Alteration of Rice Root Endophytic Bacterial Community Composition by Meloidogyne graminicola and Identification of Potential Biocontrol Agent

Abstract Introduction Rice root gall is a severe infection caused by the rice root-knot nematode Meloidogyne graminicola . Overuse of chemical nematicides intensifies the need for a suitable biocontrol agent. Nematode infestation in plants alters the associated microbiome; however, their correlations need to be better understood. Hence, this work aimed to unravel the changes in indigenous endophytic bacterial community composition of rice root because of infection caused by M. graminicola and also to identify dominant bacteria strains as a potential biological control agent. Material & Methods The endophytic bacterial community of non-infected rice root and gall was analysed using a 16 S rRNA gene-based metagenomics approach. The dominant endophytic bacterial community was further isolated and screened for its PGP and nematicidal activity using bacterial cell suspension and culture filtrate to identify a potential biocontrol agent. Result and Discussion Our results show that nematode infection has altered the bacterial community composition, and a distinct community existed between gall and non-infected roots. This shift in the microbial community is associated with reduced species richness due to infection. We also observed that a few endophytic genera like Chryseobacterium , Rhizobium , Gemmata , and Pseudomonas that were unique to gall are reported to have been associated either with nematode or may have been recruited by plants as a growth promoter to combat nematode infection. Other bacterial endophytes that are specific to the non-infected root microbiome, like Delftia , Bacillus , Pantoea , Acidovorax , and Azorhizobium , are hypothesised to remain associated with rice seeds, and they possess biological control/plant growth promotion abilities. Further, after screening all isolates, Enterobacter sp. strain SSNI 8 isolated from a non-infected root was evaluated for its efficiency in acting as a nematicidal agent against M. graminicola , and we found that the strain showed 90% nematode mortality with its culture filtrate which may possess some secondary metabolites antagonistic to the nematode. Conclusion Overall, this study provided a comprehensive view of endophytes associated with gall in non-infected roots and identified a potential biocontrol agent.