Flow Cytometric Sorting for 'omics
Currently we run two projects, which combine the use of omics methods with flow cytometric cell sorting.
In collaboration with the Joint Genome Institute under the Emerging Technologies Opportunity Program (ETOP) we developed a fluorescence in situ hybridization (FISH) method to flow cytometrically sort taxonomically defined bacteria from plankton samples for subsequent genomic analysis. Our main target, the uncultured Cryomorphaceae clade VIS6, is suspected to be a main player in the degradation of diatom derived polysaccharides in the aftermath of spring phytoplankton blooms in the North Sea at Helgoland. Our approach will gain genomic insights into this yet uncultured clade and will allow for predictions of its metabolic capacity. The advantage over standard metagenomic binning is that by combining FISH and FACS genomic information is gained from taxonomically well-defined populations.
In a second project we push the combination FISH and FACS further and combine cell sorting with metaproteomics. Proteomic analyses are one step closer to the metabolism of microorganisms and give valuable insights into the activity of the organisms of interest. In pilot studies we could identify several hundreds of peptides from one million of phylogenetically stained and sorted cells. This project is part of the DFG research unit FOR 2406 (Proteogenomics Of Marine Polysaccharide Utilization - POMPU).
Find >>here<< more information on the subproject 2: In situ mechanisms of polysaccharide degradation of key bacteroidetal genera in spring algae blooms.
Southern Pacific Gyre
The Southern Pacific Ocean (SPG) is the most remote ocean region on earth. It is characterized by clearest waters and extreme nutrient limitation. Due to its extreme oligotrophy it is often referred to as an ‘oceanic desert’. In a cruise in December 2015 to January 2016 we took part of a research cruise across the SPG from Chile to New Zealand to explore the microbial community and its capabilities to cope with such extreme conditions. We took the on-board sequencing pipeline with us on board and have some 200 FISH preparations on board. After two years in the project we see patterns in the microbial community and discover yet undescribed bacterial clades. It is our goal to characterize those novel clades by targeted flow cytometry and metagenomics.