Metagenomic insights into microbial ecology and antibiotic resistance in floating rice cultivation within coal mining subsidence water areas

Balancing cultivated land protection, energy security, and ecological restoration in coal mining subsidence water accumulation areas (CMSWAA) remains a critical challenge. Here, we investigate an innovative floating rice cultivation system in Guqiao Town, Huainan City, China, using metagenomic sequencing of rhizosphere soil, bottom sediment, and water. Distinct microbial communities were identified across environmental compartments: Chloroflexota, Pseudomonadota, and Actinomycetota dominated the rhizosphere soil and sediment, driving cellulose degradation, nitrogen cycling, and methane production, while Cyanobacteriota, Pseudomonadota, and Actinomycetota in water facilitated polysaccharide degradation and photosynthetic carbon fixation. Functional annotation revealed that carbohydrate and amino acid metabolism were predominant, supporting active organic matter transformation and nutrient cycling. CAZy analysis indicated the enrichment of glycosyltransferases and glycoside hydrolases, highlighting their roles in polysaccharide metabolism and soil aggregate stabilization. Additionally, transposase-related genes suggested enhanced microbial adaptability to dynamic environmental conditions. Antibiotic resistance gene analysis demonstrated the dominance of vancomycin and multidrug resistance genes, indicating strong anthropogenic selection pressures and potential ecological risks associated with non-point source pollution. This study provides the first comprehensive metagenomic characterization of microbial metabolic functions in a floating rice cultivation system within the unique CMSWAA habitat, offering a scientific basis for ecological restoration and sustainable agricultural management. • Floating rice cultivation first applied in coal mining subsidence water areas • Metagenomes profiled across water, soil, and rhizosphere niches • Aquatic and terrestrial niches show distinct metabolic and biogeochemical pathways • Microbial community divergence drives C–N cycling dynamics and methane production • High vancomycin and multidrug resistance genes indicate agricultural pollution risks