Recent projects

More details will follow after publication.

Comparative Genomics of Members of the Marine SAR11 Clade

 

The SAR11 clade of marine Alphaproteobacteria is the most abundant group of heterotrophic bacterioplankton in nearly all oceanic surface layers and regularly constitutes to more than 25% of the total prokaryotic community. The genome sequence of Candidatus Pelagibacter ubique HTCC1062, the first sequenced strain of this cluster, showed exciting adaptations to the marine environment and a very streamlined genome which encoded for only 1354 proteins including a gene for proteorhodopsin. Data from different time series studies and recent metagenomic data indicated a high microdiversity within the SAR11 clade. Based on a comparison of the HTCC1062 genome with the Sargasso Sea WGS data, we concluded that extraordinarily high allelic variation and genome rearrangements appeared to mask the conservation of many genome properties in native SAR11 populations, leading to overestimates of functional species diversity. To assess the genomic background of microdiversity in the SAR11 clade, we sequenced and compared five genomes from SAR11 strains isolated at the same time from the same drop of water. Oceanic systems can differ greatly in nutrient concentrations and productivity. In order to investigate the genomic adaptations of SAR11 bacteria to a rather cold, highly productive coastal environments (off the Oregon Coast) and an oligotrophic subtropical gyre system (off Bermuda), we isolated a new SAR11 strain from the Sargasso Sea (HTCC7211), sequenced its genome and compared it to the existing genomes of the coastal strains.

 

 

 

Culturing of bacteria from the water column of ice-covered lakes in the McMurdo Dry Valleys, Antarctica.

 

        Lakes in the McMurdo Dry Valleys of Antarctica are characterized by a permanent ice cover and little or no anthropogenic influence. Although many bacterial cultures have been obtained from these habitats, recent culture-independent studies indicate that the most abundant microbes in these systems are not yet cultivated. By using dilution-to-extinction cultivation methods with sterilized and nutrient-amended lake water as media, after 24 weeks incubation we isolated 148 chemotrophic psychrotolerant bacterial cultures from surface water of Lake Fryxell as well as the east and west lobes of Lake Bonney. Screening of the 16S rRNA genes of the cultures by restriction fragment length polymorphism (RFLP) yielded 57 putatively pure cultures grouped into 18 clusters. Sequencing of 16S rRNA genes of randomly selected representatives of each RFLP cluster revealed that the corresponding isolates belong to the Alphaproteobacteria (6 RFLP patterns), Betaproteobacteria (6 RFLP patterns), Bacteroidetes (4 RFLP patterns) and Actinobacteria (2 RFLP patterns). Phylogenetic analysis of the sequences showed that the vast majority of the isolates were not closely related to previously described species. Thirteen of 18 RFLP patterns shared a 16S rDNA sequence similarity of 97% or less with the closest described species and four isolates had a sequence similarity of 93% or less with the nearest described species. Phylogenetic analysis showed that these sequences were representatives of deeply branching organisms in the respective phylum. A comparison of the isolates with 16S rRNA clone libraries prepared from the same environments showed substantial overlap, indicating that dilution-to-extinction culturing in natural lake water media can help isolate some of the most abundant organisms in these perennially ice covered lakes.