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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. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 10 5  copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 10 5  copies per gram dry weight) based on  pmoA  gene. Mangrove surface layers harbored more abundant  pmoA  gene than intertidal mudflat, but less  pmoA  genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more  pmoA  gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of  mcrA  gene (8.51 × 10 8  copies per gram dry weight) and  pmoA  gene (1.56 × 10 7  copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of  mcrA  gene-harboring communities in nSCS and stratification of  mcrA  and  pmoA  gene diversity and abundance in the Mai Po Nature Reserve.

frontiers in microbiology

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