Cell Sorting for Genomics
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 first target, the uncultured Cryomorphaceae clade VIS6, is one of the main player in the degradation of diatom derived polysaccharides in the aftermath of spring phytoplankton blooms in the North Sea at Helgoland. Our approach gained valuable insights into the metabolic capacity of this yet uncultured clade. By complementing existing metagenomic bins with genomic data from our sorted cells, we could describe three species of the novel Candidatus genus Abditibacter: A. vernus, A. forsetii, and A. autumni (Grieb et al. 2020a; Grieb et al. 2020b). Members of Cand. Abditibacter are aerobic, proteorhodopsin-containing Flavobacteria, with small genomes and with a capacity to degrade and respire simple carbohydrates like laminarin and peptides.
In essence, the developed pipeline helps complementing existing metagenomic bins from taxonomically well-defined populations and facilitates the targeted retrieval of genomic information from rare taxa.
Currently, we are working on other Flavobacteria taxa using this combined metagenomics and sorting approach. Please find more information on the webpage of Taylor Priest
Cell Sorting for Proteomics
Predicting metabolic function based on (meta-)genomic annotations alone has its limits. Expressed proteins are one step closer to the metabolism of a microorganism and its ecological role in the environment.
In this project we push the combination FISH and FACS further and combine cell sorting with metaproteomics. 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.
Grace Ho is currently doing her PhD on this project.
Southern Pacific Gyre
The Southern Pacific Ocean (SPG) is the most remote oceanic region on earth, characterized by clearest waters and extreme nutrient limitation. Due to its extreme oligotrophy it is often referred to as an ‘oceanic desert’. In a joint research cruise with the Department of Biogeochemistry we sailed across the SPG to explore the microbial community and its capabilities to cope with such extreme conditions. The cruise took place in December 2015 to January 2016 in a track across the oligotrophic gyre from Chile to New Zealand. After a first screening with an on-board sequencing pipeline and on-board FISH analyses (Reintjes et al., 2019) we focussed on characterizing novel clades by targeted flow cytometry and metagenomics. Nine metagenomes from three stations from the oligotrophic gyre centre from three surface layers have been constructed and are currently being analysed. One of the hypotheses we are following is how the microbial community can withstand such high solar irradiance prevalent in the SPG and how its metabolism is adapted to such an extreme environment.
Dr. Monike Oggerin is working on this projekt.