Articles | Volume 22, issue 17
https://doi.org/10.5194/bg-22-4449-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/bg-22-4449-2025
© Author(s) 2025. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Research article
| 
09 Sep 2025
Research article |
| 09 Sep 2025
| 09 Sep 2025
Methanogenesis by CO2 reduction dominates lake sediments with different organic matter compositions
Guangyi Su
CORRESPONDING AUTHOR
Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Department of Surface Waters – Research and Management, 6047 Kastanienbaum, Switzerland
Julie Tolu
Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Department of Water resources and Drinking water, 8600 Duebendorf, Switzerland
Clemens Glombitza
Department of Environmental Systems Sciences, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
Jakob Zopfi
Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
Moritz F. Lehmann
Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
Mark A. Lever
Department of Environmental Systems Sciences, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
Carsten J. Schubert
Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Department of Surface Waters – Research and Management, 6047 Kastanienbaum, Switzerland
Department of Environmental Systems Sciences, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland
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Cited articles
Bartosiewicz, M., Przytulska, A., Birkholz, A., Zopfi, J., and Lehmann, M. F.: Controls and significance of priming effects in lake sediments, Glob. Chang. Biol., 30, 1–13, https://doi.org/10.1111/gcb.17076, 2024.
Bastviken, D., Tranvik, L. J., Downing, J. A., Crill, P. M., and Enrich-Prast, A.: Freshwater methane emissions offset the continental carbon sink, Science, 331, 50–50, https://doi.org/10.1126/science.1196808, 2011.
Bechtel, A. and Schubert, C. J.: A biogeochemical study of sediments from the eutrophic Lake Lugano and the oligotrophic Lake Brienz, Switzerland, Org. Geochem., 40, 1100–1114, https://doi.org/10.1016/j.orggeochem.2009.06.009, 2009.
Bélanger, É., Lucotte, M., Moingt, M., Paquet, S., Oestreicher, J., and Rozon, C.: Altered nature of terrestrial organic matter transferred to aquatic systems following deforestation in the Amazon, Appl. Geochem., 87, 136–145, https://doi.org/10.1016/j.apgeochem.2017.10.016, 2017.
Berberich, M. E., Beaulieu, J. J., Hamilton, T. L., Waldo, S., and Buffam, I.: Spatial variability of sediment methane production and methanogen communities within a eutrophic reservoir: Importance of organic matter source and quantity, Limnol. Oceanogr., 65, 1336–1358, https://doi.org/10.1002/lno.11392, 2020.
Beulig, F., Røy, H., Glombitza, C., and Jørgensen, B. B.: Control on rate and pathway of anaerobic organic carbon degradation in the seabed, P. Natl. Acad. Sci. USA, 115, 367–372, https://doi.org/10.1073/pnas.1715789115, 2018.
Blair, N. E., Leithold, E. L., Thanos Papanicolaou, A. N., Wilson, C. G., Keefer, L., Kirton, E., Vinson, D., Schnoebelen, D., Rhoads, B., Yu, M., and Lewis, Q.: The C-biogeochemistry of a Midwestern USA agricultural impoundment in context: Lake Decatur in the intensively managed landscape critical zone observatory, Biogeochemistry, 138, 171–195, https://doi.org/10.1007/s10533-018-0439-9, 2018.
Burrus, D., Thomas, R. L., Dominik, J., and Vernet, J.-P.: Recovery and concentration of suspended solids in the upper Rhone River by continuous flow centrifugation, Hydrol. Process., 3, 65–74, https://doi.org/10.1002/hyp.3360030107, 1989.
Chikaraishi, Y., Naraoka, H., and Poulson, S. R.: Hydrogen and carbon isotopic fractionations of lipid biosynthesis among terrestrial (C3, C4 and CAM) and aquatic plants, Phytochemistry, 65, 1369–1381, https://doi.org/10.1016/j.phytochem.2004.03.036, 2004.
Cloern, J. E., Canuel, E. A., and Harris, D.: Stable carbon and nitrogen isotope composition of aquatic and terrestrial plants of the San Francisco Bay estuarine system, Limnol. Oceanogr., 47, 713–729, https://doi.org/10.4319/lo.2002.47.3.0713, 2002.
Conrad, R.: Quantification of methanogenic pathways using stable carbon isotopic signatures: a review and a proposal, Org. Geochem., 36, 739–752, https://doi.org/10.1016/j.orggeochem.2004.09.006, 2005.
Conrad, R.: Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: A mini review, Pedosphere, 30, 25–39, https://doi.org/10.1016/S1002-0160(18)60052-9, 2020.
Conrad, R., Noll, M., Claus, P., Klose, M., Bastos, W. R., and Enrich-Prast, A.: Stable carbon isotope discrimination and microbiology of methane formation in tropical anoxic lake sediments, Biogeosciences, 8, 795–814, https://doi.org/10.5194/bg-8-795-2011, 2011.
Conrad, R., Klose, M., and Enrich-Prast, A.: Acetate turnover and methanogenic pathways in Amazonian lake sediments, Biogeosciences, 17, 1063–1069, https://doi.org/10.5194/bg-17-1063-2020, 2020.
Cranwell, P. A.: Monocarboxylic acids in lake sediments: Indicators, derived from terrestrial and aquatic biota, of paleoenvironmental trophic levels, Chem. Geol., 14, 1–14, https://doi.org/10.1016/0009-2541(74)90092-8, 1974.
Cranwell, P. A.: Decomposition of aquatic biota and sediment formation: organic compounds in detritus resulting from microbial attack on the alga Ceratium hirundinella, Freshwater Biol., 6, 41–48, https://doi.org/10.1111/j.1365-2427.1976.tb01589.x, 1976.
Dai, J., Sun, M.-Y., Culp, R. A., and Noakes, J. E.: Changes in chemical and isotopic signatures of plant materials during degradation: Implication for assessing various organic inputs in estuarine systems, Geophys. Res. Lett., 32, L13608, https://doi.org/10.1029/2005GL023133, 2005.
Davidson, T. A., Audet, J., Jeppesen, E., Landkildehus, F., Lauridsen, T. L., Søndergaard, M., and Syväranta, J.: Synergy between nutrients and warming enhances methane ebullition from experimental lakes, Nat. Clim. Change, 8, 156–160, https://doi.org/10.1038/s41558-017-0063-z, 2018.
Dean, W. E. and Gorham, E.: Magnitude and significance of carbon burial in lakes, reservoirs, and peatlands, Geology, 26, 535, https://doi.org/10.3133/fs05899, 1998.
DelSontro, T., Kunz, M. J., Kempter, T., Wüest, A., Wehrli, B., and Senn, D. B.: Spatial heterogeneity of methane ebullition in a large tropical reservoir, Environ. Sci. Technol., 45, 9866–9873, https://doi.org/10.1021/es2005545, 2011.
Demirel, B. and Scherer, P.: The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review, Rev. Environ. Sci. Biotechnol., 7, 173–190, https://doi.org/10.1007/s11157-008-9131-1, 2008.
Downing, J. A., Prairie, Y. T., Cole, J. J., Duarte, C. M., Tranvik, L. J., Striegl, R. G., McDowell, W. H., Kortelainen, P., Caraco, N. F., Melack, J. M., and Middelburg, J. J.: The global abundance and size distribution of lakes, ponds, and impoundments, Limnol. Oceanogr., 51, 2388–2397, https://doi.org/10.4319/lo.2006.51.5.2388, 2006.
Eglinton, G. and Hamilton, R. J.: Leaf epicuticular waxes, Science, 156, 1322–1335, https://doi.org/10.1126/science.156.3780.1322, 1967.
Ernst, L., Steinfeld, B., Barayeu, U., Klintzsch, T., Kurth, M., Grimm, D., Dick, T. P., Rebelein, J. G., Bischofs, I. B., and Keppler, F.: Methane formation driven by reactive oxygen species across all living organisms, Nature, 603, 482–487, https://doi.org/10.1038/s41586-022-04511-9, 2022.
Ficken, K. J., Li, B., Swain, D. L., and Eglinton, G.: An n-alkane proxy for the sedimentary input of submerged/floating freshwater aquatic macrophytes, Org. Geochem., 31, 745–749, https://doi.org/10.1016/S0146-6380(00)00081-4, 2000.
Gallina, N., Beniston, M., and Jacquet, S.: Estimating future cyanobacterial occurrence and importance in lakes: a case study with Planktothrix rubescens in Lake Geneva, Aquat. Sci., 79, 249–263, https://doi.org/10.1007/s00027-016-0494-z, 2017.
Glombitza, C., Pedersen, J., Røy, H., and Jørgensen, B. B.: Direct analysis of volatile fatty acids in marine sediment porewater by two-dimensional ion chromatography-mass spectrometry, Limnol. Oceanogr.-Meth., 12, 455–468, https://doi.org/10.4319/lom.2014.12.455, 2014.
Grasset, C., Mendonça, R., Villamor Saucedo, G., Bastviken, D., Roland, F., and Sobek, S.: Large but variable methane production in anoxic freshwater sediment upon addition of allochthonous and autochthonous organic matter, Limnol. Oceanogr., 63, 1488–1501, https://doi.org/10.1002/lno.10786, 2018.
Han, X., Schubert, C. J., Fiskal, A., Dubois, N., and Lever, M. A.: Eutrophication as a driver of microbial community structure in lake sediments, Environ. Microbiol., 22, 3446–3462, https://doi.org/10.1111/1462-2920.15115, 2020.
Han, X., Tolu, J., Deng, L., Fiskal, A., Schubert, C. J., Winkel, L. H. E., and Lever, M. A.: Long-term preservation of biomolecules in lake sediments: potential importance of physical shielding by recalcitrant cell walls, PNAS Nexus, 1, pgac076, https://doi.org/10.1093/pnasnexus/pgac076, 2022.
Hansen, L. K., Jakobsen, R., and Postma, D.: Methanogenesis in a shallow sandy aquifer, Rømø, Denmark, Geochim. Cosmochim. Ac., 65, 2925–2935, https://doi.org/10.1016/S0016-7037(01)00653-6, 2001.
Hedges, J. I., Clark, W. A., Quay, P. D., Richey, J. E., Devol, A. H., and Santos, M.: Compositions and fluxes of particulate organic material in the Amazon River, Limnol. Oceanogr., 31, 717–738, https://doi.org/10.4319/lo.1986.31.4.0717, 1986.
IPCC, 2021: Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change, edited by: Masson-Delmotte, V., Zhai, P., Pirani, A., Connors, S. L., Péan, C., Berger, S., Caud, N., Chen, Y., Goldfarb, L., Gomis, M. I., Huang, M., Leitzell, K., Lonnoy, E., Matthews, J. B. R., Maycock, T. K., Waterfield, T., Yelekçi, O., Yu, R., and Zhou, B., Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA, https://doi.org/10.1017/9781009157896, 2021.
Jetten, M. S. M., Stams, A. J. M., and Zehnder, A. J. B.: Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp., FEMS Microbiol. Lett., 88, 181–198, https://doi.org/10.1111/j.1574-6968.1992.tb04987.x, 1992.
Kawamura, K., Ishiwatari, R., and Ogura, K.: Early diagenesis of organic matter in the water column and sediments: Microbial degradation and resynthesis of lipids in Lake Haruna, Org. Geochem., 11, 251–264, https://doi.org/10.1016/0146-6380(87)90036-2, 1987.
Kristensen, E., Ahmed, S. I., and Devol, A. H.: Aerobic and anaerobic decomposition of organic matter in marine sediment: Which is fastest?, Limnol. Oceanogr., 40, 1430–1437, https://doi.org/10.4319/lo.1995.40.8.1430, 1995.
Kuivila, K. M., Murray, J. W., Devol, A. H., and Novelli, P. C.: Methane production, sulfate reduction and competition for substrates in the sediments of Lake Washington, Geochim. Cosmochim. Ac., 53, 409–416, https://doi.org/10.1016/0016-7037(89)90392-X, 1989.
Ladd, S. N., Nelson, D. B., Schubert, C. J., and Dubois, N.: Lipid compound classes display diverging hydrogen isotope responses in lakes along a nutrient gradient, Geochim. Cosmochim. Ac., 237, 103–119, https://doi.org/10.1016/j.gca.2018.06.005, 2018.
Lamb, A. L., Wilson, G. P., and Leng, M. J.: A review of coastal palaeoclimate and relative sea-level reconstructions using δ13C and C
Larsen, S., Andersen, T., and Hessen, D. O.: Climate change predicted to cause severe increase of organic carbon in lakes, Glob. Change Biol., 17, 1186–1192, https://doi.org/10.1111/j.1365-2486.2010.02257.x, 2011.
Lehmann, M. F., Bernasconi, S. M., Barbieri, A., and McKenzie, J. A.: Preservation of organic matter and alteration of its carbon and nitrogen isotope composition during simulated and in situ early sedimentary diagenesis, Geochim. Cosmochim. Ac., 66, 3573–3584, https://doi.org/10.1016/S0016-7037(02)00968-7, 2002.
Lehmann, M. F., Carstens, D., Deek, A., McCarthy, M., Schubert, C. J., and Zopfi, J.: Amino acid and amino sugar compositional changes during in vitro degradation of algal organic matter indicate rapid bacterial re-synthesis, Geochim. Cosmochim. Ac., 283, 67–84, https://doi.org/10.1016/j.gca.2020.05.025, 2020.
Lever, M. A. and Teske, A. P.: Diversity of methane-cycling archaea in hydrothermal sediment investigated by general and group-specific PCR primers, Appl. Environ. Microb., 81, 1426–1441, https://doi.org/10.1128/AEM.03588-14, 2015.
Li, B., Wang, H., Lai, A., Xue, J., Wu, Q., Yu, C., Xie, K., Mao, Z., Li, H., Xing, P., and Wu, Q. L.: Hydrogenotrophic pathway dominates methanogenesis along the river-estuary continuum of the Yangtze River, Water Res., 240, 120096, https://doi.org/10.1016/j.watres.2023.120096, 2023.
Liu, Y. and Whitman, W. B.: Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea, Ann. NY Acad. Sci., 1125, 171–189, https://doi.org/10.1196/annals.1419.019, 2008.
Liu, Y., Conrad, R., Yao, T., Gleixner, G., and Claus, P.: Change of methane production pathway with sediment depth in a lake on the Tibetan plateau, Palaeogeogr. Palaeocl., 474, 279–286, https://doi.org/10.1016/j.palaeo.2016.06.021, 2017.
Lyu, Z., Shao, N., Akinyemi, T., and Whitman, W. B.: Methanogenesis, Curr, Biol., 28, R727–R732, https://doi.org/10.1016/j.cub.2018.05.021, 2018.
McMurdie, P. J. and Holmes, S.: Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, 1–11, https://doi.org/10.1371/journal.pone.0061217, 2013.
Meier, D., van Grinsven, S., Michel, A., Eickenbusch, P., Glombitza, C., Han, X., Fiskal, A., Bernasconi, S., Schubert, C. J., and Lever, M. A.: Hydrogen–independent CO2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states, ISME Communications, 4, ycae089, https://doi.org/10.1093/ismeco/ycae089, 2024.
Mendonça, R., Müller, R. A., Clow, D., Verpoorter, C., Raymond, P., Tranvik, L. J., and Sobek, S.: Organic carbon burial in global lakes and reservoirs, Nat. Commun., 8, 1–6, https://doi.org/10.1038/s41467-017-01789-6, 2017.
Meyers, P. A. and Ishiwatari, R.: Lacustrine organic geochemistry-an overview of indicators of organic matter sources and diagenesis in lake sediments, Org. Geochem., 20, 867–900, https://doi.org/10.1016/0146-6380(93)90100-P, 1993.
Meyers, P. A. and Takeuchi, N.: Environmental changes in Saginaw Bay, Lake Huron recorded by geolipid contents of sediments deposited since 1800, Environ. Geol., 3, 257–266, https://doi.org/10.1007/BF02473517, 1981.
O'Leary, M. H.: Carbon isotope fractionation in plants, Phytochemistry, 20, 553–567, https://doi.org/10.1016/0031-9422(81)85134-5, 1981.
Opsahl, S. and Benner, R.: Early diagenesis of vascular plant tissues: Lignin and cutin decomposition and biogeochemical implications, Geochim. Cosmochim. Ac., 59, 4889–4904, https://doi.org/10.1016/0016-7037(95)00348-7, 1995.
Parsons, T. R., Stephens, K., and Strickland, J. D. H.: On the Chemical Composition of Eleven Species of Marine Phytoplankters, J. Fish. Res. Board Can., 18, 1001–1016, https://doi.org/10.1139/f61-063, 1961.
R Core Team: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing [online], https://www.r-project.org/ (last access: 20 January 2025), 2024.
Randlett, M.-E., Sollberger, S., Del Sontro, T., Müller, B., Corella, J. P., Wehrli, B., and Schubert, C. J.: Mineralization pathways of organic matter deposited in a river–lake transition of the Rhone River Delta, Lake Geneva, Environ. Sci. Process Impacts, 17, 370–380, https://doi.org/10.1039/C4EM00470A, 2015.
Raymond, P. A. and Bauer, J. E.: Riverine export of aged terrestrial organic matter to the North Atlantic Ocean, Nature, 409, 497–500, https://doi.org/10.1038/35054034, 2001.
Ritalahti, K. M., Amos, B. K., Sung, Y., Wu, Q., Koenigsberg, S. S., and Löffler, F. E.: Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains, Appl. Environ. Microb., 72, 2765–2774, https://doi.org/10.1128/AEM.72.4.2765-2774.2006, 2006.
Rotaru, A.-E., Shrestha, P. M., Liu, F., Shrestha, M., Shrestha, D., Embree, M., Zengler, K., Wardman, C., Nevin, K. P., and Lovley, D. R.: A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane, Energy Environ. Sci., 7, 408–415, https://doi.org/10.1039/C3EE42189A, 2014.
Schaedler, F., Lockwood, C., Lueder, U., Glombitza, C., Kappler, A., and Schmidt, C.: Microbially mediated coupling of Fe and N cycles by nitrate-reducing Fe (II)-oxidizing bacteria in littoral freshwater sediments, Appl. Environ. Microb., 84, 1–14, https://doi.org/10.1128/AEM.02013-17, 2018.
Schellekens, J., Buurman, P., and Pontevedra-Pombal, X.: Selecting parameters for the environmental interpretation of peat molecular chemistry – A pyrolysis-GC/MS study, Org. Geochem., 40, 678–691, https://doi.org/10.1016/j.orggeochem.2009.03.006, 2009.
Schubert, C. J. and Nielsen, B.: Effects of decarbonation treatments on δ13C values in marine sediments, Mar. Chem., 72, 55–59, https://doi.org/10.1016/S0304-4203(00)00066-9, 2000.
Schulz, S. and Conrad, R.: Effect of algal deposition on acetate and methane concentrations in the profundal sediment of a deep lake (Lake Constance), FEMS Microbiol. Ecol., 16, 251–259, https://doi.org/10.1016/0168-6496(94)00088-E, 1995.
Schulz, S. and Conrad, R.: Influence of temperature on pathways to methane production in the permanently cold profundal sediment of Lake Constance, FEMS Microbiol. Ecol., 20, 1–14, https://doi.org/10.1016/0168-6496(96)00009-8, 1996.
Schwarz, J. I. K. K., Eckert, W., and Conrad, R.: Response of the methanogenic microbial community of a profundal lake sediment (Lake Kinneret, Israel) to algal deposition, Limnol. Oceanogr., 53, 113–121, https://doi.org/10.4319/lo.2008.53.1.0113, 2008.
Shi, W., Sun, M. Y., Molina, M., and Hodson, R. E.: Variability in the distribution of lipid biomarkers and their molecular isotopic composition in Altamaha estuarine sediments: Implications for the relative contribution of organic matter from various sources, Org. Geochem., 32, 453–467, https://doi.org/10.1016/S0146-6380(00)00189-3, 2001.
Smith, K. S. and Ingram-Smith, C.: Methanosaeta, the forgotten methanogen?, Trends Microbiol., 15, 150–155, https://doi.org/10.1016/j.tim.2007.02.002, 2007.
Sobek, S., Durisch-Kaiser, E., Zurbrügg, R., Wongfun, N., Wessels, M., Pasche, N., and Wehrli, B.: Organic carbon burial efficiency in lake sediments controlled by oxygen exposure time and sediment source, Limnol. Oceanogr., 54, 2243–2254, https://doi.org/10.4319/lo.2009.54.6.2243, 2009.
Sobek, S., DelSontro, T., Wongfun, N., and Wehrli, B.: Extreme organic carbon burial fuels intense methane bubbling in a temperate reservoir, Geophys. Res. Lett., 39, 2–5, https://doi.org/10.1029/2011GL050144, 2012.
Sollberger, S., Corella, J. P., Girardclos, S., Randlett, M. E., Schubert, C. J., Senn, D. B., Wehrli, B., and DelSontro, T.: Spatial heterogeneity of benthic methane dynamics in the subaquatic canyons of the Rhone River Delta (Lake Geneva), Aquat. Sci., 76, 89–101, https://doi.org/10.1007/s00027-013-0319-2, 2014.
Su, G., Niemann, H., Steinle, L., Zopfi, J., and Lehmann, M. F.: Evaluating radioisotope-based approaches to measure anaerobic methane oxidation rates in lacustrine sediments, Limnol. Oceanogr.-Meth., 17, 429–438, https://doi.org/10.1002/lom3.10323, 2019.
Su, G., Zopfi, J., Yao, H., Steinle, L., Niemann, H., and Lehmann, M. F.: Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments, Limnol. Oceanogr., 65, 863–875, https://doi.org/10.1002/lno.11354, 2020.
Su, G., Lehmann, M. F., Tischer, J., Weber, Y., Lepori, F., Walser, J.-C., Niemann, H., and Zopfi, J.: Water column dynamics control nitrite-dependent anaerobic methane oxidation by Candidatus “Methylomirabilis” in stratified lake basins, ISME J., 17, 693–702, https://doi.org/10.1038/s41396-023-01382-4, 2023.
Tolu, J., Gerber, L., Boily, J.-F., and Bindler, R.: High-throughput characterization of sediment organic matter by pyrolysis–gas chromatography/mass spectrometry and multivariate curve resolution: A promising analytical tool in (paleo)limnology, Anal. Chim. Acta., 880, 93–102, https://doi.org/10.1016/j.aca.2015.03.043, 2015.
Tolu, J., Rydberg, J., Meyer-Jacob, C., Gerber, L., and Bindler, R.: Spatial variability of organic matter molecular composition and elemental geochemistry in surface sediments of a small boreal Swedish lake, Biogeosciences, 14, 1773–1792, https://doi.org/10.5194/bg-14-1773-2017, 2017.
Valentine, D. W., Holland, E. A., and Schimel, D. S.: Ecosystem and physiological controls over methane production in northern wetlands, J. Geophys. Res., 99, 1563, https://doi.org/10.1029/93JD00391, 1994.
Volkman, J. K.: A review of sterol markers for marine and terrigenous organic matter, Org. Geochem., 9, 83–99, https://doi.org/10.1016/0146-6380(86)90089-6, 1986.
Volkman, J. K., Johns, R. B., Gillan, F. T., Perry, G. J., and Bavor, H. J.: Microbial lipids of an intertidal sediment – I. Fatty acids and hydrocarbons, Geochim. Cosmochim. Ac., 44, 1133–1143, https://doi.org/10.1016/0016-7037(80)90067-8, 1980.
Volkman, J. K., Barrett, S. M., Blackburn, S. I., Mansour, M. P., Sikes, E. L., and Gelin, F.: Microalgal biomarkers: A review of recent research developments, Org. Geochem., 29, 1163–1179, https://doi.org/10.1016/S0146-6380(98)00062-X, 1998.
West, W. E., Coloso, J. J., and Jones, S. E.: Effects of algal and terrestrial carbon on methane production rates and methanogen community structure in a temperate lake sediment, Freshwater Biol., 57, 949–955, https://doi.org/10.1111/j.1365-2427.2012.02755.x, 2012.
West, W. E., McCarthy, S. M., and Jones, S. E.: Phytoplankton lipid content influences freshwater lake methanogenesis, Freshwater Biol., 2261–2269, https://doi.org/10.1111/fwb.12652, 2015.
Whiticar, M. J.: Carbon and hydrogen isotope systematics of bacterial formation and oxidation of methane, Chem. Geol., 161, 291–314, https://doi.org/10.1016/S0009-2541(99)00092-3, 1999.
Whiticar, M. J. J., Faber, E., and Schoell, M.: Biogenic methane formation in marine and freshwater environments: CO2 reduction vs. acetate fermentation – Isotope evidence, Geochim. Cosmochim. Ac., 50, 693–709, https://doi.org/10.1016/0016-7037(86)90346-7, 1986.
Xiao, K.-Q., Beulig, F., Røy, H., Jørgensen, B. B., and Risgaard-Petersen, N.: Methylotrophic methanogenesis fuels cryptic methane cycling in marine surface sediment, Limnol. Oceanogr., 63, 1519–1527, https://doi.org/10.1002/lno.10788, 2018.
Xu, L., Zhuang, G. C., Montgomery, A., Liang, Q., Joye, S. B., and Wang, F.: Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea, Environ. Microbiol., 23, 641–651, https://doi.org/10.1111/1462-2920.15110, 2021.
Zhao, B., Ma, J., Zhao, Q., Laurens, L., Jarvis, E., Chen, S., and Frear, C.: Efficient anaerobic digestion of whole microalgae and lipid-extracted microalgae residues for methane energy production, Bioresource Technol., 161, 423–430, https://doi.org/10.1016/j.biortech.2014.03.079, 2014.
Zhou, J., Smith, J. A., Li, M., and Holmes, D. E.: Methane production by Methanothrix thermoacetophila via direct interspecies electron transfer with Geobacter metallireducens, mBio, 2–3, https://doi.org/10.1128/mbio.00360-23, 2023.
Zhuang, G.-C., Heuer, V. B., Lazar, C. S., Goldhammer, T., Wendt, J., Samarkin, V. A., Elvert, M., Teske, A. P., Joye, S. B., and Hinrichs, K.-U.: Relative importance of methylotrophic methanogenesis in sediments of the Western Mediterranean Sea, Geochim. Cosmochim. Ac., 224, 171–186, https://doi.org/10.1016/j.gca.2017.12.024, 2018.
Short summary
In Lake Geneva, we studied how different types of organic matter affect methane production. Despite varying sources, like algae and land-based materials, both deep and delta areas are significant methane sources, and methane was mainly produced through CO2 reduction. Surprisingly, the origin of organic matter did not strongly influence methane production rates or pathways. Our findings highlight the need to better understand microbial processes to predict methane emissions from lakes.
In Lake Geneva, we studied how different types of organic matter affect methane production....
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