Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea

The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH ₃) oxidation to nitrite (NO ₂⁻) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH ₃ oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH ₂OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH ₂OH or an initial oxidation product other than NH ₂OH. We now show through combined physiological and stable isotope tracer analyses that NH ₂OH is both produced and consumed during the oxidation of NH ₃ to NO ₂⁻ by Nitrosopumilus maritimus , that consumption is coupled to energy conversion, and that NH ₂OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH ₃ by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH ₂OH, the archaea possibly catalyzing NH ₂OH oxidation using a novel enzyme complex.