Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

Frontiers in Microbiology
Zhi-Chao ZhouJi-Dong Gu

Abstract

Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 10(6) copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 10(6) copies per gram dry weight) was observed, but higher abundance (6.9 × 10(6) to 1.02 × 10(8) copies per gram dry weight) was found in subsurface samples of both sediment types. Aero...Continue Reading

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Datasets Mentioned

BETA
KF595310
KF596336

Methods Mentioned

BETA
PCR
electrophoresis
phylogenetic profiles

Software Mentioned

Fast Unifrac
Unifrac
CloVR
MrBayes
Clustal W
R
Dendrogram
R script
Rstudio
Fastgroup

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