The overuse of chemical fungicides against fungal pathogens adversely affects soil and plant health, resulting in environmental problems and food safety. Therefore, biocontrol is considered as an environmentally friendly and cost-effective green technique in environmental protection and agricultural production. We obtained a bacterial strain N23 from a contaminated plate which showed significant inhibition to anthracnose. The strain N23 was identified as Bacillus velezensis based on 16S rRNA gene, gyrA gene, and whole-genome sequence. The bacterium N23 was able to suppress the mycelial growth of numerous plant pathogenic fungi on solid media. Tomato seeds treated with strain N23 showed significantly higher germination levels than untreated ones. Moreover, strain N23 effectively reduced the lesion area of pepper anthracnose disease in planta. The gene clusters responsible for antifungal metabolites (fengycin, surfactin, and iturin) were identified in the genome sequence of N23 based on genome mining and PCR. Furthermore, methanol extracts of the bacterial culture caused significant inhibition in growth of the fungal Colletotrichum sp. and Botrytis cinerea. These findings suggested that B. velezensis N23 could be a potential biocontrol agent in agricultural production and a source of antimicrobial compounds for further exploitation.

Pseudomonas nitroreducens L4 was isolated from the interior of cotton plants, which showed strong biocontrol activity against Verticillium dahlia and other fungal pathogens. To elucidate the biocontrol mechanism, the genome sequence of L4 was sequenced using the Illumina and Nanopore sequencing platform. The assembled genome of L4 consisted of a single circular chromosome was 6,229,472 bp, with an average GC content of 64.95 %, 5,629 protein-coding genes, 72 tRNA, 16 rRNA and 1 tm RNA. Six secondary metabolite biosynthetic gene clusters are identified in the genome. The genome sequence provided a theoretical basis for analyzing the biocontrol mechanism of this strain.

The soil-borne oomycete pathogen Phytophthora capsici poses a serious threat to plant growth and results in substantial economic impact on the pepper industry. Therefore, the isolation of multifunctional biocontrol agents has become a major research priority. In this study, we isolated a biocontrol strain, Bacillus subtilis Z-294, which demonstrated strong inhibition of P. capsici in both plate and greenhouse experiments. This strain Z-294 exhibited broad-spectrum antagonistic activities as well as plant growth-promoting ability. Phylogenetic analysis based on core-genome and average nucleotide identity (ANI) further identified Z-294 as B. subtilis. Importantly, we found that the strain Z-294 alleviates the P. capsici disease through mechanisms associated with changes in the plant microbiome. Plants treated with Z-294 showed higher alpha-diversity. The application of B. subtilis Z-294 showed that the relative abundance of Alphaproteobacteria, Bacilli, Bacteroidia, Agaricomycetes, and Eurotiomycetes increased, while the relative abundance of Gammaproteobacteria and Sordariomycetes declined. Strain Z-294 holds great promise as a multifunctional biocontrol agent for the sustainable management of diseases and the enhancement of plant health, laying a solid foundation for its future agricultural applications.

The root rot of Lycium barbarum represents the most severe soil-borne disease that impedes its production. The management of this disease primarily relies on chemical agents, which pose risk to both the environment and human health. In this study, we isolated Bacillus strains as potential biological control agents. Bai2-32 exhibited the strongest antagonistic activity against all five Fusarium species and demonstrated broad-spectrum antifungal activities. Field experiments further displayed that Bai2-32 provided excellent biocontrol efficacy. To understand the possible genetic determinants for biocontrol traits, we performed genome sequencing. The genome of B. mojavensis Bai2-32 consists of a 4,055,438 bp circular chromosome with a GC content of 43.67%, containing 3986 protein-coding genes. Phylogenetic analysis of Bacillus strains, utilizing a single core-genome approach, clearly placed the strain Bai2-32 within the B. mojavensis clade. Predictive analysis revealed that the genome encoded lipopeptides such as surfactin and fengycin, in addition to several active metabolite synthesis gene clusters. The results further support the potential of B. mojavensis Bai2-32 for application in agricultural production and suggest that it may be a promising biocontrol agent for further studies.