Endophytic bacterial taxonomic and functional diversity in the seeds of wheat genotypes from different agroecologies

Plant genotype and agroecology influence the composition and functionality of seed endophytic bacterial communities. Taxonomic analysis of 123 wheat seeds endophytic bacteria classified these into 23 genera predominantly under Firmicutes followed by Actinobacteria and Proteobacteria. Genus Bacillus was most abundant (30.7%) followed by Streptomyces (18.4%) with other representative genera such as Stenotrophomonas, Paenibacillus, Mixta, Enterobacter, Micrococcus, Pantoea, Alkalihalobacillus, Cortiobacterium, and more. Across agroecologies, the core microbiota of seeds consists of Bacillus, Streptomyces, Paenibacillus, and Stenotrophomonas, with maximum diversity and abundance observed in seeds of the North Western Plain Zone of India. Seed endophytic bacteria had PGP traits; nitrogen fixation (n = 101), production of IAA (n = 65), siderophores (n = 43), ammonia (n = 82) and solubilization of phosphate (n = 47), potassium (n = 37), and zinc (n = 8). The isolates produced HCN and hydrolytic enzymes and displayed antagonism against fungal pathogens. Overall, the information generated on wheat seeds’ endophytic bacterial taxonomy and beneficial traits may pave the path for the development of novel bioinoculants.