Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting

► AOA and AOB play roles under different conditions during composting. ► Both AOA and AOB amoA gene abundance correlate to the difference in the PAO rate. ► Archaea dominate ammonia oxidation during the thermophilic and cooling stages. ► Bacteria relate to ammonia oxidation during the mesophilic and maturation stages.