Staff

Carsten Schubert

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Prof. Dr. Carsten Schubert

Department Surface Waters Research & Management

About Me

Projects
See projects on the webpage of the group Biogeochemistry


Research interests
•    Genesis, aerobic and anaerobic oxidation of methane in freshwater systems
•    Understanding food chains using stable isotopes
•    Isotopic (C,N,O,H) and organic geochemical investigations in respect to the cycling of nutrients (C,N) and the preservation/degradation of organic matter
•    Investigation of the nitrogen cycle (amino-sugars and amino acids as the main nitrogen compounds in organisms, stable isotopes on bulk and single compounds to understand food webs)
•    Determination and use of biomarkers in organic materials (sediments, plankton, and bacteria), especially alkenones, n-alkanes, fatty-acids, alcohols, sterols, ether-lipids and lignin for identifying key processes taking place today or in the past (palaeo-reconstructions)

 

Teaching

  • Lecture: Isotopes and Biomarkers in Biogeochemistry at ETH Zürich
  • Laboratory: Isotopes and Biomarkers in Biogeochemistry at ETH Zürich


PhD students

  • 2021-    Bastiaan Drost, Blue Green Biodiversity Project
  • 2020-    Grégoire Saboret, Isotopes and food chains

Postdocs in research group

  • 2021-            Maja Illic, Blue Green Biodiversity
  • 2021-2022    Sigrid vanGrinsven, Methanogenesis and dependence of organic material

Field experience

8 Oceanographic cruises (2 times as chief scientist) to the Arctic, Pacific Ocean, Atlantic Ocean, Black Sea and numerous lake sampling campaigns


Reviewer for Journals, Funding agencies

Nature, Science, Nature Communications, Nature Climate Change, Nature Geosciences, Scientific Reports, Geology, Marine Chemistry, Palaeoceanography, Geochimica et Cosmochimica Acta, Journal of Geophysical Research, Marine Geology, Limnology & Oceanography, Environmental Science & Technology, Organic Geochemistry, Gcubed, Global Biogeochemical Cycles, FEMS Microbial Ecology, Chemical Geology, Journal of Earth System Science, Journal of Great Lakes Research, Archives of Microbiology, Aquatic Microbial Ecology, Aquatic Geochemistry, Continental Shelf Research, Journal of Chromatography A, Environmental Microbiology, Ecological Monographs

Reviewer for Funding agencies

ERC Grants, European Science Foundation
DFG, German research foundation
NSF, National Science Foundation, USA
NWO Earth and Life Science, Dutch research council
SNF, Swiss National Science Foundation
Academy of Finland
Fondecyt, Chilean national research funding
U.S.-Israel Binational Science Foundation
NERC, National Science Foundation, UK
Darwin Center for Biogeosciences (Netherlands)
American Chemical Society Petroleum Fund
French National Research Agency

Publications
Eawag Publications

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Curriculum Vitae

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Publications

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De Jonge, C., Dubois, N., Ladd, S. N., Deng, L., Gajendra, N., Haghipour, N., … Lever, M. (2025). Holocene environmental change in Rotsee and its impact on sedimentary carbon storage. Journal of Paleolimnology, 73, 311-327. doi:10.1007/s10933-025-00361-3, Institutional Repository

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.
Klatt, A., De Jonge, C., Nelson, D. B., Reyes, M., Schubert, C. J., Dubois, N., & Ladd, S. N. (2025). Algal lipid distributions and hydrogen isotope ratios reflect phytoplankton community dynamics. Geochimica et Cosmochimica Acta, 394, 205-219. doi:10.1016/j.gca.2025.02.013, Institutional Repository

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 (δ2HLipid) 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 δ2HLipid values (δ2HLipid1/Lipid2) from short-chain fatty acids, phytosterols and phytol. Comparing these data with phytoplankton cell counts, we found that δ2HC16:0 Acid/Sterol and δ2HSterol/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 δ2HLipid1/Lipid2 values based on δ2HC16:0 Acid, δ2HSterol and δ2HPhytol values from batch cultures of individual algal groups and their biovolume in Rotsee and evaluated the role of heterotrophy on δ2HLipid1/Lipid2 values using a model incorporating δ2HC16:0 Acid and δ2HSterol values from microzooplankton. Annually-integrated and amount-weighted δ2HLipid1/Lipid2 values measured in Rotsee were within 2 to 20 ‰ of the mean of modeled algal δ2HLipid1/Lipid2 values, demonstrating a strong link with the phytoplankton community composition, while δ2HLipid1/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 δ2HLipid1/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.
Knies, J., Ahn, Y., Ebner, B., Smik, L., Jang, K., Nam, S. I., … Schubert, C. J. (2025). Arctic fjord ecosystem adaptation to cryosphere meltdown over the past 14,000 years. Communications Earth & Environment, 6(1), 298 (8 pp.). doi:10.1038/s43247-025-02251-y, Institutional Repository

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.
Ladd, S. N., Nelson, D. B., Matthews, B., Dyer, S., Limberger, R., Klatt, A., … Schubert, C. J. (2025). Taxon-specific hydrogen isotope signals in cultures and mesocosms facilitate ecosystem and hydroclimate reconstruction. Geochimica et Cosmochimica Acta, 390, 199-210. doi:10.1016/j.gca.2024.12.002, Institutional Repository

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.
Lürig, M. D., Matthews, B., Schubert, C. J., & Kishida, O. (2025). Nutritional effects on the expression of cryptic pigmentation in freshwater isopods. Oikos. doi:10.1002/oik.11664, Institutional Repository

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.
Saboret, G., Moccetti, C., Wassenaar, L. I., Matthews, B., Aquino, N. J., Janssen, D. J., … Schubert, C. J. (2025). Impact of glaciers on trophic dynamics and polyunsaturated fat accumulation in Southern Greenland Fjord ecosystems. Global Change Biology, 31(1), e70044 (19 pp.). doi:10.1111/gcb.70044, Institutional Repository

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.
Su, G., Tolu, J., Glombitza, C., Zopfi, J., Lehmann, M. F., Lever, M. A., & Schubert, C. J. (2025). Methanogenesis by CO 2 reduction dominates lake sediments with different organic matter compositions. Biogeosciences, 22(17), 4449-4466. doi:10.5194/bg-22-4449-2025, Institutional Repository

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.
Bauersachs, T., Schubert, C. J., Mayr, C., Gilli, A., & Schwark, L. (2024). Branched GDGT-based temperature calibrations from Central European lakes. Science of the Total Environment, 906, 167724 (11 pp.). doi:10.1016/j.scitotenv.2023.167724, Institutional Repository

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 IR6Me, 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 IR6Me is here proposed, after which MBT'5Me-reconstructed MAATs from lacustrine archives should be regarded as unreliable.
Doda, T., Ramón, C. L., Ulloa, H. N., Brennwald, M. S., Kipfer, R., Perga, M. E., … Bouffard, D. (2024). Lake surface cooling drives littoral-pelagic exchange of dissolved gases. Science Advances, 10(4), eadi0617 (9 pp.). doi:10.1126/sciadv.adi0617, Institutional Repository

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.
Gajendra, N., Deng, L., Eglinton, T. I., Schubert, C. J., & Lever, M. A. (2024). Impacts of temperature and fluid seepage on organic matter composition in sediments of an active hydrothermal basin. Organic Geochemistry, 196, 104829 (15 pp.). doi:10.1016/j.orggeochem.2024.104829, Institutional Repository

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.
Khatun, S., Berg, J. S., Jézéquel, D., Moiron, M., Escoffier, N., Schubert, C. J., … Perga, M. E. (2024). Long-range transport of littoral methane explains the metalimnetic methane peak in a large lake. Limnology and Oceanography, 69(9), 2095-2108. doi:10.1002/lno.12652, Institutional Repository

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.
Meier, D., van Grinsven, S., Michel, A., Eickenbusch, P., Glombitza, C., Han, X., … Lever, M. A. (2024). Hydrogen–independent CO2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states. ISME Communications, 4(1), ycae089 (15 pp.). doi:10.1093/ismeco/ycae089, Institutional Repository

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.
Saboret, G., Moccetti, C., Takatsu, K., Janssen, D. J., Matthews, B., Brodersen, J., & Schubert, C. J. (2024). Glacial meltwater increases the dependence on marine subsidies of fish in freshwater ecosystems. Ecosystems, 27, 779-796. doi:10.1007/s10021-024-00920-1, Institutional Repository

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.
Saboret, G., Drost, B. J. W., Kowarik, C., Schubert, C. J., Gossner, M. M., & Ilić, M. (2024). Quantifying the utilisation of blue, green and brown resources by riparian predators: a combined use of amino acid isotopes and fatty acids. Methods in Ecology and Evolution, 15(8), 1450-1462. doi:10.1111/2041-210X.14371, Institutional Repository

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.
Schorn, S., Graf, J. S., Littmann, S., Hach, P. F., Lavik, G., Speth, D. R., … Milucka, J. (2024). Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility. Nature Communications, 15(1), 5293 (14 pp.). doi:10.1038/s41467-024-49602-5, Institutional Repository

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.
Ehrenfels, B., Baumann, K. B. L., Niederdorfer, R., Mbonde, A. S., Kimirei, I. A., Kuhn, T., … Callbeck, C. M. (2023). Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika. Nature Communications, 14, 6591 (13 pp.). doi:10.1038/s41467-023-42391-3, Institutional Repository

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.
Ehrenfels, B., Junker, J., Namutebi, D., Callbeck, C. M., Dinkel, C., Kalangali, A., … Wehrli, B. (2023). Isotopic signatures induced by upwelling reveal regional fish stocks in Lake Tanganyika. PLoS One, 18(11), e0281828 (29 pp.). doi:10.1371/journal.pone.0281828, Institutional Repository

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.
Gajendra, N., Berg, J. S., Vogel, H., Deng, L., Wolf, S. M., Bernasconi, S. M., … Lever, M. A. (2023). Carbohydrate compositional trends throughout Holocene sediments of an alpine lake (Lake Cadagno). Frontiers in Earth Science, 11, 1047224 (17 pp.). doi:10.3389/feart.2023.1047224, Institutional Repository

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.
Panieri, G., Knies, J., Vadakkepuliyambatta, S., Lee, A. L., & Schubert, C. J. (2023). Evidence of Arctic methane emissions across the mid-Pleistocene. Communications Earth & Environment, 4, 109 (11 pp.). doi:10.1038/s43247-023-00772-y, Institutional Repository

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.
Saboret, G., Stalder, D., Matthews, B., Brodersen, J., & Schubert, C. J. (2023). Autochthonous production sustains food webs in large perialpine lakes, independent of trophic status: evidence from amino acid stable isotopes. Freshwater Biology, 68(5), 870-887. doi:10.1111/fwb.14071, Institutional Repository

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.
Woszczyk, M., & Schubert, C. J. (2023). Methane and nitrous oxide emissions from an anthropogenically transformed Lake (Lake Licheńskie, Poland). Journal of Geophysical Research: Biogeosciences, 128(12), e2023JG007594 (21 pp.). doi:10.1029/2023JG007594, Institutional Repository

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.
van Grinsven, S., & Schubert, C. (2023). Soil-biodegradable plastic films do not decompose in a lake sediment over 9 months of incubation. Biogeosciences, 20(19), 4213-4220. doi:10.5194/bg-20-4213-2023, Institutional Repository

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.
Baumann, K. B. L., Thoma, R., Callbeck, C. M., Niederdorfer, R., Schubert, C. J., Müller, B., … Bürgmann, H. (2022). Microbial nitrogen transformation potential in sediments of two contrasting lakes is spatially structured but seasonally stable. mSphere, 7(1), e01013-21 (20 pp.). doi:10.1128/msphere.01013-21, Institutional Repository

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.
Berg, J. S., Lepine, M., Laymand, E., Han, X., Vogel, H., Morlock, M. A., … Lever, M. A. (2022). Ancient and modern geochemical signatures in the 13,500-year sedimentary record of Lake Cadagno. Frontiers in Earth Science, 9, 754888 (16 pp.). doi:10.3389/feart.2021.754888, Institutional Repository

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.
Han, X., Tolu, J., Deng, L., Fiskal, A., Schubert, C. J., Winkel, L. H. E., & Lever, M. A. (2022). Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls. PNAS Nexus, 1(3), 1-15. doi:10.1093/pnasnexus/pgac076, Institutional Repository

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.
Hudson, C. M., Ladd, S. N., Leal, M. C., Schubert, C. J., Seehausen, O., & Matthews, B. (2022). Fit and fatty freshwater fish: contrasting polyunsaturated fatty acid phenotypes between hybridizing stickleback lineages. Oikos, 2022(7), e08558 (14 pp.). doi:10.1111/oik.08558, Institutional Repository

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.
van Grinsven, S., Meier, D. V., Michel, A., Han, X., Schubert, C. J., & Lever, M. A. (2022). Redox zone and trophic state as drivers of methane-oxidizing bacterial abundance and community structure in lake sediments. Frontiers in Environmental Science, 10, 857358 (22 pp.). doi:10.3389/fenvs.2022.857358, Institutional Repository

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.
Callbeck, C. M., Ehrenfels, B., Baumann, K. B. L., Wehrli, B., & Schubert, C. J. (2021). Anoxic chlorophyll maximum enhances local organic matter remineralization and nitrogen loss in Lake Tanganyika. Nature Communications, 12, 830 (11 pp.). doi:10.1038/s41467-021-21115-5, Institutional Repository

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.
Callbeck, C. M., Canfield, D. E., Kuypers, M. M. M., Yilmaz, P., Lavik, G., Thamdrup, B., … Bristow, L. A. (2021). Sulfur cycling in oceanic oxygen minimum zones. Limnology and Oceanography, 66(6), 2360-2392. doi:10.1002/lno.11759, Institutional Repository

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.
Fiskal, A., Anthamatten, E., Deng, L., Han, X., Lagostina, L., Michel, A., … Lever, M. A. (2021). Carbon sources of benthic fauna in temperate lakes across multiple trophic states. Biogeosciences, 18(14), 4369-4388. doi:10.5194/bg-18-4369-2021, Institutional Repository

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.
Fiskal, A., Gaillard, A., Giroud, S., Malcic, D., Joshi, P., Sander, M., … Lever, M. A. (2021). Effects of macrofaunal recolonization on biogeochemical processes and microbiota - a mesocosm study. Water, 13(11), 1599 (25 pp.). doi:10.3390/w13111599, Institutional Repository

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.
Graf, J. S., Schorn, S., Kitzinger, K., Ahmerkamp, S., Woehle, C., Huettel, B., … Milucka, J. (2021). Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature, 591, 445-450. doi:10.1038/s41586-021-03297-6, Institutional Repository

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 endosymbiosis1,2. 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.
Liao, S., Wang, K. J., Xue, Y., Huo, J., Santos, E., Wang, J., … Huang, Y. (2021). Novel methyl-branched alkenones with up to five double bonds in saline lakes. Organic Geochemistry, 156, 104243 (9 pp.). doi:10.1016/j.orggeochem.2021.104243, Institutional Repository

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 C38:5Me (brC38:5Me) 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.
Madeira, C., Madeira, D., Ladd, N., Schubert, C. J., Diniz, M. S., Vinagre, C., & Leal, M. C. (2021). Conserved fatty acid profiles and lipid metabolic pathways in a tropical reef fish exposed to ocean warming – an adaptation mechanism of tolerant species?. Science of the Total Environment, 782, 146738 (13 pp.). doi:10.1016/j.scitotenv.2021.146738, Institutional Repository

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.
Mohr, W., Lehnen, N., Ahmerkamp, S., Marchant, H. K., Graf, J. S., Tschitschko, B., … Kuypers, M. M. M. (2021). Terrestrial-type nitrogen-fixing symbiosis between seagrass and a marine bacterium. Nature, 600, 105-109. doi:10.1038/s41586-021-04063-4, Institutional Repository

Symbiotic N2-fixing microorganisms have a crucial role in the assimilation of nitrogen by eukaryotes in nitrogen-limited environments1,2,3. 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 symbiont2,4. 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.
Müller, B., Thoma, R., Baumann, K. B. L., Callbeck, C. M., & Schubert, C. J. (2021). Nitrogen removal processes in lakes of different trophic states from on-site measurements and historic data. Aquatic Sciences, 83(2), 37 (13 pp.). doi:10.1007/s00027-021-00795-7, Institutional Repository

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.
Philippi, M., Kitzinger, K., Berg, J. S., Tschitschko, B., Kidane, A. T., Littmann, S., … Kuypers, M. M. M. (2021). Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nature Communications, 12, 4774 (12 pp.). doi:10.1038/s41467-021-25000-z, Institutional Repository

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.
Sauer, S., Hong, W. L., Yao, H., Lepland, A., Klug, M., Eichinger, F., … Knies, J. (2021). Methane transport and sources in an Arctic deep-water cold seep offshore NW Svalbard (Vestnesa Ridge, 79°N). Deep Sea Research Part I: Oceanographic Research Papers, 167, 103430 (17 pp.). doi:10.1016/j.dsr.2020.103430, Institutional Repository

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‰.
Sertić Perić, M., Nielsen, J. M., Schubert, C. J., & Robinson, C. T. (2021). Does rapid glacial recession affect feeding habits of alpine stream insects?. Freshwater Biology, 66(1), 114-129. doi:10.1111/fwb.13621, Institutional Repository

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.
Stockhecke, M., Bechtel, A., Peterse, F., Guillemot, T., & Schubert, C. J. (2021). Temperature, precipitation, and vegetation changes in the Eastern Mediterranean over the last deglaciation and Dansgaard-Oeschger events. Palaeogeography, Palaeoclimatology, Palaeoecology, 577, 110535 (13 pp.). doi:10.1016/j.palaeo.2021.110535, Institutional Repository

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 (δ2Hwax) 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.
Stopelli, E., Duyen, V. T., Prommer, H., Glodowska, M., Kappler, A., Schneider, M., … Berg, M. (2021). Carbon and methane cycling in arsenic-contaminated aquifers. Water Research, 200, 117300 (8 pp.). doi:10.1016/j.watres.2021.117300, Institutional Repository

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.
Stücheli, P. E., Larsen, T., Wehrli, B., & Schubert, C. J. (2021). Amino acid and chlorin based degradation indicators in freshwater water systems. Geochimica et Cosmochimica Acta, 304, 216-233. doi:10.1016/j.gca.2021.04.006, Institutional Repository

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 ‰).
Van Grinsven, S., Oswald, K., Wehrli, B., Jegge, C., Zopfi, J., Lehmann, M. F., & Schubert, C. J. (2021). Methane oxidation in the waters of a humic-rich boreal lake stimulated by photosynthesis, nitrite, Fe(III) and humics. Biogeosciences, 18(10), 3087-3101. doi:10.5194/bg-18-3087-2021, Institutional Repository

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.
Woszczyk, M., & Schubert, C. J. (2021). Greenhouse gas emissions from Baltic coastal lakes. Science of the Total Environment, 755, 143500 (12 pp.). doi:10.1016/j.scitotenv.2020.143500, Institutional Repository

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).
Han, X., Schubert, C. J., Fiskal, A., Dubois, N., & Lever, M. A. (2020). Eutrophication as a driver of microbial community structure in lake sediments. Environmental Microbiology, 22(8), 3446-3462. doi:10.1111/1462-2920.15115, Institutional Repository

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.
Lehmann, M. F., Carstens, D., Deek, A., McCarthy, M., Schubert, C. J., & Zopfi, J. (2020). Amino acid and amino sugar compositional changes during in vitro degradation of algal organic matter indicate rapid bacterial re-synthesis. Geochimica et Cosmochimica Acta, 283, 67-84. doi:10.1016/j.gca.2020.05.025, Institutional Repository

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.
Robinson, C. T., Schweizer, P., Larsen, A., Schubert, C. J., & Siebers, A. R. (2020). Beaver effects on macroinvertebrate assemblages in two streams with contrasting morphology. Science of the Total Environment, 722, 137899 (9 pp.). doi:10.1016/j.scitotenv.2020.137899, Institutional Repository

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.
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Methane oxidation coupled to oxygenic photosynthesis in anoxic waters

Freshwater lakes represent large methane sources that, in contrast to the Ocean, significantly contribute to non-anthropogenic methane emissions to the atmosphere. Particularly mixed lakes are major methane emitters, while permanently and seasonally stratified lakes with anoxic bottom waters are often characterized by strongly reduced methane emissions. The causes for this reduced methane flux from anoxic lake waters are not fully understood. Here we identified the microorganisms and processes responsible for the near complete consumption of methane in the anoxic waters of a permanently stratified lake, Lago di Cadagno. Interestingly, known anaerobic methanotrophs could not be detected in these waters. Instead, we found abundant gamma-proteobacterial aerobic methane-oxidizing bacteria active in the anoxic waters. In vitro incubations revealed that, among all the tested potential electron acceptors, only the addition of oxygen enhanced the rates of methane oxidation. An equally pronounced stimulation was also observed when the anoxic water samples were incubated in the light. Our combined results from molecular, biogeochemical and single-cell analyses indicate that methane removal at the anoxic chemocline of Lago di Cadagno is due to true aerobic oxidation of methane fuelled by in situ oxygen production by photosynthetic algae. A similar mechanism could be active in seasonally stratified lakes and marine basins such as the Black Sea, where light penetrates to the anoxic chemocline. Given the widespread occurrence of seasonally stratified anoxic lakes, aerobic methane oxidation coupled to oxygenic photosynthesis might have an important but so far neglected role in methane emissions from lakes.
Milucka, J.; Kirf, M.; Lu, L.; Krupke, A.; Lam, P.; Littmann, S.; Kuypers, M. M. M.; Schubert, C. J. (2015) Methane oxidation coupled to oxygenic photosynthesis in anoxic waters, ISME Journal, 9(9), 1991-2002, doi:10.1038/ismej.2015.12, Institutional Repository

Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago di Cadagno)

Anaerobic oxidation of methane (AOM) has been investigated in sediments of a high alpine sulfate-rich lake. Hot spots of AOM could be identified based on geochemical and isotopic evidence. Very high fractionation of methane (α=1.031) during oxidation was observed in the uppermost sediment layers, where methane is oxidized most likely with sulfate-containing bottom waters. However, we could not exclude that other electron acceptors such as iron, or manganese might also be involved. Light carbon isotope values (δ13C=−10‰ vs. Vienna Pee Dee Belemnite [VPDB]) of sedimentary carbonates at 16–20 cm sediment depth are indicative of a zone where methane was oxidized and the resulting bicarbonate ions were used for carbonate precipitation. 16S rRNA gene analysis revealed the presence of sequences belonging to the marine benthic groups B, C, and D and to the recently described clade of AOM-associated archaea (AAA). Catalyzed reporter deposition-FISH analysis revealed a high abundance of Deltaproteobacteria, especially of free-living sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus branch of Deltaproteobacteria in the AOM zone. Here, loose aggregations of AAA cells were found, suggesting that AAA might be responsible for oxidation of methane in Lake Cadagno sediments.
Schubert, C. J.; Vazquez, F.; Lösekann-Behrens, T.; Knittel, K.; Tonolla, M.; Boetius, A. (2011) Evidence for anaerobic oxidation of methane in sediments of a freshwater system (Lago di Cadagno), FEMS Microbiology Ecology, 76(1), 26-38, doi:10.1111/j.1574-6941.2010.01036.x, Institutional Repository

Nutrient regime shift in the western North Atlantic indicated by compound-specific δ15N of deep-sea gorgonian corals

Despite the importance of the nitrogen (N) cycle on marine productivity, little is known about variability in N sources and cycling in the ocean in relation to natural and anthropogenic climate change. Beyond the last few decades of scientific observation, knowledge depends largely on proxy records derived from nitrogen stable isotopes (δ15N) preserved in sediments and other bioarchives. Traditional bulk δ15N measurements, however, represent the combined influence of N source and subsequent trophic transfers, often confounding environmental interpretation. Recently, compound-specific analysis of individual amino acids (δ15N-AA) has been shown as a means to deconvolve trophic level versus N source effects on the δ15N variability of bulk organic matter. Here, we demonstrate the first use of δ15N-AA in a paleoceanographic study, through analysis of annually secreted growth rings preserved in the organic endoskeletons of deep-sea gorgonian corals. In the Northwest Atlantic off Nova Scotia, coral δ15N is correlated with increasing presence of subtropical versus subpolar slope waters over the twentieth century. By using the new δ15N-AA approach to control for variable trophic processing, we are able to interpret coral bulk δ15N values as a proxy for nitrate source and, hence, slope water source partitioning. We conclude that the persistence of the warm, nutrient-rich regime since the early 1970s is largely unique in the context of the last approximately 1,800 yr. This evidence suggests that nutrient variability in this region is coordinated with recent changes in global climate and underscores the broad potential of δ15N-AA for paleoceanographic studies of the marine N cycle.
Sherwood, O. A.; Lehmann, M. F.; Schubert, C. J.; Scott, D. B.; McCarthy, M. D. (2011) Nutrient regime shift in the western North Atlantic indicated by compound-specific δ15N of deep-sea gorgonian corals, Proceedings of the National Academy of Sciences of the United States of America PNAS, 108(3), 1011-1015, doi:10.1073/pnas.1004904108, Institutional Repository

Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika)

Here we provide the first direct evidence for the anammox process (anaerobic ammonium oxidation) in a lacustrine system, Lake Tanganyika, the second largest lake in the world. Incubations with 15N labelled nitrate showed that anammox occurred in the suboxic water layer at 100-110 m water depth. Anammox rates up to 10 nM N2 h-1 are comparable to those reported for the marine water column. Up to ∼13% of produced N2 could be attributed to the anammox process whereas the remainder was related to denitrification. Typical lipid biomarkers characteristic of f anammox bacteria were found in filtered water from the depths where anammox occurred, thus supporting the presence of anammox bacteria. Further evidence is provided by fluorescence in situ hybridization (FISH), revealing up to 13 000 anammox bacteria cells per ml or 1.4% of all DAPI (4′-6-Diamidino-2-phenylindole)-stained cells. Phylogenetic analyses of partial 16S rRNA genes indicated the presence of sequences most closely related to the known anammox bacterium Candidatus 'Scalindua brodae' (95.7% similarity). Using the incubation results, a total loss of 0.2 Tg N2 per year linked to anammox was estimated for the Northern basin of Lake Tanganyika.
Schubert, C. J.; Durisch-Kaiser, E.; Wehrli, B.; Thamdrup, B.; Lam, P.; Kuypers, M. M. M. (2006) Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika), Environmental Microbiology, 8(10), 1857-1863, doi:10.1111/j.1462-2920.2006.01074.x, Institutional Repository

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