Fig. 5

Maximum likelihood phylogenetic trees of Nitrospira spp. based on (left) AmoA and (right) HaoA amino acid sequences. Only complete or nearly complete sequences are included. The strength of support for internal nodes was assessed by performing bootstrap replicates, with the obtained values shown as colored circles (top left legend). The comammox Nitrospira clades and subclades are indicated by colored boxes, and the colour font of clade A sequences in the AmoA tree refers to their membership on the HaoA tree. Gamma- and betaproteobacterial AOB sequences were used to root the trees. Shapes next to the sequence names denote the environment from where the MAGs were recovered (color code as in Fig. 1)