Comparative genomics-based insights into <i>Xanthomonas indica</i> , a non-pathogenic species of healthy rice microbiome with bioprotection function

<i>Xanthomonas</i> species are major pathogens of plants and have been studied extensively. There is increasing recognition of the importance of non-pathogenic species within the same genus. With this came the need to understand the genomic and functional diversity of non-pathogenic <i>Xanthomonas</i> (NPX) at the species and strain level. This study reports isolation and investigation into the genomic diversity and variation in NPX isolates, chiefly <i>Xanthomonas indica</i>, a newly discovered NPX species from rice. The study establishes the relationship of <i>X. indica</i> strains within clade I of Xanthomonads with another NPX species, <i>X. sontii</i>, also associated with rice seeds. Identification of highly diverse strains, open-pan genome, and systematic hyper-variation at the lipopolysaccharide biosynthetic locus when compared to pathogenic <i>Xanthomonas</i> indicates the acquisition of new functions for adaptation. Furthermore, comparative genomics studies established the absence of major virulence genes such as type III secretion system and effectors, which are present in the pathogens, and the presence of a known bacterial-killing type IV secretion system (X-T4SS). The diverse non-pathogenic strains of <i>X. indica</i> and <i>X. sontii</i> were found to protect rice from bacterial leaf blight pathogen, <i>X. oryzae</i> pv. <i>oryzae</i> (Xoo). The absence of phenotype of an X-T4SS mutant suggests redundancy in the genetic basis of the mechanisms involved in the bioprotection function, which may include multiple genetic loci, such as putative bacteriocin-encoding gene clusters and involvement of other factors such as nutrient and niche competition apart from induction of innate immunity through shared microbial-associated molecular patterns. The rice-NPX community and its pathogenic counterpart can be a promising model for understanding plant-microbe-microbiome interaction studies.IMPORTANCEThe <i>Xanthomonas</i> group of bacteria is known for its characteristic lifestyle as a phytopathogen. However, the discovery of non-pathogenic <i>Xanthomonas</i> (NPX) species is a major shift in understanding this group of bacteria. Multi-strain, in-depth genomic, evolutionary and functional studies on each of these NPX species are still lacking. This study on diverse non-pathogenic strains provides novel insights into genome diversity, dynamics, and evolutionary trends of NPX species from rice microbiome apart from its relationship with other relatives that form a sub-clade. Interestingly, we also uncovered that NPX species protect rice from pathogenic <i>Xanthomonas</i> species. The plant protection property shows their importance as a part of a healthy plant microbiome. Furthermore, finding an open pan-genome and large-scale variation at lipopolysaccharide biosynthetic locus indicates a significant role of the NPX community in host adaptation. The findings and high-quality genomic resources of NPX species and the strains will allow further systematic molecular and host-associated microbial community studies for plant health.