<i>Bacteria</i> rather than <i>Archaea</i> dominate microbial ammonia oxidation in an agricultural soil

TLDR

Agricultural ecosystems receive about 25 % of the world’s nitrogen input, and ammonia‑oxidizing prokaryotes—now known to include both Bacteria and Archaea—carry out the first step of the nitrogen cycle. The study aimed to determine whether ammonia oxidation in soil is predominantly performed by Archaea, as suggested by their high abundance. The authors found that Bacteria, not Archaea, functionally dominate ammonia oxidation in the tested agricultural soil, with bacterial amoA activity and CO₂ assimilation linked to oxidation while archaeal genes were numerically more abundant but inactive.

Abstract

Agricultural ecosystems annually receive approximately 25% of the global nitrogen input, much of which is oxidized at least once by ammonia-oxidizing prokaryotes to complete the nitrogen cycle. Recent discoveries have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex soil environment it remains unclear whether ammonia oxidation is exclusively or predominantly linked to Archaea as implied by their exceptionally high abundance. Here we show that Bacteria rather than Archaea functionally dominate ammonia oxidation in an agricultural soil, despite the fact that archaeal versus bacterial amoA genes are numerically more dominant. In soil microcosms, in which ammonia oxidation was stimulated by ammonium and inhibited by acetylene, activity change was paralleled by abundance change of bacterial but not of archaeal amoA gene copy numbers. Molecular fingerprinting of amoA genes also coupled ammonia oxidation activity with bacterial but not archaeal amoA gene patterns. DNA-stable isotope probing demonstrated CO(2) assimilation by Bacteria rather than Archaea. Our results indicate that Archaea were not important for ammonia oxidation in the agricultural soil tested.