Responses of archaeal, bacterial, and functional microbial communities to growth season and nitrogen fertilization in rice fields

Fertilization provides excess N to soil microorganisms, thus possibly affecting soil microbial abundance, activity, and community composition during rice cultivation. The abundance and diversity of archaeal, bacterial, and functional microbial communities in rice soils upon different N fertilization regimes (no fertilizer, urea, and controlled-release fertilizer) were investigated by sampling four seasonal growth stages (seedling, tillering, vegetative, maturing) under field conditions. The abundance of bacteria was significantly affected by fertilization and seasonal time, while that of the archaea was not significantly affected. Analysis of terminal restriction fragment polymorphism (T-RFLP) of 16S rRNA genes showed no effect of N fertilization on the archaeal and bacterial community composition, but changes with plant growth time. This result was confirmed by the patterns of pyrosequencing of bacterial 16S rRNA genes. The function of the methanogenic microbial community was assayed at maturing plant growth stage by determining CH4 production rates and stable isotope fractionation in the absence and presence of methyl fluoride, an inhibitor of acetoclastic methanogenesis. N fertilization had a pronounced effect on the CH4 production rate but not on the pathway of CH4 formation. Additionally, the abundance of functional microbial communities related to CH4 and N2O emissions was measured by qPCR of functional genes. Similarly to the taxonomic composition, rice growth season showed a significant effect on the abundance of the functional microbial communities represented by the mcrA, pmoA, nirK, nirS, and nosZ genes, while N addition had usually no significant effect. A similar result was also obtained by correlation analysis between CH4 and N2O emission rates and abundances of the functional microbial gene copies. In summary, rice growth time had pronounced effects on abundance, composition, and function of microbial communities in the rice soil, while the effect of N fertilization was negligible on the level of both specific functional genes and taxonomic 16S rRNA genes