Dr. Stefanie Böhnke-Brandt

Research Division 2: Marine Biogeochemistry
FE Marine Geosystems

room: 12-337
phone: +49 431 600-1234
E-Mail: sboehnke-brandt@geomar.de

Wischhofstraße 1-3
D-24148 Kiel

Research interests

My main research interest aims at a better understanding of how abiotic dynamics and biotic interactions affect microbial diversity, activity, and metabolic strategies. Here my focus lies on the identification and characterization of key enzymes catalyzing autotrophic CO2 fixation processes in marine environments. In order to circumvent the bottleneck of culturability I use functional metagenomic and develop activity-based screens to seek CO2 reducing enzymes like e.g. RubisCO or CODH.

Range of Methods

functional Screen establishment // standard molecular work // sensor triggered in situ sampling and incubations // transposon mutagenesis // biochemical enzyme characterization // overexpression // aerobic and anaerobic cultivations // HPLC measurements // spectrophotometric analyses // FPLC // database searches // Amplicon sequence processing // qPCR // Electrophoretic Mobility Shift Assay (EMSA) // DNA/RNA isolation from challenging sample materials // constructing metagenomic libraries // protein purifications // Western-Blot // functional metagenomics // specific enzyme activity measurements // complementation experiments // NGS amplicon library preparation

Scientific Career

since 01/2018*
Postdoc at the GEOMAR Helmholtz Centre for Ocean Research Kiel (Geomicrobiology)

Postdoc at the University of Hamburg (Molecular Biology of Microbial Consortia)

PhD at the University of Hamburg (Molecular Biology of Microbial Consortia): „A novel function-based screen for detecting RubisCO active clones from metagenomic libraries: elucidating the role of RubisCO associated enzymes“
(PI: Prof. Dr. Mirjam Perner)

Diploma (M. Sc. equivalent) in microbiology, genetics and law (criminal law), University of Hamburg

Diploma Thesis at the University of Hamburg (Microbiology and Biotechnology): “Investigating structure and dynamic of ammonia oxidizing populations in tide influenced habitats of the river Elbe“
(PI: PD A. Pommerening-Röser)

Studies of Biology at the University of Hamburg

*Parental leave     2016 and 2019

Engagements and memberships


  • since 2020 - Lecturer within the modules MSc Biological Oceanography (MNF-bioc-101) and MSc Geoscience (MNF-geow-103), GEOMAR
  • annually since 2020 - Contributing supervisor, block courses for Master students (MNF-bioc-279, MNF-bioc-379, and MNF-bioc-202), including cruises, seminar, lecture and practical course, GEOMAR
  • annually from 2012 to 2015 - Supervisor, functional metagenomics block course for Masters students, including seminar and practical course, University of Hamburg
  • since 2010 - Supervision of technical staff, various undergraduates and trainees


PhD bursary from the graduate school C1-Chemistry in Resource and Energy Management (C1-REM) funded by the state excellence initiative (Lexi) Hamburg


Böhnke, S., Scheffen, M., Erb, T., & Perner, M. (2022) An activity-based metagenomic screen uncovers novel perception into enzymatically catalyzed decrease of ribulose-1,5-bisphosphate (in preparation)

Hansen, C., Kleint, C., Böhnke, S., Klose, L., Adam, N., Sass, K., Perner, M., Dittmar, T. & Koschinsky, A. (2022) The impact of variable Fe concentrations on Fe-binding ligands, dissolved organics and microbial communities in hydrothermal plumes – an experimental study. (in preparation)

Gebert, J., Zander, F., Bergmann, L., Krohn, I., Böhnke, S. & Perner, M. (2022) Linking microbial community composition, microbial biomass and extrapolymeric substances to organic matter lability gradients in sediments of the tidal Elbe. (in preparation)

Böhnke, S. & Perner, M. (2022) Approaches to unmask functioning of the uncultured microbial majority from extreme habitats on the seafloor. Frontiers in Microbiology 29;13:845562. doi: 10.3389/fmicb.2022.845562

Böhnke, S. & Perner, M. (2019) Seeking active RubisCOs from the currently uncultured microbial majority colonizing deep-sea hydrothermal vent environments. The ISME Journal 13, 2475-2488. doi: 10.1038/s41396-019-0439-3

Böhnke, S., Sass, K., Gonnella, G., Diehl, A. Kleint, C., Bach, W., Zitoun, R., Koschinsky, A., Indenbirken, D., Sander, S. G., Kurtz, S., and Perner, M. (2019) Parameters Governing the Community Structure and Element Turnover in Kermadec Volcanic Ash and Hydrothermal Fluids as Monitored by Inorganic Electron Donor Consumption, Autotrophic CO2 Fixation and 16S Tags of the Transcriptome in Incubation Experiments, Frontiers in Microbiology, 10: 2296. doi: 10.3389/fmicb.2019.02296

Böhnke, S. & Perner, M., Unraveling RubisCO form I and form II regulation in an uncultured organism from a deep-sea hydrothermal vent via metagenomic and mutagenesis studies, Frontiers in Microbiology (2017), 8: 1303. doi: 10.3389/fmicb.2017.01303.

Gonnella, G., Böhnke, S., Indenbirken, D., Garbe-Schönberg, D., Seifert, R., Mertens, C., Kurtz, S. & Perner, M. Endemic hydrothermal vent species identified in the open ocean seed bank, Nature Microbiology (2016), 1(8):16086. doi: 10.1038/nmicrobiol.2016.86.

Böhnke, S. & Perner, M. A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity, The ISME Journal (2015), 9 (3): 735-745. doi: 10.1038/ismej.2014.163

Rabausch, U., Jürgensen, J., Ilmberger, N., Böhnke, S., Fischer, S., Schubach, B., Schulte, M.M. & Streit, W.R. Functional screening of metagenome and genome libraries for detection of novel flavonoid modifying  enzymes, Applied and Environmental Microbiology (2013), 79 (15): 4551-4563. doi: 10.1128/AEM.01077-13.

Perner, M., Gonnella, G., Hourdez, S., Böhnke, S., Kurtz, S. & Girguis, P. In-situ chemistry and microbial community compositions in five deep-sea hydrothermal fluid samples from Irina II in the Logatchev field, Environmental Microbiology (2013), 15 (5) 1551-1560. doi: 10.1111/1462-2920.12038.

Selected national and international conference contributions

Stefanie Böhnke-Brandt*,Christian T. Hansen, Charlotte Kleint, Lukas Klose, Nicole Adam-Beyer, Katharina Sass, Thorsten Dittmar, Andrea Koschinsky, and Mirjam Perner (2022), Poster: Iron amendment to hydrothermal plumes induces shifts in microbial communities and provide first insights into the microbial organic iron-ligand production, VAAM (Düsseldorf, Germany)

Böhnke, S*. and Perner, M. (2018), Talk: An activity-based metagenomic screen reveals: RubisCO is not the only enzyme that converts ribulose-1,5-bisposphate. 17th international Symposium on Microbial Ecology (ISME17) (Leipzig, Germany).

Sass, K.*, Böhnke, S. and Perner, M. (2018) Talk: Iron, sulfide and hydrogen cycling in Kermadec Arc hydrothermal fluids: microbial turnover rates coupled to transcriptomics give insight into biogeochemical processes. Goldschmidt, Boston, USA

Perner, M.*, Böhnke, S., Sass, K. (2018) Talk:Turnover rates coupled to transcriptomics reveal dominant microorganisms responsible for cycling iron, sulfide and hydrogen in Kermadec Arc hydrothermal fluids. VAAM (Wolfsburg, Germany

Böhnke, S*. and Perner, M. (2018) Poster: Metagenomic and mutagenesis studies uncover novel features for regulating RubisCO expression in an uncultured deep-sea vent bacterium. VAAM (Marburg, Germany)

Böhnke, S*. and Perner, M. (2015) VAAM Talk: A novel function-based screen suited to seek RubisCOs from metagenomic libraries: Improving our understanding of RubisCO regulation and activation mechanisms. (Marburg, Germany)

Böhnke, S*. and Perner, M. (2014) Talk: A novel function- based screen for detecting RubisCO active clones from metagenomic libraries: elucidating the role of RubisCO associated enzymes. Institutions Internal Seminar of the Biocentre Klein Flottbek (Hamburg, Germany)

Böhnke, S*. and Perner, M. (2013) Poster: Functional metagenomics: Seeking CO2-reducing enzymes using newly established screening approaches. VAAM (Bremen, Germany)

Böhnke, S*. and Perner, M. (2012) Poster: Novel function based approaches for seeking CO2 reducing enzymes on a metagenomic scale. Gorden Research Conference (GRC) (Bosten, USA),

Böhnke, S*. and Perner, M. (2012) Talk: Hydrothermal deep-sea systems: Oasis for seeking novel CO2-reducing enzymes by using functional metagenomics. sommer school of the C1-REM graduate school (Hamburg, Germany)

Böhnke, S*. and Perner, M. (2012) Talk: Function based screening of CO2 reducing enzymes by using metagenomic libraries from hydrothermal deep-sea systems. 14th international Symposium on Microbial Ecology (ISME14) (Copenhagen, Denmark)

Böhnke, S*. and Perner, M. (2011) Talk: Hydrothermal deep-sea habitats: A resource for novel CO2 reducing enzymes. sommer school of the C1-REM graduate school (Hamburg, Germany),

Böhnke, S*. and Perner, M. (2011) Talk: Autotrophic carbon fixation: Advances in biogeochemical interactions, with function based approaches on a metagenomic level as a prospect. CAREX Conference (Dublin, Ireland)

*presenting author