Molecular characterization and in vitro evaluation of endophytic bacteria against major pathogens of rice

Thirty one isolates of endophytic bacteria were collected from different plant sources together with Bacillus subtilis var. amyloliquefaciens (FZB24) that was obtained from Novozymes South Asia Pvt. Ltd. to screen against major pathogens of rice. All the isolates were characterized on the basis of biochemical and phenotypic analysis. Therefore, following these tests, it can be concluded that 31 isolates exhibited differences and they were subjected to partial 16S-rDNA gene sequencing using polymerase chain reaction for phylogenetic analysis. The molecular characterization through amplification of 16S rDNA fragment to an amplicon size of 546 bp confirmed that the thirty one isolates were Bacillus. The PCR analysis showed that all the 31 isolates were found to have the genes for iturin A, 30 isolates for surfactin, 27 isolates for bacillomycin D and one isolate was found to have gene for zwittermicin A. The biosynthetic gene for the production of ACC deaminase was also identified among 11 endophytic Bacillus isolates. The random amplified polymorphic DNA (RAPD) analysis showed more similarity among the isolates isolated from the same ecosystem as compared to the isolates collected from different ecosystems. Among the endophytic bacterial isolates tested against the major pathogens of rice viz., Pyricularia grisea, Rhizoctonia solani and Xanthomonas oryzaepv. oryzae in vitro, Bacillus subtilis var. amyloliquefaciens (FZB24) was found to be effective in inhibiting growth of all the three pathogens and it was also found to promote the growth of rice seedling by registering significantly higher vigour index in roll towel method.