Oxygen availability shapes microbial community composition and function to determine antibiotic resistance genes and expression during composting: A pilot-scale study.

Temperature was considered the primary factor reducing antibiotic resistance genes (ARGs) during composting, with oxygen availability serving as the fundamental driver of temperature differences. However, how different oxygen levels shaped the composition and function of microbial communities, and subsequently affected ARGs and resistance expression during composting, remained unclear. Here, a pilot-scale long-term thermophilic aerobic and mesophilic facultative composting were constructed with metagenomics and stress (Oxygen/Antibiotic) plate screening to reveal the resistance potential and direct risk. The ratios of aerobic, facultative, and anaerobic bacteria were 1:0.94:0.75 in aerobic composting, and 1:0.96:0.99 in facultative composting. Metabolic functions were significantly enriched in aerobic composting, promoting temperature rise (peak 54 °C). In facultative composting, functions related to horizontal gene transfer and transcription/translation were enriched. Compared with mesophilic facultative composting, aerobic composting significantly reduced ARGs abundance (from 4.80 to 3.59 CPC) and mobility (from 3.66 to 2.27 CPC). ARGs hosts in aerobic composting were widely distributed, predominantly among aerobic microorganisms, while ARGs hosts in facultative composting were more concentrated, mostly among facultative anaerobes. The relative abundance of culturable antibiotic-resistant bacteria (25.00% vs. 15.88%) and active antibiotic-resistant pathogens (44.04% vs. 6.68%) were significantly higher in facultative composting than in aerobic composting. This study revealed the pathway by which oxygen shaped the composition and function of microorganisms with different oxygen requirements, thereby influencing compost antibiotic resistance, providing a theoretical basis for the safe application of manure to agricultural fields.