Cover crops and manure compost shift microbial functions and diversity in Southeastern sandy soils

Abstract Organic inputs are vital to sustainable agriculture because of their capacity to improve soil nutrients and nourish soil microbial communities. However, it is still not well known how organic inputs modify soil microbial functions. Here, we studied the effects of cover crop inclusion and manure compost amendment on maicrobial communities in sandy soils under organic vegetable production. Two manure composts (with and without) and four cover crop treatments, that is, cereal rye ( Secale cereale L.), hairy vetch ( Vicia villosa ), the mixture of the two, and no cover crop control, were fully crossed and established in the fields in 2020. After 2 years of repeated treatments, soils were collected for biogeochemical and microbial analyses in 2022. We found limited treatment effects on microbial alpha diversity, but both manure compost application and cover crop inclusion altered microbial community structure, in which cereal rye and hairy vetch had distinct effects. In addition, hairy vetch and cereal rye increased the abundances of dominant soil bacterial and fungal taxa, respectively. Organic inputs altered C and N‐cycling extracellular enzyme activities (EA), which correlated with soil biogeochemical properties and microbial diversity. The changes in predicted microbial functions are likely to have a significant impact on long‐term soil fertility.