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We hypothesized that community patterns associated with agricultural practices would be most evident in the uppermost soil layer, and that potentially plant-pathogenic taxa would be more abundant under soybean monoculture. Bacterial community composition varied with soil depth but not among agricultural practices. In contrast, fungal community composition was associated with both soil depth and practice. The only significant pairwise difference was found between soybean monoculture and the most diversified rotation involving cover crops and high nitrogen fertilization. When practices were compared within each soil layer, differences in both bacterial and fungal composition were detected only in the uppermost layer. Here, the bacterial community was associated with extractable phosphorus and pH. Few bacterial bioindicator taxa were detected, and no potentially plant-pathogenic taxa were found under soybean monoculture. 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