Long-Term Pig Manure Amendment Mitigates Soil Acidification and Boosts Sweet Potato Productivity in Latosolic Red Soil via Enhanced Nutrient Availability and Microbiome Reshaping

Organic amendments can mitigate soil acidification and degradation, yet their long-term effects on soil microbiome, functions, and crop productivity remain underexplored in latosolic red soils. This study aimed to elucidate how different fertilization regimes reshape soil microbial communities and predicted functions, and how these changes link to sweet potato productivity after 15 years. Soil and plant samples were collected from a 15-year field experiment on latosolic red soil under five treatments: no fertilizer (CK), chemical fertilizer alone (NPK), and chemical fertilizer combined with commercial manure (NPK + CM), pig manure (NPK + PM), or rice straw (NPK + RS). Soil properties, bacterial and fungal communities, and predicted functions (FAPROTAX, FUNGuild) were analyzed. The results showed that long-term NPK alone significantly acidified soil (pH decreased by 1.49 units), whereas NPK + PM increased pH by 1.38 units relative to NPK, and also increased soil organic carbon, available nutrients, and sweet potato yield (by 31% compared with NPK). Soil pH was strongly associated with reshaping the microbial community. NPK + PM enriched beneficial phyla (e.g., Myxococcota, Nitrospirota, Latescibacterota, Entotheonellaeota, and Mortierellomycota) and enhanced predicted chemoheterotrophic, predatory or exoparasitic, and saprotrophic functions. Variance partitioning showed that nutrients, key microbial taxa, and predicted functions jointly explained productivity variation (adjusted R2 = 0.9386). Thus, chemical fertilizer combined with pig manure is an effective strategy to mitigate soil acidification and improve sweet potato productivity by regulating soil nutrient-microbiome interactions. Our findings support reshaping the microbiome via organic amendments for sustainable agriculture in acidic soils.