Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization

Abstract

The phylogenetic relationships of 49 Acinetobacter strains, 46 of which have previously been classified into 18 genomic species by DNA-DNA hybridization studies, were investigated using the nucleotide sequence of gyrB, the structural gene for the DNA gyrase B subunit. The phylogenetic tree showed linkages between genomic species 1 (Acinetobacter calcoaceticus), 2 (Acinetobacter baumannii), 3 and TU13; genomic species 6, BJ15, BJ16 and BJ17; genomic species 5, BJ13 (synonym of TU14) and BJ14; genomic species 7 (Acinetobacterjohnsoni~, I 0 and 11; and genomic species 8 and 9. The phylogenetic grouping of Acinetobacter strains based on gyrB genes was almost congruent with that based on DNA-DNA hybridization studies. Consequently, gyrB sequence comparison can be used to resolve the taxonomic positions of bacterial strains a t the level of genomic species. However, minor discrepancies existed in the grouping of strains of genomic species 8,9 and BJ17. The phylogenetic tree for these strains was reconstructed from the sequence of rpoD, the structural gene for the RNA polymerase u 7 O factor. The latter tree was 100% congruent with the grouping based on DNA-DNA hybridization. The reliability of DNA-DNA hybridization may be superior to that of sequence comparison of a single protein-encoding gene in resolving closely related organisms since the former method measures the homologies between the nucleotide sequences of total genomic DNAs. Three strains that have not been characterized previously by DNA-DNA hybridization seem to belong to two new genomic species, one including strain ATCC 33308 and the other including strains ATCC 31012 and MBlC 1332.

Proposal of Pseudorhodobacter ferrugineus gen. nov., comb. nov., for a non-photosynthetic marine bacterium, Agrobacterium ferrugineum, related to the genus Rhodobacter.

“…gyrB sequencing. The protocol for determining the gyrB sequences was almost the same as that described by Yamamoto and Harayama (1995 T were amplified by PCR using primers UP-1E (Yamamoto et al, 1999) and UP-2r (Yamamoto and Harayama, 1995 Phylogenetic analysis. The phylogenetic analysis based on nucleotide sequences of 16S rRNA and 23S rRNA and amino acid sequences of DNA gyrase B subunit were performed.…”

Pseudoalteromonas peptidolytica sp. nov., a novel marine mussel-thread-degrading bacterium isolated from the Sea of Japan.

“…Nine of 17 well-described species of the genus Pseudoalteromonas showed 16S rDNA sequence similarities of 98 %. To circumvent this limitation, the more rapidly evolving gyrB gene (Edgell & Doolittle, 1997) has been used as a high-resolution molecular identification marker for distinguishing strains of Vibrio (Venkateswaran et al, 1998), the Bacillus cereus group (Yamada et al, 1999), Acinetobacter (Yamamoto et al, 1999), Pseudomonas (Yamamoto & Harayama, 1995, 1996, Shewanella and now Pseudoalteromonas.…”

Taxonomic re-evaluation of whorl-forming Streptomyces (formerly Streptoverticillium) species by using phenotypes, DNA–DNA hybridization and sequences of gyrB, and proposal of Streptomyces luteireticuli (ex Katoh and Arai 1957) corrig., sp. nov., nom. rev.

“…However, more comparative data, including DNA-DNA hybridization and phenetic data, are needed to evaluate whether this method is a useful tool for discrimination at species level in Streptomyces. Furthermore, phylogenetic analysis of partial sequences of the gyrB gene, which encodes the B subunit of DNA gyrase, has been used for classification of several types of bacteria and has been shown to be a useful tool for discrimination at species level (Yamamoto & Harayama 1995, 1996, 1998Yamamoto et al, 1999;Kasai et al, 2000). Therefore, we undertook phylogenetic analysis based on partial gyrB gene sequences for reclassification of the whorlforming Streptomyces species, which are suspected to include many synonyms because of their similar morphology and narrow range of sugars utilized for growth.…”