Endophytic bacterial communities and spatiotemporal variations in cotton roots in Xinjiang, China

Endogenous bacteria are important for maintaining the health and other ecologically relevant functions of cotton plants. However, little is known about the community structures and diversity of endophytic bacteria in cotton plants. In our study, we used the Illumina amplicon sequencing technology to study the endophytic bacteria found in cotton root tissue in Xinjiang, China. A total of 60.84 × 10⁶ effective sequences of the 16S rRNA gene in the V5-V6 variable region revealed a large number of operational taxonomic units (OTUs), namely 81-338 OTUs, at a cut-off level of 3% and a sequencing depth of 50 000 sequences. Among the 23 classes identified, Gammaproteobacteria was the dominant group, followed by Alphaproteobacteria, Actinobacteria, and Bacillus. The diversity of endogenous bacteria differed at different growth periods, with the most OTUs detected in seedlings (654), followed by the budding stage (381), flowering stage (350), and flocking stage (351). A total of 217 OTUs were common to all four stages. Pantoea tags were more common to the Shihezi region, whereas Erwinia labels were more common to the Hami region. These results suggest that the dynamics of endophytic bacterial communities are affected by plant growth stage. This highlights the relevance of microbial diversity studies in improving our understanding of endophyte communities.