen, das «System See» noch besser zu verstehen und wo nötig frühzeitig auf unerwünschte Entwicklungen reagieren zu können.

River networks' universal fractal structure not only defines their hydrology and connectivity, but has also profound biological consequences, especially regarding stability and persistence of organismal populations. While rivers' scaling features are captured by Optimal Channel Networks, knowledge on adequate network topologies has hitherto been only partially transferred across geo- and biosciences. Consequently, ecologists have often studied riverine populations via random networks not respecting real rivers' scaling character. Here we show that an alleged property of such random networks (branching probability) is a scale-dependent quantity that does not reflect any recognized metric of rivers' fractal character, and hence cannot be a driver of ecological dynamics. Moreover, we show that random networks lead to biased estimates of population stability and persistence, while only Optimal Channel Networks yield estimates comparable to real rivers. We hence advocate Optimal Channel Networks as model landscapes for realistic and generalizable projections of ecohydrological dynamics in riverine networks.

Rivers regulated by dams display several ecosystem alterations due to modified flow and sediment regimes. Downstream from a dam, ecosystem degradation occurs because of reduced disturbance, mostly derived from limitations on flow variability and sediment supply. In the last decade, most flow restoration/dam impact mitigation was oriented towards the development of environmental flows. Flow variability (and consequent disturbance) can be reintroduced by releasing artificial high flows (experimental floods). Flow-sediment interactions during experimental floods represent strong ecosystem drivers, influencing nutrient dynamics, and metabolic and functional properties. In river networks, sediment and water inputs from tributaries generate points of discontinuity that can drive major changes in environmental conditions, affecting habitat structure and determining functional differences between upstream and downstream. However, despite the relevance for management, flow/sediment relations during environmental flows - and more importantly during experimental floods - remain poorly understood, mostly due to the lack of empirical evidence. In this study, we examined how a major tributary (source of water and sediments) modified the physical habitat template of a regulated river, thereby influencing ecological and geomorphological responses to experimental floods. Methods combined high-resolution drone mapping techniques with a wide range of biological samples collected in field surveys before, during, and after experimental floods in an alpine river. Data were used to quantify changes in relevant functional and structural ecosystem properties, relating ecological responses to geomorphological dynamics. Results highlight the importance of tributaries in restoring ecosystem properties lost after damming, enhancing the resilience of the system. In addition, we observed that disturbance legacy played a fundamental role in determining ecological conditions of a river prior to experimental floods, thus confirming that considering flow variability and sediment availability is crucial in adaptive dam management and environmental flows design.

Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature. Collectively, we demonstrated that exogenous nutrient supply and immobilization are critical control points for decomposition of organic matter.

Dispersal is a central biological process tightly integrated into life-histories, morphology, physiology and behaviour. Such associations, or syndromes, are anticipated to impact the eco-evolutionary dynamics of spatially structured populations, and cascade into ecosystem processes. As for dispersal on its own, these syndromes are likely neither fixed nor random, but conditional on the experienced environment. We experimentally studied how dispersal propensity varies with individuals' phenotype and local environmental harshness using 15 species ranging from protists to vertebrates. We reveal a general phenotypic dispersal syndrome across studied species, with dispersers being larger, more active and having a marked locomotion-oriented morphology and a strengthening of the link between dispersal and some phenotypic traits with environmental harshness. Our proof-of-concept metacommunity model further reveals cascading effects of context-dependent syndromes on the local and regional organisation of functional diversity. Our study opens new avenues to advance our understanding of the functioning of spatially structured populations, communities and ecosystems.

Changing weather patterns and receding glaciers are predicted to increase flow intermittency in alpine streams. If aquatic macroinvertebrate communities largely comprise taxa adapted to perennial flows, an increase in flow intermittency substantially reduces biodiversity and affects functional processes. We conducted a before-after-control-impact field experiment to examine how macroinvertebrate communities in an alpine headwater stream responded to and recovered from a repeated experimental increase in flow intermittency. Flow in one channel was manipulated to simulate increased summer intermittency (June–September) over two consecutive years, whilst an adjacent channel served as a control. We monitored the density of benthic macroinvertebrates, periphyton and organic matter at approximately monthly intervals over three years during the snow-free period. Before manipulation, both channels had similar ecological properties. The flow manipulation reduced the overall macroinvertebrate density, and especially the proportional rheophile density, across both years. Recovery of the macroinvertebrate community following experimental flow intermittency took more than a year, and longer than our study period. This could be due to long aquatic life stages, dispersal limitation and biotic interactions. We conclude that climate-induced changes in alpine stream flow regimes can lead to a fundamental shift in macroinvertebrate assemblages through local extinctions, mostly of rheophilic species.

Monitoring of aquatic habitats for water quality and biodiversity requires regular sampling, often in off-shore locations and underwater. Such sampling is commonly performed manually from research vessels, or if autonomous, is constrained to permanent installations. Consequentially, high frequency ecological monitoring, such as for harmful algal blooms, are limited to few sites and/or temporally infrequent. Here, we demonstrate the use of MEDUSA, an Unmanned Aerial-Aquatic Vehicle which is capable of performing underwater sampling and inspection at up to 10 m depth, and is composed of a multirotor platform, a tether management unit and a tethered micro Underwater Vehicle. The system is validated in the task of vertical profiling of Chlorophyll-a levels in freshwater systems by means of a custom solid sample filtering mechanism. This mechanism can collect up to two independent samples per mission by pumping water through a pair of glass-fibre GF/F filters. Chlorophyll levels measured from the solid deposits on the filters are consistent and on par with traditional sampling methods, highlighting the potential of using UAAVs to sample aquatic locations at high frequency and high spatial resolution.

The phylogeographic patterns of many taxa on New Zealand's South Island are characterized by disjunct distributions that have been attributed to Pleistocene climatic cycles and the formation of the Southern Alps. Pleistocene glaciation has been implicated in shaping the contemporary genetic differentiation between populations of the aquatic snail Potamopyrgus antipodarum. We investigated whether similar phylogeographic patterns exist for the snail's locally adapted trematode parasite, Atriophallophorus winterbourni. We found evidence for a barrier to gene-flow in sympatry between cryptic, but ecologically divergent species. When focusing on the most common of these species, disjunct geographic distributions are found for mitochondrial lineages that diverged during the Pleistocene. The boundary between these distributions is found in the central part of the South Island and is reinforced by low cross-alpine migration. Further support for a vicariant origin of the phylogeographic pattern was found when assessing nuclear multilocus SNP data. Nuclear and mitochondrial population differentiation was concordant in pattern, except for populations in a potential secondary contact zone. Additionally, we found larger than expected differentiation between nuclear- and mitochondrial-based empirical Bayes F_ST estimates (global F_ST: 0.02 vs. 0.39 for nuclear and mitochondrial data, respectively). Population subdivision is theoretically expected to be stronger for mitochondrial genomes due to a smaller effective population size, but the strong difference here, together with mitonuclear discordance in a putative contact zone, is potentially indicative of divergent gene flow of nuclear and mitochondrial genomes.

Competition for limited resources is a major force in structuring ecological communities. Species minimum resource requirements (R*s) can predict competitive outcomes and evolve under selection in simple communities under controlled conditions. However, whether R*s predict competitive outcomes or demonstrate adaptive evolution in naturally complex communities is unknown. We subjected natural phytoplankton communities to three types of resource limitation (nitrogen, phosphorus, light) in outdoor mesocosms over 10 weeks. We examined the community composition weekly and isolated 21 phytoplankton strains from seven species to quantify responses to the selection of R* for these resources. We investigated the evolutionary change in R*s in the dominant species, Desmodesmus armatus. R*s were good predictors of species changes in relative abundance, though this was largely driven by the success of D. armatus across several treatments. This species also demonstrated an evolutionary change in R*s under resource limitation, supporting the potential for adaptive trait change to modify competitive outcomes in natural communities.

Recently, a plethora of studies reporting insect declines has been published. Even though the common theme is decreasing insect richness, positive trends have also been documented. Here, we analysed nationwide, systematic monitoring data on aquatic insect richness collected at 438 sites in Switzerland from 2010 to 2019. In addition to taxonomic richness, we grouped taxa in accordance with their ecological preferences and functional traits to gain a better understanding of trends and possible underlying mechanisms. We found that in general, richness of aquatic insects remained stable or increased with time. Warm-adapted taxa, common feeding guilds and pesticide-tolerant taxa showed increasing patterns while cold-adapted, rarer feeding guilds and pesticide-sensitive taxa displayed stable trends. Both climate and land-use-related factors were the most important explanatory variables for the patterns of aquatic insect richness. Although our data cover the last decade only, our results suggest that recent developments in insect richness are context-dependent and affect functional groups differently. However, longer investigations and a good understanding of the baseline are important to reveal if the increase in temperature- and pesticide-tolerant species will lead to a decrease in specialized species and a homogenization of biotic communities in the long term.

Lakes are often described as sentinels of global change. Phenomena like lake eutrophication, algal blooms, or reorganization in community composition belong to the most studied ecosystem regime shifts. However, although regime shifts have been well documented in several lakes, a global assessment of the prevalence of regime shifts is still missing, and, more in general, of the factors altering stability in lake status, is missing. Here, we provide a first global assessment of regime shifts and stability in the productivity of 1,015 lakes worldwide using trophic state index (TSI) time series derived from satellite imagery. We find that 12.8% of the lakes studied show regime shifts whose signatures are compatible with tipping points, while the number of detected regime shifts from low to high TSI has increased over time. Although our results suggest an overall stable picture for global lake dynamics, the limited instability signatures do not mean that lakes are insensitive to global change. Modeling the interaction between lake climatic, geophysical, and socioeconomic features and their stability properties, we find that the probability of a lake experiencing a tipping point increases with human population density in its catchment, while it decreases as the gross domestic product of that population increases. Our results show how quantifying lake productivity dynamics at a global scale highlights socioeconomic inequalities in conserving natural environments.

Ecological and evolutionary processes can occur at similar time scales and, hence, influence one another. There has been much progress in developing metrics that quantify contributions of ecological and evolutionary components to trait change over time. However, many empirical evolutionary ecology studies document trait differentiation among populations structured in space. In both time and space, the observed differentiation in trait values among populations and communities can be the result of interactions between nonevolutionary (phenotypic plasticity, changes in the relative abundance of species) and evolutionary (genetic differentiation among populations) processes. However, the tools developed so far to quantify ecological and evolutionary contributions to trait changes are implicitly addressing temporal dynamics because they require directionality of change from an ancestral to a derived state. Identifying directionality from one site to another in spatial studies of eco-evolutionary dynamics is not always possible and often not meaningful. We suggest three modifications to existing partitioning metrics so they allow quantifying ecological and evolutionary contributions to changes in population and community trait values across spatial locations in landscapes. Applying these spatially modified metrics to published empirical examples shows how these metrics can be used to generate new empirical insights and to facilitate future comparative analyses. The possibility of applying eco-evolutionary partitioning metrics to populations and communities in natural landscapes is critical as it will broaden our capacity to quantify eco-evolutionary interactions as they occur in nature.

Übermässige Stickstoff- und Phosphoreinträge in die Umwelt gehören zusammen mit Änderungen der Land- und Gewässernutzung, der Übernutzung natürlicher Ressourcen, der Umweltverschmutzung, invasiven gebietsfremden Arten und dem Klimawandel zu den Hauptgründen des Biodiversitätsrückgangs. Überschüsse dieser Nährstoffe verändern und reduzieren die Artenzahlen, die Zusammensetzung von Lebensgemeinschaften, Interaktionen zwischen Arten sowie Ökosystemprozesse. Die flächendeckenden Einträge, die heute mehrheitlich aus der Landwirtschaft stammen, vereinheitlichen zudem die Standortbedingungen weiträumig, was den Verlust regionaler Besonderheiten verursacht. Dies alles kann nicht nur zum irreversiblen Verschwinden von Arten und zum Verlust genetischer und funktioneller Diversität führen, sondern beeinträchtigt auch Ökosystemleistungen wie zum Beispiel die Trinkwasserqualität und verschiedene Waldfunktionen. Entsprechend können neben der Biodiversität weitere Schutzgüter wie Wasser-, Boden-, Luftqualität, Treibhausgasbilanz und Gesundheit ebenfalls beeinträchtigt werden. Ursachen und Auswirkungen dieser Einträge sind wissenschaftlich gut belegt.
Der vorliegende Artikel soll einen Einstieg in das Thema bieten. Es werden die Wirkungsweisen übermässiger Stickstoff- und Phosphoreinträge auf die Biodiversität thematisiert, diskutiert, wie sich die Stickstoffdeposition über die Luft und Phosphorgehalte in Seen im Laufe der Zeit verändert haben und wie sich aus naturwissenschaftlicher Sicht beurteilen lässt, ob Einträge und Gehalte von Stickstoff und Phosphor übermässig sind. Schlussendlich werden wirkungsvolle Handlungsansätze im Landwirtschafts- und Ernährungssystem präsentiert.

The dreissenids, quagga mussel Dreissena bugensis and zebra mussel D. polymorpha, are invasive freshwater mussels in Europe and North America. These species strongly impact aquatic ecosystems, such as the food web through their high abundance and filtration rate. They spread quickly within and between waterbodies, and have the ability to colonize various substrates and depths. The zebra mussel invaded and established in Swiss lakes in the 1960s, whereas the quagga mussel was not detected until 2014. We collected all available data from cantonal as well as local authorities and other institutions to describe the colonization pattern of quagga mussels in perialpine lakes north of the Alps. We also collected data regarding the distribution of larval stages of the mussels, the so-called veliger larvae. We observed that in lakes colonized by the quagga mussel, veligers are present the whole year round, whereas they are absent in winter in lakes with only zebra mussels. Additionally, we present detailed information about the invasion and colonization pattern of quagga mussels in Lake Constance. Quagga mussels colonized the lakeshore within a few years (~ 2016-2018), outcompeted zebra mussels, and have reached densities > 5000 ind. m^-2 in the littoral zone, even at 80 m densities above 1000 ind. m^-2 were found at some locations. At the end of the article, we discussed possibilities on how the spread of quagga mussels within and among northern perialpine lakes should be monitored and prevented in the future.

1. Shifts in microbial communities and their functioning in response to environmental change result from contemporary interspecific and intraspecific diversity changes. Interspecific changes are driven by ecological shifts in species composition, while intraspecific changes are here assumed to be dominated by evolutionary shifts in genotype frequency. Quantifying the relative contributions of interspecific and intraspecific diversity shifts to community change thus addresses the essential, yet understudied question as to how important ecological and evolutionary contributions are to total community changes. This debate is to date practically constrained by (a) a lack of studies integrating across organizational levels and (b) a mismatch between data requirements of existing partitioning metrics and the feasibility to collect such data, especially in microscopic organisms like phytoplankton.
2. We experimentally assessed the relative ecological and evolutionary contributions to total phytoplankton community changes using a new design and validated its functionality by comparisons to established partitioning metrics. We used a community of coexisting Emiliania huxleyi and Chaetoceros affinis with initially nine genotypes each. First, we exposed the community to elevated CO₂ concentration for 80 days (~50 generations) to induce interspecific and intraspecific diversity changes and a total abundance change. Second, we independently manipulated the induced interspecific and intraspecific diversity changes in an assay to quantify the corresponding ecological and evolutionary contributions to the total change. Third, we applied existing partitioning metrics to our experimental data and compared the outcomes.
3. Total phytoplankton abundance declined to one-fifth in the high CO₂ exposed community compared to ambient conditions. Consistently across all applied partitioning metrics, the abundance decline could predominantly be explained by ecological shifts and to a low extent by evolutionary changes.
4. We discuss potential consequences of the observed community changes on ecosystem functioning. Furthermore, we explain that the low evolutionary contributions likely resulted of intraspecific diversity changes that occurred irrespectively of CO₂. We discuss how the assay could be upscaled to more realistic settings, including more species and drivers. Overall, the presented calculations of eco-evolutionary contributions to phytoplankton community changes constitute another important step towards understanding future phytoplankton shifts, and eco-evolutionary dynamics in general.

Advancing understanding of the complexities and expansive spatial scales of river ecology can be enhanced through the application of remote sensing. We obtained satellite (Quickbird) and airborne (LIDAR, hyperspectral, multispectral, and thermal) imagery data of an alluvial gravel-bed river floodplain in western Montana to quantify both riparian and aquatic habitats and processes. LIDAR data provided a detailed bare earth DEM and vegetation canopy DEM. We classified river hydraulics and aquatic habitats using a combination of the satellite multispectral, airborne hyper-spectral, and LIDAR data coupled with spatially-explicit acoustic Doppler velocity profile data of water depth and velocity. Velocity, depth, and Froude classifications were aggregated into similar hydraulic zones of river habitat classes. Thermal imagery data were coupled with field measurements of temperature and radon gas tracer to identify patterns of water exchange between the alluvial aquifer and the surface. We found a high complexity of aquatic surface temperatures and radon tracer linked to groundwater discharge from the alluvial aquifer. Airborne hyperspectral data were used to identify “hot spots” of periphyton production, which coincided with the complex nature of groundwater–surface water exchange. Airborne hyperspectral data provided differentiation of vegetation patches by dominant species. When the hyperspectral data were coupled to LIDAR first return metrics, we were able to determine vegetation canopy height and relative vegetation patch age classes. The integration of these various remote sensing sources allowed us to characterize the distribution and abundance of floodplain aquatic and riparian species and model processes of change through space and time.

Aphids have evolved tight relationships with heritable endosymbionts, i.e., bacteria hosted within their tissues. Besides the primary endosymbiont Buchnera aphidicola, aphids host many facultative secondary endosymbionts with functions they may or may not benefit from. The different phenologies, lifestyles, and natural enemies of aphid species are predicted to favor the selection for distinct endosymbiont assemblages, as well as the emergence of intra-specific genetic diversity in the symbiotic bacteria. In this study, we (1) investigated the diversity of endosymbionts associated with four species from the genus Aphis in the field, and (2) we characterized the genetic diversity of Hamiltonella defensa, an endosymbiont that protects aphids against parasitoid wasps. We observed strong differences in the composition of endosymbiont communities among the four aphid species. H. defensa was clearly the dominant symbiont, although its abundance in each species varied from 25 to 96%. Using a multilocus sequence-typing approach, we found limited strain diversity in H. defensa. Each aphid species harbored two major strains, and none appeared shared between species. Symbiont phylogenies can thus help to understand the (seemingly limited) mobility of endosymbionts in aphid communities and the selection forces driving strain diversification.

While aquatic (blue) and terrestrial (green) food webs are parts of the same landscape, it remains unclear whether they respond similarly to shared environmental gradients. We use empirical community data from hundreds of sites across Switzerland and a synthesis of interaction information in the form of a metaweb to show that inferred blue and green food webs have different structural and ecological properties along elevation and among various land-use types. Specifically, in green food webs, their modular structure increases with elevation and the overlap of consumers’ diet niche decreases, while the opposite pattern is observed in blue food webs. Such differences between blue and green food webs are particularly pronounced in farmland-dominated habitats, indicating that anthropogenic habitat modification modulates the climatic effects on food webs but differently in blue versus green systems. These findings indicate general structural differences between blue and green food webs and suggest their potential divergent future alterations through land-use or climatic changes.