Hybrid de novo whole genome assembly of lipopeptide producing novel Bacillus thuringiensis strain NBAIR BtAr exhibiting antagonistic activity against Sclerotium rolfsii

• Published in: Microbial pathogenesis 2024-10, Vol.195, p.106867, Article 106867
• Main Authors: Kukreti, Aditya, Kotasthane, Anil Sudhakar, Tandon, Ashwarya Lalit, Nekkanti, Aarthi, Prasannakumar, Muthakapalli Krishnareddy, Devanna, Pramesh, Aravindaram, Kandan, Sreedevi, Kolla, Sushil, Satya Nand, Manjunatha, Channappa
• Format: Article
• Language: English
• Subjects: Antifungal potential; Biosynthetic gene clusters; CRISPR elements; Genomic islands; Insertion sequences; Prophage
• ISSN: 0882-4010; 1096-1208; 1096-1208
• DOI: 10.1016/j.micpath.2024.106867

Bacillus thuringiensis Berliner is recognized as a predominant bioinsecticide but its antifungal potential has been relatively underexplored. A novel B. thuringiensis strain NBAIR BtAr was isolated and morphologically characterized using light and scanning electron microscopy, revealing presence of bipyramidal, cuboidal, and spherical parasporal crystals. The crude form of lipopeptides was extracted from NBAIR BtAr and assessed for its antagonistic activity in vitro, and demonstrated 100 % inhibition of Sclerotium rolfsii Sacc. at a minimum inhibitory concentration of 50 μL of the crude lipopeptide extract per mL of potato dextrose agar. To identify the antagonistic genes responsible, we performed whole genome sequencing of NBAIR BtAr, revealing the presence of circular chromosome of 5,379,913 bp and 175,362 bp plasmid with 36.06 % guanine-cytosine content and 5814 protein-coding sequences. Average nucleotide identity and whole genome phylogenetic analysis delineated the NBAIR BtAr strain as konkukian serovar. Gene ontology analysis revealed associations of 1474, 1323, and 1833 genes with biological processes, molecular function, and cellular components, respectively. Antibiotics & secondary metabolite analysis shell analysis of the whole genome yielded secondary metabolites biosynthetic gene clusters with 100 %, 85 %, 40 %, and 35 % similarity for petrobactin, bacillibactin, fengycin, and paenilamicin, respectively. Also, novel biosynthetic gene clusters, along with antimicrobial genes, including zwittermicin A, chitinase, and phenazines, were identified. Moreover, the presence of eight bacteriophage sequences, 18 genomic islands, insertion sequences, and one CRISPR region indicated prior occurrences of genetic exchange and thus improved competitive fitness of the strain. Overall, the whole genome sequence of NBAIR BtAr is presented, with its taxonomic classification and critical genetic attributes that contribute to its strong antagonistic activity against S. rolfsii. •To the best of our knowledge, this is the first report of the in vitro activity of lipopeptides extracted from Bacillus thuringiensis against Sclerotium rolfsii.•Hybrid de novo genome assembly of NBAIR BtAr enhanced genome assembly precision and advanced the identification and expansion of known antagonistic gene families.•Secondary metabolite BGCs i.e. petrobactin, bacillibactin, fengycin, and paenilamicin produced by NRPS/PKS clusters and other mycolytic genes like zwiitermicin A involve