Diversity of endophytic bacterial community in rice roots and their roles in phosphate solubilization and plant growth

Abstract

Root endophytic bacteria have significant beneficial effects on plant growth and health, while specific coexisting pathogenic bacteria can cause various diseases. In this study, we assessed the diversity and cultivability of the endophytic bacterial community in rice roots with a focus on their capacity for phosphate solubilization and impact on plant growth. Employing PacBio Single Molecule Real-Time (SMRT) and Sanger sequencing, we generated 16S rRNA gene libraries using metagenomic DNA extracted from the roots of three field-grown rice plants, along with genomic DNA from 156 associated bacterial isolates. QIIME 2-based microbiome analysis revealed dominant classified species at diverse taxonomic levels, including Arcobacter marinus, Paraburkholderia kururiensis, Lactobacillus plantarum, and Lactobacillus brevis. Furthermore, we effectively isolated 25.97% of rice root endophytic bacteria, with a notable 33.33% of pure culture endophytic bacteria exhibiting phosphate solubilization abilities. Finally, we revealed the inhibitory role of Burkholderia vietnamiensis and the growth promoting role of Paraburkholderia kururiensis subsp. Kururiensis in both the monocot model Brachypodium distachyon and the dicot Arabidopsis thaliana. Our study provided novel insight into the microbiome structure in rice roots and its potential to benefit rice cultivation and enhance overall crop health.