Microbial consortium augmentation reshapes endophytic microbiome to enhance antioxidant activity and yield in black rice (Oryza sativa L. var. indica)

Black rice ( Oryza sativa L. indica ), is valued for its rich nutritional value and unique phytochemical composition. It is a significant source of anthocyanins, that contribute to its characteristic dark purple hue, along with other essential nutrients. The endophytic microbiome plays a pivotal role in plant growth, nutrient acquisition and the biosynthesis of health-promoting metabolites (antioxidants). Modulation of the endophytic bacterial community through beneficial microbial inoculants offers a promising strategy for improving crop productivity and functional quality. However, field-based evidence linking microbiome dynamics with black rice plant growth, antioxidant potential, and soil biological activity remains limited. A field experiment was conducted to evaluate the effects of a consortium of endophytic plant growth-promoting bacteria consisting of Bacillus subtilis , AMR1; Kluyvera sp. PO2S7; Enterobacter sp. SES19 on black rice. Plants were inoculated with the bacterial consortium, and plant growth, yield, antioxidant attributes (TPC, TFC, DPPH, and anthocyanin), and soil enzyme activities were assessed. The endophytic bacterial community was profiled using 16 S rRNA amplicon sequencing, followed by diversity, taxonomic, functional, and correlation network analyses to investigate microbiome modulation and its association with plant physiological and biochemical traits. The consortium promoted plant growth, mitigated stress responses, enhanced antioxidant activity, soil fertility and improved the yield of black rice ( Oryza sativa L.) compared to single bacterial inoculation and uninoculated control plants. Stress enzyme activities, including catalase, peroxidase, and superoxide dismutase, were notably reduced, indicating alleviation of oxidative stress. Simultaneously, antioxidant activity such as total polyphenol content (TPC), total flavonoid content (TFC) in plant tissues was enhanced by 56.63%, 62.7% respectively in comparison to control, supporting improved physiological resilience. High-throughput sequencing of the endophytic microbiome after the application of consortium demonstrated a distinct shift in microbial community structure, with an increased abundance of beneficial taxa such as Bacillus , Rhizobium , Agrobacterium , Enterobacter etc. associated with nutrient acquisition, stress tolerance, and growth promotion and yield. These findings suggest that microbial consortium can effectively reprogram the endophytic microbiome, offering a sustainable strategy for enhancing black rice productivity under diverse environmental conditions.