Background: The impacts of the conversion of natural to agricultural ecosystem on soil biodiversity and ecosystem functions are still disputable. Here, we compared the soil biodiversity (bacteria and fungi) and ecosystem functions of citrus orchards in different stages of succession (5–30 years) with those in adjacent natural ecosystems. Different management strategies were also considered for one of this stage (15 years). Results: The results indicate that changes from natural vegetation land to citrus orchards would lead to reduced soil bacterial diversity, as well as significant declines in multiple ecosystem functions associated with C cycle after 30 years of citrus plantation. However, the functions associated with N and P cycle were enhanced by the plantation. Citrus plantation negatively affected the C cycle by reducing the soil microbial diversity. Reduction in soil bacterial biodiversity was indirectly driven by increased soil acidification resulting from citrus plantation, while wheat straw addition could alleviate the reduction (15-year stage). Compared with natural vegetation, citrus plantation also reduced the relative abundance of multiple phylotypes, including Alphaproteobacteria, Deltaproteobacteria, Subgroup_6, Subgroup_4, Anaerolineae and Bacteroidia. The ecological clusters of soil bacteria and fungi were significantly associated with multiple ecosystem functions, suggesting that citrus planting altered multiple ecosystem functions via ecological clusters. Conclusions: Taken together, our results indicate that soil biodiversity, soil functions and C:N:P coupling are sensitive to the conversion of natural vegetation land to agricultural land, and further suggest that proper management of soil acidification can address some negative impacts of land use conversion on soil biodiversity and functions.
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