Metal(loid) contamination shifts microbial carbon and nitrogen cycling potential in paddy soils

Trace metal(loid) contamination in paddy soils derived from either geogenic sources or mining activities is widely occurring in mid-south to south China and south to south east Asia. Due to their toxicities, these trace metal(loid)s may influence microbial community assembly and carbon/nitrogen (C/N) cycling. However, how metal(loid) contamination reshapes community composition, functional potential, and genomic traits of key functional microorganisms remains unclear. Here, we collected paddy soil samples from mid-south to south China and classified them into low- and high-contamination groups based on the Nemerow index. The associations among contamination level, microbial community composition, C/N-cycling potential, and genomic traits of key functional microorganisms were examined by combining soil physicochemical characterization, 16S rRNA gene amplicon sequencing, metagenomics, and metagenome-assembled genome (MAG) reconstruction. Bacterial and archaeal richness did not differ significantly between contamination levels, whereas community composition varied markedly. Methane oxidation genes were enriched in high-contamination soils, whereas methanogenesis genes were more abundant in low-contamination soils. Denitrification- and dissimilatory nitrate reduction to ammonium (DNRA)-related genes increased under heavy contamination, whereas several nitrogen fixation genes declined. Environmental association analyses identified As, Cd, Pb, Cr, and Zn as key variables associated with C/N cycling genes. Several MAGs carried both elemental cycling genes and metal(loid)-response or transformation genes, suggesting potential multifunctionality in contaminated paddy soils. Overall, metal(loid) contamination, together with associated edaphic variation, reorganized microbial communities and redistributed C/N cycling potential. This work provides a genomic basis for identifying microorganisms that could serve as bioindicators or functional targets in contaminated paddy soils.