Farming systems shape distinct ARGs removal pathways: Biotic-driven in large-scale composting versus abiotic-driven in free-range systems.

Current research on antibiotic resistance genes (ARGs) removal during manure composting has primarily focused on differences across animal species. However, how farming practices, which fundamentally differ in feed composition, antibiotic use, and rearing density, shape ARGs removal patterns and underlying mechanisms remains poorly understood. Here we compared manure composting between large-scale (LS) and free-range (FR) systems and revealed fundamentally divergent causal pathways governing ARGs dynamics. LS achieved higher removal rates of total ARGs (93% vs 57%) and total mobile genetic elements (MGEs; 93% vs 77%) than FR, operating through a biotic-driven mechanism: composting conditions suppressed specialized bacterial consortia that served as primary ARGs hosts, with biotic factors exerting a dominant effect on ARGs variation (path coefficient: r = 0.92). In contrast, FR relied on an abiotic-factor-dominated dual-suppression mechanism, with the abiotic latent variable exerting a dominant negative effect on ARGs abundance (r = -0.59), while biotic contributions were minimal (r = 0.26). Driven by their distinct feed origins, key nutritional components diverged significantly between systems: nitrogen-related factors [total nitrogen (TN) + protein (P)] dominated ARGs variation in LS (56.86%), whereas TS was the predominant driver in FR (76.06%). FR also exhibited greater microbial richness and a wider variety of genera, but lacked specialized ARG-hosting consortia, explaining its lower removal efficiency. Collectively, our findings reveal system-associated differences in the mechanistic pathways of ARGs removal between the two farming systems, underscoring the potential necessity for system-specific composting strategies.