Research

Main Research Objectives

  • Investigation of fundamental physiological and ecological properties of comammox bacteria.
  • Structural and biochemical characterization of key enzymes of comammox and canonical nitrifying microorganisms.
  • Insights into effects that changing environmental conditions have on comammox bacteria.
  • Quantification of the greenhouse gas production by comammox, and assessment of a potential role of comammox as "green microbes" in agriculture and biotechnology.
  • Integrative analysis of the obtained data in the context of nitrification ecology in natural and technical systems.

The Comammox Research Platform joins experts from Microbiolgy and Microbial Ecology, Structural Biology, and Ecosystem Science to address these research topics in a highly collaborative, interdisciplinary approach.

 

Microbiology and Microbial Ecology

The Microbiology and Microbial Ecology group headed by Prof. Holger Daims and Prof. Michael Wagner will tackle the ecophysiology of comammox bacteria, using selected laboratory cultures (model organisms) as well as uncultured comammox in environmental samples. Based on (meta)genome, (meta)transcriptome, and (meta)proteome analyses, hypotheses on metabolic features of comammox organisms will be developed and experimentally tested in physiological experiments. Using state-of-the-art techniques such as microrespirometry, Raman microspectroscopy, and nanoscale secondary ion mass spectrometry (NanoSIMS), the metabolic activity of comammox bacteria will be monitored. The consumption and production of dissolved and gaseous nitrogen compounds will be quantified and related to comammox metabolism by using isotope approaches in close collaboration with the Ecosystem Science group. Protein structures will be analyzed together with the Structural Biology group, and targeted physiological experiments will be designed based on the protein structural and biochemical data.

Participating Researchers: Prof. Holger Daims, Prof. Michael Wagner, Dr. Shurong Liu

 

Structural Biology

The Structural Biology group led by Prof. Kristina Djinovic-Carugo will apply an innovative pipeline for protein crystallization and structure determination to characterize the three-dimensional structures of key comammox enzymes at the scale of single atoms. The obtained structural data will form the basis of specific biochemical and physiological studies (in-house and with external collaboration partners) to achieve first insights into the functioning of important enzymes for nitrification, such as nitrite oxidoreductase. Suitable target proteins will be identified based on the genome-informed metabolic pathway reconstruction done by the Microbial Ecology group. Where possible, catalytically critical protein structural features will be mapped to the protein sequences. This information will be used by the Structural Biology and Microbial Ecology groups to infer physiological properties of uncultured comammox organisms from metagenomic sequence data.

Participating Researchers: Prof. Kristina Djinovic-Carugo, Dr. Georg Mlynek

 

Ecosystem Science

The Ecosystem Science group headed by Prof. Andreas Richter will study nitrification in different types of samples from a process perspective. Isotope pool dilution and fractionation analyses will be applied for quantifying nitrification rates and for source partitioning of nitrification (by-)products. Samples rich in comammox organisms and/or canonical nitrifiers will be selected and incubation experiments will be carried out together with the Microbial Ecology group. In this collaboration, the results of process-based isotope assays will be set in context with data from molecular and in situ microbial activity analyses to estimate the relative contributions of comammox and other nitrifying microbes to overall nitrification in a system.

Participating Researchers: Prof. Andreas Richter, Prof. Michael Wagner, Dr. Shurong Liu