Pathways and organisms involved in ammonia oxidation and nitrous oxide emission

Ammonia oxidation is a central step in the global nitrogen cycle that involves several different-conditions and metabolic bioprocesses, including aerobic versus anaerobic ammonia oxidation, and autotrophic versus heterotrophic ammonia oxidation. With the development and application of metagenomics and other modern molecular approaches, some new organisms (particularly ammonia-oxidizing archaea) and novel pathways related to ammonia oxidation have been identified. Consequently, the understanding of nitrogen cycling processes and the microorganisms that mediate them have been greatly improved. Here the authors summarize the biochemistry, microbiology, and ecophysiology of these organisms (including autotrophic ammonia-oxidizing bacteria, heterotrophic nitrifying bacteria, anaerobic ammonia-oxidizing bacteria, and ammonia-oxidizing archaea) and discuss the current knowledge and important concepts associated with their corresponding pathways. Factors influencing their distribution, abundance, community structure and potential ammonia oxidation rates in natural and engineered ecosystems are also addressed. Furthermore, the mechanism of nitrous oxide emission during these processes and the specific control strategies are explained or proposed. The significant roles of these organisms in novel biological wastewater treatment processes are also evaluated. Finally, several urgent issues and significant perspectives related to these novel pathways and players have been addressed to evoke the involvement of researchers in broadening future studies.