Lakes are expected to experience longer summer stratification and shorter winter mixing due to climate-induced warming. These changes will impact biogeochemical cycles, but how shifts in mixing might influence lake nitrogen removal via denitrification remains unconstrained. Here we used ¹⁵N-tracer assays, molecular techniques and flux measurements to establish the seasonal dynamics of denitrification in a eutrophic lake in Switzerland. We find that denitrification was disproportionately active during the winter mixed regime, potentially driven by a previously unrecognized chitinolytic–denitrifying microbial consortium. Moreover, denitrification was strongly governed by the relative availabilities of particulate organic carbon and nitrate. Leveraging these insights enabled accurate simulation of denitrification in a lake model, revealing that a worst-case climate scenario may shorten the mixing period by ~27 days and reduce denitrification by 8–13%, increasing nitrogen export to downstream ecosystems. We conclude that lake microbial denitrification, and its associated denitrifying consortium, will be weakened by climate change.

Accelerated soil erosion due to land use is a far-reaching problem for today's society. Soil degradation leads to outwash and redistribution of soil organic matter, which not only impacts soils but also adjacent ecosystems by downstream eutrophication of freshwater bodies. Despite the severity of the problem and the ever-growing footprint of agriculture, little is known about the long-term effects of past soil degradation periods on catchment soils and lake systems. This study addresses this question by analyzing a sediment sequence retrieved from Lake Lavijärvi, located near the city of Sortavala, north of Lake Ladoga in the Republic of Karelia, Russia, which has witnessed a period of intensive farming at the beginning of the twentieth century, followed by abandonment of the land post-World War II. We applied a multi-proxy approach using geophysical properties, the geochemical and isotopic composition of the bulk sediment, as well as the distribution of sedimentary leaf waxes and their relative ages (compound-specific radiocarbon dating). With the beginning of industrialization (ca. 1900 CE), we observed severe soil erosion, evident as maxima in magnetic susceptibility and Ti concentrations, as well as high sediment mass accumulation rates. Intensive farming led to a reduction of soil-carbon-residence times (mean transfer time, MTT), indicated by the washout and deposition of pre-aged soil organic carbon. During the same time, the lake became eutrophic and varves were deposited, due to a surplus of soil-derived nutrients. Decreasing MTT after World War II reflected depopulation and land abandonment that resulted in stabilization of catchment soils. Even though soil erosion declined and the trophic status of Lake Lavijärvi returned to more oligotrophic conditions during the post-war period, the lake still suffers from anoxia today. We show that land-use legacies exert a major influence on freshwater ecosystems decades after land-use relaxation.

Methane (CH₄) accumulation in the oxic metalimnion is a common yet poorly resolved feature of deep stratified lakes. In Lake Geneva, lateral transport from the Rhône delta has been suggested but lacks spatial validation. Here, we quantify the role of lateral advection in shaping metalimnetic CH₄ using high-resolution in situ CH₄ measurements, δ¹³C-CH₄ analyses, and a three-dimensional Lagrangian particle-tracking model. Elevated metalimnetic CH₄ (up to 1143 nM) near the Rhône delta becomes isotopically enriched, likely from prolonged residence and partial oxidation during summer stratification. While additional sources may contribute, comparisons of in situ measurements with particle-tracking simulations suggest circulation gyres may distribute deltaic CH₄. Moreover, isotope- and transport-based indicators suggest more coherent coupling in the epilimnion than in the metalimnion. These results demonstrate that horizontal advection can be an important driver of metalimnetic CH₄ and highlight the importance of circulation-driven lateral transport for assessing CH₄ fluxes from large, stratified lakes.

Phytoplankton cells exude a wide array of chemicals in the water column, generating a localized microenvironment known as the phycosphere. Although it is now well accepted that the phycosphere mediates interactions between phytoplankton and bacteria, the chemical gradients around individual phytoplankton cells have never been explicitly measured, and their shape has been classically assumed to be set by ideal diffusion. Here we used Raman microspectroscopy to obtain micrometer-scale measurements of the concentration profile of a phytoplankton metabolite (fucoxanthin) around individual phytoplankton cells of different species, having radii between 2.5 and 60 µm. We found that fucoxanthin concentration decreases more rapidly with distance from the cell than predicted by ideal diffusion, showing that the phycosphere includes compounds whose diffusion is characterized by nonideal effects. We explain this observation using a space-dependent diffusivity model where nonideality arises from viscosity and solubility gradients in the extracellular environment. Our results suggest an onion-structured model of the phycosphere, in which small hydrophilic solutes that obey ideal diffusion generate broad but weak gradients, whereas insoluble compounds are retained within 10 to 20 µm from the phytoplankton cell surface and yield steep gradients of organic matter. These observations, supported by evidence that fucoxanthin can act as an effective chemoattractant for marine bacteria, show the existence of strong and highly localized chemical cues with potentially far-reaching impacts on microbial interactions in aquatic environments. These findings highlight the importance of directly measuring the microscale chemical landscape experienced by marine microbes.

Cryptic pigmentation is a key phenotypic adaptation that helps many benthic invertebrates evade visual predators. However, little is known about whether and how the expression of pigmentation phenotypes that match the habitat background is influenced by the availability of nutritional resources. Here we investigated whether variation in both the background and the nutritive composition of benthic substrates affect the expressed pigmentation of a freshwater isopod, Asellus hilgendorfii. We collected isopods and their predominant substrate from 17 locations across Hokkaido, northern Japan, and quantified substrate background and nutritional composition (total protein, 18 amino acids, and C:N and C:P ratios). We found that variation in isopod pigmentation was better explained by the substrate's nutritive composition than by its background darkness. Specifically, isopods were more pigmented when substrates had intermediate C:P ratios, lower C:N ratios, and a higher proportion of tryptophan – an essential amino acid involved in the isopods' pigmentation pathway. These results are consistent with previous experiments showing that isopods reared under diets with higher protein concentrations developed more pigmentation, advancing our understanding about the environmental sources of phenotypic variation in natural populations. By demonstrating that nutritional constraints may shape the expression of key phenotypic adaptations in natural populations, our study opens new directions for exploring how organisms navigate adaptive landscapes; particularly in those organisms that rely on pigmentation for signaling and camouflage. Finally, we demonstrate how macronutrients, amino acids, and elemental ratios can serve as biotracers in ecological studies of adaptation, offering new opportunities to examine how stoichiometric traits influence phenotypic plasticity and adaptive capacity, especially in detritivorous taxa.

Lakes, ponds, and reservoirs (hereafter: "lakes") are important sources of the greenhouse gases carbon dioxide (CO₂) and methane (CH₄). Emissions of CO₂ and CH₄ from lakes are regulated in part by in-lake processes, including the production and storage of gases in the lower parts of the water column (bottom waters). However, while substantial efforts have been made to improve estimates of greenhouse gas emissions from lakes, limited data on gas concentrations along depth profiles have prevented the incorporation of bottom-water processes in global emission estimates. Here, we present GHG-depths: the largest existing dataset of depth-profile CO₂ and CH₄ measurements worldwide, including 522 lakes across 38 countries and all seven continents. These data include contributions from 45 research teams and 56 published studies, totaling 2558 discrete sampling events. As global change continues to alter biogeochemical cycling in lakes, these data can help improve mechanistic models to better predict greenhouse gas production and emission from lakes worldwide.

The availability of trophic niches is a key driver of biodiversity, promoting adaptive radiation through evolutionary processes. However, most research has focused on how species adapt to trophic niches as adults, largely overlooking the fact that many taxa undergo significant ontogenetic dietary shifts. Here, we address this gap by investigating individual dietary shifts in an incipient adaptive radiation of Arctic charr (Salvelinus alpinus), where distinct piscivorous and planktivorous lacustrine morphs have diverged. Using eye lens isotopes, we reconstructed dietary histories at the individual level, tracing resource use from maternal nutrients to adult diet. Our analyses revealed three key dimensions in which ontogenetic dietary shifts diverge: early-life diets, the stability of dietary transitions, and the degree of plasticity in dietary shifts. These findings suggest that the early phases of adaptive radiation are accompanied by a complete divergence of ontogenetic dietary shifts. We advocate for a more integrated approach to understanding dietary shifts within evolutionary processes and call for further exploration of these patterns across diverse taxa.

Glacier retreat is rapidly transforming landscapes, creating thousands of new lakes that act as natural laboratories of ecological succession. In these newly formed ecosystems, colonizing animals must meet their requirements for essential organic nutrients, such as long-chain polyunsaturated fatty acids (LC-PUFAs). Here, we combined compound-specific stable isotope analyses of amino acids with fatty acid analysis to trace the origins and transfer of organic nutrients to fish (Arctic char) across a glacial-to-lacustrine lake succession in southern Greenland. Through lake succession, primary sources of nutrients shifted, coinciding with a 60% increase in LC-PUFA concentration in individual fish. In early glacial stages, Arctic char appeared to compensate for low LC-PUFA availability through endogenous biosynthesis of docosahexaenoic acid and, when connected to the fjord, by assimilating marine-derived nutrients via egg cannibalism. Overall, our results demonstrate that glacier retreat reshapes not only physical landscapes but also organic nutrient availability, with cascading consequences for animal physiology, ecosystem connectivity, and potentially long-term evolutionary trajectories.

Understanding the mechanisms shaping food chain length (FCL) has long been central to food web ecology. FCL is a key determinant of stability, energy flow efficiency, and biodiversity maintenance, but there is an ongoing debate about its underlying drivers. It is particularly important in meta-ecosystems, where predator trophic position (TP) is influenced by multiple energy channels. In this study, we focused on spiders in riparian ecosystems, which rely on resources linked to distinct energy channels: blue (algal herbivory), green (terrestrial herbivory), and brown (terrestrial detritivory). We applied nitrogen isotope analysis of amino acids to estimate the TP of both spiders and their prey. This method is a powerful tool for determining TP from a single sample and even allows for capturing decomposer trophic steps. However, the TP estimate requires special care for riparian spiders, as spiders show a specific trophic discrimination factor (TDF_Glx-Phe), and that energy channel use can confound the TP estimate. Our detailed food web resolution supports the use of specific parameters for spiders, particularly the low trophic discrimination factor (TDF_Glx-Phe ~ 2‰), and raises caution about the importance of estimating resource use of predators to estimate their TP. We show that the primary factor driving variation in spider TP is the energy channel they utilize, from blue (TP ~ 2.9) to green (TP ~ 3.6) to brown (TP ~ 4.1). This increase was largely due to prey omnivory in green channels, and microbial and fungal decomposers serving as an initial trophic step between litter and invertebrate detritivores in brown channels. We propose that this pattern is likely influenced by differences in basal nutritional quality, which increases from brown (low) to green (medium) and to blue (high) sources. This suggests that shifts in energy channels within meta-ecosystems in the course of global change (e.g., climate warming, eutrophication and land-use change) may significantly impact FCL, with significant consequences for trophic interactions, nutrient fluxes, and biomagnification processes.

Plant wax hydrogen isotopes (δ²H) preserved in lake sediments provide valuable insights into past climatic changes. However, lake catchments often experience local shifts in vegetation type that can yield distinct isotopic signatures in the sediments, potentially obscuring hydroclimatic signals. Here, we compile regional plant wax data and test different approaches to correct for the impact of changes in vegetation type over time to isolate precipitation δ²H values (δ²H_prc) since the Younger Dryas (12.9–11.7 ka) from a sediment record from Rotsee (central Switzerland). Our method intercomparison shows that n-alkane relative abundances produced the most accurate δ²H_prc estimates, agreeing with an independent speleothem fluid-inclusion δ²H record from Milandre Cave. This indicates that sedimentary plant wax δ²H values represent a vegetation-weighted community signal. Precipitation was ²H-depleted during the Younger Dryas (∼−75‰), and then δ²H_prc values increased sharply into the Holocene. During the early Holocene (∼10 ka), δ²H_prc values of ∼−55‰ were reached, consistent with maximum summer insolation, followed by a gradual long-term decline toward the present, reflecting Neoglacial cooling and consistent with modern δ²H_prc values (∼−67‰). Importantly, while plant wax δ²H values declined sharply due to deforestation beginning in the Roman period, this impact is effectively corrected for by using the relative abundance of n-alkanes. These findings underscore the need for site-specific vegetation corrections to produce robust hydroclimate reconstructions from plant-wax isotopes, especially in lakes with small catchments, thereby enhancing comparability of sedimentary records with climate models and deepening our understanding of past climate–vegetation–human interactions.

We present a data set of trace gas (TG; CH₄, N₂O and H₂S) concentrations and associated hydrochemical parameters (temperature, EC, pH, ORP, TOC, DOC, HCO₃^-, Cl^-, SO42−, NO₃^-, δ¹³C_DIC) in the water columns of Polish inland freshwater lakes. This data set acts as the first comprehensive source of information on the distribution of TG in lakes of central-eastern Europe. Despite the fact that this region displays relatively high limnicity, it is considerably understudied with regard to the occurrence of TG in lakes. This data set was created to fulfill this gap in biogeochemical knowledge and to provide data which can improve assessing and modelling of TG emissions from aquatic systems. The observations were collected monthly between July 2019 and September 2022 from different water depths in representative sites of three lakes in central (L. Łódzko-Dymaczewskie and L. Dębno) and western (L. Trześniowskie) Poland. The lakes showed different trophic conditions, depths as well as catchment characteristics. The database involves 358 records of CH₄/N₂O and 507 values of H₂S.

Bacterial endosymbionts of the family Candidatus Azoamicaceae obligately associate with anaerobic ciliates belonging to the class Plagiopylea. The symbionts' unique role for their host involves anaerobic respiration of nitrate and generation of adenosine triphosphate (ATP), analogous to the role of mitochondria in aerobic eukaryotes. As this symbiosis remains so far uncultured, insights into its functioning have been mainly inferred from environmental metagenomes. Here, we investigated the distribution and environmental role of this symbiosis in the anoxic basins of two freshwater lakes, Zug and Lugano (Switzerland), over a course of several years. We found that the environmental niche of the ciliate host is defined by the combined effects of sulfide, oxygen, and nitrate, the latter of which is essential for the symbiont's respiratory function. Moreover, the distribution and abundance of ciliates with denitrifying endosymbionts in the water column suggest that they may substantially contribute to nitrate consumption in Lake Zug. Our microscopic analyses further demonstrated a coordinated division of the Ca. Azoamicus ciliaticola symbionts and their ciliate hosts, implying a vertical inheritance of denitrifying symbionts. These observations offer new insights into the evolution of ciliates with denitrifying endosymbionts and their ecological role in oxygen-depleted lake waters.

Methane (CH₄) production in lacustrine sediments is known to be spatially heterogeneous, varying both horizontally and vertically. Porewater methane concentrations often differ between locations within a lake and with depth within the sediment profile. The drivers of this heterogeneity are often not well understood. Here, we explore methane cycling in the sediments of Lake Constance, the 2^nd largest perialpine lake in Europe, with well-documented sedimentary methane production. We use a novel radiocarbon (¹⁴C) based approach to determine the origin and age of buried carbon pools, as well as that of CO₂ and CH₄ in sediment porewaters at two locations with contrasting sediment supply, dominated by either allochthonous or autochthonous inputs. We show that porewater CO₂ is predominantly derived from inorganic carbon inputs, whereas CH₄ is produced from a mixture of CO₂-derived and organic carbon-derived substrates. At the allochthonous-dominated location, a larger fraction of the CH₄ seemed to be produced from organic substrates than in the autochthonous location, where the ¹⁴C signals of CO₂ and CH₄ were more comparable to one another. Furthermore, ¹⁴C contents of lignin-derived phenols and fatty acids, as proxies for mineral-associated and free organic matter respectively, suggest that the "recalcitrant" carbon pool contributes to the methane production in centennial-aged sediments. Microbial community data further suggest active methane production in these old sediments, challenging concepts of permanent organic carbon burial in deeper sediment layers and on the recalcitrance of the buried material.

Reliable paleotemperature proxies are essential for reconstructing past climate. To refine interpretation of the MBT'_5ME index, based on bacterial brGDGT lipids, a year-long study was conducted in Rotsee, Switzerland, a seasonally stratified lake with a 4–21°C temperature range. Suspended particulate matter was collected monthly from the epilimnion and the hypolimnion, complemented by surface sediments and surrounding soils. Both intact polar (IPL) and core lipid (CL) brGDGTs were analyzed alongside 16S rRNA gene data to disentangle environmental (temperature, dissolved oxygen, and pH) and biological (microbial community) controls on brGDGT compositions. In the stratified epilimnion, MBT'_5ME values showed a muted response to summer warming (r = 0.59, p < 0.1), whereas the isomer ratio (IR) correlated more strongly with temperature (r = 0.68, p < 0.05). MBT'_5ME and IR were also significantly correlated (r = 0.93, p < 0.0001), providing a novel diagnostic tool to identify sedimentary GDGTs derived from surface waters. In the seasonally anoxic hypolimnion, MBT'_5ME correlated with pH (r = 0.79, p < 0.01) and IR with dissolved oxygen (r = −0.65 and p < 0.05). Microbial DNA analysis revealed low Acidobacterial abundances (<0.4% of reads), suggesting MBT'_5ME patterns are not solely driven by this phylum. Instead, hypolimnion IPL-brGDGTs correlated with gene abundance of several other bacteria, indicating broader microbial contributions. Surface sediments reflected an integrated water column signal, while also showing evidence for additional in situ IPL-brGDGT production. Overall, findings demonstrate that stratification onset drives MBT'_5ME variability, while epilimnion temperature exerts stronger control on IR, refining their application in paleoclimate proxies.

To assess the long-term impact of climate change and human influence on lakes and their sedimentary carbon storage, paleo-environmental approaches using well-dated lake sediment cores can be employed. Here, we reconstruct carbon mass accumulation rates for organic and inorganic carbon since 13 ka BP in Rotsee, a perialpine lake near the Swiss Alps, using a 12-m sediment core. A multiproxy approach (XRF, carbon and nitrogen isotopes, organic macromolecule chemical compositions, aDNA) was used to explore changes in the lake system that affect sedimentary carbon storage. The Early Holocene (11.8–7 cal ka BP) was characterized by a mixed phytoplankton and watershed-derived provenance of organic matter, and the deposition of inorganic and organic sedimentary carbon. Warming during the Holocene Thermal Maximum (9.8–8.8 cal ka BP) increased sedimentary carbon storage. In the Mid- to Late Holocene (7–1 cal ka BP), the sedimentary record indicates an increased influx of allochthonous, vascular plant-derived organic matter, and low production or conservation of phytoplankton-derived carbon. Organic carbon storage increased, while inorganic carbon became negligible. Larger deforestation events, potentially during Neolithic times (around 4 ka BP), but especially during Roman times (2 ka BP), coincided with further increased organic carbon MARs. Recent sediments, influenced by eutrophication in the last century, show higher carbon accumulation rates compared to earlier Holocene periods. Rotsee serves as a case study of how climate warming and human land use changes have influenced lake development and sedimentary carbon6 storage, with broader implications for understanding carbon dynamics in high altitude lakes and their future carbon balance.

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.

The Arctic cryosphere is the epicentre of acute global change impact, with abrupt warming and amplification driving rapid sea ice decline and irreversible glacial ice loss. A key challenge is understanding how the cryosphere meltdown will impact Arctic marine carbon cycles and ecosystems. Here, we use organic geochemical biomarkers to trace the contribution of different planktonic groups to organic carbon in Arctic fjord sediments (Kongsfjorden, Svalbard) during past warmer and colder (than present) climate states. We show that phytoplankton community structures changed abruptly with variable sea ice cover and glacial ice loss. Our results imply that future deglaciation of Svalbard fjords will likely increase primary productivity in a “blue” (summer ice-free) scenario; however, the potential for fjords to serve as hotspots of marine organic carbon burial will likely be constrained due to warmer, stratified waters and reduced meltwater-induced supply of critical nutrients.

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.

The primary production of fjords across the Arctic and Subarctic is undergoing significant transformations due to the climatically driven retreat of glaciers and ice sheets. However, the implications of these changes for upper trophic levels remain largely unknown. In this study, we employ both bulk and compound-specific stable isotope analyses to investigate how shifts at the base of fjord food webs impact the carbon and energy sources of consumers. Focusing on two rapidly changing fjords in Southern Greenland, we used the migratory Arctic char as an indicator species, sampling populations along environmental gradients within the fjords, building upon the assumption that char populations feed primarily close to their natal stream, thereby integrating a dietary gradient. Our analysis of bulk stable isotopes in Arctic char tissue confirmed this premise, revealing a consistent change in resource use from the outer to the inner fjord, which nonetheless served as preferred feeding grounds. Essential amino acid analysis further indicated shifts in carbon and nitrogen sources, consistent with changes in nutrient use near glacier inputs characterized by low turbidity and high iron levels. Notably, these changes in the source of primary production were associated with shifts in trophic positions and the transfer of polyunsaturated fatty acids, with Arctic char in glacier-influenced inner fjords feeding at lower trophic level (size-corrected) and accumulating higher levels of high-quality docosahexaenoic acid (DHA). These findings highlight the usefulness of new analytical tools in revealing that glacial retreat can substantially alter food web dynamics, enhancing both carbon flow and the nutritional quality of fish in fjord ecosystems. The two Southern Greenland fjords studied could represent the future of other fjords, where retreating glaciers become land-terminating and glacial inputs decrease. Our study underscores the critical role of glacier dynamics in affecting high-level consumers, such as salmonids, with implications for fjords globally.

Microbial methane production is a key reaction involved in the terminal step of anaerobic degradation of organic matter. The energy substrates of methane-producing microorganisms are largely generated during the breakdown of larger organic molecules by fermentative microorganisms, wherein the products of fermentation may vary with the chemical compositions of these larger molecules. Due to differences in energy substrates among methane-producing microorganisms, it is thus possible that organic matter compositional variations select for different communities of methane producers. Here, we investigate the sources and compositions of OC in sediments of Lake Geneva and how both are potentially linked to methane production. Differences in dominant long-chain fatty acid abundances and carbon isotopic compositions suggest the predominance of diagenetically altered phytoplankton-derived OC at a profundal site (PS) and temporally highly variable sources of both aquatic and terrestrial OC in a deltaic location. Despite these differences, radiotracer-based methanogenesis rate measurements and stable isotopic signatures of methane indicate significant methane production that is dominated by CO₂ reduction (>95 % of total methanogenesis) in both locations. Matching this interpretation, members of well-known CO₂-reducing Methanoregula sp. dominate both sites. Similarly, no clear effect of OC source on methane production rates was evident. Our data demonstrate that OC of diverse sources and diagenetic states supports microbial methane production, but the data do not indicate a clear impact of the OC source on the dominant methanogenic pathway or the community structure of methanogenic microorganisms in lacustrine sediments.

Branched glycerol dialkyl glycerol tetraethers (brGDGTs) are common in lake sediments, where they are frequently employed to infer mean annual air temperatures (MAAT) or air temperatures of months above freezing (MAF) using the MBT'_5Me lipid paleothermometer. The reliable reconstruction of such temperatures, however, requires robust calibration functions. Here, we investigated brGDGT distributions in surface sediments from 41 freshwater lakes located along an altitudinal gradient across the Alps (Central Europe) and spanning a MAAT range from 1.3 to 12.9 °C. Linear regression analysis demonstrates that fractional abundances of brGDGTs are strongly correlated with MAAT and MAF allowing to establish regional MBT'_5Me-based transfer functions: MAAT (°C) = −2.19 + 31.91 × MBT'_5Me (r² = 0.72; RMSE = 1.51 °C) and MAF (°C) = 4.81 + 15.64 × MBT'_5Me (r² = 0.64, RMSE = 0.92 °C). Stepwise forward selection yielded the following, alternate temperature calibrations: MAAT (°C) = 7.11 + 67.66 × Ib – 13.54 × IIIa (r² = 0.72; RMSE = 1.47 °C) and MAF (°C) = 5.19 + 16.22 × Ia (r² = 0.66; RMSE = 0.98 °C). Our results demonstrate that the above calibration functions allow precise temperature reconstructions using lacustrine sediment records. However, our data also show that high-altitude lakes are more prone to warm bias and that lakes characterized by comparatively high abundances of 6-methyl brGDGTs show aberrant behaviors with temperature offsets up to ∼7 °C. Determining the IR_6Me, as an independent control complementary to the MBT'_5Me, is thus essential to validate the robustness of brGDGT-based temperature reconstructions of past climates. A cut-off value of 0.50 for the IR_6Me is here proposed, after which MBT'_5Me-reconstructed MAATs from lacustrine archives should be regarded as unreliable.

The extent of littoral influence on lake gas dynamics remains debated in the aquatic science community due to the lack of direct quantification of lateral gas transport. The prevalent assumption of diffusive horizontal transport in gas budgets fails to explain anomalies observed in pelagic gas concentrations. Here, we demonstrate through high-frequency measurements in a eutrophic lake that daily convective horizontal circulation generates littoral-pelagic advective gas fluxes one order of magnitude larger than typical horizontal fluxes used in gas budgets. These lateral fluxes are sufficient to redistribute gases at the basin-scale and generate concentration anomalies reported in other lakes. Our observations also contrast the hypothesis of pure, nocturnal littoral-to-pelagic exchange by showing that convective circulation transports gases such as oxygen and methane toward both the pelagic and littoral zones during the daytime. This study challenges the traditional pelagic-centered models of aquatic systems by showing that convective circulation represents a fundamental lateral transport mechanism to be integrated into gas budgets.

Marine sediments are one of the largest organic carbon (OC) sinks on Earth. Yet, major knowledge gaps remain in our understanding of sedimentary OC cycling, particularly regarding temperature-induced alteration processes of OC from different sources. Here, we investigate OC-rich sediments of Guaymas Basin (Gulf of California) across two hydrothermal areas, one with only conductive geothermal heating and the other additionally experiencing seepage of hydrocarbon-rich fluids from deeper layers. We use Pyrolysis-Gas Chromatography/Mass Spectrometry (Py-GC/MS) to investigate diagenetic OC changes and show that cold control sites in both hydrothermal areas are dominated by similar contributions of lipid-derived compounds, nitrogenous (likely protein-derived) compounds, carbohydrates, and polyaromatic hydrocarbons (PAHs). These OC compound groups are largely derived from phytoplankton detritus from overlying water. Conductively heated sediments, which reach in situ temperatures of ∼ 80 °C, have similar general OC compositions and contents to these cold sites, but show evidence of diagenetic modifications of individual carbohydrate groups in deeper layers. By contrast, strong decreases in carbohydrate and nitrogenous compound abundances at the seep sites indicate that these compound groups are not only modified but also selectively degraded at the higher temperatures (>80 °C) of these sites. Increases in pyrolysis products of PAHs, prist-1-ene, and alkanes with depth, moreover, show that import of OC by deep hydrothermal fluids contributes significantly to sedimentary OC pools mainly in deeper layers of these sites. Our study provides the first comprehensive analysis of major OC compound groups in Guaymas Basin sediment and indicates that the supply of OC by hydrothermal fluid flow only has minor impacts on particulate organic matter compositions at the seafloor, even at active seep sites. We furthermore show that temperatures up to ∼ 80 °C already result in thermochemical modifications of organic matter (OM) that are potentially linked to the onset of kerogen formation. The sequence and time scales of chemical modifications and activations in relation to temperature are an important subject for future investigations.

In large and stratified lakes, substantial methane stocks are often observed within the metalimnion. The origin of the methane (CH₄) accumulated in the metalimnion during stratification, which can sustain significant emissions during convective mixing, is still widely debated. While commonly attributed to the transport of methane produced anaerobically ex situ, recent evidence suggests that oxic in situ methane production could also contribute to metalimnetic methane peaks. Here, we assessed the origin, that is, pelagic CH₄ production or transport of sublittoral CH₄ through the interflow, of metalimnetic methane in Lake Geneva, the largest lake in Western Europe. Microbial diversity data do not support the hypothesis of oxic methane production in the metalimnion. In contrast, both spatial and temporal surveys of methane show that maxima occur at depths and sites most affected by the Rhône River inflow. Methane δ¹³C values point to an anaerobic sublittoral methane source, within a biogeochemical hotspot close to the river delta region, and an efficient transport across several kilometers in a vertically well-constrained metalimnion. Our current findings emphasize the indirect role of river interflows for the long-range transport of CH₄ produced in sediment biogeochemical hotspots, even for large lakes where sublittoral habitats represent a fairly limited fraction of the lake volume.

Emissions of microbially produced methane (CH₄) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH₄ production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH₄ producing Archaea and methanogenesis pathways across time–resolved sedimentary records of five Swiss lakes with well–characterized trophic histories. Despite higher CH₄ concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO₂-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO₂-reduction with hydrogen (H₂) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO₂-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO₂-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H₂ as an electron shuttle.

In a warming world, the input of glacier meltwater to inland water ecosystems is predicted to change, potentially affecting their productivity. Meta-ecosystem theory, which posits that the nutrient availability in the recipient ecosystem can determine the extent of cross-ecosystem boundary utilization, can be useful for studying landscape-scale influences of glacier meltwater on inland waters. Here, we investigate how the input of glacier meltwater in a river system in Southern Greenland influences the utilization of marine subsidies in freshwater fish. Our study system comprised four sites, with controls for glacial meltwater and marine subsidies, harboring a partially migrating population of arctic char, meaning that some individuals migrate to the ocean and others remain in freshwaters, and two fully resident populations as a freshwater reference. We assessed the incorporation of marine carbon in freshwater resident char using both bulk and amino acid stable isotope analysis of muscle tissue. In the population with partial migration, marine subsidies were a significant resource for resident char individuals, and estimates of trophic position suggest that egg cannibalism is an important mechanism underlying the assimilation of these marine subsidies. In proglacial streams, namely those with high glacial meltwater, the total dependence on marine subsidies increased and reached 83% because char become cannibals at smaller sizes. In the configuration of our focal meta-ecosystem, our results suggest that the importance of marine subsidies to freshwater fish strengthens within increasing meltwater flux from upstream glaciers.

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.

Food webs are crucial for understanding how carbon and nutrients flow within ecosystems, influencing sustainability and carbon fluxes. Ecosystems are interconnected, exchanging energy, nutrients, and organic matter—a concept captured by meta-ecosystem theory. Consequently, changes in one ecosystem can have cascading effects on others. This interconnectedness becomes increasingly important as global change drives significant alterations in food webs. Therefore, there is a pressing need to characterize food web functioning in complex settings, such as meta-ecosystems, and to study how these webs are impacted by global change. [...]

Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d⁻¹. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.

The factors that govern the geographical distribution of nitrogen fixation are fundamental to providing accurate nitrogen budgets in aquatic environments. Model-based insights have demonstrated that regional hydrodynamics strongly impact nitrogen fixation. However, the mechanisms establishing this physical-biological coupling have yet to be constrained in field surveys. Here, we examine the distribution of nitrogen fixation in Lake Tanganyika – a model system with well-defined hydrodynamic regimes. We report that nitrogen fixation is five times higher under stratified than under upwelling conditions. Under stratified conditions, the limited resupply of inorganic nitrogen to surface waters, combined with greater light penetration, promotes the activity of bloom-forming photoautotrophic diazotrophs. In contrast, upwelling conditions support predominantly heterotrophic diazotrophs, which are uniquely suited to chemotactic foraging in a more dynamic nutrient landscape. We suggest that these hydrodynamic regimes (stratification versus mixing) play an important role in governing both the rates and the mode of nitrogen fixation.

Lake Tanganyika’s pelagic fish sustain the second largest inland fishery in Africa and are under pressure from heavy fishing and global warming related increases in stratification. The strength of water column stratification varies regionally, with a more stratified north and an upwelling-driven, biologically more productive south. Only little is known about whether such regional hydrodynamic regimes induce ecological or genetic differences among populations of highly mobile, pelagic fish inhabiting these different areas. Here, we examine whether the regional contrasts leave distinct isotopic imprints in the pelagic fish of Lake Tanganyika, which may reveal differences in diet or lipid content. We conducted two lake-wide campaigns during different seasons and collected physical, nutrient, chlorophyll, phytoplankton and zooplankton data. Additionally, we analyzed the pelagic fish–the clupeids Stolothrissa tanganicae, Limnothrissa miodon and four Lates species–for their isotopic and elemental carbon (C) and nitrogen (N) compositions. The δ¹³C values were significantly higher in the productive south after the upwelling/mixing period across all trophic levels, implying that the fish have regional foraging grounds, and thus record these latitudinal isotope gradients. By combining our isotope data with previous genetic results showing little geographic structure, we demonstrate that the fish reside in a region for a season or longer. Between specimens from the north and south we found no strong evidence for varying trophic levels or lipid contents, based on their bulk δ¹⁵N and C:N ratios. We suggest that the development of regional trophic or physiological differences may be inhibited by the lake-wide gene flow on the long term. Overall, our findings show that the pelagic fish species, despite not showing evidence for genetic structure at the basin scale, form regional stocks at the seasonal timescales. This implies that sustainable management strategies may consider adopting regional fishing quotas.

Carbohydrates are a ubiquitous constituent of organisms and contribute significantly to sedimentary organic carbon pools. Yet, the factors that control the degradation and long-term preservation of sedimentary carbohydrates are not well understood. Here, we investigate carbohydrate pool sizes and chemical compositions in high-altitude, meromictic Lake Cadagno (Switzerland) over a 13,500-year-old sedimentary succession that has recorded past changes from oxic to anoxic conditions and consists mostly of intercalations of lacustrine sediments and terrestrial-derived sediments. Analyses of the organic matter chemical composition by pyrolysis gas chromatography/mass spectrometry (Py-GC/MS) show that carbohydrates are selectively preserved over other organic matter constituents over time. The carbohydrate pyrolysis products levosugars (potentially cellulose-derived) and (alkyl)furans and furanones (potentially pectin-derived) dominate both lacustrine and terrestrially derived sediment layers, suggesting aquatic and terrestrial-derived sources of these compounds. Carbohydrate monomer analyses indicate galactose and glucose as dominant monomers and show no clear differences between aquatic and terrestrial organic matter. No clear impacts of past changes in redox conditions on carbohydrate compositions were observed. Our study shows that carbohydrates are a major contributor to sedimentary organic carbon burial in Lake Cadagno and indicates the effective preservation of both aquatic and terrestrial derived carbohydrates over millennia in lake sediments.

During the Pleistocene, Earth's climate changed dramatically. The mid-Pleistocene transition (MPT; ~1.3-0.7 million years (Ma)) featured an important ice volume increase at both poles. The evolution of large Arctic ice sheets caused the sequestration of methane as free gas and hydrates in subseabed sediments. Ice volume changes, associated with variable pressures and temperatures, perturbed those giant reservoirs, causing methane leakages. Here, we present borehole data from the Arctic-Atlantic gateway region, providing foraminiferal stable carbon isotope and source-specific biomarker evidence that reveals three main seafloor leakage episodes that occurred prior to and across the mid-Pleistocene transition. By combining borehole data with hydrate stability modelling, we propose that tectonic stress changes associated with large ice volume early build-up and wastage during the mid-Pleistocene controlled episodic methane leakages from subsurface reservoirs. Our data indicate methane release, showing a potential scenario for vast Arctic areas storing methane that are now affected by ongoing ice volume decrease.

1. Lakes are recipients of allochthonous organic matter and nutrients. However, the importance of these subsidies for food webs and how they vary with lake trophic status remains unclear, especially for large lakes.
2. We assessed the source and fate of organic matter and nutrients in seven perialpine lakes across a gradient of trophic status. We measured carbon and nitrogen stable isotopes of amino acids of lake-residing Atlantic trout, Salmo trutta, to determine the source of primary production (i.e., how carbon is fixed in the ecosystem) and how it is transferred through food webs, respectively. Based on essential amino acid carbon fingerprinting, we estimated the probability of organic carbon originating from autochthonous (algal), allochthonous (terrestrial plant), and recycled (bacterial) sources. In addition, we used amino acid δ¹⁵N to track how this primary production is transferred to consumers in general, and by using different trophic amino acids (glutamic acid and alanine), identify the trophic pathways involving either metazoan or protozoans.
3. We found a high likelihood of autochthonous origin of organic carbon (86 ± 9%) in trout that contrasted with allochthonous origins of particulate organic matter and some sediments. We showed that those estimates are good proxies of source reliance. Our results also highlighted the importance of bacterial origin of organic carbon in fish (12%). The likely autochthonous origin of this carbon was supported by trophic markers (Ala δ¹⁵N) that suggest the role of protists in transferring recycled organic carbon up the food web. While the sources of nitrogen sustaining food webs varied among lakes, we found a conserved carbon fingerprinting of fish. Overall, this suggests an uncoupling between the source of nutrients and organic carbon in large perialpine lakes.
4. Across a wide range of trophic status (c. 2 orders of magnitude range of phosphorus concentration), several lines of evidence suggested that perialpine lake food webs shared a common reliance on autochthonous and bacterial production.
5. Our study is the first to quantify the dependence on allochthonous organic carbon in lake food webs based on new amino acid stable isotope markers (carbon fingerprinting and Ala δ¹⁵N) and shows promise for estimating the source of carbon fixation in ecosystems. Our results support previous suggestions that terrestrial organic carbon is a relatively minor source for aquatic consumers despite contributing to the pool of organic matter, and more importantly, its contribution does not vary substantially with trophic status in perialpine lakes.

For over 50 years Lake Licheńskie (LLi), central Poland, has been involved in the cooling system of two power plants (PP). Owing to the discharge of cooling waters the lake was prone to considerable environmental changes which involved its thermal structure, mixing regime and water parameters. In this study we investigated how the man-made transformations affected greenhouse gas emissions (GHG; CH₄ and N₂O) from the lake. The GHG emissions in Lake Licheńskie were monitored at the deepest site from December 2014 to November 2015 and between March 2022 and February 2023. The values obtained were compared to reference lakes encompassing 10 natural and undisturbed inland and coastal lakes in Poland. Our results revealed that LLi was a net source of CH₄ and N₂O to the atmosphere but the fluxes were low. The mean annual diffusive fluxes were 0.21–0.38 mmol·m⁻² d⁻¹ for CH₄ and 4.90–7.40 μmol·m⁻² d⁻¹ for N₂O. The CH₄ emissions were significantly lower than in most of reference lakes, while the N₂O emissions were comparable. Therefore, the human intervention resulted in reduction of CH₄ release from LLi but it had minor effect on the N₂O. The most likely reason for the low direct fluxes of GHGs from the surface waters was the high flushing rate of the lake and export of dissolved gases to adjacent lakes and canals. Hence, the overall emission from the connected lake and canal system was not mitigated by the man-made changes to the lake system.

Agriculture relies heavily on the use of plastic mulch films, which increase crop yields and can lower water demands. In recent years, soil-biodegradable mulch films have been marketed to replace the non-biodegradable, conventional polyethylene-based mulch films. These biodegradable mulch films are designed to be ploughed into the soil after use to be biodegraded in situ by soil microorganisms. However, research has shown that part of the mulch film material may be transported from the fields to neighboring environments, including aquatic ecosystems. Research on potential biodegradation of soil-biodegradable plastics in freshwater habitats is lacking. Here, we investigated the mineralization of soil-biodegradable agricultural mulch films in freshwater lake sediments of Lake Lucerne, Switzerland. Two types of commercial soil-biodegradable mulch films were incubated within lake sediment cores, along with traditional polyethylene (PE) plastic, and the production of CO₂ and CH₄ was followed over time relative to non-plastic-containing control sediments. After the 40-week incubation period, the films were visually intact and showed no signs of mineralization. Gas analyses showed no additional production of either CO₂ or CH₄ in the degradable mulch film incubations, compared to the control or PE plastic incubations. We conclude that these two used soil-biodegradable mulch films have a low biodegradability in lake sediments, likely reflecting that the microbial community structure in the lake sediment lacks active microbial degraders. Our results highlight the importance of preventing transport of soil-biodegradable mulch films from agricultural soils to surrounding aquatic environments.

The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N₂O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions.

Although lake sediments are globally important organic carbon sinks and therefore important habitats for deep microbial life, the deep lacustrine biosphere has thus far been little studied compared to its marine counterpart. To investigate the impact of the underexplored deep lacustrine biosphere on the sediment geochemical environment and vice versa, we performed a comprehensive microbiological and geochemical characterization of a sedimentary sequence from Lake Cadagno covering its entire environmental history since formation following glacial retreat. We found that both geochemical gradients and microbial community shifts across the ∼13.5 kyr subsurface sedimentary record reflect redox changes in the lake, going from oxic to anoxic and sulfidic. Most microbial activity occurs within the top 20 cm of sediment, where millimolar sulfate concentrations diffusing in from the bottom water are almost completely consumed. In deeper sediment layers, organic carbon remineralization is much slower but microorganisms nonetheless subsist on fermentation, sulfur cycling, metal reduction, and methanogenesis. The most surprising finding was the presence of a deep, oxidizing groundwater source. This water source generates an inverse redox gradient at the bottom of the sedimentary sequence and could contribute to the remineralization of organic matter sequestered in the energy-limited deep subsurface.

Even though lake sediments are globally important organic carbon (OC) sinks, the controls on long-term OC storage in these sediments are unclear. Using a multiproxy approach, we investigate changes in diatom, green algae, and vascular plant biomolecules in sedimentary records from the past centuries across five temperate lakes with different trophic histories. Despite past increases in the input and burial of OC in sediments of eutrophic lakes, biomolecule quantities in sediments of all lakes are primarily controlled by postburial microbial degradation over the time scales studied. We, moreover, observe major differences in biomolecule degradation patterns across diatoms, green algae, and vascular plants. Degradation rates of labile diatom DNA exceed those of chemically more resistant diatom lipids, suggesting that chemical reactivity mainly controls diatom biomolecule degradation rates in the lakes studied. By contrast, degradation rates of green algal and vascular plant DNA are significantly lower than those of diatom DNA, and in a similar range as corresponding, much less reactive lipid biomarkers and structural macromolecules, including lignin. We propose that physical shielding by degradation-resistant cell wall components, such as algaenan in green algae and lignin in vascular plants, contributes to the long-term preservation of labile biomolecules in both groups and significantly influences the long-term burial of OC in lake sediments.

Long-chain polyunsaturated fatty acids are biologically important lipids that are unevenly distributed between and throughout environments. This heterogeneity can affect the evolution of metabolic processes, as populations adapt to the resource landscape that they encounter. Here, we compare fatty acid phenotypes of stickleback over two time scales of evolutionary divergence: between two lineages with different metabolic capacities for fatty acid synthesis (i.e. different copy number of the fatty acid desaturase gene; FADS2) that independently colonized European freshwaters during the Pleistocene and Holocene; and between two ecotypes within each lineage that have diverged more recently (~150 years) in different habitats (i.e. lake and stream). We measured fatty acid profiles of wild-caught and lab-reared fish for each lineage and ecotype combination after rearing lab fish on a diet deficient in omega-3 long-chain polyunsaturated fatty acids. Since these lineages hybridize in nature, we also measured profiles of lab-reared hybrids and backcrosses raised on the same deficient diet. Wild fish showed strong compositional differences in fatty acids between habitats, lineages and sexes. Common garden fish had generally lower polyunsaturated fatty acid levels than wild fish, and females had lower omega-6:omega-3 than males. Fish from the lineage with fewer FADS2 copies also had lower levels of docosahexaenoic acid. Overall, we document divergence in fatty acid phenotypes between stickleback lineages with different histories of freshwater colonization, and between ecotypes in the early stages of adaptive population divergence.

Eutrophication is expected to increase methane production in freshwater sediments worldwide over the coming decades. Methane-oxidizing bacteria (MOB) consume a significant fraction of this sedimentary methane, but the factors that control their distributions and activities are not understood. By combining genetic approaches (pmoA, 16S rRNA gene, metagenomics) with geochemical and sedimentological analyses, we investigate the role of trophic state, electron acceptors, oxygen (O₂) and methane fluxes, and potential methylotrophic partner organisms in driving the distributions, abundances, and community compositions of MOB across five lakes in central Switzerland. Although methane fluxes were highest in the eutrophic lakes, methanotrophic abundances peaked in oxic and anoxic sediments of an oligotrophic lake. In all lakes, Type I gammaproteobacterial Methylococcaceae dominated oxic and suboxic bottom water and surface sediments, showing strong correlations with abundances of putatively methylotrophic Methylophilaceae, whereas Type II alphaproteobacterial Methylocystaceae increased in deeper, anoxic sediment layers. Methanotrophic bacteria belonging to the NC10 phylum were predominantly detected within denitrifying sediment of the oligotrophic lake, matching their presumed nitrite-dependent lifestyle. While dominant MOB taxa at the genus-level follow vertical distributions of different aerobic and anaerobic respiration reactions, trophic state at the time of sediment deposition was the best predictor of MOB community structure at the operational taxonomic unit (OTU) level. Elevated methane fluxes combined with low MOB abundances in surface sediments of eutrophic lakes, moreover, support the notion that in eutrophic lakes a major portion of sedimentary methane bypasses the biological methane filter and escapes to overlying water.

In marine and freshwater oxygen-deficient zones, the remineralization of sinking organic matter from the photic zone is central to driving nitrogen loss. Deep blooms of photosynthetic bacteria, which form the suboxic/anoxic chlorophyll maximum (ACM), widespread in aquatic ecosystems, may also contribute to the local input of organic matter. Yet, the influence of the ACM on nitrogen and carbon cycling remains poorly understood. Using a suite of stable isotope tracer experiments, we examined the transformation of nitrogen and carbon under an ACM (comprising of Chlorobiaceae and Synechococcales) and a non-ACM scenario in the anoxic zone of Lake Tanganyika. We find that the ACM hosts a tight coupling of photo/litho-autotrophic and heterotrophic processes. In particular, the ACM was a hotspot of organic matter remineralization that controlled an important supply of ammonium driving a nitrification-anammox coupling, and thereby played a key role in regulating nitrogen loss in the oxygen-deficient zone.

The sulfur cycle is an important, although understudied facet of today's modern oxygen minimum zones (OMZs). Sulfur cycling is most active in highly productive coastal OMZs where sulfide-rich sediments interact with the overlying water column, forming a tightly coupled benthic-pelagic sulfur cycle. In such productive coastal systems, highly eutrophic and anoxic conditions can result in the benthic release of sulfide leading to an intensification of OMZ-shelf biogeochemistry. Active blooms involving a succession of sulfide-oxidizing bacteria detoxify sulfide and reduce nitrate to N₂, while generating nitrite and ammonium that augment anammox and nitrification. Furthermore, the abiotic interactions of sulfide with trace metals may have the potential to moderate nitrous oxide emissions. While sulfide/sulfur accumulation events were previously considered to be rare, new evidence indicates that events can develop in OMZ shelf waters over prolonged periods of anoxia. The prevalence of these events has ramifications for nitrogen loss and greenhouse gas emissions, including other linked cycles involving carbon and phosphorous. Sulfur-based metabolisms and activity also extend into the offshore OMZ as a result of particle microniches and lateral transport processes. Moreover, OMZ waters ubiquitously host a community of organosulfur-based heterotrophs that ostensibly moderate the turnover of organic sulfur, offering an exciting avenue for future research. Our synthesis highlights the widespread distribution and multifaceted nature of the sulfur cycle in oceanic OMZs.

Background Lake Tanganyika is the longest (673 km) and second deepest (1,470 m) freshwater lake in the world. The lake is part of the East African Rift and its pelagic food web sustains the second largest inland fishery in Africa. The fish stocks are under dual pressure through heavy fishing and a long-term decline in biological productivity, caused by increasing water column stratification due to climate change.
The productivity of the pelagic ecosystem depends on the internal nutrient cycling, which is governed by the limnological cycle: Lake Tanganyika is heavily stratified in the rainy season (October-April) with nutrient-depleted surface waters; in the dry season (May-September), southerly trade winds lead to an upwelling and convective mixing of nutrientrich water masses in the south basin, promoting high biological productivity, whereas the north and central basins maintain a weakened, but persistent stratification of the upper water column. [...]

Previous studies have shown that microbially produced methane can be a dominant carbon source of lacustrine sedimentary macrofauna in eutrophic lakes, most likely through grazing on methane-oxidizing bacteria. Here we investigate the contributions of different carbon sources to macrofaunal biomass across five lakes in central Switzerland that range from oligotrophic to highly eutrophic. Macrofaunal communities change with trophic state, with chironomid larvae dominating oligotrophic and tubificid oligochaetes dominating eutrophic lake sediments. The ¹³C-isotopic data suggest that the average contribution of methane-derived carbon to the biomass of both macrofaunal groups is similar but consistently remains minor, ranging from only ∼1 % in the oligotrophic lake to at most 12 % in the eutrophic lakes. The remaining biomass can be explained by the assimilation of detritus-derived organic carbon. Low abundances of methane-cycling microorganisms in macrofaunal specimens, burrows, and surrounding sediment based on 16S ribosomal RNA (rRNA) gene sequences and copy numbers of genes involved in anaerobic and aerobic methane cycling (mcrA, pmoA) support the interpretation of isotopic data. Notably, 16S rRNA gene sequences of macrofauna, including macrofaunal guts, are highly divergent from those in tubes or sediments. Many macrofaunal specimens are dominated by a single 16S rRNA phylotype of Fusobacteria, α-, β-, γ-, or ε-Proteobacteria, Bacteroidetes, or Parcubacteria. This raises the question of whether dominant lake macrofauna live in so far uncharacterized relationships with detrital organic-matter-degrading bacterial endosymbionts.

Macroinvertebrates are widespread in lake sediments and alter sedimentary properties through their activity (bioturbation). Understanding the interactions between bioturbation and sediment properties is important given that lakes are important sinks and sources of carbon and nutrients. We studied the biogeochemical impact of macrofauna on surface sediments in 3-month-long mesocosm experiments conducted using sediment cores from a hypoxic, macrofauna-free lake basin. Experimental units consisted of hypoxic controls, oxic treatments, and oxic treatments that were experimentally colonized with chironomid larvae or tubificid worms. Overall, the presence of O₂ in bottom water had the strongest geochemical effect and led to oxidation of sediments down to 2 cm depth. Relative to macrofauna-free oxic treatments, chironomid larvae increased sediment pore water concentrations of nitrate and sulfate and lowered porewater concentrations of reduced metals (Fe²⁺, Mn²⁺), presumably by burrow ventilation, whereas tubificid worms increased the redox potential, possibly through sediment reworking. Microbial communities were very similar across oxic treatments; however, the fractions of α-, β-, and γ-Proteobacteria and Sphingobacteriia increased, whereas those of Actinobacteria, Planctomycetes, and Omnitrophica decreased compared to hypoxic controls. Sediment microbial communities were, moreover, distinct from those of macrofaunal tubes or feces. We suggest that, under the conditions studied, bottom water oxygenation has a stronger biogeochemical impact on lacustrine surface sediments than macrofaunal bioturbation.

Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis^1,2. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution³. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation⁴. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron–sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.

Long-chain alkenones, a class of highly specific and widely used lipid biomarkers found in ocean and lake sediments, have been so far found as straight-chain alkyl ketones with 2 to 4 double bonds. Jaraula et al. (2010) reported assignments of a series of tri- to penta-unsaturated alkenones as straight-chain C₃₈ methyl (C₃₈Me) and C₃₉ ethyl (C₃₉Et) alkenones in Lake Fryxell, Antarctica. The same series of compounds were later found in sediments from Lake Van (Randlett et al., 2014). The structure assignments by Jaraula et al (2010) were primarily based on strong ions at [M-43]⁺ for C₃₈ alkenones and [M-57]⁺ for C₃₉ alkenones, which were interpreted as a loss of CH₃CO and CH₃CH₂CO groups. However, such fragmentation is atypical for common straight-chain methyl and ethyl alkenones. In this study, we reanalyzed Lake Van sediment samples. We show these new C₃₈ and C₃₉ alkenones elute earlier than the common straight-chain C₃₈Me and C₃₉Et alkenones on a mid-polarity GC column. After hydrogenation, mass spectra of these new alkenones show distinct peaks at m/z 72 or 86 caused by McLafferty rearrangement, indicating a methyl substitution at the α position of the carbonyl group in these C₃₈ and C₃₉ alkenones (i.e., α-methyl-branched C₃₈Me and C₃₉Et). Our new assignments as methyl-branched alkenones are further confirmed by the synthesis of an analog α-methyl C₂₅ methyl ketone and comparison of mass spectra. Double bond positions for branched C_38:5Me (brC_38:5Me) are found to be Δ⁴, Δ⁷, Δ¹⁴, Δ²¹ and Δ²⁸ based on the mass spectrum of corresponding dimethyl disulfide adducts. Analysis of Lake Van alkenone data reveals that based on brC₃₈Me shows a trend similar to for the past 270 ka, suggesting that the degree of unsaturation of branched alkenones is also sensitive to temperature.

limate warming is causing rapid spatial expansion of ocean warm pools from equatorial latitudes towards the subtropics. Sedentary coral reef inhabitants in affected areas will thus be trapped in high temperature regimes, which may become the “new normal”. In this study, we used clownfish Amphiprion ocellaris as model organism to study reef fish mechanisms of thermal adaptation and determine how high temperature affects multiple lipid aspects that influence physiology and thermal tolerance. We exposed juvenile fish to two different experimental conditions, implemented over 28 days: average tropical water temperatures (26 °C, control) or average warm pool temperatures (30 °C). We then performed several analyses on fish muscle and liver tissues: i) total lipid content (%), ii) lipid peroxides, iii) fatty acid profiles, iv) lipid metabolic pathways, and v) weight as body condition metric. Results showed that lipid storage capacity in A. ocellaris was not affected by elevated temperature, even in the presence of lipid peroxides in both tissues assessed. Additionally, fatty acid profiles were unresponsive to elevated temperature, and lipid metabolic networks were consequently well conserved. Consistent with these results, we did not observe changes in fish weight at elevated temperature. There were, however, differences in fatty acid profiles between tissue types and over time. Liver showed enhanced α-linolenic and linoleic acid metabolism, which is an important pathway in stress response signaling and modulation on environmental changes. Temporal oscillations in fatty acid profiles are most likely related to intrinsic factors such as growth, which leads to the mobilization of energetic reserves between different tissues throughout time according to organism needs. Based on these results, we propose that the stability of fatty acid profiles and lipid metabolic pathways may be an important thermal adaptation feature of fish exposed to warming environments.

Symbiotic N₂-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments^1,2,3. Particularly among land plants, N₂-fixing symbionts occur in a variety of distantly related plant lineages and often involve an intimate association between host and symbiont^2,4. Descriptions of such intimate symbioses are lacking for seagrasses, which evolved around 100 million years ago from terrestrial flowering plants that migrated back to the sea⁵. Here we describe an N₂-fixing symbiont, 'Candidatus Celerinatantimonas neptuna', that lives inside seagrass root tissue, where it provides ammonia and amino acids to its host in exchange for sugars. As such, this symbiosis is reminiscent of terrestrial N₂-fixing plant symbioses. The symbiosis between Ca. C. neptuna and its host Posidonia oceanica enables highly productive seagrass meadows to thrive in the nitrogen-limited Mediterranean Sea. Relatives of Ca. C. neptuna occur worldwide in coastal ecosystems, in which they may form similar symbioses with other seagrasses and saltmarsh plants. Just like N₂-fixing microorganisms might have aided the colonization of nitrogen-poor soils by early land plants⁶, the ancestors of Ca. C. neptuna and its relatives probably enabled flowering plants to invade nitrogen-poor marine habitats, where they formed extremely efficient blue carbon ecosystems⁷.

Freshwater lakes are essential hotspots for the removal of excessive anthropogenic nitrogen (N) loads transported from the land to coastal oceans. The biogeochemical processes responsible for N removal, the corresponding transformation rates and overall removal efficiencies differ between lakes, however, it is unclear what the main controlling factors are. Here, we investigated the factors that moderate the rates of N removal under contrasting trophic states in two lakes located in central Switzerland. In the eutrophic Lake Baldegg and the oligotrophic Lake Sarnen, we specifically examined seasonal sediment porewater chemistry, organic matter sedimentation rates, as well as 33-year of historic water column data. We find that the eutrophic Lake Baldegg, which contributed to the removal of 20 ± 6.6 gN m⁻² year⁻¹, effectively removed two-thirds of the total areal N load. In stark contrast, the more oligotrophic Lake Sarnen contributed to 3.2 ± 4.2 gN m⁻² year⁻¹, and had removed only one-third of the areal N load. The historic dataset of the eutrophic lake revealed a close linkage between annual loads of dissolved N (DN) and removal rates (NRR = 0.63 × DN load) and a significant correlation of the concentration of bottom water nitrate and removal rates. We further show that the seasonal increase in N removal rates of the eutrophic lake correlated significantly with seasonal oxygen fluxes measured across the water–sediment interface (R² = 0.75). We suggest that increasing oxygen enhances sediment mineralization and stimulates nitrification, indirectly enhancing denitrification activity.

Biological N₂ fixation was key to the expansion of life on early Earth. The N₂-fixing microorganisms and the nitrogenase type used in the Proterozoic are unknown, although it has been proposed that the canonical molybdenum-nitrogenase was not used due to low molybdenum availability. We investigate N₂ fixation in Lake Cadagno, an analogue system to the sulfidic Proterozoic continental margins, using a combination of biogeochemical, molecular and single cell techniques. In Lake Cadagno, purple sulfur bacteria (PSB) are responsible for high N₂ fixation rates, to our knowledge providing the first direct evidence for PSB in situ N₂ fixation. Surprisingly, no alternative nitrogenases are detectable, and N₂ fixation is exclusively catalyzed by molybdenum-nitrogenase. Our results show that molybdenum-nitrogenase is functional at low molybdenum conditions in situ and that in contrast to previous beliefs, PSB may have driven N₂ fixation in the Proterozoic ocean.

We investigate the uppermost 60 cm of sediment in active pockmarks of a deep-water methane seep site from Vestnesa Ridge offshore NW Svalbard. Using video guided core sampling with a remotely operated vehicle we collected push cores directly from bacterial mats within two active pockmarks, Lunde and Lomvi. Pore water analyses show very shallow sulphate methane transition zones and transport-reaction modelling suggests a considerable amount of dissolved methane passing through the sediment water interface due to upwards advection of an aqueous fluid not previously reported from Vestnesa Ridge. In addition, we show that the amount of methane that bypasses the benthic methane filter greatly increases with higher aqueous fluid advection rate. Recent changes in methane flux are evident from lipid biomarker, seep carbonate, and δ¹³C-organic carbon profiles in both pockmarks. Hydrocarbons at this cold seep site are supplied both by deep thermogenic sources from below the gas hydrate stability zone but also to a significant degree by microbial methanogenesis which dominates the signature in our shallow sediment cores with δ¹³C–CH₄ values as low as −77‰.

1. Glacial retreat, accompanied by shifts in riparian vegetation and glacier meltwater inputs, alters the energy supply and trophic structure of alpine stream food webs. Our goal in this study was to enhance understanding of dietary niches of macroinvertebrates inhabiting different alpine streams with contrasting glacial and non‐glacial (groundwater, precipitation, snowmelt) water inputs in conjunction with seasonal and habitat‐specific variation in basal resource availability.
2. We measured a range of stream physico‐chemical attributes as well as carbon and nitrogen isotopes (δ¹³C, δ¹⁵N) of macroinvertebrates and primary food sources at seven sites across seasons within a Swiss glaciated catchment (Val Roseg) undergoing rapid glacial retreat (1-2 km between 1997 and 2014). Sampling sites corresponded to streams used in a previous (1997/1998) study within the same alpine catchment.
3. Physico-chemical attributes showed wide variation in environmental conditions across streams and seasons. Significant correlation among physico‐chemical proxies of glacier meltwater (phosphate‐P, total inorganic carbon, conductivity, turbidity) and macroinvertebrate δ¹³C, δ¹⁵N, and size‐corrected standard ellipse area (a proxy for feeding niche width) values showed that the extent of glacial water input shapes the energy base among alpine streams. Feeding niche differences among common alpine stream insect taxa (Chironomidae, Baetidae, Heptageniidae) were not significant, indicating that these organisms probably are plastic in feeding behaviour, opportunistically relying on food resources available in a particular stream and season.
4. Seasonal trends in macroinvertebrate δ¹³C largely followed patterns in periphyton δ¹³C values, indicating that autochthonous resources were the main consumer energy source within the stream network, as shown previously. The overall range in macroinvertebrate δ¹³C (-33.5 to -18.4‰) and δ¹⁵N (-6.9 to 6.7‰) values also corresponded to values measured in the previous study, suggesting that macroinvertebrates altered diets in line with changes in environmental conditions and food resources during a period of rapid glacial retreat. Our results suggest that environmental changes brought on by rapid glacial retreat have not yet caused a profound change in the trophic structure within these fluvial networks.

We here estimate past temperature and hydroclimate variations in eastern Anatolia for marine isotope stages 4 to 1 (MIS4 to MIS1) respectively using branched glycerol dialkyl glycerol tetraethers (brGDGTs) and the hydrogen isotopic composition of n-C₂₉ leaf-wax n-alkanes (δ²H_wax) stored in the sedimentary record of Lake Van (Turkey). Our millennial-scale lipid biomarker records reflect warm and wet conditions during interstadials/interglacials and colder and dryer periods with increased evapotranspiration and aridity during stadials/glacials. The degree of methylation of the 5-methyl brGDGTs (MBT´_5me) indicates increasing mean annual air temperatures (MAT) during stadial/interstadial transitions, that characterize Dansgaard-Oeschger events, and during the last glacial termination.
Based on the effects of changes in precipitation amount on apparent enrichment factors between the δ²H of the C₂₉n-alkanes and δ²H of precipitation, a total increase in annual precipitation of about 200 mm during transitions from stadials to interstadials, and of 300-350 mm during glacial-interglacial transitions can be determined, in line with previous paleoclimate reconstructions for the Eastern Mediterranean.
High sterol concentrations in sediments deposited during warm and humid interstadials reflect increases in lake level, vegetation density and algal blooms, whereas lower values of the branched versus isoprenoid tetraethers ratio (BIT) likely reflects the increased niche of Thaumarchaeota resulting from enhanced windiness and mixing of the water column during colder periods. This quantitative hydroclimate reconstruction from Lake Van (Turkey), as it is optimally situated to respond to North Atlantic climate change via changes in the large-scale wind fields shed light into millennial-scale global climate variability.

Geogenic arsenic (As) contamination of groundwater is a health threat to millions of people worldwide, particularly in alluvial regions of South and Southeast Asia. Mitigation measures are often hindered by high heterogeneities in As concentrations, the cause(s) of which are elusive. Here we used a comprehensive suite of stable isotope analyses and hydrogeochemical parameters to shed light on the mechanisms in a typical high-As Holocene aquifer near Hanoi where groundwater is advected to a low-As Pleistocene aquifer. Carbon isotope signatures (δ¹³C-CH₄, δ¹³C-DOC, δ¹³C-DIC) provided evidence that fermentation, methanogenesis and methanotrophy are actively contributing to the As heterogeneity. Methanogenesis occurred concurrently where As levels are high (>200 µg/L) and DOC-enriched aquitard pore water infiltrates into the aquifer. Along the flowpath to the Holocene/Pleistocene aquifer transition, methane oxidation causes a strong shift in δ¹³C-CH₄ from -87‰ to +47‰, indicating high reactivity. These findings demonstrate a previously overlooked role of methane cycling and DOC infiltration in high-As aquifers.

Lakes cover a global area that is about 35 times smaller than the oceans, but carbon burial in lakes and oceans are on the same order of magnitude. Hence, understanding the processes for such high organic carbon burial in lacustrine systems is essential. We applied proxies typically used for marine environments including amino acid (AA) content and their nitrogen stable isotope composition to the water columns and sediments of three lakes that differ in their trophic states and depositions rates of sedimentary terrestrial organic matter. Additionally, we used carbon isotope fingerprinting of AAs to characterise their sources and fates. We show that this set of proxies tracks sources and degradation processes in eutrophic lakes with high sedimentary total organic carbon and nitrogen content. Those lakes also have a high total hydrolysable amino acid (THAA) content as well as higher pigment concentrations. While the Chlorin degradation Index (CI) showed increasing values with depth, the patterns were less consistent for the Degradation Index (DI). In general, all parameters failed to describe degradation in the most oligotrophic lake due to the very low organic carbon and nitrogen content in the sediment. We show that AAs are mostly of autochthonous origin and that AA contribute 5-45 % to the organic material in plankton, POM, and sediment. Proxies based on AA for bacterial reworking (ΣV) or trophic level (TL) showed increasing values in the water column but relatively stable values in the sediments. Furthermore, we show that methanotrophic bacteria led to increased values for the bacterial reworking proxy (ΣV) and extraordinarily low δ¹³C AA values (-30 to -60 ‰).

Small boreal lakes are known to contribute significantly to global CH₄ emissions. Lake Lovojärvi is a eutrophic lake in southern Finland with bottom water CH₄ concentrations up to 2 mM. However, the surface water concentration, and thus the diffusive emission potential, was low (< 0.5 µM). We studied the biogeochemical processes involved in CH₄ removal by chemical profiling and through incubation experiments. δ¹³C-CH₄ profiling of the water column revealed a methane-oxidation hotspot just below the oxycline and zones of CH₄ oxidation within the anoxic water column. In incubation experiments involving the addition of light and/or oxygen, CH₄ oxidation rates in the anoxic hypolimnion were enhanced 3-fold, suggesting a major role for photosynthetically fueled aerobic CH₄ oxidation. We observed a distinct peak in CH₄ concentration at the chlorophyll-a maximum, caused by either in situ CH₄ production or other CH₄ inputs such as lateral transport from the littoral zone. In the dark anoxic water column at 7 m depth, nitrite seemed to be the key electron acceptor involved in CH₄ oxidation, yet additions of Fe(III), anthraquinone-2,6-disulfonate and humic substances also stimulated anoxic CH₄ oxidation. Surprisingly, nitrite seemed to inhibit CH₄ oxidation at all other depths. Overall, this study shows that photosynthetically fueled CH₄ oxidation can be a key process in CH₄ removal in the water column of humic, turbid lakes, thereby limiting diffusive CH₄ emissions from boreal lakes. Yet, it also highlights the potential importance of a whole suite of alternative electron acceptors, including humics, in these freshwater environments in the absence of light and oxygen.

Coastal lakes (CL) act as limnetic–β-oligohaline systems located on non-tidal coastlines in fresh and salt water mixing zone. Owing to considerable terrestrial nutrient input and a high autochthonous productivity CLs release greenhouse gases (GHG) to the ambient atmosphere, however, neither emission from the system was assessed nor controls on the emission were recognized so far. In this study we attempted to quantify diffusive emissions of CH₄, CO₂ and N₂O from CLs based on data collected from seven lakes located on a south coast of the Baltic Sea in Poland. Lake water samples were collected with quarterly resolution along salinity, water depth and wind fetch gradients. From our data it emerged that the concentrations of GHGs were determined by temperature. CH₄ showed dependence on salinity, lake water depth and wind fetch. N₂O was controlled by dissolved O₂ and NO₃⁻ and CO₂ was largely related to wind fetch. It also appeared that concentrations of N₂O and CO₂ were influenced by terrestrial nutrient input. The mean fluxes of CH₄, CO₂ and N₂O for the whole system were 21.7 mg·m⁻²·d⁻¹, 12.7 g·m⁻²·d⁻¹ and 0.74 mg·m⁻²·d⁻¹, respectively which was equivalent to 7.9 g CH₄·m⁻²·y⁻¹, 4.6 kg CO₂·m⁻²·y⁻¹ and 269 mg N₂O·m⁻²·y⁻¹. CH₄ and N₂O were released throughout the year and CO₂ was predominantly emitted during winter. We showed that diffusive emissions of the GHGs showed relationships to the surface area of the lakes as well as the ratio of catchment area to lake area (CA/LA). The study would benefit from further extension with higher resolution analyses of the lakes over longer timescales and quantification of ebullitive GHG emission (CH₄ in particular).

Lake sediments are globally important carbon sinks. Although the fate of organic carbon in lake sediments depends significantly on microorganisms, only few studies have investigated controls on lake sedimentary microbial communities. Here we investigate the impact of anthropogenic eutrophication, which affects redox chemistry and organic matter (OM) sources in sediments, on microbial communities across five lakes in central Switzerland. Lipid biomarkers and distributions of microbial respiration reactions indicate strong increases in aquatic OM contributions and microbial activity with increasing trophic state. Across all lakes, 16S rRNA genes analyses indicate similar depth‐dependent zonations at the phylum‐ and class‐level that follow vertical distributions of OM sources and respiration reactions. Yet, there are notable differences, such as higher abundances of nitrifying Bacteria and Archaea in an oligotrophic lake. Furthermore, analyses at the order‐level and below suggest that changes in OM sources due to eutrophication cause permanent changes in bacterial community structure. By contrast, archaeal communities are differentiated according to trophic state in recently deposited layers, but converge in older sediments deposited under different trophic regimes. Our study indicates an important role for trophic state in driving lacustrine sediment microbial communities and reveals fundamental differences in the temporal responses of sediment Bacteria and Archaea to eutrophication.

Amino acids (AA) and, more recently, amino sugars (AS) in marine or lacustrine sediments have been increasingly used as paleoproxies. In order to assess AA and AS compositional changes during simulated microbial degradation, as well as to understand the importance of amino-compound re-synthesis by microbes during early diagenesis, decomposition experiments (300 days) were performed with algal (Fragilaria crotonensis) organic matter (OM)/quartz-sand mixtures under controlled redox conditions. Despite expected greater overall degradability under oxic conditions, decomposition kinetics of the bulk algal OM, as well as the total particulate AA and AS were similar under oxic and anoxic conditions, following exponential decay kinetics consistent with the observed mobilization and transfer of large parts of the particulate organic carbon (C) and nitrogen (N) into the dissolved inorganic and organic C and N pools. Carbon-normalized AA and AS yields suggest relative enrichment of amino compounds during partial decomposition, indicating the production and accumulation of microbial biomass during early diagenesis, independent of the redox environment. Moreover, AA and AS compositional changes, such as the relative enrichment of the AA glycine and the AS muramic acid (MurA), and the decrease in the molar ratio of glucosamine and galactosamine (GlcN:GalN) during degradation in both redox systems, were consistent with significant bacterial re-synthesis and the preferential preservation of bacterial biomaterial with increasing diagenesis. Large disparities between different bacterial amino-sugar based estimates of bacterial contribution indicate that bacterial end-member compositions are not currently known well enough to make these bacterial-biomarker constraints quantitative. However, the overall trends are consistent, indicating substantial turnover of eukaryotic into bacterial OM on short time scales of weeks to months. Together these results suggest that the influence of bacterial reworking in conserving sedimentary OM via its transfer into more refractory OM pools may be substantially greater than previously appreciated. We also investigated established amino-compound based indicators of OM degradation, bacterial synthesis, and sediment reactivity. Despite discrepancies, which we attribute to different susceptibilities of the respective indicators towards degradational changes on different time-scales, the tested indices were overall consistent with past data. These results therefore confirm their value as universal indicators of OM diagenesis. Together, our data highlight the vital role of bacterial reworking on the composition of sedimentary OM, with important implications for the alteration of primary geochemical signatures during early sedimentary diagenesis and their use as proxies in paleoenvironmental studies.

Beaver populations are increasing throughout Europe and especially in Switzerland. Beaver are major ecological engineers of fluvial systems, dramatically influencing river morphology, ecohydrology and, consequently, aquatic and terrestrial biota. This study compared macroinvertebrate assemblages and trophic structure at two beaver complexes with contrasting topography in Switzerland over an annual cycle. One complex (Marthalen) was in a low gradient open basin, whereas the other complex (Flaach) flowed through a higher gradient ravine-like basin. Both complexes were embedded in an overall agricultural landscape matrix. Water physico-chemistry differed between the two complexes with nitrogen, phosphorus, and DOC being higher at Marthalen than at Flaach. Both complexes showed strong seasonality in physico-chemistry, but retention of nutrients (N, P) was highest in summer and only at Marthalen. Both complexes also showed strong seasonality in macroinvertebrate assemblages, although assemblages differed substantially between complexes. At Marthalen, macroinvertebrate assemblages were predominantly lentic in character at 'pool' sites within the complex. At Flaach, lotic macroinvertebrate assemblages were common at most sites with some lentic taxa also being present. Dietary shifts based on carbon/nitrogen stable isotopes occurred in spring and summer among sites at both complexes (autochthonous resource use increasing over allochthonous resource use downstream), although being most pronounced at Marthalen. In contrast, similar resource use across sites occurred in winter within both complexes. Although beaver significantly influenced fluvial dynamics and macroinvertebrate assemblage structure at both complexes, this influence was most pronounced at Marthalen where beaver caused the system to become more wetland in character, e.g., via higher hydraulic residence time, than at Flaach. We conclude that topography can shape beaver effects on fluvial systems and resident biota.