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.

Continuous monoculture alters rhizosphere soil conditions and microbial community structure, but the integrated soil biochemical, microbial, and metabolomic responses of pepper (Capsicum annuum L.) rhizosphere soils remain insufficiently characterized. Here, we compared uncropped/non-continuously cropped pepper soil (Y0) with soil under 10 years of pepper monoculture (Y10) using soil physicochemical assays, enzyme measurements, 16S rRNA and ITS amplicon sequencing, untargeted UHPLC-Q Exactive HFX metabolomics, and predictive functional profiling. Long-term monoculture markedly separated Y10 from Y0 in multivariate analyses. Y10 soils showed higher organic matter, available nitrogen, available phosphorus, available potassium, and electrical conductivity in soil-water extracts, whereas microbial biomass carbon and pH were lower. Soil enzyme profiles also differed between treatments. Microbial alpha diversity declined under Y10, and bacterial and fungal community structures were clearly separated between treatments. At the taxonomic level, Acidobacteriota and several oligotrophic bacterial taxa were relatively enriched in Y0, whereas Proteobacteria, Bacteroidota, Chloroflexi, Bacillota, Pseudomonas, Bacillus, and several fungal genus-level taxa increased in Y10. Untargeted metabolomics revealed extensive remodeling of rhizosphere metabolites, with 413 up-regulated and 21 down-regulated differential metabolites in Y10. Differential metabolites were mainly associated with carboxylic acids and derivatives, benzene and substituted derivatives, fatty acyls, aromatic-compound transformation, sulfur metabolism, alkaloid biosynthesis, and microbial metabolism. Correlation analyses further linked key microbial taxa with soil pH, microbial biomass carbon, available nutrients, electrical conductivity, and enzyme activities. These results indicate that long-term pepper monoculture is associated with coordinated shifts in soil chemical status, microbial community composition, and metabolite profiles. The study provides an integrated basis for understanding rhizosphere changes under pepper continuous-cropping systems while recognizing that functional predictions and metabolite annotations require experimental validation.