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.

Contact

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

Team

Dr. Helmut Bürgmann Microbial Ecology Tel. +41 58 765 2165 Send Mail
Karin Beck Tel. +41 58 765 2150 Send Mail
Dr. Robert Niederdorfer Tel. +41 58 765 2215 Send Mail
Dr. Sasikaladevi Rathinavelu Tel. +41 58 765 2210 Send Mail
Dr. Matthew Blair Tel. +41 58 765 2228 Send Mail
Denise Wälchli Tel. +41 58 765 2158 Send Mail

Current Projects

Wastewater is a source of antibiotic resistant bacteria. We study their dissemination in the aquatic environment, and strategies to remove them.

Antibiotic resistance as an emerging environmental contaminant
Niches and traits of methanotroph bacteria in stratified lakes are studied with the ultimate goal to improve process models.

MOBtrait: Methanotrophs in stratified lakes
We study the microbial community composition, identify the key players and their activity in the nitrogen transformation processes in freshwater lakes.

Nitrogen cycling and microbial community dynamics in lakes
We study the ecological stability of anammox biofilms, which are responsible for the autotrophic Nitrogen removal in mixed nitritation-anammox systems.

Ecological stability of anammox biofilms

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.

Collaboration
Lake Kivu project team

 

Publication

Methane sources and sinks in Lake Kivu

Unique worldwide, Lake Kivu stores enormous amounts of CH4 and CO2. A recent study reported that CH4 concentrations in the lake have increased by up to 15% in the last 30 years and that accumulation at this rate could lead to catastrophic outgassing by ∼2100. This study investigates the present-day CH4 formation and oxidation in Lake Kivu. Analyses of 14C and 13C in CH4 and potential carbon sources revealed that below 260 m, an unusually high ∼65% of the CH4 originates either from reduction of geogenic CO2 with mostly geogenic H2 or from direct inflows of geogenic CH4. Aerobic CH4 oxidation, performed by close relatives of type X CH4-oxidizing bacteria, is the main process preventing CH4 from escaping to the atmosphere. Anaerobic CH4 oxidation, carried out by CH4-oxidizing archaea in the SO42−-reducing zone, was also detected but is limited by the availability of sulfate. Changes in 14CCH4 and 13CCH4 since the 1970s suggest that the amount of CH4 produced from degrading organic material has increased due to higher accumulation of organic matter. This, as well as the sudden onset of carbonates in the 1960s, has previously been explained by three environmental changes: (1) introduction of nonnative fish, (2) amplified subaquatic inflows following hydrological changes, and (3) increased external inputs due to the fast growing population. The resulting enhancement of primary production and organic matter sedimentation likely caused CH4 to increase. However, given the large proportion of old CH4 carbon, we cannot exclude an increased inflow of geogenic H2 or CH4.
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.

Collaboration
Lake Kivu project team

Publication

Local conditions structure unique archaeal communities in the anoxic sediments of meromictic Lake Kivu

Meromictic Lake Kivu is renowned for its enormous quantity of methane dissolved in the hypolimnion. The methane is primarily of biological origin, and its concentration has been increasing in the past half-century. Insight into the origin of methane production in Lake Kivu has become relevant with the recent commercial extraction of methane from the hypolimnion. This study provides the first culture-independent approach to identifying the archaeal communities present in Lake Kivu sediments at the sediment-water interface. Terminal restriction fragment length polymorphism analysis suggests considerable heterogeneity in the archaeal community composition at varying sample locations. This diversity reflects changes in the geochemical conditions in the sediment and the overlying water, which are an effect of local groundwater inflows. A more in-depth look at the archaeal community composition by clone library analysis revealed diverse phylogenies of Euryarchaeota and Crenarachaeota. Many of the sequences in the clone libraries belonged to globally distributed archaeal clades such as the rice cluster V and Lake Dagow sediment environmental clusters. Several of the determined clades were previously thought to be rare among freshwater sediment Archaea (e.g., sequences related to the SAGMEG-1 clade). Surprisingly, there was no observed relation of clones to known hydrogentrophic methanogens and less than 2 % of clones were related to acetoclastic methanogens. The local variability, diversity, and novelty of the archaeal community structure in Lake Kivu should be considered when making assumptions on the biogeochemical functioning of its sediments.
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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