Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.halophile ͉ lateral gene transfer ͉ convergence ͉ prokaryotic evolution ͉ rhodopsins U ntil recently, halophilic archaea (haloarchaea) were thought to be the only cells capable of thriving in saltern crystallizers. These impoundments contain Ϸ37% NaCl, at the limits of tolerance for this environmental factor. Further concentration of thalassic (seawater-derived) hypersaline water leads to precipitation of magnesium salts and sterility. Fluorescent in situ hybridization indicates that one crystallizer morphotype, well defined large rods, corresponds to a bacterium of the Cytophaga cluster (1), within the Bacteroides͞Chlorobi group. This organism represents 10-20% of the cells in climax crystallizer communities (spring and summer in temperate latitudes). Representative strains (as defined by 16S rRNA sequences) have been isolated from the same environment and described as the previously uncharacterized genus and species Salinibacter ruber (2).The closest cultivated relative of S. ruber (henceforth Salinibacter) is Rhodothermus marinus (89% 16S rRNA sequence similarity), a slightly halophilic thermophile isolated from marine hot springs (2). Salinibacter displays many remarkable similarities to haloarchaea, one being a very high concentration of potassium in the cytoplasm (3). This property is associated, as in haloarchaea, with a high content of acidic amino acids and a low content of hydrophobic residues in bulk protein, necessary for protein solubility at such high ionic strength (4). Cell integrity requires high salt concentrations in both cases, and growth only occurs at Ͼ2 M NaCl. Both Salinibacter and the haloarchaea are aerobic heterotrophs that exploit the large stock of organic nutrients produced in previous stages of seawater concentration, mostly by the green alga Dunaliella, and they use a similar range of organic compounds as carbon and energy sources (5). Like haloarchaea, Salinibacter contains a high proportion of carotenoids in its membrane, pro...

The variability in genome content among closely related strains of prokaryotes has been one of the most remarkable discoveries of genomics. One way to approach the description of this so-called pan-genome is to compare one reference strain genome with metagenomic sequences from the environment. We have applied this approach to one extreme aquatic habitat, saturated brines in a solar saltern. The genome of Haloquadratum walsbyi strain DSM 16790 was compared to an environmental metagenome obtained from the exact site of its isolation. This approach revealed that some regions of the strain genome were scarcely represented in the metagenome. Here we have analyzed these genomic islands (GI) in the genome of DSM 16790 and compared them with the complete sequence of some fosmids from the environmental library. Two of the islands, GI 2 and GI 4, overlapped with two large guanine and cytosine (GC)-rich regions that showed evidence of high variability through mobile elements. GI 3 seemed to be a phage or phage-remnant acquired by the reference genome, but not present in most environmental lineages. Most differential gene content was related to small molecule transport and detection, probably reflecting adaptation to different pools of organic nutrients. GI 1 did not possess traces of mobile elements and had normal GC content. This island contained the main cluster of cell envelope glycoproteins and the variability found was different from the other GIs. Rather than containing different genes it consisted of homologs with low similarity. This variation might reflect a phage evasion strategy.

Background: Mature saturated brine (crystallizers) communities are largely dominated (>80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present.