Figure 2
Phylogenetic evidence for the presence and transcriptional activity of NC10 in OMZs. (a) Particulate methane monooxygenase subunit A (PmoA) gene phylogeny. PmoA sequences (n=53) recovered from the ETNP and GD are highlighted in bold within the larger clade of NC10-like sequences from other studies, separated from PmoA of aerobic methanotrophic clades and an ammonia monooxygenase (AmoA) outgroup. Phylogeny was inferred based on Maximum Likelihood (ML) analysis of 88 amino acids using the Dayhoff substitution model. Bootstrap values greater than 70 are shown, along with NCBI Accession numbers for database sequences. Numbers in parentheses represent the number of unique sequences included in each collapsed node—Taxon identifiers and Accession numbers for all sequences are in Supplementary Figure S2. The scale bar represents 50 amino-acid changes per 100 amino acids. (b) Heme-copper oxidases (HCO) phylogeny following that of Ettwig et al. (2012), with putative nitric oxide dismutases (NODs) shown in green, including two full-length sequences (labeled ETNP) assembled from OMZ NC10 transcript fragments. The sequences used for assembly were those with top matches (bit score>50) to Ca. M. oxyfera via BLASTX against the NCBI-nr database. Phylogeny was inferred by ML analysis of 520 amino acids based on the Le and Gascuel_2008 model. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. (c, d) Alignment of the qNor quinol-binding (c) and catalytic (d) sites showing putative NOD (green) compared with canonical qNor (red) sequences, following that of Ettwig et al. (2012). Numbering reflects residue numbers of G. stearothermophilus. Shading highlights conserved residues in canonical qNors where amino-acid replacement has occurred in putative NODs.
