Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils

Flooded paddy soils are global sources of the greenhouse gas methane. Net methane fluxes from paddy fields reflect the sum of methane generation in the anoxic zone and methane consumption in the oxic zone, which are driven by methanogenic archaea and methanotrophic bacteria, respectively. Furthermore, methanogenic archaea produce methane utilizing hydrogen or acetate generated by hydrogen-producing bacteria or acetogenic bacteria, respectively. Therefore, methane emissions are regulated and orchestrated by hydrogen production, acetogenesis, methanogenesis, and methane oxidation. However, a comprehensive understanding of the microbial consortia that regulate methane emissions has yet to be achieved owing to the lack of simultaneous assessments of microbial drivers involved in these four processes, especially the production of hydrogen and acetate, which are primary substrates for methanogenesis. In this study, the transcriptional profiles of genes encoding the enzymes that catalyze each process were comprehensively investigated by shotgun RNA sequencing analysis (metatranscriptomics). Seasonal and spatial transitions in soil redox potentials and the transcriptional activities of methanogens indicated active methane metabolism in paddy soils 5 weeks after waterlogging, when the soil redox conditions of the surface (0–1 cm depth; S layer) and subsurface (5–7 cm depth; D layer) were the most divergent. Deep metatranscriptomics focusing on such soils suggested that: (1) in the anoxic D layer, rather than in the oxic S layer, Deltaproteobacteria, Acidobacteria, and Planctomycetes actively generate hydrogen; (2) Deltaproteobacteria, Betaproteobacteria, Acidobacteria, and Alphaproteobacteria generate acetate; (3) utilizing these products as substrates for methanogenesis, the archaea Methanocella, Methanoregula, and Methanosaeta actively produce methane; (4) concurrently, in the oxic S layer, methanotrophs related to Methylocystis and Methylogaea oxidize methane. The present study represents the first comprehensive report of the community structure and dynamics of the microbial consortia underpinning the methane emissions from paddy fields.