Activity and composition of the methanogenic archaeal community in soil vegetated with wild versus cultivated rice

Wild rice (Oryza rufipogon) is a problematic weed in fields of cultivated rice (Oryza sativa). We hypothesized that the composition and/or the activity of the methanogenic microbial communities might be different in soil grown with cultivated versus wild rice. We used samples from Hainan, China, where wild rice grew on a field adjacent to cultivated rice. The composition of the methanogenic archaeal community was analyzed in samples of rice soil by targeting the 16S rRNA gene. Analysis of the terminal restriction fragment length polymorphism (T-RFLP) showed similar patterns in soil from wild versus cultivated rice. Sequences of archaeal 16S rRNA genes also showed similar composition in soil from wild versus cultivated rice, revealing the presence of Methanosarcinaceae, Methanosaetaceae, Methanobacteriales, Methanocellales (Rice Cluster I), Rice Cluster II, Crenarchaeota Group I.3 and Crenarchaeota Group I.1b. Incubation of soil samples under anoxic conditions generally resulted in vigorous CH4 production after a lag phase of 7–8 days. Production of CH4 was partially inhibited by methyl fluoride, a specific inhibitor of acetoclastic methanogenesis, resulting in nearly stoichiometric accumulation of acetate. CO2 was produced without lag phase. The δ13C of the produced CO2 was slightly lower in soil grown with cultivated rice versus wild rice, reflecting the δ13C of organic matter, which was about −29‰ for cultivated rice soil and about −24‰ for wild rice soil. The δ13C of the produced CH4 and the acetate that accumulated in the presence of CH3F was much more negative in cultivated versus wild rice soil, mainly since the isotopic fractionation factors for hydrogenotrophic methanogenesis were higher for soil from cultivated rice (α = 1.054) versus wild rice (α = 1.039). However, the percentage contribution of hydrogenotrophic methanogenesis to total CH4 production was similar in both soils (27–35%). In conclusion, although the two soils exhibited different δ13C values of soil organic matter and derived products, they were similar with respect to rates and composition of the methanogenic communities.