Objectives The effects of the combined application of chemical fertilizer with different organic materials on soil nutrient content, soil microbial biomass stoichiometric ratios and microbial community structures were studied in Yellow clayey paddy soil, to understand the response of microbial community structure to nutrient changes and the microbial biomass stoichiometric changes.

Methods The research based on a 12-years field experiment beginning since 2011, under single rice cropping system. Soil samples were collected in five treatment plots, including no fertilization (CK), chemical fertilizers (NPK), and chemical fertilizers with milk vetch (NPKGM), cow manure (NPKCM), and rice straw (NPKRS). Soil organic matter (SOM), dissolved organic carbon (DOC), dissolved organic nitrogen (DON), inorganic nitrogen (IN), total nitrogen (TN) and available phosphorous (AP) contents, the microbial biomass carbon (MBC), nitrogen (MBN) and phosphorus (MBP) contents were measured. The microbial community structure was analyzed by phospholipid fatty acid (PLFA) method.

Results Compared with NPK, long-term combined application with milk vetch, cow manure and rice straw improved soil organic matter and nutrient content. NPKCM treatment exhibited the highest promotion effect, with the increment in SOM, TN, and AP by 40.7%, 41.6%, and 108.6%, respectively. Compared with CK, long-term combined application treatments increased the soil MBC/MBN, but decreased MBC/MBP and MBN/MBP (P<0.05), with the lowest MBC/MBP recorded in NPKCM. Compared to NPK, combined applications increased soil bacteria, fungi, actinomycetes, and total microbial biomass, and reduced fungi/bacteria ratios (F/B) and G⁺/G⁻ ratio. Redundancy analysis showed that soil TN (P<0.05) was the most important environmental factor affecting soil microbial community, followed by soil TP (P<0.05). Linear regression analysis indicated that MBC/MBN had negative correlation with DOC/(DON+IN), MBC/MBP had positive correlation with DOC/AP, and MBN/MBP had positive correlation with (DON+IN)/AP. Correlation analysis proved that the changes in the stoichiometric ratio of microbial biomass was closely related to the ratios of F/B and G⁺/G⁻.

Conclusions The combined application of chemical fertilizer with organic materials could effectively increase soil organic matter and nutrient content, change the stoichiometric characteristics of soil microbial biomass and microbial community. Cow manure shows the best combined application effect due to its low stoichiometric ratio. The ratios of F/B and G⁺/G⁻ were correlated with the stoichiometric ratio of soil microbial biomass. The reconstruction of community structure may be an effective strategy for soil microorganisms to respond to changes in substrate stoichiometric ratio in Yellow clayey paddy soil.