Abstract
Aerobic ammonia oxidation is crucial to the nitrogen cycle and is only known to be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] and a single lineage of archaea belonging to the Nitrososphaeria class of Thermoproteota [ammonia-oxidizing Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture only a limited subset of the full diversity of this clade. Here, we describe several genomes of AOA from metagenomic sequencing of a hot spring microbial mat, representing several poorly characterized basal lineages that may be important for understanding the early evolution of archaeal ammonia oxidation. These genomes include a novel genus most closely related to Nitrososphaera as well as novel species belonging to the genera Nitrosotenuis, Nitrososphaera and Nitrosotalea. Furthermore, the distributions and phylogenetic relationships of key metabolic genes support a history of vertical inheritance of ammonia oxidation and carbon fixation from the last common ancestor of crown group AOA.