Figure 1.

Phylogeny of Ca. Nitrosomirales and other AOA orders; phylogenomic inference of AOA species affiliated to the orders Nitrosopumilales (blue, basal lineage #1), Nitrososphaerales (green, basal lineage #2), Ca. Nitrosomirales (yellow, basal lineage #3), and Ca. Nitrosocaldales (orange, basal lineage #4) based on concatenated sequences of 70 conserved single-copy core genes; the non-ammonia-oxidizing thaumarchaeotal genomes were used as outgroups (gray); please note that, based on the recent comparative phylogenetic analysis of AOA genomes [15], the previously defined acidophilic AOA group Ca. Nitrosotaleales has been merged with Nitrosopumilales; phylogenomic tree was constructed using the protein mixture model UL3 (three-matrix model); confidence values were provided based on 1000 bootstrap replications.