Brachymonas denitrificans gen. nov., sp. nov., an aerobic chemoorganotrophic bacterium which contains rhodoquinones, and evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes.

Abstract

The new strains of aerobic chemoorganotrophic rhodoquinone-containing bacteria previously isolated from activated sludge were studied from taxonomic and phylogenetic viewpoints. These strains were Gramnegative, nonmotile coccobacilli, had a strictly respiratory type of metabolism with oxygen or nitrate as the terminal acceptor, produced catalase and oxidase, and contained both ubiquinone-8 and rhodoquinone-8 as major quinones. DNA-DNA reassociation studies revealed that the new strains were highly related to each other at hybridization levels of more than 74%, suggesting the genetic coherency of the isolates as a single species. The 16S rRNA gene from one of the isolates, strain AS-P1, was amplified in vitro and sequenced directly. Sequence comparisons and a distance matrix tree analysis revealed that strain AS-P 1 was most closely related to Comamonas testosteroni, a representative of the beta subclass of the Proteobacteria, but the level of sequence similarity between the two appeared to be low enough to warrant different generic allocations. The strains were differentiated from related organisms by a number of phenotypic and chemotaxonomic properties. Thus, we conclude that the isolates should be placed in a new genus and species of the beta subclass of the Proteobacteria, for which we propose the name Brachymonas denitrificans. Evolutionary relationships of rhodoquinone producers to bacterial species with various quinone classes were discussed on the basis of 16S rRNA sequence information.

Phylogenetic relationships among members of the Comamonadaceae, and description of Delftia acidovorans (den Dooren de Jong 1926 and Tamaoka et al. 1987) gen. nov., comb. nov.

“…Hiraishi et al (1995) found Brachymonas denitriJicans to group with Comamonas testosteroni but used too few reference sequences to adequately infer the relationship of this species with other members of the Comamonadaceae. The cells of this species are nonmotile coccobacilli or short rods (Hiraishi et al, 1995). They have a similar cell morphology to strains 7087 and 12022 (results not shown), but the three strains are not phylogenetically related according to their 16s rRNA gene sequences.…”

“…The following organic compounds can be utilized as carbon and energy sources : acetate, acetamide [reported as a variable reaction by Tamaoka et al ( 1 987) and Willems et al (1991b) De Vos et al (1985), Palleroni (1984), Tamaoka et al (1987) andWillems et al (1991b);b, De Vos et al (1985), Palleroni (1984), Tamaoka et al (1987) and Willems et al (1991b);c, Palleroni (1984) and Willems et al (1990Willems et al ( , 1992b; d, Palleroni (1984) and Willems et al (1989); e, Kersters & De Ley (1984), Urakami et al (1995) and Willems et al (1991a);h Bradbury (1984) and Willems et al (1987Willems et al ( , 1991a; g , Hiraishi et al (1991); h, Hiraishi et al (1995) -gens et al (1996);j, Hamana et al (1994), Krieg (1984), Pot et al (1992a, b) (199 1 b) analysis. The type strain is ATCC 15668T (den Dooren de Jong 7T; Stanier 14T; ACM 489T; LMG 1226T NCIB 968 1' ) .…”

“…On the basis of 16s rRNA sequences, Hiraishi (1 994) demonstrated that Rhodoferax fermentans was most closely related to Comamonas testosteroni, and later Hiraishi et al (1995) assigned Rhodoferax fermentans and the newly described Brachymonas denitriJicans to this family. Two strains from activated sludge and the Baltic Sea were found to be related to Comamonas testosteroni using in situ hybridization with oligonucleotide probes (Koivula & Hantula, 1997), but their phylogenetic position and taxonomic status are not known.…”

“…Comparative sequence analysis of the 16s rRNA gene is currently one of the most powerful and reliable methods to estimate phylogenetic relationships among bacterial taxa. Prior to the commencement of this study, only four 16s rDNA sequences of bacteria belonging to the family Comarnonadaceae were available (Hiraishi, 1994;Hiraishi et al, 1995;Yang et al, 1985). The purpose of this study was to use 16s rDNA sequence similarity analysis to elucidate the precise phylogenetic relationships among members of the Comamonadaceae and to provide a more complete set of 16s rDNA sequences for future taxonomic studies.…”

Activity and Community Composition of Denitrifying Bacteria in Poly(3-hydroxybutyrate-co-3-hydroxyvalerate)-Using Solid-phase Denitrification Processes

“…Nucleotide sequences of nirS and nosZ gene clones were determined as described for 16S rRNA gene sequences. For comparison, nosZ genes from the previously described denitrifying bacteria Brachymonas denitrificans strain AS152 20) and Diaphorobacter nitroreducens strain NA10B T 24,25) were PCR-amplified, subcloned and sequenced as described above. In addition, Aquitalea sp.…”