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.

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.