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Microbial communities play a key role in maintaining agroecosystem functioning and sustainability, but their response to excessive animal manure application and relevant mechanisms have not been thoroughly elucidated to date. This study investigated the responses of soil bacterial and fungal communities to pig manure (PM) amendment in red paddy soils. High-throughput sequencing revealed that PM amendment significantly reduced the relative abundance of Acidobacteria yet increased that of Bacteroidetes, Ignavibacteriae, Firmicutes, and Rozellomycota. The Cu and available phosphorus were the primary impact factors influencing bacterial and fungal diversity, respectively. Bacterial alpha-diversity tended to sharply decrease when the content of soil Cu was >30.70 mg kg⁻¹, while fungal alpha-diversity did not continuously increase when the content of soil available phosphorus was >82.84 mg kg⁻¹ …