Cotton stubble return and subsoiling alter soil microbial community, carbon and nitrogen in coastal saline cotton fields

Long-term cotton stubble return and subsoiling improve root growth and soil properties and alter microbial colonization in the rhizosphere. However, it is unknown if cotton stubble return and subsoiling would change the soil microbial biomass carbon (MBC) and nitrogen (MBN) sequestration by changing the microbial community in coastal saline soil. We used an experiment to quantify the effects of stubble management (removal or return), tillage (non-subsoiling or subsoiling), and soil compartments (non-rhizosphere or rhizosphere) on the bacterial and fungal communities after 9-year treatments. Soil compartments were the main factor affecting the soil bacterial community. The abundance of Bacillus, Pseudomonas, and Sphingomonas in the rhizosphere soil increased by 63.64%, 20.40%, and 109.24%, respectively, compared to the non-rhizosphere soil. Moreover, Bacillus was increased by both stubble return and subsoiling. The Chao1, Simpson, and Shannon indices in alpha diversity of the bacterial community were increased by rhizosphere soil, stubble return, and subsoiling. The MBC and MBN in the rhizosphere soil was 22.4% and 13.2% higher than in the non-rhizosphere soil. Stubble management was the main factor affecting the fungal community composition. Stubble return significantly increased some fungal abundance, e.g., Cephalotrichum and Fusarium, by 243.11% and 95.24% than stubble removal. The abundance of Cephalotrichum, Fusarium, and Alternaria in the rhizosphere soil was significantly higher than that in the non-rhizosphere soil. The Chao1, Simpson, and Shannon indices of the fungal community were only significantly increased by stubble return. Compared with cotton stubble removal, stubble return increased MBC and MBN by 31.8% and 23.0%, respectively. The effects of the plant growth promoting rhizobacteria (PGPR) (Bacillus and Pseudomonas) on rhizosphere microbial community and MBC and MBN were higher than those of pathogenic fungi (Fusarium and Alternaria) from Structural Equation Models (SEM). Our results suggest that long-term cotton stubble return and subsoiling could play a role in improving soil microbial community and C and N and enhance the sustainability of coastal saline soil.