Using pyrosequencing and quantitative PCR to analyze microbial communities

Methyl coenzyme M reductase A (mcrA) gene-based investigation of methanogens in the mudflat sediments of Yangtze River estuary, China

Methanogen populations of an intertidal mudflat in the Yangtze River estuary of China were investigated based on the methyl coenzyme M reductase A (mcrA) gene using 454-pyrosequencing and quantitative real-time polymerase chain reaction (qPCR). Samples were collected at six depths from three locations. In the qPCR analyses, a mean depth-wise change of mcrA gene abundance was observed from (1.23 ± 0.13) × 10(7) to (1.16 ± 0.29) × 10(8) per g dried soil, which was inversely correlated with the depletion of sulfate (R(2) = 0.74; α = 0.05) and salinity (R (2) = 0.66; α = 0.05). The copy numbers of mcrA was at least 1 order of magnitude higher than dissimilatory sulfate reductase B (dsrB) genes, likely indicating the importance of methanogenesis at the mudflat. Sequences related to the orders Methanomicrobiales, Methanosarcinales, Methanobacteriales, Methanococcales and the uncultured methanogens; Rice Cluster I (RC-I), Zoige cluster I (ZC-I) and anaerobic methane oxidizing archaeal lineage-1 (ANME-1) were detected. Methanomicrobiales and Methanosarcinales dominated the entire sediment layers, but detectable changes of proportions were observed with depth. The hydrogenotrophic methanogens Methanomicrobiales slightly increased with depth while Methanosarcinales showed the reverse. Chao1 and ACE richness estimators revealed higher diversity of methanogens near the surface (0-10 cm) when compared with the bottom sediments. The near-surface sediments were mainly dominated by the family Methanosarcinaceae (45 %), which has members that can utilize substrates that cannot be used by sulfate-reducing bacteria. Overall, current data indicate that Methanosarcinales and Methanomicrobiales are the most dominant methanogens within the entire depth profile down to 100 cm, with higher abundance and diversity of methanogens in the deeper and upper sediment layers, respectively.