Deciphering the genetics of antagonism and antimicrobial resistance in Bacillus velezensis HU-91 by whole genome analysis

Bacillus species are well reported plant growth promoting rhizobacteria which play an important role in improving soil fertility, nutrient recycling, and controlling phytopathogens. Their use as biocontrol agents is an ecofriendly strategy but being a rhizospheric community, they could harbor antimicrobial resistance genes. In current study, rhizobacteria were isolated from the mono cropped wheat. Ten out of 50 isolates showed antifungal activity against Fusarium spp., an economically important pathogen of wheat. The strain HU-91 with highest antifungal activity showed the biochemical traits of lipopeptide production. It also resisted multiple antibiotics of different classes (index ≥ 0. 2) and categorized as multidrug resistant bacteria. The strain HU-91 was identified as Bacillus velezensis based on its 16S rRNA homology (99%). Whole genome analysis of B. velezensis HU-91 revealed 76 contigs with a total length of 3,952,697 bp, GC content 46.3%, and a total of 3912 genes. Functional classification of genome predicted genes involved in drug resistance, and antagonism. A detailed genome analysis identified CAZymes and 10 biosynthetic gene clusters involved in antagonism. Various antimicrobial resistance genes associated with the resistance to different antimicrobial classes such as β lactam, tetracyclines, aminoglycosides, fluoroquinolones, macrolides, sulfonamide, and lincosamides were also found in the genome of HU-91. Furthermore, HU-91 lacked plasmid but harbored a well-developed CRISPR Cas system. The underlying mechanisms involved in the antimicrobial resistance were depicted as intrinsic based on the genes encoding production of antibiotics degrading enzymes and efflux pumps. These findings depict that HU-91 adapts the intrinsic mechanisms of drug resistivity to tolerate environmental stress. The lack of plasmid and presence of CRISPR Cas system advocate its safety to be used as bioinoculant.