Dr. Martina Herrmann


Phone: +49 (0)3641 (9)49459










As a scientific coordinator of the German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig at the Friedrich Schiller University, I am strongly involved in projects addressing microbial biodiversity in terrestrial environments such as in the framework of the iDiv platforms CRC AquaDiva (subsurface/aquifer biodiversity) and the Jena Experiment (soil microbial diversity). Using next generation sequencing approaches, we are addressing the question if plant biodiversity influences soil microbial biodiversity and how far down in the soil such effects may reach (Jena Experiment). In the CRC AquaDiva, especially in the BIODIV3 project, we aim to get more insight into the diversity of prokaryotic and eukaryotic microorganisms in aquifers.

In addition, I am interested in different aspects of the microbial ecology of the nitrogen cycle. Ongoing projects focus on distribution patterns of microorganisms involved in nitrification, denitrification, and anammox and their activities in forest soils (master project Danny Schelhorn), savanna soils (master project Saskia Rughöft) and in aquifers (PhD project Swatantar Kumar). 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.


23. Herrmann M., Opitz S., Harzer R., Totsche K. U., Küsel K. (accepted) Attached and suspended denitrifier communities in pristine limestone aquifers harbor high fractions of potential authotrophs oxidizing resduced iron and sulfur compounds. Microb Ecol.



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

21. 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

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

19. 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



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

17. Herrmann, M; Rusznyak, A; Akob, DM; Schulze, I; Opitz, S; Totsche, KU; 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, Appl Environ Microbiol 81, 2384-2394. doi:10.1128/AEM.03269-14.

16. 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. 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 (2014): Carbon flow from volcanic CO2 into soil microbial communities of a wetland mofette. ISME J, 9, 746-759. 

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; Hinrich, 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)

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 at the Leibniz-Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena

2004–2005 Postdoctoral researcher at the 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)


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)

Jun.-Prof. Dr. Anke Hildebrandt (Institute of Geosciences, Friedrich Schiller University Jena)

Dr. Valerie Schwab-Lavric (Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena)

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