Postdoc Tel.: +49-441-798-3839 Mail:  felix.milke [at] uni-oldenburg.de

Current Research

Prokaryotes rarely survive as isolated species. Despite ever more sophisticated culturing methods, a vast majority of organisms refuse to grow outside its environmental condition. It is known that biological interactions among prokaryotes enable and stabilize growth of prokaryotes. Together, these organisms form groups or communities that can be understood as super-organisms, similar to multicellular organisms. And that evolution favored its development via processes such as streamlining.

In my current research, I aim to infer these groups of microbes from a biogeographic perspective. Once identified, I further try to understand their distribution in the global oceans by modelling their dispersal via large-scale ocean currents. I hypothesize that the distribution of free-living prokaryotes is much more deterministic than previously assumed.

Professional Experience

07/2023-present Postdoctoral researcher, ICBM, University of Oldenburg

07/2022-07/2023 Postdoctoral researcher, Organic Farming and Cropping Systems, University of Kassel

04/2022-12/2022 Postodoctoral researcher, ICBM, University of Oldenburg

Education

2022 Dr. rer. Nat. “Biogeography of the Atlantic and Pacific Ocean Microbiome”, ICBM, University of Oldenburg

2018 M.Sc. Marine Environmental Sciences, University of Oldenburg

2014 B.Sc. Environmental Sciences, University of Oldenburg

General Interest

I try to understand how the oceans’ conditions structure microbial communities, considering not only biological processes, but also physical structuring via global ocean currents. Their interplay forms the known biogeographic patterns. In that regard, the oceans display an interesting environment, where a point is connected to all other points in the oceans via travelling times in the range of days to hundreds of years. The implied synchrony in microbial community structures can reveal fine-scale differences resulting from evolutionary diversification on short time-scales.

With nowadays bioinformatic tools we can infer nearly complete genomes from metagenomic data that allows us to go beyond mere biogeographic patterns and instead analyze microbial communities and their genomic identity on the level of population genetics. This scientific field emerged from macroecological studies and is nowadays utilized also for microbial ecology. I am convinced that it holds great potential to deepen our understanding of microbial diversification.

List of Publications

[2023] Milke, F., Meyerjürgens, J., Simon, M. Ecological mechanisms and current systems shape the modular structure of the global oceans’ prokaryotic seascape. Nature Communications 14 (1), 6141. https://doi.org/10.1038/s41467-023-41909-z

[2023] Tran, D.Q., Milke, F., Niggemann, J., Simon, M. The diatom Thalassiosira rotula induces distinct growth responses and colonization patterns of Roseobacteraceae, Flavobacteria and Gammaproteobacteria. Environmental Microbiology. https://doi.org/10.1111/1462-2920.16506

[2023] Dlugosch, L., Bunse, C., Bunk, B., Böttcher, L., Tran, D.Q., Dittmar, T., Hartmann, M., Heinrichs, M., Hintz, N.H., Milke, F., Mori, C., Niggemann, J., Spröer, C., Striebel, M., Simon, M. Naturally induced biphasic phytoplankton spring bloom reveals rapid and distinct substrate and bacterial community dynamics. FEMS Microbiology Ecology 99 (8). https://doi.org/10.1093/femsec/fiad078

[2022] Milke, F., Wagner-Doebler, I., Wienhausen, G., Simon, M. Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean. The ISME Journal 16 (12), 2653-2665. https://doi.org/10.1038/s41396-022-01318-4

[2022] Aguilar-Cruz, Y., Milke, F., Leinberger, J., Poehlein, A., Zotz, G., Brinkhoff, T. Diversity and putative metabolic function of prokaryrotic communities in tank bromeliads along an elevation gradient in tropical Mexico. Frontiers in Mirobiology 13, 945488. https://doi.org/10.3389/fmicb.2022.945488

[2022] Sauer, S., Dlugosch, L., Milke, F., Brinkhoff, T., Kammerer, D.R., Stintzing, F.C., Simon, M. Succession of bacterial and fungal communities during fermentation of medicinal plants. Fermentation 8 (8), 383. https://doi.org/10.3390/fermentation8080383

[2022] Milke, F., Sanchez-Garcia, S., Dlugosch, L., McNichol, J., Fuhrman, J., Simon, M., Wagner-Döbler, I. Composition and biogeography of planktonic pro- and eukaryotic communities in the Atlantic Ocean: Primer choice matters. Frontiers in Microbiology 13, 895875. https://doi.org/10.3389/fmicb.2022.895875

[2022] Leinberger, J., Milke, F., Christodoulou, M., Poehlein, A., Caraveo-Patiño, J., Teske, A., Brinkhoff, T. Microbial epibiotic community of the deep-sea galatheid squat lobster Munidopsis alvisca. Scientific Reports 12 (1), 2675. https://doi.org/10.1038/s41598-022-06666-x

[2021] Giebel, H.A., Arnosti, C., Badewien, T.H., Bakenhus, I., Balmonte, J.P., Billerbeck, S., Dlugosch, L., Henkel, R., Kuerzel, B., Meyerjürgens, J., Milke, F., Voss, D., Wienhausen, G., Wietz, M., Winkler, H., Wolterink, M., Simon, M. Microbial growth and organic matter cycling in the Pacific Ocean along a latitudinal transect between subarctic and subantarctic waters. Frontiers in Marine Science 8, 764383. https://doi.org/10.3389/fmars.2021.764383

[2021] Degenhardt, J., Khodami, S., Milke, F., Waska, H., Engelen, B., Arbizu, P.M. The three domains of life within the discharge area of a shallow subterranean estuary at a high energy beach. Frontiers in Environmental Science 9, 642098. https://doi.org/10.3389/fenvs.2021.642098

[2017] Bakenhus, I., Dlugosch, L., Billerbeck, S., Giebel, H.A., Milke, F., Simon, M. Composition of total and cell-proliferating bacterioplankton community in early summer in the North Sea – roseobacters are the most active component. Frontiers in Microbiology 8, 1771. https://doi.org/10.3389/fmicb.2017.01771