Soil microbial communities play an essential role in driving multiple functions (i.e., multifunctionality) that are central to the global biogeochemical cycles. Long-term fertilization has been reported to reduce the soil microbial diversity, however, the impact of fertilization on multifunctionality and its relationship with soil microbial diversity remains poorly understood. We used amplicon sequencing and high-throughput quantitative-PCR array to characterize the microbial community compositions and 70 functional genes in a long-term experimental field station with multiple inorganic and organic fertilization treatments. Compared with inorganic fertilization, the application of organic fertilizer improved the soil multifunctionality, which positively correlated with the both bacterial and fungal diversity. Random Forest regression analysis indicated that rare microbial taxa (e.g. Cyanobacteria and Glomeromycota) rather than the dominant taxa (e.g. Proteobacteria and Ascomycota) were the major drivers of multifunctionality, suggesting that rare taxa had an over-proportional role in biological processes. Therefore, preserving the diversity of soil microbial communities especially the rare microbial taxa could be crucial to the sustainable provision of ecosystem functions in the future.

Relationships between various soil attributes and the diversity of bacteria. Solid dark line represents a significant linear relationship that fitted the ordinary least-squares (OLS) regression model, and the light green and purple shaded area shows the 95% and 99% confidence interval of the fit, respectively. PAO, potential ammonium oxidation; DEA, denitrification enzyme activity; SBR, Soil basal respiration; βG, β-glucosidase; NAG, N-acetyl-b-glucosaminidase; TN, total nitrogen; TC, total carbon; Nitrific, nitrification related genes; Denitrific, denitrification related genes; C-Degra, Carbon degradation related genes; C-Fix, Carbon fixation related genes; P-Cycling, Phosphorus cycling related genes; and S-Cycling, Sulphur cycling related genes. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)