Environmental microbial genomics is a new emerging field that enables us to look at parts of the ocean that were obscure until recently. With present estimates suggesting that ~99.8% of the microorganisms in most environments are not amenable to growth in pure culture, very little is known about their physiology and biogeochemical functions in the ocean. This problem can be now bypassed by accessing the genomes of these microorganisms and identifying protein coding genes and biochemical pathways that will shed light on their physiological properties and ecological function. The Roseobacter clade accounts for up to 40% of the bacterial communities in certain oceanic areas. Furthermore, different Roseobacter clusters account for up to 26% of all 16S rRNA genes identified in surface Bacterial Artificial Clone (BAC) libraries. Therefore, the Roseobacter clade, exhibiting a diverse heterotrophic physiology, appears to be a substantial component of marine bacterial communities.
The proposed research will use, in general, novel molecular biology, and bioinformatics techniques to explore the metabolic properties of planktonic members of the Roseobacter clade and to discover alternative ways to harvest energy.
The specific aims of the proposed research are: (1) to construct High Molecular Weight DNA fosmid and BAC libraries from the Mediterranean Sea and North Sea; (2) to BAC-end sequence these libraries in order to archive the gene inventory of uncultured microorganisms from these environments; (3) to produce a searchable dataset of the random sequences; (4) to select interesting BAC and fosmid clones based on the end sequencing and to sequence the entire selected clones in order to analyze the genomes of uncultured microorganisms and their role in the environment; (5) to screen the BAC libraries with PCRs and primers specific for the Roseobacter clade, e.g. starting with the 16S rRNA gene, genes encoding enzymes of the aerobic anoxygenic photosynthesis and other metabolic pathways unique to Roseobacter; (6) to apply bioinformatics techniques to identify and characterize novel proteins involved in anoxygenic photosynthesis and other pathways to harvest energy, e.g. CO oxidation, Mn2+ oxidation; (6) to isolate so far uncultured Roseobacter strains to complement the metagenomic analyses with physiological and gene expression studies.
Individuals working in the project:
Thorsten Brinkhoff, Oded Beja, Sarah Hahnke, Thomas Langer, Meinhard Simon