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.  

Our goals are:

• to identify, characterize and quantify key players in important microbial processes in freshwater systems, e.g. anaerobic methane oxidation, degradation of chitin and amino-compounds, methanogenesis.
  
  
• 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 of freshwater ecosystems.
  
  
• to conduct and support applied research on microbial risks 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.

Projects

Currently ongoing projects:

• Degradation and transformation of organic nitrogen compounds in the water column and sediments (DONLAC) [...]
• Antibiotic resistance as an emerging environmental contaminant:
  
  • Sources and fate of Antibiotic resistance in a mid-sized lake (Lake Geneva) [...]
  • Prevalence of Antibiotic Resistance Genes in Fresh Water Ecosystems in Switzerland (MSc project)
• Microbial diversity and function in Urine Waste treatment reactors and Microbial Fuel Cells (DUNOX/ECUT) [...]
• Diversity of methanogens in Lake Kivu sediments (MSc project) […]
• Microbial resistance and resilience against changes of foodweb structures […]
  
  

Collaborations:

• Microbial biodiversity in alpine streams (MICROLINK) - Remo Freimann, Chris Robinson, Eco [...]
• Cell extraction from aquifer biofilms – Fabio Ugolini, Martin Schroth, Josef Zeyer, ETHZ
• Food-web and ecosystem responses to global change: testing ecological theory in aquatic mesocosms – Julia Birtel, Blake Matthews, Eco
  
• qPCR biases - Robert Brankatschk [...], Josef Zeyer, ETHZ
  

Concluded projects:

• Methane cycling and diversity of methanotrophs in Lake Kivu (finished) [...]
• Specific enrichment of DNA fragments (GeneBeads) (finished) [...]
• Influence of hypolimnetic oxygenation systems on microbial diversity and metal fluxes – Lee Bryant […]

Equipment

List of our methodological capabilities and equipment.

Teaching

• Vorlesung ETHZ: Stoffwechsel von Mikroorganismen [...]

Team

• Helmut Bürgmann, group leader
• Karin Beck, technician
• Nadine Czekalski, PhD student
• Krista Köllner, PhD student
• Remo Freimann, PhD student (Eco/Surf)
• Karen Sullam, PhD student, scientific guest (Fulbright stipendiate)
• José Santos, scientific assistant
• Hannah Bruderer, intern
  
  

Co-supervised students:

• Julia Birtel, PhD student (Eco)
  “Food-web and ecosystem responses to global change: testing ecological theory in aquatic mesocosms” [...]
  
• Remo Freimann, PhD student (Eco)
  “Terrestrial/aquatic linkages in microbial biodiversity in alpine floodplains: shifting role of bacteria in ecosystem functioning (MICROLINK)” [...]
  
• Sarina Jenni, PhD student (Process Engineering)
  “Nitrogen removal from urine with partial nitritation / anammox” [...]
  
• Fabio Ugolini (ETHZ)
  “In-Situ extraction of microorganisms from aquifer sediments” [...]
  
• Dörte Carstens, PhD student (Surf)
  “Degradation and transformation of lacustrine organic nitrogen compounds: microbiology and biogeochemistry” [...]
  

Former members, guests and supervised students:

• Radhika Sigdel, MSC student (IHE-UNESCO)
  
• Susma Bhattarai, MSc student and scientific assistant
• Tina Wunderlin, MSc student
• Manuel Pesaro, PostDoc
• Lee Bryant, PhD student VirginiaTech, scientific guest
  
• Natascha Pasche, PhD Student
• Nina Bircher, Bachelor student