Objectives We studied the soil microbial community, enzyme activity, and physicochemical properties after continuous applying organic fertilizer and liming for different years, to find out the remediation ways for acidification and possible indicators for the health of paddy soil.

Methods A pair of commercial organic fertilizer (ChM) and quicklime application experiments were conducted in a typical acid purple mud paddy field of eastern Hunan Province since 2014 under double-rice cropping system. 2.25 t/hm² of ChM or quicklime was applied before transporting of early and late rice, taking no ChM and lime application as the corresponding controls. On the third (in 2017) and seventh year (in 2021), 0−15 cm top soils were sampled at the late rice ripening stage for the determination of microbial phospholipid fatty acids (PLFAs), enzyme activities and physicochemical properties. The correlation coefficients between soil physicochemical and biological properties were used to construct the structural equation models, and the sensitive indicators were screened by their correlation coefficients with the soil PLFAs and enzyme activities.

Results In 2017, ChM application elevated the gram-negative bacteria (G⁻) PLFAs content by 23%, reduced the G⁺/G⁻ ratio by 29%; and in 2021, increased the content of soil total PLFAs, bacteria, G⁺, and actinomycetes PLFAs by 16%, 13%, 28%, and 38%, respectively, decreased the saprotrophic fungi PLFAs by 19%, did not change the G⁻ PLFAs content and the G⁺/G⁻ ratio significantly. Liming reduced total soil microbial PLFAs contents by 30% in 2017, and reduced that by 36% in 2021. ChM increased urease activity by 29% in 2017, and increased the activity of soil catalase, sucrase, and urease by 63%, 82%, and 39% in 2021, respectively. Liming increased the urease activity by 25% in 2017 but decreased that by 39% in 2021, did not impact the activities of other tested enzymes. 3 and 7 years of ChM application elevated soil aeration porosity by 14% and 33%, increased total organic matter by 12% and 7%, and increased the three labile organic C fractions by 29% and 69% on average; 3 and 7 years of liming elevated soil pH by 0.6 and 0.6 units, but decreased aeration porosity by 47% and 28%, did not change the total and liable organic carbon contents significantly, but increased fine particle organic C content by 24% and 9%, and the coarse particle organic C content by 100% and 21%, and 7-years liming decreased available N but increased available P content. Soil physical, chemical and biological indices positively responded to continuous ChM but negatively to liming in general, and the response in 7 years became more positive than in 3 years to ChM, and that was opposite to liming. According to the multivariate structural model analysis, continuous ChM application enhanced the total microbial PLFAs and urease activity mainly through increase the coarse particulate organic C content and the consequent liable organic carbon content, while cumulative increase of lime decreased total microbial PLFAs and urease activity due to deteriorated aeration porosity, coarse particle organic carbon and available N contents.

Conclusions Continues organic fertilizer application keeps improving soil porosity, organic matter content, and the physiochemical and biological properties. Liming in short term is beneficial to improve soil physiochemical and biological properties, but would offset the benefits in long run. The coarse particulate organic carbon content plays key roles to regulate the response of soil microbial community and chemical properties to the continuous organic fertilizer application and liming, showing potential as indicator of soil health.