A synthetic Bacillus compound agent enhances cotton yield and fiber quality by regulating rhizosphere microbes and metabolites

To improve cotton yield and reduce reliance on chemical fertilizers and pesticides, we synthesized a novel compound microbial agent with cotton growth-promoting activity. Pot experiments demonstrated that application of this agent significantly promoted cotton seedling growth: chlorophyll content increased by 6.6%, root activity was enhanced by 87.69%, and malondialdehyde (MDA) content decreased by 44.36%. Furthermore, the agent treatment significantly enhanced the antioxidant enzyme activities in cotton seedlings, with catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activities increasing by 136.56%, 125.00%, and 45.73%, respectively. Field plot trials showed that the agent increased cotton yield by 20.00%-24.34% and improved fiber quality, with the spinning consistency index, breaking fiber strength, and elongation increased by 7.35%, 7.48%, and 3.06%, respectively. Further analyses of nutrient contents in cotton leaves, rhizosphere soil physicochemical properties, amplicon sequencing, and untargeted metabolomics revealed that, compared with the control group: nitrogen (N), phosphorus (P), and potassium (K) contents in cotton leaves increased by 33.27%, 68.24%, and 37.76%, respectively; rhizosphere soil pH decreased by 2.78%, while available phosphorus (AP), organic matter (OM), and total phosphorus (TP) increased by 33.43%, 17.40%, and 73.26%, respectively; bacterial community Chao1 index decreased by 7.93%, whereas the Shannon index increased by 0.29%; fungal community Chao1 and Shannon indices increased by 17.54% and 1.07%, respectively. At the genus level, the relative abundances of <i>Iamia</i>, <i>Polycyclovorans</i>, <i>Arenimonas</i>, and <i>Verticillium</i> increased by 43.48%, 10.51%, 31.27%, and 67.58%, respectively, whereas those of <i>Bacillus</i> and <i>Fusarium</i> decreased by 35.37% and 21.00%, respectively. Moreover, the secondary metabolite composition in rhizosphere soil was altered: terpenoid and nitrogen-containing compound contents increased, while phenol content decreased, with significant accumulation of tryptamine, L-tryptophan, and serotonin. This study confirms that the novel compound microbial agent enhances cotton yield and fiber quality via synergistic mechanisms, providing effective technical support for the development of green cotton production.