Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils

Recent studies of ammonia-oxidizing archaea (AOA) suggested their significant contributions to global nitrogen cycling, and phylogenetic analysis categorized AOA into a novel archaeal phylum, the Thaumarchaeota. AOA are ubiquitous in terrestrial ecosystems, have unique mechanisms for nitrification, better adaptation to low-pH pressures, and strikingly lower ammonia requirements compared with ammonia-oxidizing bacteria (AOB). Previous perceptions that microbial ammonia oxidation in acidic soils was minimal, and entirely meditated by autotrophic bacteria and occasionally by heterotrophic nitrifiers have been dramatically challenged, and the dominant nitrifying groups urgently called for re-assessment. Controversially, the relative contributions of AOA and AOB to autotrophic ammonia oxidation have been reported to vary in different soils, but ammonia substrate availability, which was largely restricted under acidic conditions, seemed to be the key driver. Theoretically predicted ammonia concentrations in acidic soils below the substrate threshold of AOB and remarkably high ammonia affinity of AOA raised the supposition that thaumarchaea could represent the dominant ammonia-oxidizing group in ammonia-limited acidic environments. Recently, the functional dominance of thaumarchaea over its bacterial counterpart and autotrophic thaumarchaeal ammonia oxidation in acidic soils has been compellingly confirmed by DNA-stable isotope probing (SIP) experiments and the cultivation of an obligate acidophilic thaumarchaeon, Nitrosotalea devanaterra. Here, we review the currently available knowledge concerning the history and progress in our understanding of the ammonia-oxidizing microorganisms (AOB and AOA) and the mechanisms of nitrification in nutrient-depleted acidic soils, present the possible mechanisms shaping the distinct niches of AOA and AOB, and thus strengthen the assumption that AOA dominate over AOB in ammonia oxidation of acidic soils.