As a glycophyte plant, pepper (Capsicum annuum L.) is widely cultivated worldwide, but its growth is susceptible to salinity damage, especially at the seedling stage. Here, we conducted a study to determine the physiological and transcriptional differences between two genotype seedlings (P300 and 323F3) with contrasting tolerance under salt stress. The P300 seedlings were more salt-tolerant and had higher K⁺ contents, higher antioxidase activities, higher compatible solutes, and lower Na⁺ contents in both their roots and their leaves than the 323F3 seedlings. During RNA-seq analysis of the roots, more up-regulated genes and fewer down-regulated genes were identified between salt-treated P300 seedlings and the controls than between salt-treated 323F3 and the controls. Many ROS-scavenging genes and several SOS pathway genes were significantly induced by salt stress and exhibited higher expressions in the salt-treated roots of the P300 seedlings than those of 323F3 seedlings. Moreover, biosynthesis of the unsaturated fatty acids pathway and protein processing in the endoplasmic reticulum pathway were deeply involved in the responses of P300 to salt stress, and most of the differentially expressed genes involved in the two pathways, including the genes that encode mega-6 fatty acid desaturases and heat-shock proteins, were up-regulated. We also found differences in the hormone synthesis and signaling pathway genes in both the P300 and 323F3 varieties under salt stress. Overall, our results provide valuable insights into the physiological and molecular mechanisms that affect the salt tolerance of pepper seedlings, and present some candidate genes for improving salt tolerance in pepper.

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.

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.

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.