Impact of Organic Fertilizer Substitution on Soil Microbial Communities and Cotton Yield in Xinjiang

Organic fertilizer substitution for chemical fertilizers is an important strategy for sustainable agriculture. This study aimed to investigate the effects of different organic nitrogen substitution ratios for a chemical nitrogen fertilizer on the soil microbial community structure in cotton fields. A three-year field experiment was conducted in Changji, Xinjiang, China, with six treatments: no fertilization (CK), a single application of chemical fertilizer (CF), and organic nitrogen substituting for 25% (T1), 50% (T2), 75% (T3), and 100% (T4) of a chemical nitrogen fertilizer. High-throughput sequencing was used to analyze the bacterial and fungal community structures. Results showed that organic substitution treatments significantly increased the bacterial Simpson and Shannon diversity indices compared to CK. At the phylum level, organic substitution treatments increased the relative abundance of Proteobacteria (1.27–22.44%), Gemmatimonadota (3.50–9.33%), and Actinobacteriota (17.25–38.57%) compared to CK. For fungi, organic substitution treatments improved the Simpson and Shannon indices, with the T2, T3, and T4 treatments showing significant increases. Organic substitution treatments increased the relative abundance of Ascomycota (2.05–14.75%), Basidiomycota (0.41–178.44%), and Glomeromycota (6.15–502.88%) compared to CK, while Rozellomycota was exclusively present in organic substitution treatments. Cotton yield data showed that the T1 treatment produced the highest seed cotton yield over the three-year study period, with significant increases of 6.19% compared to the CF treatment in the third year. These findings suggest that organic fertilizer substitution can effectively improve the soil microbial community structure and diversity, with moderate to high substitution ratios showing the most beneficial effects for maintaining soil health in cotton fields.