Dynamics of endophytic and epiphytic bacterial communities of Indian cultivated and wild rice (Oryza spp.) genotypes

Metabolic and structural profiles of the epiphytic, endophytic and rhizoplanic bacterial communities of three Indian cultivated rice (Oryza sativa var. Sabita/Swarna/Swarna-Sub1) and one wild rice (O. eichingeri) genotypes differing in life span and cultural practices viz. hydrology and fertilizer doses were analyzed through Biolog-Ecoplate assay, and culture-dependent and culture-independent approaches (denaturing gradient gel electrophoresis-DGGE). Overall microbial population dynamics and diversity was more in the wild genotype than the cultivated ones viz. wild > Sabita > Swarna and Swarna-Sub1. Microbial community metabolism was more in the roots according to wild > Sabita > Swarna and Swarna-Sub1. The DGGE profile of the endophytes of Swarna roots was distinct from those of the other parts of different rice genotypes. The microbial communities in different parts of the cultivated varieties produced higher Shannon-Weaver and lower Simpson's indices, but lower McIntosh index than those of the wild species. The principal components reflected similar trends of effects of carbohydrate and phenolic compounds in Biolog-ecoplate assay which suggested that the substrates would influence the assay of the microbial communities. Broadly, microbial dynamics in different parts of the four rice genotypes represent the structural differences of the phytonic microbial communities which would help to understand the interaction of microbes with different categories of rice genotypes.