Cucumber Fusarium wilt is a worldwide soil-borne disease that seriously restricts the yield and quality of cucumber. The rhizosphere soil microbiome, as the first line of defense against pathogens invading plant roots, plays a key role in rhizosphere immune formation and function. The purpose of this study was to reveal the key microecological factors and dominant microbial flora affecting cucumber resistance and susceptibility to Fusarium wilt by analyzing the physical and chemical properties and microbial flora of rhizosphere soil with different degrees of susceptibility and resistance to cucumber Fusarium wilt, thereby laying a foundation to establish cucumber resistance to the Fusarium wilt rhizosphere core microbiome. Firstly, Illumina Miseq sequencing technology was used to evaluate the physical and chemical properties and microbial groups of cucumber rhizosphere soil at different health levels, and the key environmental factors and microbial factors related to cucumber Fusarium wilt were screened out. Subsequently, PICRUSt2 and FUNGuild were used to predict the functions of rhizosphere bacteria and fungi. Combined with functional analysis, the possible interactions among soil physical and chemical properties, cucumber rhizosphere microorganisms, and Fusarium wilt were summarized. The results showed that the available potassium content in the rhizosphere soil of healthy cucumber decreased by 10.37% and 0.56%, respectively, compared with the rhizosphere soil of severely susceptible cucumber and mildly susceptible cucumber. Exchangeable calcium content increased by 25.55% and 5.39%; the α diversity Chao1 index of bacteria and fungi in the rhizosphere soil of healthy cucumber was significantly lower than that in the rhizosphere soil of seriously infected cucumber, and the MBC content of its physical and chemical properties was also significantly lower than that in the rhizosphere soil of seriously infected cucumber. There was no significant difference in the Shannon and Simpson diversity indexes between healthy cucumber rhizosphere soil and seriously infected cucumber rhizosphere soil. The results of the β diversity analysis showed that the bacterial and fungal community structure of healthy cucumber rhizosphere soil was significantly different from that of severely and mildly infected cucumber rhizosphere soil. At the genus level, through statistical analysis, LEfSe analysis, and RDA analysis, the key bacterial and fungal genera with potential biomarker values were screened out as SHA_26, Subgroup_22, MND1, Aeromicrobium, TM7a, Pseudorhodoplanes, Kocuria, Chaetomium, Fusarium, Olpidium, and Scopulariopsis, respectively. The bacteria SHA_26, Subgroup_22, and MND1 related to cucumber Fusarium wilt inhibition belong to Chloroflexi, Acidobacteriota, and Proteobacteria, respectively. Chaetomiacea belongs to Sordariomycates. The results of functional prediction showed that changes to the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway in the bacterial microbiota were concentrated in tetracycline biosynthesis, selenocompound metabolism, lipopolysaccharide biosynthesis, etc., which were mainly involved in the metabolism of terpenoids and polyketides, energy metabolism, metabolism of other amino acids, glycan biosynthesis and metabolism, lipid metabolism, cell growth and death, transcription, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The difference in fungi was mainly dung saprotroph–ectomycorrhizal–soil saprotroph–wood saprotroph. Through the correlation analysis and functional predictions of the key environmental factors, microbial flora, and cucumber health index in cucumber rhizosphere soil, we determined that the inhibition of cucumber Fusarium wilt was a synergistic effect of environmental factors and microbial flora, and a model diagram was drawn to briefly explain its mechanism. This work will provide a basis for the biological control of cucumber Fusarium wilt in the future.

Paenibacillus polymyxa strain PJH16, isolated and tested by our team, suppresses cucumber Fusarium wilt as an efficient biocontrol agent. For further investigation, the strain has been combined with two other Bacillus strains (Bacillus velezensis VJH504 and Bacillus subtilis JNF2) to enhance biocontrol ability, which formed high-efficiency microbial agents in the current study. The methodological target taken is based on achieving the optimal growth conditions of the combined microbial agents; hence, the medium composition and culture conditions were optimized through a single-factor test, orthogonal test and response surface methodology. Following this, the effectiveness of the microbial combination was assessed through pot experiments, which provided a theoretical foundation for the synthesis of microbial flora to significantly control cucumber Fusarium wilt. The results showed excellent compatibility, proving suitable for the proliferation and growth of Paenibacillus polymyxa PJH16, Bacillus velezensis VJH504, and Bacillus subtilis JNF2 strains together, specifically, when the inoculation amounts were adjusted to 4% of each. Using the single-factor test and orthogonal test analysis, the optimum composition of culture medium for the composite strain was identified as 3% glucose as the optimal carbon source, 2% yeast extract powder as the preferred nitrogen source, and 1% dipotassium hydrogen phosphate as the most suitable inorganic salt. Furthermore, the optical density (OD₆₀₀) of the composite strain solution reached its highest level at 3.16 under the following culture conditions: inoculation volume of 200 µL, 171 rpm culture speed, 21.6 h culture time, 30 °C cultural temperature, and an initial pH of 7.0. The pot experiment demonstrated that the mixed bacterial solution achieved a relative control efficacy of 93.4% against cucumber Fusarium wilt, which was significantly superior to that of single- strain or pesticide treatment, and also promoted cucumber growth. In summary, the microbial flora synthesized by the three Bacillus strains displayed a high bacterial concentration, following the optimization of culture conditions, and exerted remarkable control and growth-promoting effects on cucumber Fusarium wilt. This finding holds great significance for future developments of composite microbial agents.

Anthracnose is a widespread plant disease affecting vegetables, flowers, crops, and fruit trees, causing significant economic losses. It occurs at various stages of pepper growth, leading to rotting and shedding in later stages. The aim of this study was to explore the relationship with anthracnose occurrence by analyzing the physicochemical properties and microbiota changes in the inter-root soil of pepper under different susceptibility levels to reveal the key microecological factors and dominant microbial populations and to provide reference for ecological control. Illumina Miseq sequencing was first used to evaluate the physicochemical properties and microbial taxa in pepper inter-root soil across different health statuses and identify key parameters associated with anthracnose. Subsequently, PICRUSt2 (systematic genetic Investigation of communities by Reconstruction of observed States 2) and FUNGuild (Fungi Functional Guild) V1.0 online platform were used to predict the activities of inter-root bacteria and fungi. The findings indicated that healthy peppers had significantly higher inter-root soil nutrient levels and enzyme activity compared to sensitive peppers. There were significant differences between their community structures. In alpha-diversity analysis, inter-root soil microbial richness and diversity were significantly higher in healthy peppers than in susceptible peppers. At the bacterial taxonomic level, the comparative prevalence of Acidobacteria in highly resistant plants, resistant plants, and susceptible plants decreased sequentially. At the genus level, the relative abundance of Vicinamibacteraceae and RB41 was markedly elevated in disease-resistant inter-root soils than in disease-susceptible soils. At the fungal level, the comparative prevalence of Ascomycetes in highly resistant plants, resistant plants, and susceptible plants increased sequentially. Differences in function are mainly manifested in apoptosis and mycelial development.

Auxin/indoleacetic acid (Aux/IAA) family genes respond to the hormone auxin, which have been implicated in the regulation of multiple biological processes. In this study, all 25 Aux/IAA family genes were identified in Tartary buckwheat (Fagopyrum tataricum) by a reiterative database search and manual annotation. Our study provided comprehensive information of Aux/IAA family genes in buckwheat, including gene structures, chromosome locations, phylogenetic relationships, and expression patterns. Aux/IAA family genes were nonuniformly distributed in the buckwheat chromosomes and divided into seven groups by phylogenetic analysis. Aux/IAA family genes maintained a certain correlation and a certain species-specificity through evolutionary analysis with Arabidopsis and other grain crops. In addition, all Aux/IAA genes showed a complex response pattern under treatment of indole-3-acetic acid (IAA). These results provide valuable reference information for dissecting function and molecular mechanism of Aux/IAA family genes in buckwheat.

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.

Plant cuticular wax serves as a critical component for defense against biotic and abiotic stresses, with its biosynthetic pathway regulated by the ECERIFERUM (CER) gene family. This study presents the first genome-wide identification of 79 CER genes (CalCERs) in pepper (Capsicum annuum L.), which are distributed across all 12 chromosomes. Phylogenetic analysis classified CalCERs into five clades, with clade-specific conservation of exon–intron architectures and protein motifs. Promoter cis-element analysis revealed enrichment of light-responsive elements, abscisic acid (ABA), jasmonic acid (JA), and stress-responsive regulatory motifs, indicating multi-pathway regulation. Transcriptomic data highlighted tissue-specific expression patterns, such as the root-predominant express gene CalCER1-2 and the flower-specific express gene CalCER3-1. Under abiotic stresses (drought, salt, heat, and cold), CalCER4-2 and CalCER6-6 responded rapidly, while most genes showed delayed differential expression. Under biotic stress, CalCER3-1 and CalCER5-3 were upregulated, whereas CalCER2-2 exhibited pathogen-specific suppression, suggesting roles in modulating wax-mediated pathogen resistance. Hormone treatments revealed dynamic responses: CalCER2-2 was persistently ABA-inducible, while CalCER3-1 specifically responded to JA. This study underscores evolutionary conservation and species-specific expansion of the pepper CER family, linking their expression to wax biosynthesis and stress adaptation. These insights provide a foundation for enhancing stress resilience in crops. Future work should employ gene editing and metabolomics to validate functional mechanisms and optimize breeding strategies.