Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences

Abstract

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B9 gene (rpoB9) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB9 protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB9 gene and protein trees. The most important advantage of the use of the rpoB9 gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB9 gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.Haloarchaea, members of the family Halobacteriaceae, are a group of extremely halophilic micro-organisms that form part of the domain Archaea. At the time of writing, haloarchaeal strains are classified in 80 species of 24 genera (Burns et al., 2007; Castillo et al., 2006). Although the majority are neutrophilic, 16 alkaliphilic species have been isolated from soda lakes in Kenya, China, India, Egypt, etc. (Horikoshi, 1999;Rees et al., 2004). Strains isolated in the early 1980s are classified in the genera Natronobacterium, Natronococcus and Natronomonas (Kamekura et al., 1997), and some recent isolates are accommodated in Halalkalicoccus (Xue et al., 2005) and Natronolimnobius (Itoh et al., 2005). These five genera are so far composed exclusively of alkaliphilic strains. On the other hand, the genera Halobiforma, Halorubrum, Natrialba and Natronorubrum consist of both neutrophilic and alkaliphilic species. Since the haloalkaliphilic members lack detectable amounts of glycolipids , analysis of the 16S rRNA genes has been a major criterion for their classification at the genus level. Thus, there is a need for other targets for chemotaxonomy and complementary molecular markers for the phylogeny of the Halobacteriaceae (Wright, 2006).The DNA-dependent RNA polymerase subunit b (in bacteria) or B (in archaea) gene (rpoB) has become aThe GenBank/EMBL/DDBJ accession numbers for the rpoB9 gene sequences determined in this study are AB295622-AB29...

Trehalose/2-sulfotrehalose biosynthesis and glycine-betaine uptake are widely spread mechanisms for osmoadaptation in the Halobacteriales

“…and RpoB 0 trees (Figure 4) (Walsh et al, 2004;Enache et al, 2007;Minegishi et al, 2010). Collectively, these patterns suggest that trehalose production is an ancient trait within the Halobacteriales rather than a recent acquisition through horizontal gene transfer.…”

“…several gene loss events during Halobacteriales evolution. otsAB genes were present in all members of Halobacteriales Clade I (as defined by Walsh et al (2004), Enache et al (2007) and Minegishi et al (2010), including the genera Halovivax, Natronobacterium, Halobiforma, Natronorubrum, Haloterrigena, Halopiger, Natronolimnobius, Natrinema, Natrialba and Natronococcus), as well as the genera Halococcus, Haladaptatus, Halalkalicoccus and Halosimplex. On the other hand, otsAB genes were absent in all members of Halobacteriales clade II (as defined by Walsh et al (2004), Enache et al (2007), Minegishi et al (2010), including the genera Haloferax, Halorubrum, Halogeometricum, Haloquadratum, Haloplanus and Halobaculum), the Halorhabdus-Halomicrobium-Haloarcula clade, as well as within the genera Halobacterium and Natronomonas.…”

Protein Adaptations in Archaeal Extremophiles

“…A number of haloalkaliphilic species have been discovered in soda lakes in Egypt, Kenya, China, India, and the western United States [101]. All archaeal alkaliphiles are halophiles [102, 103].…”

Acidophilic haloarchaeal strains are isolated from various solar salts

“…Recently, DNA-dependent RNA polymerase subunit B' gene and protein sequences have been used as an alternative molecular marker in phylogenetic analysis of the family Halobacteriaceae [9,10]. Our unpublished data of the sequences of RNA polymerase H, B" and B' genes of all species of the family Halobacteriaceae (manuscript in preparation) also suggested that the strain MH1-52-1 was a representative of a novel genus.…”