Dr. Martina Herrmann


Phone: +49 (0)3641 9-494 59






  (Foto: Jan-Peter Kasper/FSU)


martina-herrmann-research1   martina-herrmann-research2

(Foto: Jan-Peter Kasper/FSU)                                                          (Foto: Patricia Geesink)

As a scientific coordinator of the German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig at the Friedrich Schiller University Jena, I am strongly involved in projects addressing microbial biodiversity in terrestrial environments such as in the framework of the iDiv platform CRC 1076 AquaDiva (subsurface/aquifer biodiversity). Using next generation sequencing approaches, we aim to get more insight into the functional diversity of prokaryotic and eukaryotic microorganisms in aquifers, and to what extent they are influenced by microorganisms originating from the soils of the respective groundwater recharge areas.

In addition, I am interested in different aspects of the microbial ecology of the nitrogen cycle. Within the subproject B05 of the CRC 1076 AquaDiva, we investigate the origin and fate of nitrate in the Critical Zone by following nitrogen cycling microbes and their activities from forest tree canopies via throughfall and seepage down to the groundwater (PhD project Markus Krüger). Along with that, we also study distribution patterns of microorganisms involved in nitrification and their activities in soils under different land use (master project Florian Deckner). Using activity assays and molecular methods such as qPCR and next generation sequencing, we want to gain more insight into which key environmental factors determine the abundance and community composition of these microbial groups and the corresponding nitrogen turnover processes in soils and aquifers.

University training and degree

1995–2001 Diploma studies in Biology, Leibniz University Hannover; thesis supervisor: Prof. Dr. Richard Pott


Advanced academic qualifications

2001–2003 PhD studies in Geobotany (magna cum laude), Leibniz University Hannover; supervisor: Prof. Dr. Richard Pott


Postgraduate professional career

Since 2012 Scientific Coordinator for iDiv at the FSU

2009–2012 Postdoctoral researcher, Institute of Ecology, Aquatic Geomicrobiology, FSU („Eigene Stelle“ granted by DFG)

2008–2009 Postdoctoral researcher, Institute of Microbiology, Leibniz University Hannover

2008 Postdoctoral researcher, Institute of Ecology, Aquatic Geomicrobiology, FSU (return grant funded by the DFG)

2005–2008 Postdoctoral researcher, Department of Microbiology, Institute of Biological Sciences, University of Aarhus, Denmark (20052007: 24 months DFG research fellowship)

2005 Postdoctoral researcher, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena

2004–2005 Postdoctoral researcher, Institute of Microbiology, Leibniz University Hannover


Other (Awards, Grants, Memberships)

Since 2016 Member of the International Society for Microbial Ecology (ISME)

Since 2009 Member of the German Association for General and Applied Microbiology (VAAM)

19972000 Scholarship granted by the Studienstiftung des Deutschen Volkes

1997 Award „Auszeichnung hervorragender studentischer Leistungen“ (Leibniz University Hannover)


 Google scholar


34. 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, accepted.

33. Herrmann M., Dam H.T., Kaster A.-K. and Küsel K. (2020) Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in oligotrophic groundwater. Environmental Microbiology, in print. Doi: 10.1111.1462-2920.14865.

32. Herrmann M, Geesink P, Lehmann R, Totsche KU, 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.



31. Yan L., Herrmann M., Kampe B., Lehmann R., Totsche K.U., Küsel K. (2019) Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Research, accepted.

30. Geesink P., Wegner C.-E., Probst A.J., Herrmann M., Dam H.T., Kaster A.-K. and Küsel K. (2019) Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in oligotrophic groundwater. Environmental Microbiology, accepted.

29. 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.

28. 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.

27. 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.



26. Kumar S., Herrmann M., Blohm A., Hilke I., Frosch T., Trumbore S.E., Küsel K: Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiology Ecology: fiy141 (2018)



25. Kumar S, Herrmann M, Thamdrup B, Schwab VF, Geesink P, Trumbore SE, Totsche KU, Küsel K: Nitrogen loss from pristine carbonate-rock aquifers of the Hainich Critical Zone Exploratory (Germany) is primarily driven by chemolithoautotrophic anammox processes. Front Microbiol, 8, 1951 (2017)

24. Lazar CS, Stoll W, Lehmann R, Herrmann M, Schwab VF, Akob DM, Nawaz A, Wubet T, Buscot F, Totsche KU, Küsel K: Archaeal diversity and CO2 fixers in carbonate/siliclastic-rock groundwater ecosystems. Archaea, Vol 2017, ID 2136287 (2017)

23. Herrmann M, Opitz S, Harzer R, Totsche KU, Küsel K: Attached and suspended denitrifier communities in pristine limestone aquifers harbor high fractions of potential autotrophs oxidizing reduced iron and sulfur compounds, Microb Ecol., 74, 2, 264277 (2017)

22. Schwab VF, Herrmann M, Roth V-N, Gleixner G, Lehmann R, Pohnert G, Trumbore S, Küsel K, Totsche KU: Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches, Biogeosciences, 14, 2697-2714 (2017) doi:10.5194/bg-2016-442.


21. Rughöft S, Herrmann M, Lazar CS, Cesarz S, Levick S, Trumbore S, Küsel K: 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. Front Microbiol, 7, 1638 (2016) (Corrigendum: Front. Microbiol. 7: 1954)

20. Nawaz A, Purahong W, Lehmann R, Herrmann M, Küsel K, Totsche KU, Buscot F, Wubet T: Superimposed pristine limestone aquifers with marked hydrochemical differences exhibit distinct fungal communities. Front Micobiol, 7, 666 (2016) doi:10.3389/fmicb.2016.00666.

19. Küsel K, Totsche KU, Trumbore SE, Lehmann R, Steinhäuser C, Herrmann M: 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 (2016) doi:10.3389/feart.2016.00032



18. Thakur MP, Herrmann M, Steinauer K, Rennoch S, Cesarz S, Eisenhauer N: Cascading effects of belowground predators on plant communities are density-dependent. Ecology and Evolution, 5(19), 4300-4314 (2015) doi:10.1002/ece3.1597

17. Herrmann M, Rusznyak A, Akob DM, Schulze I, Opitz S, Totsche KU, Küsel K: Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl Environ Microbiol, 81, 2384-2394 (2015) doi:10.1128/AEM.03269-14

16. Keiner R, Herrmann M, Küsel K, Popp J, Frosch T: 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 (2015) doi:10.1016/j.aca.2015.02.007



15. Beulig F, Heuer VB, Akob DM, Viehweger B, Elvert M; Herrmann M, Hinrichs KU, Küsel K: Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette. ISME J, 9, 746-759 (2014)

14. Wang JJ, Sickinger M, Ciobota V, Herrmann M, Rasch H, Rösch P, Popp J, Küsel K: Revealing the microbial community structure of clogging materials in dewatering wells differing in physicochemical parameters in an open-cast mining area. Water Research, 63, 222-233 (2014)

13. Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M: Oxygen availability and distance to surface environments determine the community compositon and abundance of ammonia-oxidizing prokaryotes in two superimposed limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol, 90, 39-53 (2014)



12. Risse-Buhl U, Herrmann M, Lange P, Akob DM, Pizani N, Schönborn W, Totsche KU, Küsel K: Phagotrophic protist diversity in the groundwater of a karstified aquifer morphological and molecular analysis. J Euk Microbiol, 60, 467-479 (2013)

11. Frerichs J, Oppermann BI, Gwosdz S, Möller I, Herrmann M, Krüger M: Microbial community changes at a terrestrial volcanic CO2 vent induced by soil acidification and anaerobic microhabitats within the soil column. FEMS Microbiol Ecol, 84, 60-74 (2013)



10. Herrmann M, Hädrich A, Küsel K: Predominance of thaumarchaeal ammonia oxidizer abundance and transcriptional activity in an acidic fen. Environ Microbiol, 14, 3013-3025 (2012)

9. Kofoed MVW, Stief P, Hauzmayer S, Schramm A, Herrmann M: Higher nitrate reducer diversity in macrophyte-colonized compared to unvegetated freshwater sediment. Syst Appl Microbiol, 35, 465-472 (2012)

8. Hädrich A, Heuer VB, Herrmann M, Hinrichs KU, Küsel K: Origin and fate of acetate in an acidic fen. FEMS Microbiol Ecol, 8, 338-354 (2012)



7. Herrmann M, Scheibe A, Avrahami S, Küsel K: Ammonium availability affects the ratio between ammonia-oxidizing bacteria and ammonia-oxidizing archaea in simulated creek ecosystems. Appl Environ Microbiol, 77, 1896-1899 (2011)



6. Juhler S, Revsbech NP, Schramm A, Herrmann M, Ottosen LDM, Nielsen LP: Distribution and rate of microbial processes in an ammonia-loaded air filter biofilm. Appl Environ Microbiol, 75, 3705-3713 (2009)

5. Herrmann M, Saunders AM, Schramm A: Effect of lake trophic status and rooted macrophytes on diversity and abundance of ammonia-oxidizing prokaryotes in freshwater sediments. Appl Environ Microbiol, 75, 3127-3136 (2009)



4. Herrmann M, Saunders AM, Schramm A: Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. Appl Environ Microbiol, 74, 3279-3283 (2008)



3. Herrmann M, Spröte P, Brakhage AA: Protein kinase C (PkcA) of Aspergillus nidulans is involved in penicillin production, Appl Environ Microbiol, 72, 2957-2970 (2006)

2. Herrmann M, Pust J, Pott R: The chemical composition of throughfall beneath oak, birch and pine canopies in Northwest Germany. Plant Ecol, 184, 273-285 (2006)



1. Herrmann M, Pust J, Pott R: Leaching of nitrate and ammonium in heathland and forest ecosystems in Northwest Germany under the influence of enhanced nitrogen deposition. Plant and Soil, 273, 129-137 (2005)

Prof. Dr. Beate Michalzik, Institute of Geography, Friedrich Schiller University Jena

Prof. Dr. Bo Thamdrup, Department of Biology, University of Southern Denmark, Odense

Dr. Sebastian Lücker, Faculty of Science, Microbiology, Radboud University of Nijmegen, The Netherlands

Prof. Dr. Anne-Kristin Kaster, Institute for Biological Interfaces, Karlsruhe Institute of Technology

Dr. Bernd Bendinger, Institut für Wasserressourcen und Wasserversorgung, University of Hamburg

Dr. Simone Cesarz, German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig

Prof. Dr. Nico Eisenhauer, German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig

Dr. Torsten Frosch, IPHT Jena

Dr. Anke Hildebrandt, Institute of Geosciences, Friedrich Schiller University Jena

Dr. Valerie Schwab-Lavric, Max Planck Institute for Biogeochemistry Jena

Madhav Prakash Thakur, German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig