Indicated the posibility of archaea involving in ammonia oxidation and the exist of ammonia-oxidation archaea was finally certified by the enrichments and pure cultures of several strains of AOA. Recent research has demonstrated that ammonia-oxidizing archaea may form a separate and deep-branching phylum, the Thaumarchaeota. Molecular biological research based on the HhAntag691 functional gene amoA and the 16SrRNA gene has revealed a widespread distribution of AOA. Quantitative PCR analyses found that AOA normally outnumbered their substrate competitors, such as AOB, in both soil and water, but the relative contributions of AOA and AOB in the soil nitrogen cycle remained undetermined. Some researchers believed that AOB played a more important role than AOA in soil nitrification. Jia and Conrad found that changes in potential nitrification rates were only correlated with the number of AOB amoA genes when they added substrate or inhibitor of ammonia oxidation to the soil. Subsequently, Di et al. discovered the same phenomenon in New Zealand grassland. In contrast, other researchers regarded AOA as the main drivers of ammonia oxidation in soil. Gubry-Rangin et al. reported that amoA genes. Zhang et al. confirmed the dominant role of AOA in soil nitrification by means of stable isotope probe and the quantitative analysis of archaral amoA genes. Offre et al. also demonstrated that the growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification. Differences in cell size, specific cell activity and other physiological characteristics may explain the different contributions of AOA and AOB to soil nitrification. In addition, AOA and AOB may compete mutually or exhibit functional redundancy under some conditions, whereas under other conditions the fundamental physiological differences between these organisms may lead to niche separation of AOA and AOB. Therefore, environmental factors are important in determining the different nitrification activities and relative contributions of AOA and AOB. Among all environmental factors, ammonia is the substrate of ammonia oxidation for which concentrations will directly affect nitrification activity. It was found that AOA were able to grow well and the growth of AOA was coupled with soil nitrification when the concentration of ammonia was relatively low or the supply of ammonia was through the mineralization of organic matter; however, AOB were more competitive in soil nitrification and the number of AOB amoA gene copies was greater than that of AOA when the concentration of ammonia was higher. Adaptation to long-term energy stress is believed to be a crucial factor that distinguishes AOA from AOB. Different specific affinities for substrate between AOA and AOB may explain their different growth patterns under low or high ammonia concentrations. N. maritimus exhibited a high affinity for ammonia and was able to grow and convert ammonia at an extremely low ammonia concentration, while the ammonia-oxidizing activity was completely inhibited when the ammonia concentration reached 28 mg/L. The affinity of N. maritimus for ammonia can be more than 1,000-fold greater than that of N. europaea. The affinity for ammonia of N. viennensis fell in between N. maritimus and N. europaea, and their growth was totally inhibited at ammonia concentration of 280 mg/L. Other than ammonia concentration, other environmental traits such as pH, oxygen concentration and organic carbon could affect the abundance and diversity of ammonia-oxidizing microorganisms and consequently lead to niche separation of AOA and AOB.