The diversity and density of methanogenic archaea and methane production were investigated ex situ at different growth stage of rice plants cultivated in compost treated tropical rice fields. The qPCR analysis revealed variation in methanogens population from 3.4 × 16 to 1.11 × 17 copies g−1 dws, in the year 29 and 4.37× 16 to 1.36 × 17 copies g−1 dws in the year 21. Apart from methanogens a large number of bacterial (9.6 × 19 to 1.44 × 11 copies g−1 dws) and archaeal (7.13 × 17 to 3.2 × 18 copies g−1 dws) communities were also associated with methanogenesis. Methanogen population size varied in the order: flowering > ripening > tillering > post-harvest > pre-plantation stage. The RFLP based 16S rRNA gene targeted phylogenetic analysis showed that clones were closely related to diverse group of methanogens comprising members of Methanomicrobiaceae, Methanosarcinaceae, Methanosaetaceae and RC I. Laboratory incubation studies revealed higher amount of cumulative CH4 at the flowering stage. The integration of methanogenic community structure and CH4 production potential of soil resulted in a better understanding of the dynamics of CH4 production in organically treated rice field soil. The hypothesis that the stages of plant development influence the methanogenic community structure leading to temporal variation in the CH4 production has been successfully tested.
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