Paddy field ecosystem is composed of surface water, plowed soil layer and subsoil, and the plowed soil layer is divided into two layers; thin oxidized soil layer and reduced soil layer. These soil layers are connected by percolating water. In addition, rice roots are developed and plant residues such as rice straw and stubble after rice harvest are incorporated into the plowed soil layer. These microsites are different habitats for microorganisms, and unique microbial communities inhabit depending on the microsites.

　Microbial communities in paddy field ecosystem, which are composed of virus, bacteria, archaea, fungi and protist, have impacts each other. For example, supply of methanogenic substrates by symbiotic anaerobic bacteria are required to produce methane gas, one of the greenhouse gases, by methanogenic archaea. Methane is oxidized by methanotrophs in oxidized aerobic soil. Dynamics of methanogenic archaeal and methanotorph communities are controlled by virus and protists．

　Dynamics of soil microorganisms and their interactions in a paddy field ecosystem are the current central themes of this research group. The aim is to elucidate the facts and mechanisms of microbial diversity and functions in cycling of bioelements in a paddy field ecosystem.