Maintaining oxygen above a critical threshold prevents acetate-driven phytotoxicity in industrial-scale aerobic composting: metagenomic, MAG, and enzyme-activity evidence.

Aerobic composting is a key route for organic-waste valorization, yet product utilization is often constrained by phytotoxicity and low germination index (GI), particularly under oxygen-limited operation. Here, we developed an actionable oxygen-control window (O2 ≥ 10% v/v) to mitigate acetate-associated GI inhibition by integrating process monitoring with inhibitor profiling of GI extracts, metagenomics/metagenome-assembled genomes (MAGs), and pyruvate dehydrogenase (PDH) activity measurements. Three composting modes were implemented to create contrasting oxygen regimes: mechanical composting (MC; well-aerated), forced aeration composting (FC; intermittently oxygen-limited), and static composting (SC; ventilation-supported static aerobic). Chemical profiling and mixed-effects/regression analyses identified acetate as the dominant GI-inhibiting compound relative to other candidates (e.g., ammonium, formate, chloride). A bench-scale oxygen-gradient validation experiment (0-21% O2) confirmed an oxygen dose-response of acetate accumulation: acetate reached 1163.5 and 865.4 mg/L at 0% and 5% O2, but remained near baseline at ≥ 10% O2 (85.8 and 80.2 mg/L at 10% and 21% O2, respectively; 24 h), defining an oxygen window for suppressing acetate build-up. To probe mechanism, KEGG-based pathway mapping showed that acetate-linked functions were dominated by pyruvate metabolism, and high-acetate states were associated with reduced PDH-related functional gene abundance (PDHA/B) and lower PDH activity. MAG co-occurrence and correlation analyses further linked acetate-associated states to specific MAG-level contributors (including Thermobifida fusca). Together, these results support a PDH-linked metabolic constraint under oxygen limitation that promotes acetate persistence and GI inhibition, and provide operational guidance to maintain in-pile O2 ≥ 10% (v/v) to reduce acetate-driven phytotoxicity in industrial composting of readily acidogenic wastes.