With an increase in global demand for food without unwanted environmental issues stresses a need for sustainable agriculture. Up till now, conventional agricultural methods focused on obtaining great crop yields from the use of chemical fertilizers but overlooked the hazardous concerns that are leading to soil depletion. These chemical fertilizers adversely affect soil structure, decrease fertility, damage soil flora, and lead to soil erosion. In this scenario, understanding the natural mechanisms of plant-microbe interactions in the rhizospheric environment can potentially lead a way towards eco-friendly agriculture, as the plant associating bacteria prompting phytostimulation can be the key players in unlocking sustainable alternative for conventional fertilizers. Plant growth-promoting bacteria (PGPB) are a distinct class of soil microorganisms that promote plant growth and yields by enhancing nutrient delivery and shielding the plants against diseases. N fixing bacteria such as Rhizobium and Azotobacter, for instance, fix atmospheric nitrogen into a usable form for plants, Pseudomonas and Bacillus induce root and shoot elongation by synthesizing phytohormones. These bacteria also provide protection to plants by synthesizing antimicrobial substances and increasing the competitive nature of the rhizosphere. Bacteria like Azospirillum, Enterobacter, and Flavobacterium also stimulate plant growth by producing phytohormones under specific envirnmental conditions. Utilization of PGPB as bio-stimulants in agriculture is a promising method for sustainable agriculture dependence on chemical fertilizers and maintaining soil health. This approach would play an important role in sustaining a balanced ecosystem along with increasing agricultural productivity.

For the safe use of microbiome-based solutions in agriculture, the genome sequencing of strains composing the inoculum is mandatory to avoid the spread of virulence and multidrug resistance genes carried by them through horizontal gene transfer to other bacteria in the environment. Moreover, the annotated genomes can enable the design of specific primers to trace the inoculum into the soil and provide insights into the molecular and genetic mechanisms of plant growth promotion and biocontrol activity. In the present work, the genome sequences of some members of beneficial microbial consortia that have previously been tested in greenhouse and field trials as promising biofertilizers for maize, tomato and wheat crops have been determined. Strains belong to well-known plant-growth-promoting bacterial genera such as Bacillus, Burkholderia, Pseudomonas and Rahnella. The genome size of strains ranged from 4.5 to 7.5 Mbp, carrying many genes spanning from 4402 to 6697, and a GC content of 0.04% to 3.3%. The annotation of the genomes revealed the presence of genes that are implicated in functions related to antagonism, pathogenesis and other secondary metabolites possibly involved in plant growth promotion and gene clusters for protection against oxidative damage, confirming the plant-growth-promoting (PGP) activity of selected strains. All the target genomes were found to possess at least 3000 different PGP traits, belonging to the categories of nitrogen acquisition, colonization for plant-derived substrate usage, quorum sensing response for biofilm formation and, to a lesser extent, bacterial fitness and root colonization. No genes putatively involved in pathogenesis were identified. Overall, our study suggests the safe application of selected strains as plant probiotics for sustainable agriculture.