Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber

Abstract

Background: Saturated brines are extreme environments of low diversity. Salinibacter ruber is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population.

Results: Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring S. ruber cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes.

Conclusion: The genomic organisation of S. ruber variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.

Figure 1

Salinibacter ruber DSM 13855 genome and metagenomic islands. (a) GC-content of Salinibacter ruber genome plotted with a sliding window of 1000 nucleotides. Location of integrases and IS transposases along the genome are indicated. (b) Coverage of San Diego saltern crystallizer metagenomic reads. Individual metagenomic reads were aligned to the sequenced strain genome and the alignment-sequence conservation visualized in the form of percent identity plot. Each dot on the graph represents an individual sequence read aligned along its homologous region in Salinibacter ruber DSM 13855 genome. Y axis reflects its nucleotide percent identity to syntenic region. The regions lacking representation in the metagenome are boxed and described in the text as metagenomic islands.

Figure 2

Distribution of Clusters of Orthologous Groups (COGs) in Salinibacter ruber DSM 13855 metagenomic islands, genome of Salinibacter ruber DSM 13855 and San Diego crystallizer metagenome.

Figure 3

Salinibacter ruber DSM 13855 metagenomic island 1 and San Diego crystallizer metagenome. GC-content of the island is plotted with a sliding window of 1000 nucleotides. Location of metagenomic island 1 on S. ruber DSM 13855 genome is indicated by nucleotide position number at the beginning and the end. ORF names are designated near each box.

Figure 4

Salinibacter ruber DSM 13855 metagenomic island 2 and San Diego crystallizer metagenome. GC-content of the island is plotted with a sliding window of 1000 nucleotides. Location of metagenomic island 2 on S. ruber DSM 13855 genome is indicated by nucleotide position number at the beginning and the end. ORF names are designated near each box.

Figure 5

Salinibacter ruber DSM 13855 metagenomic island 3 and San Diego crystallizer metagenome. GC-content of the island is plotted with a sliding window of 1000 nucleotides. Location of metagenomic island 3 on S. ruber DSM 13855 genome is indicated by nucleotide position number at the beginning and the end. ORF names are designated near each box.