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Blattner, Lucas and Ebner, Joshua and Zopfi, Jakob and von Fumetti, Stefanie. (2021) Targeted non-invasive bioindicator species detection in eDNA water samples to assess and monitor the integrity of vulnerable alpine freshwater environments. Ecological indicators, 129. p. 107916.

Buck, M. and Garcia, S. L. and Fernandez, L. and Gaetan , M. and Martinez-Rodriguez, G. A. and Saarenheimo, J. and Saarenheimo, Jatta and Zopfi, J. and Bertilsson, S. and Peura, S.. (2021) Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds. Scientific Data, 8. p. 131.

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

van Grinsven, Sigrid and Oswald, Kirsten and Wehrli, Bernhard and Jegge, Corinne and Zopfi, Jakob and Lehmann, Moritz F. and Schubert, Carsten J.. (2021) Methane oxidation in the waters of a humic-rich boreal lake stimulated by photosynthesis, nitrite, Fe(III) and humics. Biogeosciences, 18 (10). pp. 3087-3101.


Su, Guangyi and Zopfi, Jakob and Yao, Haoyi and Steinle, Lea and Niemann, Helge and Lehmann, Moritz F.. (2020) Manganese/iron-supported sulfate-dependent anaerobic oxidation of methane by archaea in lake sediments. Limnology and Oceanography, 65 (4). pp. 863-875.

Bagnoud, Alexandre and Guye-Humbert, Sylvia and Schloter-Hai, Brigitte and Schloter, Michael and Zopfi, Jakob. (2020) Environmental factors determining distribution and activity of anammox bacteria in minerotrophic fen soils. FEMS Microbiology Ecology, 96 (2). fiz191.

Hu, Haiyan and Wang, Baolin and Bravo, Andrea G. and Björn, Erik and Skyllberg, Ulf and Amouroux, David and Tessier, Emmanuel and Zopfi, Jakob and Feng, Xinbin and Bishop, Kevin and Nilsson, Mats B. and Bertilsson, Stefan. (2020) Shifts in mercury methylation across a peatland chronosequence: From sulfate reduction to methanogenesis and syntrophy. Journal of Hazardous Materials, 387. p. 121967.

Wirth, Stefanie B. and Bouffard, Damien and Zopfi, Jakob. (2020) Lacustrine groundwater discharge through giant pockmarks (Lake Neuchatel, Switzerland). Frontiers in Water, 2. p. 13.

Cojean, Adeline N. Y. and Lehmann, Moritz F. and Robertson, Elizabeth K. and Thamdrup, Bo and Zopfi, Jakob. (2020) Controls of H2S, Fe2 +, and Mn2 + on Microbial NO3–-Reducing Processes in Sediments of an Eutrophic Lake. Frontiers in Microbiology, 11. p. 1158.


Kallies, René and Kiesel, Bärbel and Schmidt, Matthias and Ghanem, Nawras and Zopfi, Jakob and Hackermüller, Jörg and Harms, Hauke and Wick, Lukas Y. and Chatzinotas, Antonis. (2019) Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. Marine Genomics, 47. p. 100667.

Cojean, A. N. Y. and Zopfi, J. and Gerster, A. and Frey, C. and Lepori, F. and Lehmann, M. F.. (2019) Direct O-2 control on the partitioning between denitrification and dissimilatory nitrate reduction to ammonium in lake sediments. Biogeosciences, 16 (23). pp. 4705-4718.

Su, G. Y. and Niemann, H. and Steinle, L. and Zopfi, J. and Lehmann, M. F.. (2019) Evaluating radioisotope-based approaches to measure anaerobic methane oxidation rates in lacustrine sediments. Limnology and Oceanography-Methods, 17 (8). pp. 429-438.


Bravo, Andrea G. and Zopfi, Jakob and Buck, Moritz and Xu, Jingying and Bertilsson, Stefan and Schaefer, Jeffra K. and Poté, John and Cosio, Claudia. (2018) Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by wastewater releases. ISME Journal, 12 (3). pp. 802-812.

Zimmermann, Rosalie E. and Ribolzi, Olivier and Pierret, Alain and Rattanavong, Sayaphet and Robinson, Matthew T. and Newton, Paul N. and Davong, Viengmon and Auda, Yves and Zopfi, Jakob and Dance, David A. B.. (2018) Rivers as carriers and potential sentinels for Burkholderia pseudomallei in Laos. Scientific Reports, 8 (1). p. 8674.

Weber, Yuki and Damste, Jaap Sinninghe and Zopfi, Jakob and De Jonge, Cindy and Gilli, Adrian and Schubert, Carsten J. and Lepori, Fabio and Lehmann, Moritz F. and Niemann, Helge. (2018) Redox-dependent niche differentiation provides evidence for multiple bacterial sources of glycerol tetraether lipids in lakes. Proceedings of the National Academy of Sciences of the United States of America, 115 (43). pp. 10926-10931.

Steinle, Lea and Knittel, Katrin and Felber, Nicole and Casalino, Claudia and de Lange, Gert and Tessarolo, Chiara and Stadnitskaia, Alina and Sinninghe Damsté, Jaap S. and Zopfi, Jakob and Lehmann, Moritz F. and Treude, Tina and Niemann, Helge. (2018) Life on the edge: active microbial communities in the Kryos MgCl 2-brine basin at very low water activity. ISME Journal, 12. pp. 1414-1426.


Stopelli, Emiliano and Conen, Franz and Guilbaud, Caroline and Zopfi, Jakob and Alewell, Christine and Morris, Cindy. (2017) Ice nucleators have shorter persistence in the atmosphere than other airborne bacteria. 14 (5).

Steinle, Lea and Maltby, Johanna and Treude, Tina and Kock, Annette and Bange, Hermann W. and Engbersen, Nadine and Zopfi, Jakob and Lehmann, Moritz F. and Niemann, Helge. (2017) Effects of low oxygen concentrations on aerobic methane oxidation in seasonally hypoxic coastal waters. Biogeosciences, 14 (6). pp. 1631-1645.

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

Kallies, René and Kiesel, Bärbel and Zopfi, Jakob and Wick, Lukas Y. and Chatzinotas, Antonis. (2017) Complete Genome Sequence of Alteromonas Virus vB_AspP-H4/4. Genome Announcements, 5 (43). e00914-e00917.

Camacho, Antonio and Walter, Xavier A. and Picazo, Antonio and Zopfi, Jakob. (2017) Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments. Frontiers in Microbiology, 8. p. 323.

Kallies, René and Kiesel, Bärbel and Schmidt, Matthias and Kacza, Johannes and Ghanem, Nawras and Narr, Anja and Zopfi, Jakob and Wick, Lukas Y. and Hackermüller, Jörg and Harms, Hauke and Chatzinotas, Antonis. (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 (20).


Jaquet, Stéphan and Junier, Pilar and Zopfi, Jakob and Brandl, Helmut and Curtis, Thomas. (2016) Microbiologie. In: Dans les Abysses du Léman. Lausanne, pp. 146-168.


Blees, Jan and Niemann, Helge and Erne, Markus and Zopfi, Jakob and Schubert, Carsten J. and Lehmann, Moritz F.. (2015) Spatial variations in surface water methane super-saturation and emission in Lake Lugano, southern Switzerland. Aquatic sciences, 77 (4). pp. 535-545.

Bravo, Andrea Garcia and Bouchet, Sylvain and Guédron, Stéphane and Amouroux, David and Dominik, Janusz and Zopfi, Jakob. (2015) High methylmercury production under ferruginous conditions in sediments impacted by sewage treatment plant discharges. Water research, 80. pp. 245-255.

Bergottini, V. M. and Otegui, M. B. and Sosa, D. A. and Zapata, P. D. and Mulot, M. and Rebord, M. and Zopfi, J. and Wiss, F. and Benrey, B. and Junier, Pilar. (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, 51 (6). pp. 749-755.

Naeher, Sebastian and Huguet, Arnaud and Roose-Amsaleg, Celine L. and Laverman, Anniet M. and Fosse, Celine and Lehmann, Moritz F. and Derenne, Sylvie and Zopfi, Jakob. (2015) Molecular and geochemical constraints on anaerobic ammonium oxidation (anammox) in a riparian zone of the Seine Estuary (France). Biogeochemistry, 123 (1-2). pp. 237-250.

Lehmann, M. F. and Simona, M. and Wyss, S. and Blees, J. H. and Frame, C. H. and Niemann, H. and Veronesi, M. and 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 in Earth Scienecs, 3. p. 45.


Wenk, Christine B. and Zopfi, Jakob and Blees, Jan and Veronesi, Mauro L. and Niemann, Helge and Lehmann, Moritz F.. (2014) Community N and O isotope fractionation by sulfide-dependent denitrification and anammox in a stratified lacustrine water column. Geochimica et cosmochimica acta, Vol. 125. pp. 551-563.

Blees, Jan and Niemann, Helge and Wenk, Christine B. and Zopfi, Jakob and Schubert, Carsten J. and Kirf, Matthias T. and Veronesi, Mauro and Hitz, Carmen and Lehmann, Moritz F.. (2014) Micro-aerobic bacterial methane oxidation in the chemocline and anoxic water column of deep south-Alpine Lake Lugano (Switzerland). Limnology and oceanography, Vol. 59, H. 2. pp. 311-324.

Wenk, Christine B. and Zopfi, Jakob and Blees, Jan and Gardner, Wayne S. and McCarthy, Mark and Niemann, Helge and Veronesi, Mauro and Lehmann, Moritz F.. (2014) Partitioning between benthic and pelagic nitrate reduction in the Lake Lugano south basin. Limnology and oceanography, Vol. 59, H. 4. pp. 1421-1433.

Bravo, Andrea Garcia and Cosio, Claudia and Amouroux, David and Zopfi, Jakob and Cheualley, Pierre-Alain and Spangenberg, Jorge E. and Ungureanu, Viorel-Gheorghe and Dominik, Janusz. (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, Vol. 49. pp. 391-405.

Walter, Xavier A. and Picazo, Antonio and Miracle, Maria R. and Vicente, Eduardo and Camacho, Antonio and Aragno, Michel and Zopfi, Jakob. (2014) Phototrophic Fe(II)-oxidation in the chemocline of a ferruginous meromictic lake. Frontiers in microbiology, Vol. 5. p. 713.

D'Alessandro, Marco and Erb, Matthias and Ton, Jurriaan and Brandenburg, Anna and Karlen, Danielle and Zopfi, Jakob and Turlings, Ted C. J.. (2014) Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions. Plant, Cell and Environment, 37 (4). pp. 813-826.


Wenk, Christine B. and Blees, Jan and Zopfi, Jakob and Veronesi, Mauro and Bourbonnais, Annie and Schubert, Carsten J. and Niemann, Helge and Lehmann, Moritz 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). pp. 1-12.


Martin, Gaetan and Guggiari, Matteo and Bravo, Daniel and Zopfi, Jakob and Cailleau, Guillaume and Aragno, Michel and Job, Daniel and Verrecchia, Eric and Junier, Pilar. (2012) Fungi, bacteria and soil pH : the oxalate-carbonate pathway as a model for metabolic interaction. Environmental microbiology, Vol. 14, H. 11 , S. 2960–2970.

Humbert, Sylvia and Zopfi, Jakob and Tarnawski Sonia-Estelle, . (2012) Abundance of anammox bacteria in different wetland soils. Environmental microbiology reports, Vol. 4, H. 5 , S. 484–490.


Morasch, B. and Hunkeler, D. and Zopfi, J. and Temime, B. and 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 (15). pp. 4459-4469.

Haller, L. and Tonolla, M. and Zopfi, J. and Peduzzi, R. and Wildi, W. and Poté, J.. (2011) Composition of bacterial and archaeal communities in freshwater sediments with different contamination levels (Lake Geneva, Switzerland). Water Research, 45 (3). pp. 1213-1228.