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The global demand for cotton makes sustainable cotton production an important issue that can be improved by a better understanding of the influence of soil microbes on cotton growth. We collected cotton field soils at the seedling and flowering/boll-setting (FBS) stages in order to obtain soil properties and cotton growth indices. Bacterial and fungal community compositions were assessed by high-throughput sequencing of 16S rRNA and internal transcribed spacer genes, respectively, after which the differences in microbial functions and their influencing factors at different growth stages were analyzed. Both the diversity and composition of soil bacterial and fungal communities were found to be significantly different between the seedling and FBS stages. Microbes in the seedling stage had significantly higher richness and biomass than those in the FBS stage. Compared with the seedling stage, the stability of the soil bacterial communities was decreased. The cotton growth indices at both the seedling and FBS stages were associated with compositional shifts in the bacterial community and but not the fungal community. The abundance of specific soil microbial taxa (e.g., Pseudarthrobacter, Thiobacillus, Cephalotrichum, Chaetomium, and Fusarium) were correlated with cotton growth indices at the seedling stage, being mainly regulated by soil salinity and nitrate content. Our results highlight the importance of soil microbial communities in mediating cotton growth and will be useful in providing better strategies for the improvement of cotton agriculture.

Differing Roles of Bacterial and Fungal Communities in Cotton Fields by Growth Stage