Recent Publications

Peer Reviewed & Book Chapters


2020, 2019, 2018, 2017, 2016, 2015 and older

(Individual Publication lists - see Group Members)



Akinyede R., Taubert M., Schrumpf M., Trumbore S., Küsel K. (2020) Rates of dark CO2 fixation are driven by microbial biomass in a temperate forest soil. Soil Biology and Biochemistry. 107950 Doi: 10.1016/j.soilbio.2020.107950

Cooper R.E., Wegner C.-E., McAllister S.M., Shevchenko O., Chan C.S., Küsel K. (2020) Draft genome sequence of Sideroxydans sp. strain CL21, an Fe(II)-Oxidizing bacterium. Microbiology Resource Announcements 9(2): e01444-19. Doi: 10.1128/MRA.01444-19.

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. Doi: 10.1038/s41396-020-0718-z 

Geesink P., Wegner C.-E.,  Probst A.J., Herrmann M., Dam H.T., Kaster A.-K., Küsel K. (2020) Genome‐inferred spatio‐temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in groundwater Environmental Microbiology 22(2), 726–737. Doi:10.1111/1462-2920.14865

Guerra C.A., Heintz-Buschart A., Küsel K., Sikorski J. et al. (2020) Blind spots in global soil biodiversity and ecosystem function research. Nature Communications 11 (1),1-13. 3870. Doi: 10.1038/s41467-020-17688-2

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. Microbial Ecology. Doi: 10.1007/s00248-020-01565-y

Herrmann M., Geesink P., 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: 115306. Doi: 10.1016/j.watres.2019.115306.

Heintz-Buschart A., Guerra C., Djukic I., Cesarz S., Chatzionotas A., Patoine G., Sikorski J., Buscot F., Küsel K., Wegner C.-E., Eisenhauer N. (2020) Microbial diversity-ecosystem function relationships across enviromental gradients Doi: 10.3897/rio.6e52217

Krüger M., Potthast K., Michalzik B., Tischer A., Küsel K., Deckner, F. K., Herrmann M., (2020) Drought and rewetting events enhance nitrate leaching and seepage-mediated translocation of microbes from beech forest soils.

Taubert M., Guo S., Houhou R., Bocklitz T.W., Kuesel 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.
Li Q., Cooper R.E., Wegner C.-E., Küsel K. (2020) Molecular mechanisms underpinning aggregation in Acidiphilium sp. C61 isolated from iron-rich pelagic aggregates. Microorganisms 8(3): 314. Doi: 10.3390/microorganisms8030314.

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: 115341. Doi: 10.1016/j.watres.2019.115341.



Akob, M.D., Bohu, T. Beyer. A., Fabisch, M., Woyke T., Shapiro N., Lapidus N., Klenk H-P., Küsel K. (2019) Draft genome sequence of the Mn (II)-oxidizing bacterium Oxalabobacteracea. Microbiology Resource Announcements. Doi: 10.1128/MRA.01024-19

Benk S.A., Yan L., Lehmann R., Roth V.-N., Schwab V.F., Totsche K.U., Küsel K., Gleixner G. (2019) Fuelin diversity in the subsurface: Composition and age of dissolved organic matter in the Critical Zone. Frontiers in Earth Science 7: 296. Doi: 10.3389/feart.2019.00296.

Bushman T.J., Akob D.M., Bohu T., Beyer A., Woyke T., Shapiro N., Lapidus A., Klenk H.-P., Küsel K. (2019) Draft genome sequence of Mn(II)-oxidizing bacterium Oxalobacteraceae sp. strain AB_14. Microbiology Resource Announcements 8(43): e01024-19. Doi: 10.1128/MRA.01024-19

Cooper R.E. and DiChristina T.J. (2019) Fe(III) oxide reduction by anaerobic biofilm formation-deficient S-Ribosylhomocysteine lyase (LuxS) mutant of Shewanella oneidensis. Geomicrobiology Journal 36(7): 639-650. Doi: 10.1080/01490451.2019.1605428

Hädrich A., Taillefert M., Akob D.M., Cooper R.E., Litzba U., Wagner F.E., Nietzsche S., Ciobota V., Rösch P., Popp J., Küsel 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): fiz034. Doi: 10.1093/femsec/fiz034

Herrmann M., Wegner C.-E., Taubert M., Geesink P., Lehmann K., Yan L., Lehmann R., Totsche K.U., Küsel K. (2019) Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Frontiers in Microbiology 10: article 1407. Doi: 10.3389/fmicb.2019.01407

Kügler S., Cooper R.E., Wegner C.-E., Mohr J.F., Wichard T., Küsel K. (2019) Iron-organic matter complexes accelerate microbial iron cycling in an iron-rich fen. Science of the Total Environment 646: 972-988. Doi: 10.1016/j.scitotenv.2018.07.258

Lazar C.S., Lehmann R., Stoll W., Rosenberger J., Totsche K.U., Küsel K. (2019) The endolithic bacterial diversity of shallow bedrock ecosystems. Science of the Total Environment 679: 35-44. Doi: 10.1016/j.scitotenv.2019.04.281

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): 341. Doi: 10.3390/microorganisms7090341

Overholt W., Hölzer M., Geesink P., Diezel C., Marz M., Küsel K. (2019) Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system bioRxiv preprint 880807.

Schwab V., Nowak M.E., Elder C.D., Trumbore S.E., Xu X., Gleixner G., Lehmann R., Pohnert G., Muhr J., Küsel K. (2019) 14C-free carbon is a major contributor to cellular biomass in geochemically distinct groundwater of shallow sedimentary aquifers. Water Resources Research 55(3): 2104-2121. Doi: 10.1029/2017WR022067

Schwab V., 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. Doi: 10.1029/2018WR024076

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. Doi: 10.1371/journal.pone.0212937

Wegner C.-E., Gaspar M., Geesink P., Herrmann M., Marz M., Küsel K. (2019) Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon. Applied and Environmental Microbiology 85(5): e02346-18. Doi: 10.1128/AEM.00502-19

Wegner, C.-E., Gorniak, L., Riedel, S., Westermann M., Küsel K. (2019) Lanthanide-Dependent Methylotrophs of the Family Beijerinckiaceae: Physiological and Genomic Insights.
Applied and Environmental Microbiology. 86.
Doi: 10.1128/AEM.01830-19

Wegner C.-E., Gorniak L., Riedel S., Westermann M., Küsel K. (2019) Physiological and genomic insights into lanthanide-dependent methylotrophs of the family Beijerinckiaceae. Applied and Environmental Microbiology 86 (1): e01830-19. Doi: 10.1128/AEM.01830-19

Wondraczek L., Pohnert G., Schacher F.H., Köhler A., Gottschaldt M., Schubert U.S., Küsel K., Brakhage A.A. (2019) Artificial microbial arenas: Materials for observing and manipulating microbial consortia. Advanced Materials 31, 1900284. Doi: 10.1002/adma.201900284

Xenophontos C., Taubert M., Harpole W.S., Küsel K. (2019) Phylogenetic and functional diversity have contrasting effects on the ecological functioning of bacterial communities. bioRxiv preprint 839696. Doi: 10.1101/839696.




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. Doi: 10.1016/j.orggeochem.2018.10.005

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): fiy164. Doi: 10.1093/femsec/fiy164

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. Doi: 10.1016/j.watres.2018.07.067

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): fiy141. Doi: 10.1093/femsec/fiy141

Taubert, M., Stöckel, S., Geesink, P., Girnus, S., Jehmlich, N., von Bergen, M., Rösch, P., Popp, J., and Küsel, K. 2018. Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environmental Microbiology  20(1): 369-384. Doi: 10.1111/1462-2920.14010

Howat, A.M., Vollmers, J., Taubert, M., Grob, C., Dixon, J.L., Todd, J.D., Chen, Y., Kaster, A.K., and Murrell, J.C. 2018. Comparative genomics and mutational analysis reveals a novel XoxF-utilizing methylotroph in the Roseobacter group isolated from the marine environment. Frontiers in Microbiology 9:766. Doi: 10.3389/fmicb.2018.00766

Shade, A., Dunn, R.R., Blowes, S.A., Keil, P., Bohannan, B.J.M., Herrmann, M., Küsel, K., Lennon, J.T., Sanders, S.J., Storch, D., Chase, J. (2018) Macroecology to unite all life, large and small. Trends in Ecology & Evolution 33(10): 731-744. Doi: 10.1016/j.tree.2018.08.005.



Bolanz, R.M., Grauer, C., Cooper, R.E., Göttlicher, J., Steininger, R., Perry, S., and 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: 6189-6198. Doi: 10.3389/fmicb.2018.00766

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): 5171-5188. Doi: 10.5194/bg-14-5171-2017

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 authotrophs oxidizing resduced iron and sulfur compounds. Microb. Ecol. 74(2): 264-277. Doi: 10.1007/s00248-017-0950-x

Kohlhepp, B., Lehmann, R., Seeber, P., Küsel, K., Trumbore, S. E., and Totsche, K. U. 2017. Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonatesiliciclastic alternations of the Hainich CZE, central Germany. HESS 21(12): 6091-6116. Doi: 10.5194/hess-21-6091-2017

Kwon M.J., Beulig F., Ilie L., Wildner W., Küsel K., Merbold L., Mahecha M.D., Zimov N., Zimov S.A., Heimann M., Schuur E. AG, Kostka J.E., Kolle O., Hilke I., Göckede M. (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. Doi: 10.1111/gcb.13558

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. Doi: 10.3389/fmicb.2017.01951

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/siliclastic-rock groundwater ecosystems. Archaea Vol 2017, ID 2136287. Doi: 10.1155/2017/2136287

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): 3783-3795. Doi: 10.1002/hyp.11274

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. ISME J 11: 2624-2636. Doi: 10.1038/ismej.2017.132

Nowak, M. E., Schwab, V. F., Lazar, C. S., Behrendt, T., Kohlhepp, B., Totsche, K. U., Küsel, K., and Trumbore, S. E. 2017. Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages. HESS 21(9): 4283-4300. Doi: 10.5194/hess-21-4283-2017

Schwab, V. F., Herrmann, M., Roth, V. N., Gleixner, G., Lehmann, R., Pohnert, G., Trumbore, S., Küsel, K., and Totsche, K. U. 2017. Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches. Biogeosciences 14(10): 2697-2714. Doi: 10.5194/bg-14-2697-2017

Taubert M., Grob C., Howat A.M., Burns O.J., Pratscher J., Jehmlich N., von Bergen M., Richnow H.H., Chen Y., Murrell J.C. (2017) Methylamine as nitrogen source for microorganisms from a coastal marine environment. Environmental Miicrobiology 19(6): 2246-2257. Doi: 10.1111/1462-2920.13709

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.W., Wei Z.. Hol W.H.G. (2017) Where less be more: how rare biosphere pulls ecosystem strings. ISME J. 11: 853-862. Doi: 10.1038/ismej.2016.174

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. ISME J. 11: 1075-1086 Doi: 10.1038/ismej.2016.186

Lazar C.S., Baker B.J., Seitz K., Teske A.P. (2017) Genomic reconstruction of multiple lineages of uncultered benthic archaea suggests distinct biogeochemical roles and ecological niches. The ISME Journal 11: 1118-1129. 10.1038/ismej.2016.189 Doi: 10.1038/ismej.2016.189

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: 153-160. Doi: 10.1016/j.jprot.2016.11.003

Jameson E., Taubert M., Coyotzi S., Chen Y., Eyice Ö., Schäfer H., Murrell J.C., Neufeld J.D., Dumont M.G. (2017) DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. Methods in Molecular Biology 1539. Metagenomics: Methods and Protocols: 57-74 Doi: 10.1007/978-1-4939-6691-2_5



Bonn, A., Richter, A., Vohland, K., Pettibone, L., Brandt, M., Feldmann, R., Goebel, C., Grefe, C., Hecker, S., Hennen, L., Hofer, H., Kiefer, S., Klotz, S., Kluttig, T., Krause, J., Küsel, K., Liedtke, C., Mahla, A., Neumeier, V., Premke-Kraus, M., Rillig, M. C., Röller, O., Schäffler, L., Schmalzbauer, B., Schneidewind, U., Schumann, A., Settele, J., Tochtermann, K., Tockner, K., Vogel, J., Volkmann, W., von Unger, H., Walter, D., Weisskopf, M., Wirth, C., Witt, T., Wolst, D. & D. Ziegler (2016) Grünbuch Citizen Science Strategie 2020 für Deutschland. Helmholtz-Zentrum für Umweltforschung (UFZ), Deutsches Zentrum für integrative Biodiversitätsforschung (iDiv) Halle-Jena-Leipzig. Leipzig, Museum für Naturkunde Berlin. Leibniz-Institut für Evolutions- und Biodiversitätsforschung (MfN), Berlin-Brandenburgisches Institut für Biodiversitätsforschung (BBIB), Berlin.

Taubert M., Grob C., Howat A.M., Burns O.J., Chen Y., Neufeld J.D., Murrell J.C. (2016)  Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies. In: Martin F., Uroz S. (eds) Microbial Environmental Genomics (MEG). Methods in Molecular Biology, vol 1399. Humana Press, New York, NY. DOI: 10.1007/978-1-4939-3369-3_14. Doi: 10.1007/978-1-4939-3369-3_14

European Commission, Joint Research Centre (2016) Global Soil Biodiversity Atlas - Earth Sciences Research - EU Bookshop. Contributors: Küsel K., Totsche K.U., Trumbore S.E., Buscot F.; Chapter III - Geographical and temporal distribution, p. 73.

Cooper R.E., Goff J.L., Reed B.C., Sekar R., DiChristina T.J. (2016) Breathing Iron: Molecular Mechanisms of Microbial Iron Reduction by Shewanella oneidensis. Manual of Environmental Microbiology. Fourth Edition. American Society of Microbiology. Chapter 5.2.1 Doi: 10.1128/9781555818821.ch5.2.1

Baker B.J., Saw J.H., Anders E.L., Lazar C.S., Hinrichs K.U., Teske A.P., Ettema T.J.G. (2016) Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nature Microbiology. 1(16002). -Link to abstract

Seitz K., Lazar C. S., Hinrichs K.-U., Teske A., Baker B. J. (2016) Genomic reconstruction of a novel, deeply-branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. The ISME Journal. 10. 1696-1705. -Link to abstract

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. -Link to abstract

Kohlhepp B., Lehmann R., Seeber P., Küsel K., Trumbore S.E., Totsche K.U. (2016) Pedological and hydrogeological setting and subsurface flow structure of the carbonate-rock CZE Hainich in western Thuringia, Germany Doi: 10.5194/hess-2016-374

Rughöft S., Herrmann M., Lazar C. S., Cesarz S., Levick S., Trumbore S., Küsel K. (2016) Community composition and abundance of nitrifiers and total bacterial and archaeal populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa. Frontiers in Microbiology 7:1638. (Corrigendum: Front. Microbiol. 7: 1954.) Doi: 10.3389/fmicb.2016.01954

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. -Link to abstract

Küsel K, Totsche KU, Trumbore SE, Lehmann R, Steinhäuser C and 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. Front. Earth Sci. 4:32. Doi: 10.3389/feart.2016.00032.

Tsing Bohu, Denise M. Akob, Michael Abratis, Cassandre S. Lazar, and Kirsten Küsel. (2016). Biological low pH Mn(II) oxidation in a manganese deposit influenced by metal-rich groundwater. (2016). Applied and Environmental Microbiology 82(10): 3009-3021. Doi: 10.1128/AEM.03844-15

Mori J. F., Lu S., Händel, M., Totsche K.U., Neu T. R., Vlad Iancu 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, Doi: 10.1099/mic.0.000205

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. Doi: 10.1038/nmicrobiol.2015.25

Fabisch M., Freyer G., Johnson C. A., Büchel 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. 6890. Doi: 10.1111/gbi.12162

Lazar C.S., Baker B.J., Seitz K., Hyde A.S., Dick G.J., Hinrichs K.-U., and Teske A.P. (2016) Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environmental Microbiology 18(4): 1200-1211. Doi: 10.1111/1462-2920.13142

Lu S., Peiffer S., Lazar C.S., Oldham C., Neu T.R., Ciobotă V., Näb O., Lillicrap A., Rösch P., Popp J., Küsel K. (2016) Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia. Environmental Microbiology and Environmental Microbiology Reports. -Link to abstract