Methanogenic populations involved in the degradation of rice straw in anoxic paddy soil

Abstract

Addition of straw to anoxic rice field soil stimulates production of CH 4, an important greenhouse gas. The archaeal community colonizing rice straw was investigated by molecular methods targeting the small subunit ribosomal RNA gene. Cloning and sequencing of 60 clones detected predominantly relatives of Methanobacterium spp. (38 clones) and Methanosarcina spp. (16 clones). Terminal restriction fragment length polymorphism (T-RFLP) analysis confirmed the dominance of Methanobacteriaceae and Methanosarcinaceae, and in addition showed restriction fragments characteristic for Rice cluster I (RC-I) methanogens. A new oligonucleotide probe specific for RC-I was designed. Quantitative slot blot hybridization of extracted rRNA with this probe indicated the presence of an active population of RC-I methanogens. Other methanogenic groups (e.g. Methanomicrobiaceae, Methanosaetaceae), although present and active in soil, could not be conclusively detected on rice straw. The methanogenic community pattern on straw, as revealed by T-RFLP and quantitative rRNA probing, was fairly constant with incubation time (8–57 days), but the total activity of methanogenic Archaea almost doubled. Our results indicate that the methanogens colonizing rice straw are less diverse than those inhabiting the soil.