Department Environmental Microbiology

Microbial Systems Ecology

Research areas

The focus of our research group is on basic questions on bacterial ecology and evolution: on the biological significance of phenotypic heterogeneity in clonal populations, on interactions within and between species, and on how bacteria cope with ever-changing environments. Our goal is to work on basic principles with model systems in the laboratory, and then to test these principles in more natural situations.

The group often works at the level of single cells, and asks how this perspective provides insights that could not be obtained by population experiments. One of the current specific interests is on how stochastic gene expression can promote the emergence of different phenotypes in clonal populations, and in how this shapes interactions within and between different strains and species.

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Group Leader

Selected Publications

Balaban, N. Q.; Helaine, S.; Lewis, K.; Ackermann, M.; Aldridge, B.; Andersson, D. I.; Brynildsen, M. P.; Bumann, D.; Camilli, A.; Collins, J. J.; Dehio, C.; Fortune, S.; Ghigo, J.- M.; Hardt, W.- D.; Harms, A.; Heinemann, M.; Hung, D. T.; Jenal, U.; Levin, B. R.; Michiels, J.; Storz, G.; Tan, M.-W.; Tenson, T.; Van Melderen, L.; Zinkernagel, A. (2019) Definitions and guidelines for research on antibiotic persistence, Nature Reviews Microbiology, 17, 441-448, doi:10.1038/s41579-019-0196-3, Institutional Repository
Rodríguez-Verdugo, A.; Vulin, C.; Ackermann, M. (2019) The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system, Ecology Letters, 22(5), 838-846, doi:10.1111/ele.13241, Institutional Repository
Vulin, C.; Leimer, N.; Huemer, M.; Ackermann, M.; Zinkernagel, A. S. (2018) Prolonged bacterial lag time results in small colony variants that represent a sub-population of persisters, Nature Communications, 9(1), 4074 (8 pp.), doi:10.1038/s41467-018-06527-0, Institutional Repository
Louca, S.; Polz, M. F.; Mazel, F.; Albright, M. B. N.; Huber, J. A.; O'Connor, M. I.; Ackermann, M.; Hahn, A. S.; Srivastava, D. S.; Crowe, S. A.; Doebeli, M.; Wegener Parfrey, L. (2018) Function and functional redundancy in microbial systems, Nature Ecology & Evolution, 2, 936-943, doi:10.1038/s41559-018-0519-1, Institutional Repository
D'Souza, G.; Shitut, S.; Preussger, D.; Yousif, G.; Waschina, S.; Kost, C. (2018) Ecology and evolution of metabolic cross-feeding interactions in bacteria, Natural Product Reports, 35(5), 455-488, doi:10.1039/C8NP00009C, Institutional Repository


In order to better understand natural processes and also to be able to better control the activities of microbial communities in technical systems such as wastewater treatment plants, we need to understand how microbial communities work.
Differences between individual cells can be important for biological processes.
Individual variation and cellular memory help bacteria deal with environmental fluctuations.
Even without genetic resistance bacteria can be tolerant to antibiotics.