The phylogeny of members of the family Halomonadaceae, and of flavobacteria isolated from a hypersaline Antarctic lake

Two recently described species of the genus Halomonas occur in the microbiota of some Antarctic saline and hypersaline lakes. The genera Halomonas and Deleya, which comprise the family Halomonadaceae, are difficult to differentiate on the basis of phenotypic and chemotaxonomic attributes. rRNA:DNA hybridisation studies have indicated that some Halomonas spp. have the same level of relationship to the type species of the genus Deleya, as some Deleya spp. Near complete 16S rRNA sequences of 3 Deleya spp., 3 Halomonas spp., and Halovibrio variabilis are obtained by direct sequencing of the PCR-amplified 16S rRNA gene using a-35S dATP. The members of the genera Halomonas and Deleya do not form separate monophyletic subgroups in the phylogenetic trees, derived from the sequence data, confirming the lack of any phylogenetic support for their retention as separate genera. Halovibrio variabilis also clusters within this group of organisms. All the members of the Halomonadaceae examined, and Halovibrio variabilis, possess a cytosine (C) residue at position 486 (E. coli numbering), which is an extremely rare attribute among the prokaryotes, and has been reported in only one other species, Listonella anguillarum. Several other signature characteristics which define this group within the gamma-subclass of the Proteobacteria are identified. The Jukes-Cantor distances between the members of the family Halomonadaceae, and including Halovibrio variabilis, range from 0.086 to 0.000 (the % similarities between sequences are in the range 92.6 - 100). The members of the genera Halomonas, Deleya, and Halovibrio form a monophyletic group and share common chemotaxonomic and phenotypic characteristics. Sub-groups among the members of the genera Halomonas, Deleya and Halovibrio can not be resolved on the basis of phylogenetic, chemotaxonomic or phenotypic data. It is proposed that the genera Halomonas, Deleya and Halovibrio be united in a single genus Halomonas. The new names Halomonas aquamarina comb. nov., Halomonas cupida comb. nov., Halomonas halophila comb. nov., Halomonas marina comb. nov., Halomonas pacifica comb. nov., Halomonas venusta comb. nov., Halomonas sauna comb. nov. and Halomonas variabilis comb. nov. are proposed. The descriptions of the genus Halomonas and the family Halomonadaceae are emended. The phylogenetic placement of pigmented bacteria isolated from Organic Lake, a hypersaline Antarctic Lake, is examined by the determination and analysis of their 16S rRNA sequences. Sequence signatures confirm that the pigmented bacteria from Organic Lake are members of the \flavobacteria-Bacteroides\" phylum. Comparison of the sequences of the Organic Lake strains with those of a large number of sequences available for members of the \"flavobacteria-Bacteroides\" phylum show that they are phylogenetically distinct. These organisms can also be distinguished on the basis of phenotypic and chemo-taxonomic data supporting their description as new taxa at least at the species level. The Organic Lake flavobacteria cluster within a group of organisms that contains the type species of the genus Flavobacterium Flavobacterium aquatile. Two new species of the genus Flavobacterium are described to accommodate the Organic Lake flavobacteria. The names Flavobacterium gondwanense and Flavobacterium sale gens are proposed. Potential oligonucleotide probes for the genus Halomonas (emended as proposed) some member-species of the genus Halomonas F. gondwanense and F.salegens are identified from their 16S rRNA sequences."