Summary auto-generated
This study re-evaluated the phylogenetic relationships within the family Halomonadaceae using comparative analysis of complete 23S and 16S rDNA sequences. The researchers sequenced complete 23S rDNA from 18 type strains and complete 16S rDNA from seven type strains of moderately halophilic bacteria. The genus Halomonas, which had become taxonomically problematic with numerous reclassifications, was found to be non-monophyletic. The analysis identified two distinct phylogenetic groups within Halomonas (groups 1 and 2 with 5 and 7 species respectively), while six additional Halomonas species could not be clearly assigned to either group. Notably, Halomonas marina branched separately and showed sequence similarities below the 95% reference threshold for genus separation, suggesting it warrants a separate genus. The genus Chromohalobacter formed a monophyletic group comprising four species. The researchers also proposed including Carnimonas nigrificans in the family Halomonadaceae based on phylogenetic clustering with Zymobacter palmae and high 16S rDNA sequence similarity to family members, despite initial sequence signature differences.
Key findings
- The genus Halomonas is non-monophyletic, with two major phylogenetic groups identifiable by 23S and 16S rDNA analysis, plus six additional ungrouped species showing high phenotypic heterogeneity.
- Halomonas marina forms a deeper-branching separate lineage with <95% sequence similarity to other Halomonas and Chromohalobacter species, indicating it should be reclassified as a separate genus.
- Chromohalobacter is monophyletic and forms a distinct group separate from the Halomonas phylogenetic groups, including recently reclassified species canadensis and israelensis.
- Carnimonas nigrificans should be formally included in the family Halomonadaceae based on close phylogenetic affiliation with Zymobacter palmae and high overall sequence similarity to family members.
- Complete 23S rDNA sequences provide more informative phylogenetic data than the more abundant 16S rDNA sequences and should be preferred for determining accurate bacterial phylogeny.
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Abstract
In this study, we have evaluated the phylogenetic status of the family Halomonadaceae, which consists of the genera Halomonas, Chromohalobacter and Zymobacter, by comparative 23S and 16S rDNA analyses. The genus Halomonas illustrates very well a situation that occurs often in bacterial taxonomy. The use of phylogenetic tools has permitted the grouping of several genera and species believed to be unrelated according to conventional taxonomic techniques. In addition, the number of species of the genus Halomonas has increased as a consequence of new descriptions, particularly during the last few years, but their features are too heterogeneous to justify their placement in the same genus and, therefore, a re-evaluation seems necessary. We have determined the complete sequences (about 2900 bases) of the 23S rDNA of 18 species of the genera Halomonas and Chromohalobacter and resequenced the complete 16S rDNA sequences of seven species of Halomonas. The results of our analysis show that two phylogenetic groups (respectively containing five and seven species) can be distinguished within the genus Halomonas. Six other species cannot be assigned to either of the above-mentioned groups. Furthermore, Halomonas marina forms a separate branch at a deeper level than the other species of the genus Halomonas, which suggests that it should be ascribed to a separate genus. The genus Chromohalobacter forms a monophyletic group constituted by Chromohalobacter marismortui, the recently reclassified species Chromohalobacter canadensis and Chromohalobacter israelensis and the recently proposed species Chromohalobacter salexigens. Finally, we propose to include the genus Carnimonas, with its single species Carnimonas nigrificans, in the family Halomonadaceae.