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The compositional and functional role of the endophytic bacterial community, associated with black scented rice, in correlation with its antioxidant property has been elucidated. Community dissimilarity analysis confirmed the overlapping of community in shoot and root tissues at the young stage, but not in mature plants. Proteobacteria was the most abundant phylum, in which  Agrobacterium, Pleomorphomonas, Bradyrhizobium, Novasphingobium, Caulobacter  were the most abundant genera, followed by Cyanobacteria and Planctomycetes in all three different varieties of the black rice. The antioxidant activity of mature plants was found to be higher in comparison to young plants. Intrinsically, the relative abundance of  Pleomorphomonas  and  Streptomyces  was positively correlated with total phenol content, while  Gemmata ,  unclassified Pirellulaceae ,  unclassified Stramenopiles  positively correlated with total flavonoid content and negatively correlated with Free radical scavenging activity. Accordingly, functional metagenome analysis of the endophytic microbiome revealed that naringenin -3-dioxygenase and anthocyanidin 3-O-glucosyltransferase for phenylpropanoid (flavonoid and anthocyanin) synthesis were abundant in the endophytic microbiome of mature plants. Specific enrichment of the antioxidant producing genes in the mature plant endophytic microbiome was assigned to some bacteria such as  Streptomyces, Pantoea  which might have contributed to the common pathway of flavonoid synthesis .  The genomes of endophytic isolates  Kluyvera  sp . PO2S7,  Bacillus subtilis  AMR1 and  Enterobacter sp.  SES19 were sequenced and annotated, and were found to have genes for phenylpropanoid synthesis in their genomes.

Host specific endophytic microbiome diversity and associated functions in three varieties of scented black rice are dependent on growth stage