Dr. Jakob Zopfi - Publications


Bartosiewicz, M., A. Przytulska, A. Birkholz, H. Niemann, J. Zopfi, M. F. Lehmann (2024). Controls and significance of priming effects in lake sediments.Global Change Biology; https://doi.org/10.1111/gcb.17076



Bartosiewicz, M., J. Venetz, S. Läubli, O. Sepúlveda-Steiner, D. Bouffard, J. Zopfi and M. F. Lehmann (2023). Detritus-hosted methanogenesis sustains the methane paradox in oxic lake waters. Limnology and Oceanography; Vol. 68, 248-264; https://doi.org/10.1002/lno.12263

Su, G., M.F. Lehmann, J. Tischer, Y. Weber, F. Lepori, J.-C. Walser, H. Niemann, J. Zopfi (2023). Water column dynamics controls nitrite-dependent anaerobic methane oxidation by Candidatus ‘Methylomirabilis’ in stratified lake basins. The ISME Journal; 17, pages 693–702 (2023) https://doi.org/10.1038/s41396-023-01382-4



Tischer, J. , J. Zopfi, C. Frey, P. M. Magyar, A. Brand, K. Oswald, C. Jegge, C.H. Frame, M. R. Miracle, X. Sòria-Perpinyà, E. Vicente and M.F. Lehmann (2022). Isotopic signatures of biotic and abiotic N2O production and consumption in the water column of meromictic, ferruginous Lake La Cruz (Spain). Limnology and Oceanography; Vol. 67, 1760-1775; https://doi.org/10.1002/lno.12165

Su G, Zopfi J, Niemann H and Lehmann MF (2022) Multiple Groups of Methanotrophic Bacteria Mediate Methane Oxidation in Anoxic Lake Sediments. Front. Microbiol. 13:864630. doi: 10.3389/fmicb.2022.864630

Damsté, J.S.S., Weber, Y., Zopfi, J., Lehmann, M.F. and Niemann, H., 2022. Distributions and sources of isoprenoidal GDGTs in Lake Lugano and other central European (peri-) alpine lakes: Lessons for their use as paleotemperature proxies. Quaternary Science Reviews, 277, p.107352.



Buck, M., Garcia, S.L., Fernandez, L., Martin, G., Martinez-Rodriguez, G.A., Saarenheimo, J., Zopfi, J., Bertilsson, S. and Peura, S., 2021. Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds. Scientific Data, 8(1), pp.1-10.

van Grinsven, S., K. Oswald, C. Jegge, B. Wehrli, J. Zopfi, M.F. Lehmann, C.J. Schubert (2021). Methane oxidation in the waters of a humics-rich Finnish lake stimulated by photosynthesis, nitrite, Fe(III) and humics. Biogeosciences. 18, 3087–3101; (2021) https://doi.org/10.5194/bg-18-3087-2021

Liechti, N., Zimmermann, R.E., Zopfi, J., Robinson, M.T., Pierret, A., Ribolzi, O., Rattanavong, S., Davong, V., Newton, P.N., Wittwer, M. and Dance, D.A., 2021. Whole-genome assemblies of 16 Burkholderia pseudomallei isolates from rivers in Laos. Microbiology Resource Announcements, 10(4), pp.e01226-20.

Blattner, L., Ebner, J.N., Zopfi, J. and von Fumetti, S., 2021. Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments. Ecological Indicators129, p.107916.



Bagnoud, A., Guye-Humbert, S., Schloter-Hai, B., Schloter, M., Zopfi, J. (2020). Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils. FEMS Microbiology, Ecology, 96(2). doi.org/10.1093/femsec/fiz191

Cojean, A.N.Y., M. F. Lehmann, E. K. Robertson, B. Thamdrup, J. Zopfi (2020). Controls of H2S, Fe2+, Mn2+ on microbial NO3--reducing processes in sediments of a eutrophic lake. Frontiers in Microbiology; doi.org/10.3389/fmicb.2020.01158

Hu H., Wang B., Bravo A.G., Björn E., Skyllberg U., Amouroux D., Tessierg T., Zopfi J., Feng X., Bishop K., Nilsson M.B., Bertilsson S.(2020). Shifts in mercury methylation across a peatland chronosequence: From sulfate reduction to methanogenesis and syntrophy. Journal of Hazardous Materials, Vol. 387, 5 April 2020, 121967: doi.org/10.1016/j.jhazmat.2019.121967

Lehmann, M.F., Carstens, D., A. Deek, M. McCarthy, C. J. Schubert, and J. Zopfi, (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, Vol. 283, 67-84;doi.org/10.1016/j.gca.2020.05.025

Su, G., J. Zopfi, H. Yao, L. Steinle, H. Niemann, M. F. Lehmann (2020). Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments.  Limnology & Oceanography, https://doi.org/10.1002/lno.11354

Wirth S. B., Bouffard D., Zopfi J. (2020) Lacustrine groundwater discharge through giant pockmarks (Lake Neuchatel, Switzerland). Frontiers in Water 2:13. doi: 10.3389/frwa.2020.00013

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Cojean, A.N.Y., J. Zopfi, A. Gerster, C. Frey, F. Lepori, M.F. Lehmann (2019). Direct O2 control on the partitioning between denitrification and dissimilatory nitrate reduction to ammonium in lake sediments. Biogeosciences, 16, 4705-4718, doi.org/10.5194/bg-16-4705-2019

Kallies R., Kiesel B., Schmidt M., Ghanem N., Zopfi J., Hackermüller J., Harms H., Wick L.Y., Chatzinotas A. (2019) Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. Marine Genomics, Vol. 47, Doi: 10.1016/j.margen.2019.03.002.

Su, G., H. Niemann, L. Steinle J. Zopfi, M. F. Lehmann (2019). Evaluating radioisotope-based approaches to measure anaerobic methane oxidation rates in lacustrine sediments. Limnology and Oceanography Methods, doi: 10.1002/lom3.10323.

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Yuki Weber, Jaap S. Sinninghe Damsté, Jakob Zopfi, Cindy De Jonge, Adrian Gilli, Carsten J. Schubert, Fabio Lepori, Moritz F. Lehmann, Helge Niemann (2018). Redox-dependent niche differentiation provides evidence for multiple bacterial sources of glycerol tetraether lipids in lakes. Proceedings of the National Academy of Sciencedoi.org/10.1073/pnas.1805186115

Steinle, L., K.Knittel, N. Felber, C. Casalino, G. de Lange, C. Tessarolo, A. Stadniskaia, J. S. Sinninghe Damsté, J. Zopfi, M. F. Lehmann, T. Treude, H. Niemann (2018). Life on the edge: Active microbial communities within the Kryos MgCl2-brine basin at very low water activity. The ISME Journal. doi.org/10.1038/s41396-018-0107-z

Zimmermann, R. E., Ribolzi, O., Pierret, A., Rattanavong, S., Robinson, M. T., Newton, P. N., Davong, V., Auda, Y., Zopfi, J. & Dance, D. A. (2018). Rivers as carriers and potential sentinels for Burkholderia pseudomallei in Laos. Scientific reports8(1), 8674. doi.org/10.1038/s41598-018-26684-y

Bravo, A. G., Zopfi, J., Buck, M., Xu, J., Bertilsson, S., Schaefer, J. K., Poté, J. & Cosio, C. (2018). Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases. The ISME journal12(3), 802. doi.org/10.1038/s41396-017-0007-7

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Kallies, R., Kiesel, B., Zopfi, J., Wick, L. Y., & Chatzinotas, A. (2017). Complete genome sequence of Alteromonas Virus vB_AspP-H4/4. Genome Announcements, 5(43), e00914-17.

Camacho, A., Walter, X. A., Picazo, A., Zopfi, J. (2017). Photoferrotrophy: remains of an ancient photosynthesis in modern environments. Frontiers in Microbiology, 8, 323. doi: 10.3389/fmicb.2017.00323.

Grimmeisen, F., Lehmann, M. F., Liesch, T., Goeppert, N., Klinger, J., Zopfi, J., & Goldscheider, N. (2017). Isotopic constraints on water source mixing, network leakage and contamination in an urban groundwater system. The Science of the total environment, 583, 202-213.

Stopelli, E., Conen, F., Guilbaud, C., Zopfi, J., Alewell, C., & Morris, C. E. (2017). Ice nucleators, bacterial cells and Pseudomonas syringae in precipitation at Jungfraujoch. Biogeosciences, 14(5), 1189-1196.

Kallies, R., Kiesel, B., Schmidt, M., Kacza, J., Ghanem, N., Narr, A., Zopfi, J., Wick, L. Y., Hackermüller, J., Harms, H., Chatzinotas, A. (2017). Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. Standards in Genomic Sciences, 12(1), 20. DOI: 10.1186/s40793-017-0235-5.

Steinle, L., Maltby, J., Treude, T., Kock, A., Bange, H. W., Engbersen, N., Zopfi, J., Lehmann, M. F., & Niemann, H. (2017). Effects of low oxygen concentrations on aerobic methane oxidation in seasonally hypoxic coastal waters. Biogeosciences (BG), 14(6), 1631-1645.

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Steinle L., Schmidt M, Bryant L., Haeckel M., Linke P., Sommer S., Zopfi J., Lehmann M.F., Treude T., Niemannn N. (2016). Linked sediment and water-column methanotrophy at a man-made gas blowout in the North Sea: Implications for methane budgeting in seasonally stratified shallow seas. Limnology and Oceanography. (online first) doi: 10.1002/lno.10388.

Wenk C. B., Frame C. Casciotti K.L., Koba K, Veronesi M., Niemann H., Schubert C. J. H., Zopfi J., Lehmann M. L. (2016). Differential N2O dynamics in two oxygen‐deficient lake basins revealed by stable isotope and isotopomer distributions. Limnology and Oceanography, 61(5), 1735-1749.

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Lehmann M. L., Simona M., Wyss S., Blees B., Frame C. H., Niemann H., Veronesi M. Zopfi J (2015) Powering up the “biogeochemical engine”: the impact of exceptional ventilation of a deep meromictic lake on the lacustrine redox, nutrient, and methane balances. Frontiers Earth Sciences. doi: 10.3389/feart.2015.00045

Naeher, S., A. Huguet, C.L. Roose-Amsaleg, A.M. Laverman, C. Fosse, M.F. Lehmann, S. Derenne and J. Zopfi,  2015. Molecular and geochemical constraints on anaerobic ammonium oxidation (anammox) in a riparian zone of the Seine Estuary (France). Biogeochemistry; Volume 123 (1-2), 237-250; doi 10.1007/s10533-014-0066-z

Bravo, A. G., Bouchet, S., Guédron, S., Amouroux, D., Dominik, J. and Zopfi, J. (2015). High methylmercury production under ferruginous conditions in sediments impacted by sewage treatment plant discharges. Water Research. http://dx.doi.org/10.1016/j.watres.2015.04.039

Bergottini, V. M., M. B. Otegui, D. A. Sosa, P. D. Zapata, M. Mulot, M. Rebord, J. Zopfi, F. Wiss, B. Benrey, and P. Junier, 2015. Bio-inoculation of yerba mate seedlings (Ilex paraguariensis St. Hill.) with native plant growth-promoting rhizobacteria: a sustainable alternative to improve crop yield. Biology and Fertility of Soils. DOI 10.1007/s00374-015-1012-5

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Walter, X. Alexis; Picazo-Mozo, Antonio; Miracle, Maria Rosa; Vicente, Eduardo; Camacho, Antonio, Aragno, Michel; Zopfi, Jakob, 2014. Phototrophic Fe(II)-oxidation in the chemocline of a ferruginous meromictic lake. Frontiers in Microbiology, Volume 5,  Article-No. 713; doi:10.3389/fmicb.2014.00713

Wenk, C.B.,  J. Zopfi, J. Blees , W. S. Gardner, M. McCarthy, H. Niemann, M. L. Veronesi, and M. F. Lehmann, 2014. Quantitative partitioning between benthic and pelagic nitrate reduction in the Lake Lugano south basin. Limnology Oceanography, 59(4):1421-1433.

Blees J., H. Niemann, C. B. Wenk, J. Zopfi, C. J. Schubert, M. L. Veronesi, and M. F. Lehmann, 2014. Bacterial methanotrophs drive the formation of a seasonal anoxic benthic nepheloid layer in an alpine lake. Limnology Oceanography, 59(4):1410-1420.

Bravo A. G., Cosio C., Amouroux D., Zopfi J., Chevalley P.-A., Spangenberg J. E., Ungureanu V.-G., Dominik J. (2014) Extremely elevated methyl mercury levels in water, sediment and organisms in a Romanian reservoir affected by release of mercury from a chlor-alkali plant. Water Research, 49, 391-405.

Blees J., Niemann H., Wenk C. B., Zopfi J., Schubert C. J., Kirf M., Veronesi M. L., Hitz C., Lehmann, M. F. (2014) Micro-aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south-Alpine Lake Lugano (Switzerland). Limnology and Oceanography. 59, 311–324.

Wenk C. B., Zopfi J., Blees J., Veronesi M. L., Niemann H., Lehmann M.F. (2014). Community N and O isotope fractionation by sulfide-dependent denitrification and anammox in a stratified lacustrine water column. Geochimica Cosmochimica Acta. 125, 551–563

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D’Alessandro M., Erb M., Ton J., Brandenburg A., Karlen D., Zopfi J., Turlings T.C.J. (2013) Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions. Plant Cell and Environment. doi: 10.1111/pce.12220.

Wenk C. B., Blees J., Zopfi J., Veronesi M. L., Bourbonnais A., Schubert C.J., Niemann H., Lehmann M. F. (2013).Anaerobic ammonium oxidation (anammox) bacteria and sulfide-dependent denitrifiers coexist in the water column of a meromictic south-alpine lake. Limnology and Oceanography, 58, 1–12.

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Humbert S., Zopfi J., Tarnawski S.-E. (2012). Abundance of anammox bacteria in different wetland soils. Environmental Microbiology Reports 4, 484–490.

Martin G., Guggiari M., Bravo D., Zopfi J., Cailleau G., Aragno M., Job D., Verrecchia E.V., Junier J. (2012). Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction. Environmental Microbiology 14, 2960–70.

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Morasch B., Hunkeler D., Zopfi J., Temime B., Höhener, P. (2011). Intrinsic biodegradation potential of aromatic hydrocarbons in an alluvial aquifer--potentials and limits of signature metabolite analysis and two stable isotope-based techniques. Water Research 45, 4459–4469.

Haller L., Poté J., Zopfi J., Tonolla M., Wildi W. (2011) Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland). Water Research 45: 1213-1228.

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Goldscheider N., Pronk M., Zopfi J. (2010) New insights into the transport of sediments and microorganisms in karst groundwater by continuous monitoring of particle-size distribution. Geologia Croatica 63: 137-142.

Humbert S., Tarnawski S., Conen F., Seth B., Bagnoud A., Mallet M.-P., Fromin N., Aragno M. , Zopfi J. (2010) Bactéries anammox terrestres: diversité et activité. Bulletin BGS 30: 104-108.

Humbert S., Tarnawski S., Fromin N., Mallet M.-P., Aragno M., Zopfi J. (2010) Molecular detection of anammox bacteria in terrestrial ecosystems: distribution and diversity. ISME Journal 4: 450-454.

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Pronk M., Goldscheider N., Zopfi J., Zwahlen F. (2009b) Percolation and particle transport in the unsaturated zone of a karst aquifer. Ground Water 47(3): 361-369.

Poté J., Haller L., Goldscheider N., Zopfi J., Khajehnouri F, Wildi W., (2009) Origin and spatial–temporal distribution of faecal bacteria in a bay of Lake Geneva, Switzerland. Environmental Monitoring and Assessment 154(1-4): 337-348.

Sinreich M., Flynn R., Zopfi J. (2009) Use of particulate surrogates for assessing microbial mobility in subsurface ecosystems. Hydrogeology Journal 17(1): 49-59.

Pronk M., Goldscheider N., Zopfi J. (2009a) Microbial communities in karst groundwater and their potential use for biomonitoring. Hydrogeology Journal 17(1): 37-48.

Bravo A. G., Dominik J., Bouchet S., Amouroux D., Ungureanu V.-G., Zopfi J. (2009) Methylmercury concentrations and sulphate-reducing bacteria in freshwater sediments contaminated by a chlor-alkali plant: Babeni Reservoir, Romania Source: Recent Advances in Environment, Ecosystems and Development Book Series: Energy and Environmental Engineering Series. Pages: 196-200.

Goldscheider N., Pronk M., Zopfi J. (2009) Role of sediments and suspended particles for contaminant attenuation and transport in karst aquifer systems. Carsologica Sinica, 28 (2): 20-27.

Abe Y., Aravena R., Zopfi J., Parker B., Hunkeler D. (2009c) Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods, Journal of Contaminant Hydrology 107: 10-21.

Abe Y., Zopfi J., Hunkeler D. (2009b) Effect of molecule size on carbon isotope fractionation during biodegradation of chlorinated alkanes by Xanthobacter autotrophicus GJ10. Isotopes in Environmental Health Studies 45(1): 1-9. 

Abe Y., Aravena R., Zopfi J., Shouakar-Stash O., Hunkeler D. (2009a) Carbon and chlorine isotope fractionation during aerobic oxidation and reductive dechlorination of vinyl chloride and cis-DCE. Environmental Science and Technology 43(1): 101-107.

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Abe Y., Zopfi J., Hunkeler D. (2008) Effect of molecule size on carbon isotope fractionation during biodegradation of chlorinated alkanes by Xanthobacter autotrophicus GJ10. Isotopes in Environmental Health Studies 45(1); 1-9.

Zopfi J., Böttcher M. E., and Jørgensen B. B. (2008) Biogeochemistry of iron and sulfur in Thioploca-colonized sediments in the upwelling area off central Chile. Geochim. Cosmochim. Acta, 72 (3):827-843.

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Pronk M. Goldscheider N., Zopfi, J. (2007) Particle-size distribution as indicator for fecal Bacteria contamination of drinking water from karst springs. Environ. Sci. Technol. 41(24); 8400-8405.

Goldscheider N., Haller L., Poté J., Wildi W., Zopfi J., (2007) Characterizing water circulation and contaminant transport in Lake Geneva using bacteriophage tracer experiments and limnological methods. Environ. Sci. Technol. 41(15); 5252-5258.

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Pronk M, Goldscheider N., Zopfi J (2006) Monitoring of organic carbon, natural particles and bacteria in a deep karst system, Yverdon-les-Bains, Switzerland. Proceedings of the 8th conference on limestone hydrogeology 2006, Neuchâtel Switzerland - ISBN 2-84867-143-2, p. 215-218.

Pronk M., Goldscheider N., and Zopfi J. (2006) Dynamics and interaction of organic carbon, turbidity and bacteria in a karst aquifer system - first results from the Yverdon test site (Switzerland). Hydrogeology Journal 14(4): 473-484.

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1998 - 2005

Wieland A., Zopfi J., Benthien M., Kühl M. (2005) Biogeochemistry of an iron-rich hypersaline microbial mat (Camargue, France). Microb. Ecol. 49, 34-49.

Wieland A., Zopfi J., Benthien M., Kühl, M. (2003) Biogeochemistry of an iron-rich microbial mat (Camargue, France): Oxygen, sulfur and carbon cycling. In: P. Caumette (ed.), Proceedings of the 3rd MATBIOPOL meeting, St. Raphael, 22-25 January, 2003.

Wieland A., Zopfi J., Benthien M., Kühl, M. (2002) Biogeochemistry of microbial mats in the Camargue (France). In: P. Caumette (ed.), Proceedings of the 2nd MATBIsOPOL meeting, Barcelona, 12-16 February, 2002, pp. 21-50.

Zopfi J., Kjær T., Nielsen L.-P., Jørgensen B. B. (2001) Filamentous sulfur bacteria, Thioploca, in Chilean shelf sediments: NO3- and S0 storage in relation to chemical microgradients. Appl. Environ. Microbiol. 67, 5530-5537.

Jørgensen B. B., Weber A., Zopfi J. (2001) Sulfate reduction and anaerobic methane oxidation in Black Sea sediments. Deep Sea Res. I. 48, 2097-2120.

Zopfi J., Ferdelman T. G., Jørgensen B. B., Teske A., Thamdrup B. (2001) Influence of water column dynamics on sulfide oxidation and other major biogeochemical processes in the chemocline of Mariager Fjord (Denmark). Mar. Chem. 74, 29-41.

Santegoeds C., Damgaard L., Hesselink C., Zopfi J., Lens P., Muyzer G., DeBeer D. (1999) Distribution of sulfate-reducing and methanogenic bacteria in anaerobic aggregates determined by microsensor and molecular analyses. Appl. Environ. Microbiol. 65, 4618-4629.

Otte S., Kuenen J. G., Nielsen L. P., Paerl H. W., Zopfi J., Schulz H. N., Teske A., Strotmann B., Gallardo V. A., Jørgensen B. B. (1999) Nitrogen, carbon and sulfur metabolism in natural Thioploca samples. Appl. Environ. Microbiol. 65, 3148-3157.

Zopfi J., Thamdrup B., Jørgensen B. B., Ramsing N. B., Teske A., Ferdelman T. G. (1998) Biogeochemical processes in the stratified water column of Mariager Fjord (Denmark). Mineral. Mag. 63, 1709-1710.

Wenk M., Baumgartner T., Dobovsek J., Fuchs T., Kucsera J., Zopfi J., Stucki G. (1998) Rapid Atrazine mineralisation in soil slurry and moist soil by inoculation of an Atrazine-degrading Pseudomonas sp. strain. Appl. Microbiol. Biotechnol. 49, 624-630.

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Book Chapters: 

Walter X. A., Dupraz C., Zopfi J. (2007) Les tapis microbiens et la dynamique hydrique de la tourbière de Cadagno. In: Peduzzi R., Tonolla M. et Boucher-Rodoni R. (eds). Milieux alpins et changement global Vol. 1. Editions Centre de Biologie Alpine de Piora (ISSN 1424-4993): 27-45.

Zopfi J., Ferdelman T. G., Fossing H. (2004) Distribution and fate of sulfur intermediates – sulfite, tetrathionate, thiosulfate, and elemental sulfur - in marine sediments. In: Amend J.P., Edwards K.J. and Lyons T.W. (eds.), Sulfur biogeochemistry – Past and present: Boulder Colorado, Geological Society of America. pp. 97-116.

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