Abstract
Methane oxidation coupled to nitrite reduction is mediated by ‘Candidatus Methylomirabilis oxyfera’ (M. oxyfera), which belongs to the NC10 phylum. In this study, the community composition and diversity of M. oxyfera-like bacteria of NC10 phylum were examined and compared in four different freshwater habitats, including reservoir sediments (RS), pond sediments (PS), wetland sediments (WS) and paddy soils (PAS), by using Illumina-based 16S rRNA gene sequencing. The recovered NC10-related sequences accounted for 0.4–2.5% of the 16S rRNA pool in the examined habitats, and the highest percentage was found in WS. The diversity of NC10 bacteria were the highest in RS, medium in WS, and lowest in PS and PAS. The observed number of OTUs (operational taxonomic unit; at 3% cut-off) were 97, 46, 61 and 40, respectively, in RS, PS, WS and PAS. A heterogeneous distribution of NC10 bacterial communities was observed in the examined habitats, though group B members were the dominant bacteria in each habitat. The copy numbers of NC10 bacterial 16S rRNA genes ranged between 5.8 × 106 and 3.2 × 107 copies g−1 sediment/soil in the examined habitats. These results are helpful for a systematic understanding of NC10 bacterial communities in different types of freshwater habitats.
Highlights
Methane (CH4) is the most important greenhouse gas after carbon dioxide, and responsible for ~20% of the current greenhouse effect[1]
Illumina-based 16S rRNA gene sequencing was applied to determine the presence of NC10 bacteria in the examined freshwater habitats as previously described[30]
Previous studies have indicated that anaerobic ammonium-oxidizing bacteria, which use nitrite as electron acceptor, could compete for nitrite with NC10 bacteria in wetland sediments[10]
Summary
Methane (CH4) is the most important greenhouse gas after carbon dioxide, and responsible for ~20% of the current greenhouse effect[1]. Based on 16S rRNA gene or functional gene clone libraries using specific primers, the community composition and diversity of NC10 bacteria in different freshwater habitats have previously been described separately, primarily including lakes[4,6,16], rivers[17], wetlands[7,9,10,18] and paddy fields[8,19,20]. The Illumina MiSeq platform provides researchers with a scalable, high-throughput and streamlined sequencing platform to survey microbial communities from environmental samples[23] This technique has been widely used to study microbial communities in various freshwater habitats, and have changed our understanding of microbial diversity in the environment[24,25,26]. Knowledge from comparisons of NC10 bacterial community structures in different freshwater habitats may identify habitat-specific adaptations in their physiology and evolution. We hypothesized that these habitats harbored unique NC10 bacterial assemblages
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