Cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerium (FOC), is a prevalent soil-borne disease. In this study, Bacillus subtilis JNF2, isolated from the high incidence area of cucumber Fusarium wilt in Luoyang, demonstrated significant inhibitory effects on FOC and promoted cucumber seedling growth. The biocontrol mechanism of strain JNF2 were elucidated through morphological observation, physiological and biochemical experiments, and whole genome sequence analysis. Pot experiments revealed an 81.33 ± 0.21% control efficacy against Fusarium wilt, surpassing the 64.10 ± 0.06% efficacy of hymexazol. Seedlings inoculated with JNF2 exhibited enhanced stem thickness and leaf area compared to control and hymexazol-treated plants. Physiological tests confirmed JNF2’s production of indole-3-acetic acid (IAA), siderophores, and hydrolytic enzymes, such as β-1,3-glucanase, amylase, and protease, which inhibited FOC growth and promoted plant development. Genome analysis identified genes encoding antimicrobial peptides and hydrolases, as well as a novel glycocin synthetic gene cluster. These findings underscore B. subtilis JNF2’s potential as a biocontrol agent for sustainable cucumber cultivation.

Rhizosphere microorganisms play an important role in the health and development of root systems. Investigating the microbial composition of the rhizosphere is central to understanding the inter-root microbial function of Arundo donax under various cultivation conditions. To complement the metagenomic study of the Arundo donax rhizosphere, here, an amplicon-based metagenomic survey of bacteria and fungi was selected as a practical approach to analyzing the abundance, diversity index, and community structure of rhizosphere bacteria and fungi, as well as to study the effects of different cultivation methods on rhizosphere microbial diversity. Next-generation sequencing and QIIME2 analysis were used. The results indicated that microbial community richness, diversity, and evenness of the hydroponic samples were lower than those of soil samples when examining the α diversity indices of bacteria and fungi using Chao1, ACE, and Shannon metrics. In particular, the relative abundances of Proteobacteria, Rhizobiales, and Incertae sedis in hydroponic materials were higher, while Basidiomycota, Ascomycota, and Actinobacteriota dominated the flora in soil materials when comparing the numbers of OTUs and the ACE community richness estimator. Furthermore, the rhizosphere of hydroponic A. donax contained a higher abundance of nitrogen-fixing bacteria and photosynthetic bacteria, which contribute to root formation. Additionally, there was a significant presence of Basidiomycota, Ascomycota, and Actinobacteriota in soil A. donax, which can form hyphae. This reveals that the microbial community composition of the A. donax rhizosphere is significantly different under various cultivation conditions, suggesting that employing two distinct culturing techniques for Arundo donax may alter the microbiome. Furthermore, it provides technical support for the synergistic interaction between Arundo donax and rhizosphere microorganisms so as to better use the relationship between Arundo donax and basic microorganisms to solve the problems of Arundo donax growth and ecological restoration.

In order to clarify the changes and correlations among microbial community structure and soil environmental factors in the rhizosphere soil of peppers under healthy and diseased conditions, Illumina MiSeq technology was used to perform high-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene and the ITS hypervariable region of fungi in the rhizosphere soil of peppers. The dominant species and key environmental factors affecting the occurrence of pepper Phytophthora blight were analyzed and screened, and the functions of bacteria and fungi in the samples were predicted by PICRUSt2 and FUNGuild. The results showed that except for soil pH, the contents of microbial biomass carbon, magnesium, zinc, and iron in the rhizosphere soil of healthy peppers were significantly higher than those in the diseased soil. Alpha diversity analysis showed that the diversity index of the bacterial community in healthy soil was higher than that in diseased soil, while the diversity index of the fungal community was significantly lower than that in diseased soil. The relative abundance of beneficial bacteria such as Proteobacteria, Actinobacteriota, Burkholderiales, and Rhodanobacteraceae in the rhizosphere soil of healthy peppers was higher. Pathogens such as Penicillium and Fusarium were significantly enriched in the rhizosphere soil of diseased pepper plants. The functional prediction results showed that soil bacteria were mainly metabolized, including the biosynthesis of ansamycin, the biosynthesis of vancomycin antibiotics, the biosynthesis of valine, leucine, and isoleucine, the metabolism of C5-branched dicarboxylic acid, and the biosynthesis of fatty acids. The main nutritional strategies of the fungal community are disease prototype and saprophytic. Combined with the key environmental factors, microbial composition, and correlation analysis of pepper rhizosphere soil, it is speculated that the occurrence of pepper Phytophthora blight may be related to the synergistic effect of soil nutrients and microbial flora, which provides a theoretical basis for the biological control of pepper Phytophthora blight in the future.