Objective Application of organic fertilizers is an important way to improve organic fertilizer input and soil fertility. Studying the effects of different organic fertilizers proportionally replacing chemical nitrogen fertilizers on soil fertility and the accumulation of organic carbon and its fractions can help elucidate how organic fertilizers improve paddy soil fertility and enhance carbon sequestration.

Methods The research based on a 10-year long-term fertilization experiment, located in Human Province. The soil samples were collected from the treatment plots of PK fertilization (T1) and NPK fertilization controls, and three organic substitution treatments: returning milk vetch in early rice and straw in late rice straw (T3), commercial organic fertilizer (T4), and pig manure (T5), the substitution rate for chemical N was 20% in all the three treatments. The content of soil total organic carbon (SOC) and organic carbon fractions, the activities of organic carbon metabolism related enzymes (cellobiose hydrolase, β-1,4-glucosidase and polyphenol oxidase) were analyzed, and the integrated soil fertility index (IFI) were calculated.

Results T2 significantly increased IFI, relative to T1. Compared with T2 treatment, the organic substitution treatments significantly increased IFI and SOC by 4.56%−7.80% and 2.34%−5.04%, respectively, and T5 was recorded the highest increment; T3 and T4 increased the content of soil mineral-bound organic carbon by 2.80%−3.91%, while T5 treatment increased soil particulate organic carbon content and its proportion by 18.30% and 12.63%, respectively. The T3 and T4 treatments increased the soil microbial biomass carbon content and the activities of three carbon conversion-related enzymes, which contributed to the decomposition of organic materials and their accumulation to mineral-bound organic carbon, T5 treatment enhanced the physical protection of organic carbon due to the high stability index and fatness index of organic carbon from pig manure, resulting in a significant increase in the accumulation of particulate organic carbon in the soil and its share in the total organic carbon. The results of structural equation modeling indicated that the content of particulate organic carbon was the main factor affecting soil integrated fertility.

Conclusions Long-term application of organic fertilizers promoted soil organic carbon accumulation and improved the integreted soil fertility under the condition of replacing 20% of chemical fertilizer nitrogen. Straw (including milk vetch) and commercial organic fertilizer were more conducive to enhancing the accumulation of stable soil organic carbon fractions, while pig manure was more conducive to increasing the proportion of unstable soil organic carbon accumulation (ie. particle organic carbon) and its proportion on total organic carbon pool, so resulted highest soil fertility index and the active organic carbon pool.