Rice soil methane emissions are modulated by microbial cohorts that shape redox succession over the growing season

Abstract

Rice paddies are major anthropogenic methane sources, yet the community interactions regulating emissions remain poorly resolved. This field experiment combined genome-resolved metagenomics, metatranscriptomics, and biogeochemistry to identify microbial cohorts directly and indirectly involved in methane cycling over a rice growing season. Cohorts routed reducing equivalents to different terminal electron-accepting processes and changed in abundance in response to depth and time-dependent shifts in environmental conditions. Methanogenic activity peaked late in the season in the rhizosphere and surface soil, whereas activity in 2-10 cm bulk soil peaked earlier, indicating that methanogenesis was temporally partitioned across soil compartments. Geobacter-like extracellular electron transfer was the most highly expressed alternate sink for reducing equivalents. Methane consumption was vertically partitioned between surface type I methanotrophs and deeper type II methanotrophs and anaerobic methane-oxidizing archaea. We infer that methane emissions reflect seasonal shifts in microbial cohorts that redirect methanogenic substrates through competing redox processes.