Diverse Manures Shape Heavy Metal Accumulation and Microbial Communities in Long-Term Continuous Maize Cropping

Livestock manure amendment improves soil fertility and promotes carbon sequestration, but long-term application leads to heavy metal (HM) accumulation with unknown ecological consequences. Based on a 13-year field experiment in a continuous maize cropping system, we compared chemical fertilizer (NPK) with four organic amendments (cattle, pig, chicken manure, and compost) applied on an isocarbon basis. Organic amendments significantly increased total organic carbon (TOC) by 15.8–24.3% and available phosphorus (AP) by 1.9- to 6-fold relative to NPK. Compost achieved the highest maize yield. However, pig and chicken manure led to substantial accumulation of Cu and Zn due to high background levels. Despite this, grain HM concentrations remained below safety thresholds, indicating no immediate food chain risk. Metagenomic analysis revealed that HM stress acted as a deterministic filter on the soil microbiome. Cattle manure fostered the most complex co-occurrence network (average degree: 2.70), while pig manure reduced network complexity and increased modularity (>0.92), reflecting a shift toward fragmented, survival-oriented interactions. This structural reorganization was coupled with functional shifts, including enrichment of stress-tolerant taxa (Chitinophagales, Nitrosotalea) and detoxification pathways. We recommend prioritizing cattle manure or compost over raw pig and poultry manure to balance fertility, productivity, and ecological safety in black soil regions.