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.