title: Community structure of planktonic methane-oxidizing bacteria in a subtropical reservoir characterized by dominance of phylotype closely related to nitrite reducer.
abstract: Methane-oxidizing bacteria (MOB) gain energy from the oxidation of methane and may play important roles in freshwater ecosystems. In this study, the community structure of planktonic MOB was investigated in a subtropical reservoir. Bacterial community structure was investigated through the analysis of the 16S rRNA gene. Three groups of phylogenetically distinct MOB were detected in the clone libraries of polymerase chain reaction products obtained with universal primers. The groups belonged to the class Gammaproteobacteria, the class Alphaproteobacteria, and the candidate phylum NC10. The last group, which consists of close relatives of the nitrite reducer 'Candidatus Methylomirabilis oxyfera', was frequently detected in the clone libraries of deep-water environments. The presence of 3 groups of MOB in deep water was also shown by a cloning analysis of the pmoA gene encoding particulate methane monooxygenase. The dominance of 'M. oxyfera'-like organisms in deep water was confirmed by catalyzed reporter deposition-fluorescence in situ hybridization, in which cells stained with a specific probe accounted for 16% of total microbial cells. This is the first study to demonstrate that close relatives of the nitrite reducer can be major component of planktonic MOB community which may affect carbon flow in aquatic ecosystems.
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Hisaya
authors.initials: H
authors.lastname: Kojima
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Riho
authors.initials: R
authors.lastname: Tokizawa
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Kouhei
authors.initials: K
authors.lastname: Kogure
authors.affiliation: Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Kobayashi
authors.affiliation: Center for Southeast Asian Studies, Kyoto University, Kyoto, Japan.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Itoh
authors.affiliation: Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan.
authors.forename: Fuh-Kwo
authors.initials: FK
authors.lastname: Shiah
authors.affiliation: Center for Ecological Research, Kyoto University, Otsu, Japan.
authors.forename: Noboru
authors.initials: N
authors.lastname: Okuda
authors.affiliation: The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Fukui
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D057486:Carbon Cycle; D017753:Ecosystem; D005618:Fresh Water / Q000382:microbiology; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D015723:Gene Library; D020459:Genes, rRNA; D008697:Methane / Q000378:metabolism*; D008772:Methylococcaceae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D008969:Molecular Sequence Data; D009573:Nitrites / Q000378:metabolism; D010084:Oxidation-Reduction; D010105:Oxygenases / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010933:Plankton / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013624:Taiwan
chemical_list: D001426:Bacterial Proteins; D009573:Nitrites; D012336:RNA, Ribosomal, 16S; D010105:Oxygenases; C021555:methane monooxygenase; D008697:Methane
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