Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity

Abstract

Chemical pesticides have an immense role in curbing the infection of plant viruses and soil-borne pathogens of high valued crops. However, the usage of chemical pesticides also contributes to the development of resistance among pathogens. Hence, attempts were made in this study to identify a suitable bacterial antagonist for managing viral and fungal pathogens infecting crop plants. Based on our earlier investigations, we identified Bacillus amyloliquefaciens VB7 as a potential antagonist for managing Sclerotinia sclerotiorum infecting carnation, tobacco streak virus infecting cotton and groundnut bud necrosis infecting tomato. Considering the multifaceted action of B. amyloliquefaciens VB7, attempts were made for whole-genome sequencing to assess the antiviral activity against tomato spotted wilt virus infecting chrysanthemum and antifungal action against Fusarium oxysporum f. sp. cubense (Foc). Genome annotation of the isolate B. amyloliquefaciens VB7 was confirmed as B. velezensis VB7 with accession number CP047587. Genome analysis revealed the presence of 9,231,928 reads with an average read length of 149 bp. Assembled genome had 1 contig, with a total length of 3,021,183 bp and an average G+C content of 46.79%. The protein-coding sequences (CDS) in the genome was 3090, transfer RNA (tRNA) genes were 85 with 29 ribosomal RNA (rRNA) genes and 21 repeat regions. The genome of B. velezensis VB7 had 506 hypothetical proteins and 2584 proteins with functional assignments. VB7 genome had the presence of flagellin protein FlaA with 987 nucleotides and translation elongation factor TU (Ef-Tu) with 1191 nucleotides. The identified ORFs were 3911 with 47.22% GC content. Non ribosomal pepide synthetase cluster (NRPS) gene clusters in the genome of VB7, coded for the anti-microbial peptides surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide. Antiviral action of VB7 was confirmed by suppression of local lesion formation of TSWV in the local lesion host cowpea (Co-7). Moreover, combined application of B. velezensis VB7 with phyto-antiviral principles M. Jalapa and H. cupanioides increased shoot length, shoot diameter, number of flower buds per plant, flower diameter, and fresh weight of chrysanthemum. Further, screening for antifungal action of VB7 expressed antifungal action against Foc in vitro by producing VOC/NVOC compounds, including hexadecanoic acid, linoelaidic acid, octadecanoic acid, clindamycin, formic acid, succinamide, furanone, 4H-pyran, nonanol and oleic acid, contributing to the total suppression of Foc apart from the presence of NRPS gene clusters. Thus, our study confirmed the scope for exploring B. velezensis VB7 on a commercial scale to manage tomato spotted wilt virus, groundnut bud necrosis virus, tobacco streak virus, S. sclerotiorum, and Foc causing panama wilt of banana.

Characterization of Bacillus velezensis TJS119 and its biocontrol potential against insect pathogens

“…The genus Bacillus includes several species that are highly similar, and the taxonomic status of Bacillus strains cannot be easily determined using conventional classification methods ( Hamdache et al, 2013 ). Several strains initially identified as B. amyloliquefaciens , including FZB42 ( Schilling et al, 2018 ), vb7 ( Saravanan et al, 2021 ), and SQR9 ( Feng et al, 2018 ), are now classified as B. velezensis . To determine the relationship between TJS119 and other strains of Bacillus , a phylogenetic tree based on 92 core gene sequences was constructed in this study.…”

“…Using whole-genome sequencing, Zhang et al (2022) found that B. velezensis GS-1 produces the lipopeptides surfactin, fengycin, and plantazolicin, which exhibit inhibitory effects against M. oryzae . Eight secondary metabolite-related gene clusters have been identified in B. velezensis VB7, which is protective against carnation infection by Sclerotinia sclerotiorum , cotton infection by tobacco streak virus, and tomato peanut shoot necrosis infection ( Saravanan et al, 2021 ). Meanwhile, 12 secondary metabolite-related gene clusters have been identified in B. velezensis YC89, which effectively controls red rot disease in sugarcane ( Xie et al, 2023 ).…”

In Vitro Evaluation of Some Endophytic Bacillus to Potentially Inhibit Grape and Grapevine Fungal Pathogens

“…fragariae [76], F. oxysporum f.sp. cubense [77], P. digitatum and P. italicum [78], Sclerotinia sclerotiorum [77], tomato spotted wilt virus, groundnut bud necrosis virus, and tobacco streak virus [77].…”

Antifungal Activity of Industrial Bacillus Strains against Mycogone perniciosa, the Causative Agent of Wet Bubble Disease in White Button Mushrooms

“…citri [ 29 ]. B. amyloliquefaciens VB7 has been shown to be a potential antagonist that can control a number of dangerous diseases ( Sclerotinia sclerotiorum affecting cloves, tobacco stripe virus affecting cotton, and peanut bud necrosis affecting tomatoes) and synthesizes non-ribosomal antimicrobial peptides such as surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide, as well as a number of other compounds as well [ 30 ].…”

“…Recently, various mechanisms of phytopathogen suppression by Bacillus strains have been actively studied [ 30 , 31 , 32 , 33 ]. In particular, chitinase and β-1,3-glucanase enzymes produced by B. velezensis CE 100 and the effectively lysing mycelium of Macrophomina phaseolina and Fusarium oxysporum f. sp.…”