Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing

Toshifumi Osaka, Sachiko Yoshie, Satoshi Tsuneda, Akira Hirata, Norio Iwami, Yuhei Inamori

    研究成果: Article

    116 引用 (Scopus)

    抄録

    Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [ 13C]acetate or [13C]methanol as the main carbon source and nitrate as the electron acceptor. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. Rarefaction curves for clones retrieved from 13C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria. Furthermore, we characterized nitrite reductase genes (nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. However, most of the nirS or nirK sequences retrieved from 13C-DNA were clustered in some unidentified groups. On the basis of 16S rRNA gene clone libraries retrieved from 13C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).

    元の言語English
    ページ(範囲)253-266
    ページ数14
    ジャーナルMicrobial Ecology
    52
    発行部数2
    DOI
    出版物ステータスPublished - 2006 8

    Fingerprint

    Isotopes
    Nitrates
    stable isotopes
    Methanol
    methanol
    acetate
    Acetates
    stable isotope
    acetates
    nitrates
    nitrate
    Comamonadaceae
    Bacteria
    bacterium
    Hyphomicrobiaceae
    Methylophilaceae
    gene
    rRNA Genes
    bacteria
    Rhodobacteraceae

    ASJC Scopus subject areas

    • Aquatic Science
    • Applied Microbiology and Biotechnology
    • Ecology
    • Microbiology

    これを引用

    Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing. / Osaka, Toshifumi; Yoshie, Sachiko; Tsuneda, Satoshi; Hirata, Akira; Iwami, Norio; Inamori, Yuhei.

    :: Microbial Ecology, 巻 52, 番号 2, 08.2006, p. 253-266.

    研究成果: Article

    Osaka, Toshifumi ; Yoshie, Sachiko ; Tsuneda, Satoshi ; Hirata, Akira ; Iwami, Norio ; Inamori, Yuhei. / Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing. :: Microbial Ecology. 2006 ; 巻 52, 番号 2. pp. 253-266.
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    abstract = "Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [ 13C]acetate or [13C]methanol as the main carbon source and nitrate as the electron acceptor. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. Rarefaction curves for clones retrieved from 13C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria. Furthermore, we characterized nitrite reductase genes (nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. However, most of the nirS or nirK sequences retrieved from 13C-DNA were clustered in some unidentified groups. On the basis of 16S rRNA gene clone libraries retrieved from 13C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).",
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    AU - Osaka, Toshifumi

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    AU - Hirata, Akira

    AU - Iwami, Norio

    AU - Inamori, Yuhei

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    N2 - Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [ 13C]acetate or [13C]methanol as the main carbon source and nitrate as the electron acceptor. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from 13C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. Rarefaction curves for clones retrieved from 13C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria. Furthermore, we characterized nitrite reductase genes (nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. However, most of the nirS or nirK sequences retrieved from 13C-DNA were clustered in some unidentified groups. On the basis of 16S rRNA gene clone libraries retrieved from 13C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).

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