The application of organic fertilizers, such as straw and manure, is an efficient approach to maintain soil productivity. However, the effect of these organic fertilizers on soil microbial nutrient balance has not yet been established. In this study, the effects of the long-term combined organic-inorganic fertilization on microbial community were investigated by conducting a 30-year-long field test. Overall, the following five fertilizer groups were employed: inorganic NP fertilizer (NP), inorganic NK fertilizer (NK), inorganic NPK fertilizer (NPK), NPK + manure (MNPK), and NPK + straw (SNPK). The results indicated that the mean natural logarithm of the soil C:N: P acquisition enzyme ratio was 1.04:1.11:1.00 under organic-inorganic treatments, which showed a deviation from its overall mean ratio of 1:1:1. This indicates that microbial resources do not have a balance. Vector analysis (vector angle 45 degrees) and threshold elemental ratio analysis (RC:N-TERC:N 0) further demonstrated that the microbial metabolism was limited by Nitrogen (N) under SNPK and MNPK treatments. N limitation further influenced soil microbial community structure and its dominated SOC decomposition. Specifically, Microbial communities transformed into a more oligotrophic-dominant condition (fungal, Acidobacteria, Chloroflexi) from copiotrophic-dominant (Proteobacteria, Actinobacteria) condition with increasing N limitation. Lysobacter genus and Blastocatellaceae family, in the bacterial communities along with the Mortierella elongata species in fungal communities, were markedly associated with the N limitation, which could be the critical biomarker that represented N limitation. Both correlation analysis and partial least squares path modeling showed significant positive effects of N limitation on the ratio of bacterial functional genes (Cellulase/Amylase), involved in recalcitrant SOC degradation.
