Lê Uyển Thanh, Vu Nhat Tan, Tran Thi Ngoc Huyen, To Lan Phuong, Huỳnh Ngọc Tâm, Luu Phuc Loi (2026).
Genomic characterization of Bacillus velezensis BP5 and BP103: insights into biocontrol potential against bacterial leaf spot on pepper.
Frontiers in Microbiology. 10.3389/fmicb.2026.1757903
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Genomic characterization of Bacillus velezensis BP5 and BP103: biocontrol potential against pepper bacterial leaf spot
Why this matters: Two locally isolated B. velezensis strains outperform a standard chemical bactericide against Xanthomonas euvesicatoria in vitro and carry rich biosynthetic arsenals, positioning them as candidates for sustainable bio-bactericides on pepper.
Background
Bacterial leaf spot caused by Xanthomonas euvesicatoria is a major constraint on pepper production, and reliance on chemical bactericides raises resistance and environmental concerns. Bacillus velezensis is known for antimicrobial secondary metabolites, but the genomic basis of biocontrol potential varies by strain. The authors ask whether two strains (BP5, BP103) isolated from pepper rhizosphere in the Mekong Delta, Vietnam, encode the genomic features consistent with strong biocontrol activity.
Methods
- In vitro antagonism: dual-culture assays against X. euvesicatoria, benchmarked to oxolinic acid.
- Enzymatic profiling: protease, lipase, amylase, cellulase, siderophore assays.
- Whole-genome sequencing of BP5 and BP103, followed by:
- Phylogenetic placement and average nucleotide identity (ANI) across 28 B. velezensis genomes plus B. subtilis DSM10.
- Orthology and pangenome (core/shell/unique) analysis.
- Secondary metabolite BGC prediction and CAZyme annotation (compared with commercial strain FZB42).
Key findings
Antagonism. BP5 produced the largest inhibition zone (36.7 mm), exceeding BP103 (32.1 mm) and oxolinic acid (31.3 mm). Both strains secreted protease, lipase, amylase, cellulase, and siderophores.
Genome features.
- BP5: 4.08 Mb, 46.04% GC, 4,047 protein-coding genes, 5 prophages.
- BP103: 3.91 Mb, 46.46% GC, 3,793 genes, 2 prophages.
- ANI > 98% confirmed assignment to B. velezensis, closest to strain 160.
Orthology / pangenome. Across 28 B. velezensis genomes + B. subtilis DSM10, 2,593 single-copy orthologs were identified. BP5 carried more multi-copy orthologs (388 vs 336), other orthologs (910 vs 763), unique paralogs (5 vs 1), and shell gene families (456 vs 203) than BP103. Core genome size decreased as more genomes were added, consistent with an open pangenome.
Secondary metabolites. Both strains encode 13 BGCs, including surfactin, fengycin, bacillaene, macrolactin, difficidin, bacilysin, bacillibactin, mersacidin, and locillomycin, plus four previously undescribed terpene/PKS clusters.
CAZymes. BP5 had the richest repertoire (133 genes), exceeding BP103 and FZB42 (both 129), suggesting enhanced adhesion and rhizosphere colonization capacity.
Limitations and open questions
The evidence for biocontrol efficacy is in vitro and genomic; in planta performance, field stability, and formulation are not reported. The four novel terpene/PKS clusters are predicted but not chemically characterized. Functional contributions of the expanded shell/paralog content in BP5 remain to be validated experimentally.
Original abstract
Bacillus velezensis strains BP5 and BP103, isolated from pepper rhizosphere soil in the Mekong Delta, Vietnam, displayed potent antagonistic activity against Xanthomonas euvesicatoria , which causes pepper bacterial spot. In dual-culture assays, BP5 formed the largest inhibition zone (36.7 mm), outperforming BP103 (32.1 mm) and oxolinic acid (31.3 mm). Both Gram-positive, rod-shaped strains produced extracellular protease, lipase, amylase, cellulase, and siderophores. Whole-genome sequencing revealed compact and genetically stable genomes: BP5 (4.08 Mb, 46.04% GC, 4,047 protein-coding genes, 5 prophages) and BP103 (3.91 Mb, 46.46% GC, 3,793 genes, 2 prophages). Phylogenetic reconstruction and average nucleotide identity (ANI of more than 98%) confirmed their assignment to B. velezensis , with closest relatedness to strain 160. Orthologous gene analysis across 28 B. velezensis genomes and B. subtilis DSM10 identified 2,593 single-copy genes. Compared to BP103, BP5 harbors greater numbers of multi-copy orthologs, other orthologs, and unique paralogs (388, 910, and 5 in BP5 with 336, 763, and 1 in BP103, respectively). Pangenome analysis showed that the core genome size decreased progressively with the addition of new genomes; BP5 showed more pronounced genetic divergence driven by expanded unique paralogs and shell gene families (with 456 in BP5 compared with 203 in BP103). Both strains encode 13 secondary metabolite biosynthetic gene clusters, including surfactin, fengycin, bacillaene, macrolactin, difficidin, bacilysin, bacillibactin, mersacidin, and locillomycin, plus four previously undescribed terpene/PKS. The CAZyme repertoire was richest in BP5 (133 genes), exceeding BP103 and the commercial strain FZB42 (both 129 genes), thereby enhancing adhesion and adhesion and rhizosphere colonization. These findings establish BP5 and BP103 as highly promising biocontrol agents, combining high genetic stability with diverse secondary metabolite profiles, suitable for development into sustainable microbial bio-bactericides.
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