Patricia Geesink


Phone: +49 (0)3641 9-494 63




   (Foto: Jan-Peter Kasper/FSU)


PatriciaGeesink-Research1  PatriciaGeesink-Research2

(Fotos: Jan-Peter Kasper/FSU)

DarkMicro - Exploring microbial dark matter with pL droplets

Within my phD project, I am focusing on understanding miscellaneous microbial interactions in groundwater systems of the Hainich Critical Zone Exploratory.

Considering the unculturability of the vast majority of microbial life, cultivation-independent approaches such as metagenomics are crucial as door opener to study microbial life in complex ecosystems. Recently, multiple studies could show the vast extent of the so-called Candidate Phyla, which are mainly composed of uncultured organisms. To date, there is only very little known about both ecological and metabolic properties of microorganisms belonging to those phyla, leading to their definition as “Microbial Dark Matter”. Studies that are based on the reconstruction of the genomes of these microorganisms indicate that bacteria belonging to the Candidate Phyla radiation have very small, reduced genomes and lack certain genes essential/necessary to live independently.

To find out more about the interactions between Candidate Phyla radiation bacteria and their biotic and abiotic environment, I will combine classic cultivation techniques with an innovative droplet-microfluidics platform as well as Single-Cell-derived genomic data.

Prof. Dr. Kirsten Küsel 
Dr. Carl-Eric Wegner

Since 2017: Doctoral Researcher - FSU Jena, Institute of Biodiversity ("Interactions and Metabolic Potential of Groundwater Microorganisms")

2016: Research stay at the Netherlands Institute for Ecology (NIOO) in Wageningen

2012 - 2017: Scientific and Technical Assistant, Chair of Aquatic Geomicrobiology, FSU Jena

2012: M.Sc. Biogeosciences - FSU Jena ("Characterization of the Eukaryotic life in limestone aquifers along a land use gradient")

2009: B.Sc. Biogeosciences - FSU Jena ("The effect of land use on herbivory on beech seedlings")


9. 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.

8. Herrmann M., Geesink P., Yan L., Lehmann R., Totsche K.U., Küsel K. (2019) Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater. Water Research, accepted. Doi: 10.1016/j.watres.2019.115306.

7. 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.

6. 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.



5. 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, fiy164. Doi: 10.1093/femsec/fiy164

4. 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 labelling to understand their ecosystem function. Environmental Microbiology  20: 369-384.



3. Kumar S, Herrmann M, Thamdrup B, Schwab VF, Geesink P, Trumbore SE, Totsche KU and Küsel K, 2017. Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) is Primarily Driven by  Chemolitoautotrophic Anammox Processes. Frontiers in Microbiology: 10.3389/fmicb.2017.01951.



2. Gossner MM, Pašalić E, Lange M, Lange P, Boch S, et al., 2014. Differential Responses of Herbivores and Herbivory to Management in Temperate European Beech. PLoS ONE 9(8): e104876.



1. Risse-Buhl U, Herrmann M, Lange P, Akob DM, Pizani N, Schönborn W, Totsche KU and Küsel K, 2013. Phagotrophic Protist Diversity in the Groundwater of a Karstic Aquifer - Morphological and Molecular Analysis. J. Eukaryot. Microbiol. 60(5): 467-479.