Ecological and molecular analyses of the rhizospheric methanotroph community in tropical rice soil: effect of crop phenology and land-use history

To study the effect of crop phenology and cultivation practices on methanotrophic communities, two tropical rice fields located in the upper Gangetic plain of India with similar soil type and different cropping history were selected. A laboratory incubation experiment for the enumeration of methanotrophs and for the measurement of CH4 oxidation potential was conducted on a parallel basis. The methanotroph population size was found to be significantly higher in the Banaras Hindu University (BHU), Varanasi soil than the Indian Institute of Vegetable Research (IIVR), Varanasi soil. The population size increased with the age of the plant for both the sites. The CH4 oxidation potential was higher with the BHU soil compared to the IIVR soil. The CH4 oxidation rate increased significantly from tillering to flowering to grain-filling stages, and finally there was no significant difference between the grain-filling and the grain-maturation stages. A diagnostic microarray targeting the pmoA gene and a 16S rRNA denaturing gradient gel electrophoresis (DGGE)-based approach were applied to assess the diversity of the methanotrophic community for the two sites. A broad diversity of methanotrophs was detected at both sites, including type I and type II methanotrophs of the genera Methylobacter, Methylomonas, Methylosarcina, Methylosphaera, Methylomicrobium and Methylocystis. Type II methanotrophs were found in higher abundance as compared to type I methanotrophs at both the sites. DGGE analysis indicated that the methanotroph community in BHU soil was more or less stable, while little variation was found in IIVR soil during crop growth