Research Projects

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

Metabolic Reconstruction of VIS6 /Candidatus Abditibacter from sorted cells
Metabolic Reconstruction of VIS6 /Candidatus Abditibacter from sorted cells © Max Planck Institute for Marine Microbiology/A. Grieb et al. 2020

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.

PhD Student

Grace Ho

MPI for Marine Microbiology
Celsiusstr. 1
D-28359 Bremen




+49 421 2028-9099

Grace Ho
Proteomics of 10^6 cells of sorted Polaribacter KT25
Heat map of protein amounts from 10^6 sorted Polaribacter KT25 cell extracts as comparison between untreated cells and cells after fixation, labeling and sorting. (Becher, Fuchs, unpublished) © Max Planck Institute for Marine Microbiology

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.

Microbial distribution across the SPG
Distribution of major microbial groups across the transect through the Southern Pacific Gyre. © Max Planck Institute for Marine Mikrobiology/Reintjes et al., 2019
Back to Top