Revealing microbial patterns in the rhizosphere of pecan trees asymptomatic and symptomatic for Texas root rot using a high-throughput sequencing approach

The rhizosphere harbors diverse microbial communities that play crucial roles in nutrient cycling and plant health. Understanding the composition and dynamics of these communities is essential for optimizing agricultural productivity and disease management. In this study, bacterial and fungal communities in the rhizosphere of pecan trees (Carya illinoinensis) asymptomatic and symptomatic for Texas root rot were characterized using high-throughput sequencing of the 16S rRNA gene and ITS region. The results indicated that Proteobacteria and Actinobacteria were the predominant bacterial phyla in both conditions. The predominant fungal phyla comprised Basidiomycota and Ascomycota in symptomatic conditions and Ascomycota and Mortierellomycota in asymptomatic ones. At the genus level, Streptomyces and Pseudomonas were the most abundant bacterial genera; among fungi, Scleroderma and Psathyrella were predominant in symptomatic samples and Mortierella in asymptomatic samples. alpha-diversity analysis showed significant differences in the fungal community. Specific bacterial and fungal biomarkers for asymptomatic and symptomatic conditions were identified, highlighting their importance in the pecan tree rhizosphere. A total of six bacterial and seven fungal taxa were detected in symptomatic samples, while four bacterial and 16 fungal taxa were detected in asymptomatic ones. These included genera known for their roles in soil health, such as Pseudomonas, Kaistobacter, Streptomyces, Psathyrella, Scleroderma, and Mortierella. Co-occurrence network analysis revealed higher complexity and interaction levels among microbial communities in asymptomatic samples, suggesting a healthier network supporting microbial communities. This study provides comprehensive and valuable insights into microbiome dynamics and microbial resources for future studies aimed at improving agricultural production through the study of rhizosphere microorganisms.