Department Surface Waters - Research and Management

Microbial Ecology

Aquatic microbes are essential players in freshwater ecosystems, catalyzing key processes of all major elemental cycles. My research group, Microbial Ecology contributes the microbial perspective to the department of Surface Waters’ aim of achieving an in-depth understanding of the physical and biogeochemical processes in freshwater systems, e.g. lakes and reservoirs. Our research is thus primarily driven by questions about the impact of environmental and ecological factors on aquatic microbial communities and their functions and vice-versa. For this purpose, we focus on functional groups of microbes that drive key processes in freshwater environments. 
Not all microbes are harmless, however: a second focus of our research is the role of aquatic environments and the urban water cycle for the dissemination of antibiotic resistant bacteria.
Our goals are:

  • to identify, characterize and quantify key players in important microbial processes in freshwater systems, e.g. methane oxidation, degradation of organic matter, or in the nitrogen cycle.
  • to understand the importance of diversity and microbial community structure for the resilience of microbial populations and their biochemical functions.
  • to understand the mechanisms that shape the microbial response to a dynamic environment, such as functional regulation, changing community structure, and evolutionary processes.
  • to link data on microbial populations and activities to chemical, physical, and other biological data in interdisciplinary efforts to obtain a better understanding, and better models, of freshwater ecosystems.
  • to conduct and support applied research on antibiotic resistance in freshwater systems and the microbiology of wastewater treatment systems.

Improving our basic knowledge about aquatic microbial ecology provides a foundation for sustainable management of one of our most important natural resources: Water.


Dr. Helmut Bürgmann Microbial Ecology Tel. +41 58 765 2165 Send Mail


"The power of the small” premiered at Global Science Film Festival"

20 November 2019
The Global Science Film Festival took place from the 15th to the 17th November in Zurich. In addition to films and short films, videos produced by scientists were shown – amongst those, a film by Helmut Bürgmann and Davide Ciccarese. Read more

Current Projects

Wastewater is a source of antibiotic resistant bacteria. We study their dissemination in the aquatic environment, and strategies to remove them.
Niches and traits of methanotroph bacteria in stratified lakes are studied with the ultimate goal to improve process models.
We study the microbial community composition, identify the key players and their activity in the nitrogen transformation processes in freshwater lakes.
We study the ecological stability of anammox biofilms, which are responsible for the autotrophic Nitrogen removal in mixed nitritation-anammox systems.

Previous Projects

Methane cycle of Lake Kivu

Lake Kivu (Rwanda / R. o. t. Kongo) is a large Lake in central Africa distinguished by an enormous accumulation of dissolved CO2 and methane in its Hypolimnion. We studied and modeled the processes of methane cycling and the distributions of potential methanotrophs populations in the Lake.


Lake Kivu project team



Pasche, N.; Schmid, M.; Vazquez, F.; Schubert, C. J.; Wüest, A.; Kessler, J. D.; Pack, M. A.; Reeburgh, W. S.; Bürgmann, H. (2011) Methane sources and sinks in Lake Kivu, Journal of Geophysical Research G: Biogeosciences, 116(G3), G03006 (16 pp.), doi:10.1029/2011JG001690, Institutional Repository

Archaeal populations in Lake Kivu sediments

In diesem Projekt analysierten wir die Population von Archaea, zu denen auch methanogene Organismen zählen. Die Sedimente werden lokal stark durch verschiedene Unterwasser-Quellen beeinflusst, und auch die Mikrobiellen Gemeinschaften werden dadurch stark beeinflusst.


Lake Kivu project team


Bhattarai, S.; Ross, K. A.; Schmid, M.; Anselmetti, F. S.; Bürgmann, H. (2012) Local conditions structure unique archaeal communities in the anoxic sediments of meromictic Lake Kivu, Microbial Ecology, 64(2), 291-310, doi:10.1007/s00248-012-0034-x, Institutional Repository

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