It has been proposed that free-living microorganisms exhibit ubiquitous dispersal, do not form geographically isolated populations and rarely (if ever) speciate via allopatry. We studied island-like hot spring cyanobacterial communities in which geographical isolation should be prominent and detectable if it influences the evolution of bacteria. The genetic diversity of cyanobacteria indigenous to North American, Japanese, New Zealand and Italian springs was surveyed by (i) amplification and cloning of 16S rRNA and 16S-23S internal transcribed spacer regions; (ii) lineage-specific oligonucleotide probing (used to verify the predominance of cloned sequences); and (iii) lineage-specific polymerase chain reaction (PCR) (used to search for possible rare genotypes). Phylogenetic and distribution patterns were found to be consistent with the occurrence of geographical isolation at both global and local spatial scales, although different cyanobacterial lineages were found to vary in their distribution. A lack of correspondence between biological patterning and the chemical character of springs sampled suggested that the geographical distribution of thermophilic cyanobacteria cannot be explained by the 20 potential niche-determining chemical parameters that we assayed. Thus, geographical isolation (i.e. genetic drift) must in part be responsible for driving the observed evolutionary divergences. Geographical isolation may be an important underestimated aspect of microbial evolution.

We describe the microbiota of two hypersaline saltern ponds, one of intermediate salinity (19%) and a NaCl saturated crystallizer pond (37%) using pyrosequencing. The analyses of these metagenomes (nearly 784 Mb) reaffirmed the vast dominance of Haloquadratum walsbyi but also revealed novel, abundant and previously unsuspected microbial groups. We describe for the first time, a group of low GC Actinobacteria, related to freshwater Actinobacteria, abundant in low and intermediate salinities. Metagenomic assembly revealed three new abundant microbes: a low-GC euryarchaeon with the lowest GC content described for any euryarchaeon, a high-GC euryarchaeon and a gammaproteobacterium related to Alkalilimnicola and Nitrococcus. Multiple displacement amplification and sequencing of the genome from a single archaeal cell of the new low GC euryarchaeon suggest a photoheterotrophic and polysaccharide-degrading lifestyle and its relatedness to the recently described lineage of Nanohaloarchaea. These discoveries reveal the combined power of an unbiased metagenomic and single cell genomic approach.

Using 1128 protein-coding gene families from 11 completely sequenced cyanobacterial genomes, we attempt to quantify horizontal gene transfer events within cyanobacteria, as well as between cyanobacteria and other phyla. A novel method of detecting and enumerating potential horizontal gene transfer events within a group of organisms based on analyses of “embedded quartets” allows us to identify phylogenetic signal consistent with a plurality of gene families, as well as to delineate cases of conflict to the plurality signal, which include horizontally transferred genes. To infer horizontal gene transfer events between cyanobacteria and other phyla, we added homologs from 168 available genomes. We screened phylogenetic trees reconstructed for each of these extended gene families for highly supported monophyly of cyanobacteria (or lack of it). Cyanobacterial genomes reveal a complex evolutionary history, which cannot be represented by a single strictly bifurcating tree for all genes or even most genes, although a single completely resolved phylogeny was recovered from the quartets’ plurality signals. We find more conflicts within cyanobacteria than between cyanobacteria and other phyla. We also find that genes from all functional categories are subject to transfer. However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases.

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...