NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969)

Willems, Anne; Ley, J. De; Gillis, Monique; Kersters, Karel

doi:10.1099/00207713-41-3-445

Cited by 214 publications

(129 citation statements)

References 29 publications

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“…Comprising 3% of the bacterial 16s rDNAs recovered (three clones), clone OM180 phylogenetically affiliated with Rhodoferax fermentans (9 1.8% similar), a phototrophic purple nonsulfur bacteria isolated from ditch water and activated sludge (Hiraishi et al, 1991;Hiraishi 1994), and Variovoraxparadoxus (90.9% similar), a heterotrophic bacterium isolated from soil (Willems et al 1991). R. fermentans and V. paradoxus are members of the family Comamonadaceae within subgroup p-1 of the /?-Proteobacteria and are 94.0% similar in 16s rRNA gene sequence, but do not appear to share many phenotypic traits (Willems et al 1991). In this analysis, the Comamonadaceae (R. fermentans, V. paradoxus, and C. testosteroni) were recovered as a monophyletic group within the P-Proteobacteria in 98 out of 100 bootstrap replicates, with the inclusion of clone OM180 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Rappé

Kemp

Giovannoni

1997

Limnology & Oceanography

222

195

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The phylogenetic diversity of a continental-shelf picoplankton community was examined by analyzing 16s ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, served as the source of bulk nucleic acids used in this study. A large proportion of the 169 rDNA clones recovered (33%) were related to plastid 16s r-RNA genes, including plastids from both chromophyte and chlorophyte algae. Most bacterial gene clones (75% of bacterial clones, 50% of the total) were closely related to r-RNA gene lineages that had been discovered previously in clone libraries from opcnocean marine habitats, including the SARI36 cluster (y-Proteobacteria), SAR83, SARll, and SAR116 clusters (all a-Proteobacteria), as well as the marine Gram-positive cluster (high G+C Gram-positive). Most of the remaining bacterial clones recovered were phylogenetically related to the y and /3 subclasses of the Proteobacteria, including an rDNA lineage within the type 1 methylotroph clade of the p subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of P-Proteobacteria, are features of this coastal picoplankton gene clone library that distinguish it from similar studies of oligotrophic open-ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open ocean, can account for most cells in this coastal marine bacterioplankton assemblage.

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Section: Resultsmentioning

confidence: 99%

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Rappé

Kemp

Giovannoni

1997

Limnology & Oceanography

222

195

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“…The genus Variovorax was proposed by reclassification of Alcaligenes paradoxus as Variovorax paradoxus, the single recognized species of the genus (Willems et al, 1991). Phylogenetic analyses based on 16S rRNA gene sequences showed that the genus Variovorax falls within the family Comamonadaceae of the Betaproteobacteria (Anzai et al, 2000).…”

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confidence: 99%

Variovorax dokdonensis sp. nov., isolated from soil

Yoon

Kang

2006

International Journal of Systematic and Evolutionary Microbiology

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A Gram-negative, motile and oval-or rod-shaped bacterial strain, DS-43 T , was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. The strain grew optimally at pH 7?0-8?0 and at 30 6C in the presence of 0?5 % (w/v) NaCl. Strain DS-43 T had Q-8 as the predominant ubiquinone and C 16 : 0 , C 16 : 1 v7c and/or iso-C 15 : 0 2-OH, C 18 : 1 v7c and C 17 : 0 cyclo as the major fatty acids, which are consistent with the corresponding data for the type strain (KCTC 12459 T ) of Variovorax paradoxus. The DNA G+C content was 66?0 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-43 T was most closely related to Variovorax paradoxus, the only recognized species of the genus. The level of 16S rRNA gene sequence similarity between strain DS-43 T and V. paradoxus IAM 12373 T was 97?3 %. DNA-DNA relatedness data and differential phenotypic properties demonstrated that strain DS-43 T is distinguishable from V. paradoxus. On the basis of phenotypic, phylogenetic and genetic data, it is proposed that strain DS-43 T (=KCTC 12544 T =CIP 108838 T ) be classified in the genus Variovorax as a member of a novel species, Variovorax dokdonensis sp. nov.

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“…At present, the Variovoras group consists of only V. paradoxus [49], divided into biovar I and biovar II strains. The difference between Alicaligenes and Variovorax is that the Variovorax group releases a yellow pigment into the medium, whereas Alicaligenes does not.…”

Section: Discussionmentioning

confidence: 99%

Identification and characterization of a new gene from Variovorax paradoxus Iso1 encoding N‐acyl‐d‐amino acid amidohydrolase responsible for d‐amino acid production

Lin¹,

Su²,

Tsai³

et al. 2002

European Journal of Biochemistry

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An N-acyl-D-amino acid amidohydrolase (N-D-AAase) was identified in cell extracts of a strain, Iso1, isolated from an environment containing N-acetyl-D-methionine. The bacterium was classified as Variovorax paradoxus by phylogenetic analysis. The gene was cloned and sequenced. The gene consisted of a 1467-bp ORF encoding a polypeptide of 488 amino acids. The V. paradoxus N-D-AAase showed significant amino acid similarity to the N-acyl-D-amino acid amidohydrolases of the two eubacteria Alcaligenes xylosoxydans A-6 (44-56% identity), Alcaligenes facelis DA1 (54% identity) and the hyperthermophilic archaeon Pyrococcus abyssi (42% identity). After over-expression of the N-D-AAase protein in Escherichia coli, the enzyme was purified by multistep chromatography. The native molecular mass was 52.8 kDa, which agreed with the predicted molecular mass of 52 798 Da and the enzyme appeared to be a monomer protein by gel-filtration chromatography. A homogenous protein with a specific activity of 516 UAEmg )1 was finally obtained. After peptide sequencing by LC/MS/ MS, the results were in agreement with the deduced amino acid sequence of the N-D-AAase. The pI of the enzyme was 5.12 and it had an optimal pH and temperature of 7.5 and 50°C, respectively. After 30 min heat treatment at 45°C, between pH 6 and pH 8, 80% activity remained. The N-D-AAase had higher hydrolysing activity against N-acetyl-D-amino acid derivates containing D-methionine, D-leucine and D-alanine and against N-chloroacetyl-D-phenylalanine. Importantly, the enzyme does not act on the N-acetyl-L-amino acid derivatives. The enzyme was inhibited by chelating agents and certain metal ions, but was activated by 1 mM of Co 2+ and Mg 2+ . Thus, the N-D-AAase from V. paradoxus can be considered a chiral specific and metaldependent enzyme.

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NOTES: Comamonadaceae, a New Family Encompassing the Acidovorans rRNA Complex, Including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969)

Cited by 214 publications

References 29 publications

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Phylogenetic diversity of marine coastal picoplankton 16S rRNA genes cloned from the continental shelf off Cape Hatteras, North Carolina

Variovorax dokdonensis sp. nov., isolated from soil

Identification and characterization of a new gene from Variovorax paradoxus Iso1 encoding N‐acyl‐d‐amino acid amidohydrolase responsible for d‐amino acid production

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