Genomic characterization of Bacillus velezensis BP5 and BP103: insights into biocontrol potential against bacterial leaf spot on pepper

Genome Sequence Resource of Bacillus velezensis Strain H166, a Potential Biological Control Agent for Apple Replant Disease

Bacillus velezensis strain H166, isolated from the apple rhizosphere, exhibits strong biocontrol efficacy against apple replant disease (ARD), a complex soilborne disease in which Fusarium oxysporum can act as an important fungal pathogen. To elucidate the underlying biocontrol mechanisms, a high-quality genome assembly of strain H166 was generated using PacBio HiFi sequencing. The genome of strain H166 consists of a single circular chromosome of 3,929,791 bp with a GC content of 46.5%, and contains 4,035 protein-coding genes, 86 tRNA genes, 27 rRNA genes, and 16 sRNA genes. Twelve secondary metabolite biosynthetic gene clusters were identified, including those associated with fengycin, surfactin, and bacillaene biosynthesis. These gene clusters are presumed to be closely associated with the biocontrol functions of this strain against Apple Replant Disease. The genome sequence provides important foundational data for further elucidating the molecular mechanisms underlying the biocontrol activity of B. velezensis strain H166.

Whole genome sequencing and molecular characterization of two Bacillus licheniformis strains isolated from hot springs in yellowstone ational park

Two B. licheniformis strains isolated from extreme environments are isolated from the Five Sisters hot spring in Yellowstone National Park and whole-genome sequencing reveals an open pangenome of 10,374 genes, providing a genomic foundation for future exploration of novel bioactive compounds with potential applications in drug discovery, agriculture, and biotechnology.

Pectobacterium nicotianae sp. nov., a novel pathogen causing tobacco hollow stalk disease, is phylogenetically distinct from P. brasiliense

Five Gram-negative, facultatively anaerobic bacteria were isolated from the hollow stalk tissues of tobacco plants in Yunnan, China. Based on polyphasic taxonomic data, they were identified as a new Pectobacterium species. Phylogenetic analyses of 16S rRNA and the concatenated dnaX-leuS-recA genes grouped them into a distinct monophyletic clade. Genome analyses showed high average nucleotide identity (ANIb 96.96–97.63%) and digital DNA-DNA hybridization (dDDH 76.2–80.1%) values, supporting their classification as a single species. However, three indices, including lower dDDH (67.9%), borderline ANIb (95.89%), and phylogenomic separation with 99% support, differentiate them from Pectobacterium brasiliense IPO 3540T. Comparative genomics across 24 reference strains revealed differences in virulence factors and specific plant cell wall-degrading enzyme profiles, highlighting adaptations to different hosts. Biochemical tests showed that all isolates lacked β-glucosidase and exhibited unique carbon utilization patterns; chemotaxonomically, strain 21LCBS03T produced only menaquinone MK-8. Pathogenicity experiments confirmed that four strains caused severe soft rot and hypersensitive responses on various hosts, while strain BSHS4, with a dDDH of 76.2% relative to 21LCBS03T, showed reduced virulence—possibly a subspecies. Reanalysis of 633 Pectobacterium genomes from NCBI reclassified 121 strains into this new species, exposed common misidentifications, and identified 9 candidate novel species awaiting phenotypic validation. Combining phylogenomic, virulence, phenotypic, and pathogenic data, we propose Pectobacterium nicotianae sp. nov., with 21LCBS03T (=GDMCC 1.3317T = CCTCC AB2022131T = JCM 35650T) designated as the type strain.

Genomic and phenotypic insights into the probiotic and antimicrobial potential of Bacillus amyloliquefaciens BCSIR-AJ strain from garlic chutney

Streptomyces songxianensis sp. nov. SX92T: biocontrol of tobacco black shank and modulation of the rhizosphere microbiome

Streptomyces species are well-known for their potential in biocontrol and plant growth promotion, with the rhizosphere serving a rich reservoir for novel isolates. In this study, a Streptomyces strain (SX92 T ) was isolated from the rhizosphere of healthy tobacco plants. In dual-culture assays, SX92 T displayed broad-spectrum antagonistic activity against six major fungal pathogens of tobacco, with the highest inhibition (59.22%) against Phytophthora nicotianae , the causal agent of tobacco black shank. Polyphasic taxonomic characterization, combining 16S rRNA gene phylogeny, distinctive physiological traits, chemotaxonomic markers (LL-diaminopimelic acid, major menaquinones MK-10(H₄) and MK-9(H₈), and predominant fatty acids anteiso-C₁₅:₀ and C₁₆:₀), and genome-based metrics (ANI and dDDH), clearly distinguished SX92 T from its closest relatives. Accordingly, strain SX92 T is proposed as the type strain of a novel species, Streptomyces songxianensis sp. nov. The genome of SX92 T is 9.69 Mb in size with a G + C content of 71% and contains 26 biosynthetic gene clusters, including one showing 100% similarity to the albaflavenone cluster. In field trials, application of SX92 T fermentation broth significantly improved tobacco agronomic traits and reduced black shank incidence by 44.97%. Furthermore, SX92 T treatment reshaped the rhizosphere microbiome by enriching beneficial bacteria such as Flavobacterium and altering the relative abundance of specific fungi, including a reduction in the arbuscular mycorrhizal fungus Rhizophagus irregularis . It also shifted soil enzyme activities, with increased cellulase and decreased catalase levels. These findings establish Streptomyces songxianensis SX92 T as a promising multifunctional biocontrol agent for sustainable tobacco production.

Integrating biocontrol efficacy and genomic potential of Bacillus velezensis BJ-1141: from broad-spectrum antagonism to tomato Fusarium wilt suppression.

AIMS To isolate and characterize a rhizosphere-derived Bacillus velezensis strain with biocontrol and plant growth-promoting potential, and to evaluate its efficacy against plant pathogens together with its genomic basis. METHODS AND RESULTS A bacterial strain (BJ-1141) was isolated from the rhizosphere and identified as B. velezensis based on morphological characteristics and phylogenetic analyses of 16S rRNA and gyrA gene sequences. The strain exhibited broad-spectrum antagonistic activity against 24 plant pathogenic fungi, inhibiting 23 pathogens by more than 50%, with a maximum inhibition rate of 95.57%. BJ-1141 produced hydrolytic enzymes (amylase, protease, cellulase and pectinase) and plant growth-promoting factors, including siderophores and indole-3-acetic acid (IAA). It also demonstrated phosphorus solubilization, nitrogen fixation and biofilm formation. Greenhouse experiments showed that root application of BJ-1141 effectively controlled tomato Fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici, achieving control efficacies of 81.13 - 85.93%, which were higher than those of chemical and commercial microbial treatments. In addition, BJ-1141 significantly increased plant height, biomass and chlorophyll content in tomato and lettuce seedlings. Whole-genome sequencing revealed a 3 902 965 bp genome containing 13 biosynthetic gene clusters associated with antimicrobial secondary metabolites, including surfactin, fengycin, bacillaene, difficidin, macrolactin H, bacillibactin and bacilysin. CONCLUSIONS B. velezensis BJ-1141 is a multifunctional bacterial strain with strong biocontrol efficacy and plant growth-promoting traits, supported by genomic evidence, and represents a promising candidate for sustainable crop disease management.