High-performing upland cotton shifts root-associated microbiomes under water limitation

Water scarcity significantly threatens cotton productivity, a challenge amplified by climate change and increasing competition for limited water resources. As a major source of natural fiber, cotton’s resilience to drought stress is essential for maintaining productivity and supporting global textile production. However, the mechanisms underlying this resilience, particularly the responses of root-associated microbial communities that may influence plant drought stress responses, remain unclear. Here, we quantified the plasticity of bacterial communities associated with roots of six cotton cultivars grown under water-limiting and well-watered conditions in a hot, arid environment. The highest-yielding cotton cultivars markedly shifted their root bacterial communities between irrigation treatments, whereas low-yielding cultivars were less responsive. Microbiome shifts in high-performing varieties suggest that these plants may leverage symbiotic relationships to cope with water limitation. This study links microbial communities and the performance of cotton and highlights the potential for leveraging these relationships to improve crop resilience in water-limited environments.