Phylogenetic analyses of the nitrogen-fixing genus Derxia

Xie, Cheng Hui; Yokota, Akira

doi:10.2323/jgam.50.129

Cited by 26 publications

(21 citation statements)

References 18 publications

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“…PCR-mediated amplification of 16S rRNA and nifH gene sequences and sequencing of the PCR products were carried out as described previously (Xie & Yokota, 2004). A 420 bp fragment of the nifH gene (encoding the iron protein of nitrogenase) was amplified from extracted DNA using the forward primer IGK (59-TACGGYAARGGBGGYATCGG-39) and the reverse primer AQE (59-GACGATGATYTCCTG-39) (Y=C/T; S=G/C; R=A/G; B=C/ G/T; D=A/G/T) (Poly et al, 2001).…”

Section: Methodsmentioning

confidence: 99%

Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively

Xie

Yokota

2005

International Journal of Systematic and Evolutionary Microbiology

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108

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The aim of this study was to clarify the taxonomic position of the nitrogen-fixing and hydrogen-oxidizing bacteria Alcaligenes latus strains IAM 12599 T , IAM 12664 and IAM 12665 and Pseudomonas saccharophila IAM 14368 T . It was found that the type strain of Alcaligenes latus, IAM 12599 T , showed 99?9 and 96?1 % 16S rRNA gene sequence similarity to strains IAM 12665 and IAM 12664, respectively. A comparison using DNA-DNA hybridization suggested that strains IAM 12599 T and IAM 12665 belong to a single species (89?7 %) and that strain IAM 12664 (35?1 %) forms a separate species. The phenotypic characteristics also support the conclusion that these bacteria should be identified as two species of a new genus: Azohydromonas lata gen. nov., comb. nov. (type strain IAM 12599 T =DSM 1122 T =LMG 3321 T =ATCC 29712 T ; reference strain IAM 12665=DSM 1123=LMG 3325=ATCC 29714) and Azohydromonas australica sp. nov. (type strain IAM 12664 T =DSM 1124 T =LMG 3324 T =ATCC 29713 T ).Pseudomonas saccharophila IAM 14368 T was found to be closely related to the phototrophic bacterium Roseateles depolymerans, with 96?8 % 16S rRNA gene sequence similarity, but the two bacteria are quite different with respect to their metabolism and some significant phenotypic characteristics, suggesting that they cannot be included in a single genus. Further studies on their nifH gene sequences, G+C content of the DNA and cellular fatty acid composition confirm that Pseudomonas saccharophila should be reclassified: the name Pelomonas saccharophila gen. nov., comb. nov. is proposed, with the type strain IAM 14368 T (=LMG 2256 T =ATCC 15946 T ).

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Section: Methodsmentioning

confidence: 99%

Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively

Xie

Yokota

2005

International Journal of Systematic and Evolutionary Microbiology

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108

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“…In contrast, the three isolates showed very high acetylenereducing activity and were found to possess the nifH gene, suggesting that the isolates belong to the first species of the genus Sphingomonas to be able to fix nitrogen. The phylogeny of the nifH gene has been reported to correlate well with that of the 16S rRNA gene, except for discrepancies with a few taxa (Xie & Yokota, 2004, 2005aMoulin et al, 2001;Rosado et al, 1998;Young, 1992). Therefore, the nifH gene appears to fulfil the criteria for a molecule suitable for molecular phylogeny and has been successfully used as a phylogenetic marker (Ueda et al, 1995).…”

mentioning

confidence: 99%

Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

Xie

Yokota

2006

International Journal of Systematic and Evolutionary Microbiology

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Three yellow-pigmented strains associated with rice plants were characterized by using a polyphasic approach. The nitrogen-fixing abilities of these strains were confirmed by acetylene reduction assay and nifH gene detection. The three strains were found to be very closely related, with 99?9 % 16S rRNA gene sequence similarity and greater than 70 % DNA-DNA hybridization values, suggesting that the three strains represent a single species. 16S rRNA gene sequence analysis indicated that the strains were closely related to Sphingomonas trueperi, with 99?5 % similarity. The chemotaxonomic characteristics (G+C content of the DNA of 68?0 mol%, ubiquinone Q-10 system, 2-OH as the only hydroxy fatty acid and homospermidine as the sole polyamine) were similar to those of members of the genus Sphingomonas. Based on DNA-DNA hybridization values and physiological characteristics, the three novel strains could be differentiated from other recognized species of the genus Sphingomonas. The name Sphingomonas azotifigens sp. nov. is proposed to accommodate these bacterial strains; the type strain is Y39 T (=NBRC 15497 T =IAM 15283 T =CCTCC AB205007 T ).

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“…Many members of the family Rhodocyclaceae possess biotechnological or agricultural potential, such as the ability to degrade halogenated compounds (Song et al, 2000), enhanced biological phosphate removal (Bond et al, 1995), denitrification and reduction of (per)chlorates (Achenbach et al, 2001;Coates et al, 1999) and nitrogen fixation (Xie & Yokota, 2004). It was shown that species of the Rhodocyclales represent the majority of bacterial populations in waste-treatment plants and bioreactors (Bond et al, 1995;Juretschko et al, 2002); however, none has yet been characterized as showing methylotrophy, and many members of the Rhodocyclales have been assumed to be recalcitrant to cultivation (Loy et al, 2005).…”

mentioning

confidence: 99%

Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates

Kalyuzhnaya

Marco

Bowerman

et al. 2006

International Journal of Systematic and Evolutionary Microbiology

113

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Phylogenetic analyses of the nitrogen-fixing genus Derxia

Cited by 26 publications

References 18 publications

Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively

Reclassification of Alcaligenes latus strains IAM 12599T and IAM 12664 and Pseudomonas saccharophila as Azohydromonas lata gen. nov., comb. nov., Azohydromonas australica sp. nov. and Pelomonas saccharophila gen. nov., comb. nov., respectively

Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa

Methyloversatilis universalis gen. nov., sp. nov., a novel taxon within the Betaproteobacteria represented by three methylotrophic isolates

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