Presence of 2,4-D-catabolizing Bacteria in a Japanese Arable Soil that Belong to BANA (Bradyrhizobium-Agromonas-Nitrobacter-Afipia) Cluster in .ALPHA.-Proteobacteria.

Itoh, Kazuhito; Kanda, Rie; Momoda, Yoshio; Sumita, Yoko; Kamagata, Yoichi; Suyama, Kousuke; Yamamoto, Hiroki

doi:10.1264/jsme2.2000.113

Cited by 34 publications

(32 citation statements)

References 14 publications

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“…The isolated 2,4-D-degrading bacteria were phylogenetically the same as those that have been previously reported. Major degraders belonged to the genera Burkholderia, Sphingononas, and Ralstonia as in other environments examined 6,12,15,17) . In almost all the Burkholderia spp.…”

Section: Discussionmentioning

confidence: 56%

“…The third group consists of the oligotrophic bacteria belonging to the genus Bradyrhizobium in α-Proteobacteria. They have been isolated from pristine soils in Hawaii, Canada, and Chile 17) and subsequently from an arable soil in Japan 12) . They are characterized by CadAB with 54-59% deduced amino acid identity with TftAB, and TfdAα with 43-46% identity with TfdA of the first group 13,14) .…”

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confidence: 99%

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Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacteria in Vietnamese Soils

2007

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Diverse 2,4-D and 2,4,5-T-degrading bacteria were isolated country-wide from ten Vietnamese soils, with or without a history of exposure to Agent Orange. The 353 degraders were phylogenetically grouped into three major categories; Burkholderias spp. (43.3% of all degraders), Sphingomonas spp. (40.2%), and Ralstonia spp. (15.3%) and two minor ones; Bradyrhizobium sp. (0.8%) and Nocardioides sp. (0.3%). The 2,4,5-T degraders, 65% of all degraders, were isolated from all soil samples and their 16S rRNA genes were the most homologous with that of Sphingomonas spp., Burkholderia spp. or Bradyrhizobium sp. The following four degradative genes were found by PCR: tfdA (tfdAα) in the Burkholderia spp., Ralstonia spp., Bradyrhizobium sp., and Nocardioides sp.; tfdB in all degraders; tftA (cadA) in the Sphingomonas spp., Burkholderia sp. and Bradyrhizobium sp.; tftC only in the Burkholderia sp. The degraders among Burkholderia spp. were isolated only from the central and southern sites, while those among Ralstonia spp. were found only at the north sites with one exception. The Sphingomonas spp. were isolated country-wide, but four phylogenetically different groups were found at one site, while only one group was found at the other five sites. At least three different plasmids that carried the tfd genes were found in the Burkholderia spp. and Ralstonia spp. without relation to the sites and the phylogenetic groups. These results suggest that the 2,4-D-and 2,4,5-T-degrading microbial consortia have spread countrywide and are diverse on a genetic as well as geographic basis.

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Section: Discussionmentioning

confidence: 56%

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confidence: 99%

Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacteria in Vietnamese Soils

2007

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“…In particular, the bacteria and genes involved in degradation of 2,4-Dichlorophenoxyacetic acid (2,4-D) have been intensively studied, while those involved in metabolizing other phenoxyacetic acids, for example, 4-chloro-2-methylphenoxyacetic acid (MCPA) are less well known. Numerous phylogenetically diverse bacteria using 2,4-D as the sole source of carbon have been isolated (Pemberton et al, 1979;Tonso et al, 1994;Kamagata et al, 1998;Itoh et al, 2000) and functional genes involved in the entire degradation pathway have been characterized (Don et al, 1985;Fukimori and Hausinger 1993). The first step in the degradation pathway is catalyzed by an a-ketoglutarate-dependent dioxygenase encoded by the tfdA gene (Figure 1).…”

Section: Introductionmentioning

confidence: 99%

“…Prior work has shown that diversity among the functional tfdA genes encoding this dioxygenase enzyme is high (Vallaeys et al, 1996;Kamagata et al, 1998). McGowan et al (1998) suggested classifying tfdA genes into three classes (I-III) with sequences between classes showing 75-80% homology and Kamagata et al (1998) and Itoh et al (2000) isolated 2,4-D-degrading strains possessing the tfdA-like genes tfdAa and cadA. Although bacteria and functional genes involved in MCPA degradation have been less intensively studied, several organisms isolated using 2,4-D as the sole source of carbon have been shown to degrade MCPA as well (Smejkal et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil

et al. 2008

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Expression of the functional gene tfdA involved in degradation of phenoxyacetic acids such as 2,4-dichlorophenoxyacetic acid (2,4-D) and 4-chloro-2-methylphenoxyacetic acid (MCPA) was investigated during degradation scenarios in natural unseeded soil samples. The results illustrate how messenger RNA (mRNA)-based analysis is well suited to quantitatively study the activity of specific microbial populations in soil using phenoxyacetic acid biodegradation as a model system. Via quantitative real-time PCR, a clear response to the presence of phenoxy acids was shown during degradation in soil amended with 20 mg 2,4-D or MCPA per kg soil. Further, we found a relatively high degree of correlation between expression of the functional gene and the rates of mineralization. Melting curve analyses of real-time PCR products, supported by tfdA-denaturing gradient gel electrophoresis analysis showed that, although only class I tfdA genes were apparent in the indigenous microbial population, class III tfdA genes became predominant during incubation, and were the only genes expressed during degradation of MCPA in soil. In contrast, both classes were expressed during degradation of the structurally similar compound 2,4-D. The ability to quantify microbial transcripts directly in environmental samples will have a profound impact on our understanding of microbial processes in the environment in future studies.

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“…Bradyrhizobium sp. strain RD5-C2 was isolated from a farm soil with no history of pesticide application 15) . Recently, some 2,4-D-degrading strains including Alpha-, Beta-, and Gammaproteobacteria were isolated from activated sludge 28) .…”

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2,4-Dichrolophenoxyacetic Acid-degrading Genes from Bacteria Isolated from Soil in Japan: Spread of Burkholderia cepacia RASC-type Degrading Genes Harbored on Large Plasmids

et al. 2007

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Fourteen strains of 2,4-dichrolophenoxyacetic acid (2,4-D)-degrading bacteria were isolated from soil samples from eight different sites in Japan and identified as members of the genera Burkholderia, Cupriavidus, and Sphingobium. To characterize them in view of the 2,4-D-degrading genes that they had, the strains were divided into three groups based on similarities of PCR-amplified partial nucleotide sequences of their 2,4-D-degrading genes to the sequences of well-characterized 2,4-D-degrading genes, tfdA, tfdB, and tfdC in Cupriavidus necator strain JMP134, Achromobacter xylosoxidans strain EST4002, and Sphingomonas sp. strain TFD44. The nucleotide sequences of the tfdA, tfdB, and tfdC gene homologs in eight of the 14 strains were highly similar to those in Burkholderia cepacia strain RASC. The eight strains were classified into the RASC subgroup in the EST4002 group. Southern hybridization indicated that at least one set of the putative tfdA, tfdB, and tfdC genes in each of the 14 strains was located on a replicon (ca. 90-600 kb). In particular, the RASC-type 2,4-D-degrading genes of the eight strains were located on plasmids of similar size (ca. 600 kb), and the hybridization experiments suggested that the 2,4-D-degrading genes of seven strains among the eight were located on restriction fragments of the same length. In view of the fact that the seven strains originated from six distant sites in Japan and had different 16S rRNA gene sequences, our results suggest that the RASC-type 2,4-D-degrading genes on similar plasmids were horizontally transferred among bacteria and were distributed throughout Japan.

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Presence of 2,4-D-catabolizing Bacteria in a Japanese Arable Soil that Belong to BANA (Bradyrhizobium-Agromonas-Nitrobacter-Afipia) Cluster in .ALPHA.-Proteobacteria.

Cited by 34 publications

References 14 publications

Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacteria in Vietnamese Soils

Diversity of 2,4-Dichlorophenoxyacetic Acid (2,4-D) and 2,4,5-Trichlorophenoxyacetic Acid (2,4,5-T)-Degrading Bacteria in Vietnamese Soils

Direct analysis of tfdA gene expression by indigenous bacteria in phenoxy acid amended agricultural soil

2,4-Dichrolophenoxyacetic Acid-degrading Genes from Bacteria Isolated from Soil in Japan: Spread of Burkholderia cepacia RASC-type Degrading Genes Harbored on Large Plasmids

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