Whole-genome sequence and functional insights into the salt-tolerant plant growth-promoting bacterium Priestia aryabhattai MS3

Priestia aryabhattai MS3, a plant growth-promoting (PGP) bacterium isolated from saline rice fields of Bangladesh, was subjected to whole-genome sequencing and functional analyses to understand its ecological adaptability and biofertilization potential. The genome encodes 5,387 protein-coding genes, 5 rRNAs, 33 tRNAs, and 1 tmRNA gene. Functional classification indicated enrichment in cofactor biosynthesis, amino acid metabolism, and stress response pathways, highlighting the strain’s metabolic flexibility. Approximately 40% of annotated genes were associated with stress adaptation and biotic interactions, including those encoding antioxidant enzymes (e.g., superoxide dismutase, catalase). The genome also harbors genes involved in key plant-beneficial traits, including phosphate and potassium solubilization, siderophore production, nitrogen metabolism, and phytohormone biosynthesis. Additional features supporting biofertilizer potential include genes for biofilm formation, root colonization, and CO₂ fixation (e.g., RuBisCO and associated regulators). Notably, antiSMASH analysis predicted seven secondary metabolite biosynthetic gene clusters, including those for koranimine, surfactin, and carotenoids, compounds associated with antimicrobial activity and plant growth-promotion. The genome also exhibited extensive iron acquisition mechanisms, comprising genes for heme biosynthesis, siderophore transport, ferritin-based storage, and iron-regulatory systems. Nitrogen utilization pathways were supported by genes for nitrate reduction, nitrogen fixation, and urea hydrolysis. Comparative pan-genome analysis with 96 other P. aryabhattai strains revealed an open pan-genome of 35,632 genes, with only 2,000 core genes, underscoring substantial genomic diversity and plasticity. Overall, these features highlight the potential of P. aryabhattai MS3 as a bioinoculant for saline agriculture with its versatile metabolism, stress resilience, and biosynthetic capabilities supporting sustainable crop productivity in resource-constrained environments.