Genomes of “Spiribacter”, a streamlined, successful halophilic bacterium

Abstract

BackgroundThalassosaline waters produced by the concentration of seawater are widespread and common extreme aquatic habitats. Their salinity varies from that of sea water (ca. 3.5%) to saturation for NaCl (ca. 37%). Obviously the microbiota varies dramatically throughout this range. Recent metagenomic analysis of intermediate salinity waters (19%) indicated the presence of an abundant and yet undescribed gamma-proteobacterium. Two strains belonging to this group have been isolated from saltern ponds of intermediate salinity in two Spanish salterns and were named “Spiribacter”.ResultsThe genomes of two isolates of “Spiribacter” have been fully sequenced and assembled. The analysis of metagenomic datasets indicates that microbes of this genus are widespread worldwide in medium salinity habitats representing the first ecologically defined moderate halophile. The genomes indicate that the two isolates belong to different species within the same genus. Both genomes are streamlined with high coding densities, have few regulatory mechanisms and no motility or chemotactic behavior. Metabolically they are heterotrophs with a subgroup II xanthorhodopsin as an additional energy source when light is available.ConclusionsThis is the first bacterium that has been proven by culture independent approaches to be prevalent in hypersaline habitats of intermediate salinity (half a way between the sea and NaCl saturation). Predictions from the proteome and analysis of transporter genes, together with a complete ectoine biosynthesis gene cluster are consistent with these microbes having the salt-out-organic-compatible solutes type of osmoregulation. All these features are also consistent with a well-adapted fully planktonic microbe while other halophiles with more complex genomes such as Salinibacter ruber might have particle associated microniches.

From Metagenomics to Pure Culture: Isolation and Characterization of the Moderately Halophilic Bacterium Spiribacter salinus gen. nov., sp. nov

“…This value is similar to the genomic GϩC content calculated from the complete genome sequence (62.7%) (44). This value is within the range described for members of the family Ectothiorhodospiraceae (50.5 to 69.9 mol%) (52) but different from the values reported for species of the genera Alkalilimnicola (65.6 to 67.5 mol%) (20,53), Alkalispirillum (66.2 mol%) (54), and Arhodomonas (67.0 mol%) (43).…”

“…T was confirmed when we constructed the phylogenetic tree using a concatenated sequence of 277 conserved proteins in all genomes available for members of the family Ectothiorhodospiraceae (44).…”

“…T (29,44). Comparison of the complete genome sequence with the metagenomic data sets previously obtained from several saltern ponds located in Santa Pola (with salinities of 13, 19, 33, and 37% total salts) and Isla Cristina (with 21% total salts) showed that the M19-40…”

“…S1 in the supplemental material). Besides the intermediate-salinity ponds of the Santa Pola saltern, sequences related to strain M19-40 T (analyzed by recruitment of its genome from the available metagenomes of hypersaline habitats or by comparison of 16S rRNA gene sequences from the RDP database) have been observed in ponds of a saltern in San Diego, CA, with 12 to 14% salinity and several other habitats in Asia and South America with intermediate salinities (44).…”

“…We have recently sequenced the complete genome of strain M19-40 T and assembled it into a single contig (29,44). The genome has a size of 1.7 Mbp, being the smallest genome described within the Ectothiorhodospiraceae.…”