Alkaline woody peat shifts CO₂ emissions to CH₄ by modulating microbial cross-feeding in Cd-contaminated paddy soil

Alkaline organic amendments are widely used to remediate cadmium (Cd)-contaminated paddy soils by alleviating acidification and reducing Cd bioavailability, yet their impacts on greenhouse gas emissions remain unclear. Here, we examined how alkaline woody peat (WP) regulates carbon fluxes and microbial interactions in Cd-contaminated paddy soil. Anaerobic incubation and greenhouse pot experiments, together with in situ methane monitoring and metagenomic analyses, were used to compare alkaline-modified WP with acidic WP, CaO alone, and unamended controls. Alkaline WP (AWP-2) increased soil pH from 5.5 to 7.35 and decreased exchangeable Cd from 32% to 13%, confirming its remediation effectiveness. However, this was accompanied by marked changes in greenhouse gas emissions: methane production increased by up to 3.9-fold, while carbon dioxide emissions declined. Metagenomic analyses showed that alkaline WP strongly enriched methanogenic archaea, particularly Methanosarcina, whose relative abundance reached 26.6% compared with 4.2% in the control, while suppressing microbial populations associated with CO₂-generating pathways. Functional gene profiles revealed increased abundance of mcrA and reduced representation of genes involved in complete acetate oxidation (maeA, pdc, sucA, porA, aceE, and icd). Genome-resolved analysis further showed that some microbes positively associated with methanogens lacked key genes involved in acetate oxidation to CO₂ (e.g., aceE), suggesting a reduced capacity for CO₂ generation from acetate and a greater tendency to retain carbon as acetate, thereby potentially favoring acetoclastic methanogenesis. Overall, these results highlighting a potential trade-off between Cd remediation and greenhouse gas mitigation and the need to incorporate microbially driven carbon fluxes into environmental risk assessments of alkaline amendments in contaminated paddy soils.