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

JiangbingXu, ZhongjunJia, XianguiLin, YouzhiFeng

International Center for Ecology, Meteorology and Environment (IceMe), School of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, China.

Abstract

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.

Keywords: Formate-metabolizing methanogenic archaea, Paddy soil, Stable isotope probing.