DNA-based stable isotope probing identifies formate-metabolizing methanogenic archaea in paddy soil

Paddy methane (CH4) production is biologically dominated by methanogenic archaea that metabolize a variety of organic and/or inorganic carbon sources. Though formate is easily dissimilated into H2/CO2, formate-metabolizing methanogenic archaea are distinct from CO2-utilizing methanogen taxa. The identity of formate-metabolizing methanogenic archaea in paddy soil remains elusive. In this investigation, molecular approaches based on stable isotope probing (SIP) technique were conducted to identify the formate-metabolizing methanogenic archaea in paddy soil. CH4 emission monitor, real-time quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE) analyses consistently indicated that some methanogenic archaea metabolized 13C-labeled formate in microcosm and accounted for a large portion of formate-metabolizing archaea in anoxic paddy soil. Phylogenetic identification further found that this guild was affiliated to Methanobacteriaceae. Taken together Methanobacteriaceae could be the dominant formate-metabolizing methanogenic archaea and play an important role in the CH4 production in paddy soil. These findings would extend the extant knowledge on paddy methanogenic archaea and microbial-driven paddy CH4 emission.