Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

Abstract

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

Evolutionary Ecology of Natural Comammox Nitrospira Populations

“…In fact, ammonium concentration was the variable that better explained the Nitrospira distribution in the studied waterworks. Although little is known about the range of ammonia affinities in comammox Nitrospira , as this trait has only been measured in two species ( 24 , 25 ), other ammonia oxidizers have ammonia affinities spanning several orders of magnitude ( 26 ). Likewise, canonical Nitrospira species affiliated with different lineages have shown niche differentiation based on nitrite concentration ( 27 , 28 ).…”

Evolutionary ecology of natural comammoxNitrospirapopulations

“…A possible explanation might be that the co-occurrent comammox Nitrospira species had different ammonia affinities, and they would occupy different sites in the highly porous filter material (23). So far, little is known about the variability of ammonia affinity in comammox Nitrospira as this feature has only been reported for two comammox species (24,25), however, a wide range of ammonia affinities have been observed in other ammonia oxidizers (26). Another reason could lie in the abundance of unique genes in each comammox Nitrospira species (> 250 in average ( 21)).…”

A Review of Ammonia-Oxidizing Archaea and Anaerobic Ammonia-Oxidizing Bacteria in the Aquaculture Pond Environment in China

“…Nitrosoarchaeum koreensis (10 mM L –1 ), and a strain in the AOA AC2 enrichment culture (5 mM L –1 ) ( French et al, 2012 ). It was found that group I.1b AOA species could tolerate very high ammonium concentrations ( Jung et al, 2021 ).…”

“…The latest research also showed that the AOA of group I.1a and group I.1b had a wide range of cellular ammonia affinities ( Jung et al, 2021 ). Group I.1a AOA displayed a high substrate affinity, and the ammonia apparent-half-saturation concentration Km(app), which ranged from ∼2.2 to 24.8 nM, can adapt to oligotrophic conditions, while several group I.1b species possess a wide range of affinities for NH 3 [Km(app) = ∼0.14 to 31.5 μM] ( Jung et al, 2021 ). Compared with AOB, AOA may not have the advantage of using high-concentration ammonia.…”