Prof. Kirsten Küsel

Committees and memberships


  • International board member of the International Society of Microbial Ecology (ISME)
  • Executive Committee member of the Board of the Graduate Academy Jena
  • Member of the Alliance for Terrestrial Infrastructure
  • Member of DFG Senate Commission on Water Research KoWa
  • Member of the Association for General and Applied Microbiology (VAAM)
  • Member of the European Association for Geochemistry (EAG)
  • Member of the American Society for Microbiology (ASM)

Editorial Boards


  • Associate Editor of Biogeosciences

Academic positions


  • 2014 Professor for Aquatic Geomicrobiology, Friedrich Schiller University Jena
  • 2004 Professor for Limnology, Friedrich Schiller University Jena
  • 1997 Postdoc at Environmental Protection Agency, Florida, USA
  • 1996–2003 Research assistant
  • 1995–1996 Scientific assistent, University of Bayreuth



  • 2003 Venia Legendi in Microbiology, University of Bayreuth
  • 1995 Ph.D., Prof. Harold L. Drake, Department of Ecological Microbiology, Institute of Terrestrial Ecosystem Research, University of Bayreuth. "Anaerobic microbial turnover of carbon in forest soils: acetate as a key intermediate" (summa cum laude)
  • 1992 Diploma in Geoecology, Prof. Reimer Herrmann (Department of Hydrology), University of Bayreuth. "Reductive Dechlorination of aromatic compounds in landfill leachates"



  • Collaborative Research Centre 1076 AquaDiva (Speaker)
  • Collaborative Research Centre 1127 ChemBioSys Chemical Mediators in Complex Biosystems
  • Graduate School of Excellence GSC 214 Jena School for Microbial Communication 
  • International Max-Planck-Research School for Global Biogeochemical Cycles, IMPRS
  • Research Training Group RTG 1257: Alteration and element mobility at the microbe-mineral interface

Research focus


Microorganisms control most of the global biogeochemical cycles necessary to sustain life. Iron minerals especially dominate the solid phase of porous media and their redox cycling supports key biogeochemical processes which influence the fate of organic matter or contaminant elements. Based on my interdisciplinary background, my research group is focused on the microbial processes and biogeochemistry of a variety of ecosystems from freshwater lakes and sediments, peatlands, and both pristine and heavy metal contaminated streams and aquifers. We use both molecular and cultivation-based techniques to unravel the structure/function relationships of the inherent microbial communities.



Cooper, R. E., Wegner, C.-E., Kügler, S., Poulin, R. X., Ueberschaar, N., Wurlitzer, J. D., Stettin, D., Wichard, T., Pohnert, G., Küsel, K.

(2020): Iron is not everything: unexpected complex metabolic responses between iron-cycling microorganisms. The ISME Journal (in press)

Guerra, C. A., Heintz-Buschart, A., Sikorski, J., Chatzinotas, A., Guerrero-Ramirez, N.,Cesarz, S., Beaumelle, L., ..., Buscot, F., ..., Patoine, G., Phillips, H. R. P., Winter, M., Wubet, T., Küsel, K., ..., Eisenhauer, N.

(2020): Blind spots in global soil biodiversity and ecosystem function research. Nature Communications 11(1) *

Herrmann, M., Geesink, P., Richter, R., Küsel, K.

(2020): Canopy position has a stronger effect than tree species identity on phyllosphere bacterial diversity in a floodplain hardwood forest. bioRxiv (in press) *

Herrmann, M., Geesink, P., Yan, L., Lehmann, R., Totsche, K. U., Küsel, K.

(2020): Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater. Water Research 170

Matanfack, G. A., Taubert, M., Guo, S., Houhou, R., Bocklitz, T., Küsel, K., Rösch, P., Popp, J.

(2020): Influence of Carbon Sources on Quantification of Deuterium Incorporation in Heterotrophic Bacteria: A Raman-Stable Isotope Labeling Approach. Analytical Chemistry 92(16), 11429-11437

Yan, L., Herrmann, M., Kampe, B., Lehmann, R., Totsche, K. U., Küsel, K.

(2020): Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Research 170 *

Benk, S. A., Yan, L., Lehmann, R., Roth, V.-N., Schwab, V. F., Totsche, K. U., Küsel, K., Gleixner, G.

(2019): Fueling Diversity in the Subsurface: Composition and Age of Dissolved Organic Matter in the Critical Zone. Frontiers in Earth Science 7(296) *

Geesink, P., Wegner, C.-E., Probst, A. J., Herrmann, M., Dam, H. T., Kaster, A.-K.,  Küsel, K.

(2019): Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater. Environmental Microbiology 22(2), 726-737

Hadrich, A., Taillefert, M., Akob, D. M., Cooper, R. E., Litzba, U., Wagner, F. E., Nietzsche, S., Ciobota, V., Rosch, P., Popp, J., Kusel, K.

(2019): Microbial Fe(II) oxidation by Sideroxydans lithotrophicus ES-1 in the presence of Schlöppnerbrunnen fen-derived humic acids. Fems Microbiology Ecology 95(4)

Herrmann, M., C. E. Wegner, M. Taubert, P. Geesink, K. Lehmann, L. J. Yan, R. Lehmann, K. U. Totsche, K. Kusel

(2019): Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions. Frontiers in Microbiology 10 *

Lazar, C. S., R. Lehmann, W. Stoll, J. Rosenberger, K. U. Totsche, K. Kusel

(2019): The endolithic bacterial diversity of shallow bedrock ecosystems. Science of The Total Environment 679, 35-44

Nawaz, A., Purahong, W., Herrmann, M., Küsel, K., Buscot, F., Wubet, T.

(2019): DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors. Microorganisms 7(9)

Schwab, V. F., Nowak, M. E., Elder, C. D., Trumbore, S. E., Xu, X., Gleixner, G., Lehmann, R., Pohnert, G., Muhr, J., Küsel, K., Totsche, K. U.

(2019): 14C-free Carbon is a Major Contributor to Cellular Biomass in Geochemically Distinct Groundwater of Shallow Sedimentary Bedrock Aquifers. Water Resources Research 55(3), 2104-21

Schwab, V. F., Nowak, M. E., Trumbore, S. E., Xu, X., Gleixner, G., Muhr, J., Küsel, K., Totsche, K. U.

(2019): Isolation of Individual Saturated Fatty Acid Methyl Esters Derived From Groundwater Phospholipids by Preparative High-Pressure Liquid Chromatography for Compound-Specific Radiocarbon Analyses. Water Resources Research 55(3), 2521-2531

Taubert, M., Stähly, J., Kolb, S., Küsel, K.

(2019): Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PLOS ONE 14(3), e0212937

Wegner, C. E., Gaspar, M., Geesink, P., Herrmann, M., Marz, M., Küsel, K.

(2019): Biogeochemical Regimes in Shallow Aquifers Reflect the Metabolic Coupling of the Elements Nitrogen, Sulfur, and Carbon. Applied and Environmental Microbiology 85, e02346-18

Wondraczek, L., Pohnert, G., Schacher, F. H., Kohler, A., Gottschaldt, M., Schubert, U. S., Kusel, K., Brakhage, A. A.

(2019): Artificial Microbial Arenas: Materials for Observing and Manipulating Microbial Consortia. Advanced Materials 31(24)

Ding, S., Kohlhepp, B., Trumbore, S., Küsel, K., Totsche, K. U., Pohnert, G., Gleixner, G., Schwab, V. F.

(2018): In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater. Organic Geochemistry 126, 1-12

Geesink, P., Tyc, O., Küsel, K., Taubert, M., van de Velde, C., Kumar, S., Garbeva, P.

(2018): Growth promotion and inhibition induced by interactions of groundwater bacteria. FEMS Microbiology Ecology 94(11)

Kugler, S., Cooper, R. E., Wegner, C. E., Mohr, J. F., Wichard, T., Küsel, K.

(2018): Iron-organic matter complexes accelerate microbial iron cycling in an iron-rich fen. Science of the Total Environment 646, 972-88

Kumar, S., Herrmann, M., Blohm, A., Hilke, I., Frosch, T., Trumbore, S. E., Küsel, K.

(2018): Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. Fems Microbiology Ecology 94(10)

Nawaz, A., Purahong, W., Lehmann, R., Herrmann, M., Totsche, K. U., Küsel, K., Wubet, T., Buscot, F.

(2018): First insights into the living groundwater mycobiome of the terrestrial biogeosphere. Water Research 145, 50-61

Shade, A., Dunn, R. R., Blowes, S. A., Keil, P., Bohannan, B. J. M., Herrmann, M., Küsel, K., Lennon, J. T., Sanders, N. J., Storch, D., Chase, J.

(2018): Macroecology to Unite All Life, Large and Small. Trends in Ecology & Evolution 33(10), 731-44

Taubert, M., Stöckel, S., Geesink, P., Girnus, S., Jehmlich, N., von Bergen, M., Rösch, P., Popp, J., Küsel, K.

(2018): Tracking active groundwater microbes with D2O labeling to understand their ecosystem function. Environmental Microbiology 20(1), 369-84

Bolanz, R. M., Grauer, C., Cooper, R. E., Gottlicher, J., Steininger, R., Perry, S., Küsel, K.

(2017): Incorporation of molybdenum(VI) in akaganéite (β-FeOOH) and the microbial reduction of Mo–akaganéite by Shewanella loihica PV-4. CrystEngComm 19(41), 6189-98

Cooper, R. E., Eusterhues, K., Wegner, C. E., Totsche, K. U., Küsel, K.

(2017): Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia. Biogeosciences 14(22), 5171-88

Herrmann, M., Opitz, S., Harzer, R., Totsche, K. U., Küsel, K.

(2017): Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. Microbial Ecology 74(2), 264-77

Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V., Küsel, K., Rillig, M. C., Rivett, D. W., Salles, J. F., van der Heijden, M. G. A., Youssef, N. H., Zhang, X., Wei, Z., Hol, W. H. G.

(2017): Where less may be more: how the rare biosphere pulls ecosystems strings. The ISME Journal 11(4), 853-62

Kohlhepp, B., Lehmann, R., Seeber, P., Küsel, K., Trumbore, S. E., Totsche, K. U.

(2017): Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate–siliciclastic alternations of the Hainich CZE, central Germany. Hydrology and Earth System Sciences 21(12), 6091-116

Kumar, S., Herrmann, M., Thamdrup, B., Schwab, V. F., Geesink, P., Trumbore, S. E., Totsche, K. U., Küsel, K.

(2017): Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes. Frontiers in Microbiology 8, 1951

Kwon, M. J., Beulig, F., Ilie, I., Wildner, M., Küsel, K., Merbold, L., Mahecha, M. D., Zimov, N., Zimov, S. A., Heimann, M., et al.

(2017): Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain. Global Change Biology 23(6), 2396-2412

Lazar, C. S., Stoll, W., Lehmann, R., Herrmann, M., Schwab, V. F., Akob, D. M., Nawaz, A., Wubet, T., Buscot, F., Totsche, K.-U., Küsel, K.

(2017): Archaeal Diversity and CO2 Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems. Archaea 2017, 2136287

Metzger, J. C., Wutzler, T., Dalla Valle, N., Filipzik, J., Grauer, C., Lehmann, R., Roggenbuck, M., Schelhorn, D., Weckmüller, J., Küsel, K., Totsche, K. U., Trumbore, S., Hildebrandt, A.

(2017): Vegetation impacts soil water content patterns by shaping canopy water fluxes and soil properties. Hydrological Processes 31(22), 3783-95

Mori, J. F., Scott, J. J., Hager, K. W., Moyer, C. L., Küsel, K., Emerson, D.

(2017): Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov. The ISME Journal 11(11), 2624-36

Mori, J. F., Ueberschaar, N., Lu, S., Cooper, R. E., Pohnert, G., Küsel, K.

(2017): Sticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling. The ISME Journal 11(5), 1075-86

Nowak, M. E., Schwab, V. F., Lazar, C. S., Behrendt, T., Kohlhepp, B., Totsche, K. U., Küsel, K., Trumbore, S. E.

(2017): Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages. Hydrology and Earth System Sciences 21(9), 4283-300

Schwab, V. F., Herrmann, M., Roth, V. N., Gleixner, G., Lehmann, R., Pohnert, G., Trumbore, S., Küsel, K., Totsche, K. U.

(2017): Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches. Biogeosciences 14(10), 2697-714

Starke, R., Müller, M., Gaspar, M., Marz, M., Küsel, K., Totsche, K. U., von Bergen, M., Jehmlich, N.

(2017): Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer. Journal of Proteomics 152, 153-60

Beulig, F., Urich, T., Nowak, M., Trumbore, S. E., Gleixner, G., Gilfillan, G. D., Fjelland, K. E., Küsel, K.

(2016): Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure. Nature Microbiology 1, 15025

Bohu, T., Akob, D. M., Abratis, M., Lazar, C. S., Küsel, K.

(2016): Biological low pH Mn(II) oxidation in a manganese deposit influenced by metal-rich groundwater. Applied and Environmental Microbiology 82(10), 3009-21

Fabisch, M., Freyer, G., Johnson, C. A., Buechel, G., Akob, D. M., Neu, T. R., Küsel, K.

(2016): Dominance of "Gallionella capsiferriformans' and heavy metal association with Gallionella-like stalks in metal-rich pH 6 mine water discharge. Geobiology 14(1), 68-90

Küsel, K., Totsche, K. U., Trumbore, S. E., Lehmann, R., Steinhäuser, C., Herrmann, M.

(2016): How deep can surface signals be traced in the critical zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape. Frontiers in Earth Science 4(32)

Lu, S. P., Peiffer, S., Lazar, C. S., Oldham, C., Neu, T. R., Ciobota, V., Nab, O., Lillicrap, A., Rosch, P., Popp, J., Küsel, K.

(2016): Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia. Environmental Microbiology Reports 8(1), 58-67

Miot, J., Lu, S., Morin, G., Adra, A., Benzerara, K., Küsel, K.

(2016): Iron mineralogy across the oxycline of a lignite mine lake. Chemical Geology 434, 28-42

Mori, J. F., Lu, S., Haendel, M., Totsche, K. U., Neu, T. R., Iancu, V. V., Tarcea, N., Popp, J., Küsel, K.

(2016): Schwertmannite formation at cell junctions by a new filament-forming Fe(II)-oxidizing isolate affiliated with the novel genus Acidithrix. Microbiology 162, 62-71

Nawaz, A., Purahong, W., Lehmann, R., Herrmann, M., Küsel, K., Totsche, K. U., Buscot, F., Wubet, T.

(2016): Superimposed pristine limestone aquifers with marked hydrochemical differences exhibit distinct fungal communities. Frontiers in Microbiology 7, 666

Rughoft, S., Herrmann, M., Lazar, C. S., Cesarz, S., Levick, S. R., Trumbore, S. E., Küsel, K.

(2016): Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa. Frontiers in Microbiology 7, 1638

Beulig, F., Heuer, V. B., Akob, D. M., Viehweger, B., Elvert, M., Herrmann, M., Hinrichs, K. U., Küsel, K.

(2015): Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette. The ISME Journal 9(3), 746-59

Bohu, T., Santelli, C. M., Akob, D. M., Neu, T. R., Ciobota, V., Roesch, P., Popp, J., Nietzsche, S., Küsel, K.

(2015): Characterization of pH dependent Mn(II) oxidation strategies and formation of a bixbyite-like phase by Mesorhizobium australicum T-G1. Frontiers in Microbiology 6, 734

Herrmann, M., Rusznyak, A., Akob, D. M., Schulze, I., Opitz, S., Totsche, K. U., Küsel, K.

(2015): Large Fractions of CO2-Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds. Applied and Environmental Microbiology 81(7), 2384-94

Johnson, C. A., Murayama, M., Küsel, K., Hochella, M. F., Jr.

(2015): Polycrystallinity of green rust minerals and their synthetic analogs: Implications for particle formation and reactivity in complex systems. American Mineralogist 100(10), 2091-2105

Keiner, R., Herrmann, M., Küsel, K., Popp, J., Frosch, T.

(2015): Rapid monitoring of intermediate states and mass balance of nitrogen during denitrification by means of cavity enhanced Raman multi-gas sensing. Analytica Chimica Acta 864, 39-47

Mori, J. F., Neu, T. R., Lu, S., Haendel, M., Totsche, K. U., Küsel, K.

(2015): Iron encrustations on filamentous algae colonized by Gallionella-related bacteria in a metal-polluted freshwater stream. Biogeosciences 12(18), 5277-89

Sitte, J., Loeffler, S., Burkhardt, E.-M., Goldfarb, K. C., Buechel, G., Hazen, T. C., Küsel, K.

(2015): Metals other than uranium affected microbial community composition in a historical uranium-mining site. Environmental Science and Pollution Research 22(24), 19326-41

Akob, D. M., Bohu, T., Beyer, A., Schaffner, F., Handel, M., Johnson, C. A., Merten, D., Buchel, G., Totsche, K. U., Küsel, K.

(2014): Identification of Mn(II)-Oxidizing Bacteria from a Low-pH Contaminated Former Uranium Mine. Applied and Environmental Microbiology 80(16), 5086-97

Eusterhues, K., Haedrich, A., Neidhardt, J., Küsel, K., Keller, T. F., Jandt, K. D., Totsche, K. U.

(2014): Reduction of ferrihydrite with adsorbed and coprecipitated organic matter: microbial reduction by Geobacter bremensis vs. abiotic reduction by Na-dithionite. Biogeosciences 11(18), 4953-66

Johnson, C. A., Freyer, G., Fabisch, M., Caraballo, M. A., Küsel, K., Hochella, M. F.

(2014): Observations and assessment of iron oxide and green rust nanoparticles in metal-polluted mine drainage within a steep redox gradient. Environmental Chemistry 11(4), 377-91

Mehlhorn, J., Beulig, F., Küsel, K., Planer-Friedrich, B.

(2014): Carbon dioxide triggered metal(loid) mobilisation in a mofette. Chemical Geology 382, 54-66

Opitz, S., Küsel, K., Spott, O., Totsche, K. U., Herrmann, M.

(2014): Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiology Ecology 90(1), 39-53

Wang, J. J., Sickinger, M., Ciobota, V., Herrmann, M., Rasch, H., Rosch, P., Popp, J., Küsel, K.

(2014): Revealing the microbial community structure of clogging materials in dewatering wells differing in physico-chemical parameters in an open-cast mining area. Water Research 63, 222-33
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Friedrich-Schiller-Universität Jena
Institut für Biodiversität
Dornburger Straße 159
07743 Jena

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+49 3641 949461
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+49 3641 94940
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Friedrich-Schiller-Universität Jena

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