92 Chapter 3 Enrichments of MBAE14-like Pseudomonadales IMCC2047 and Rugosibacter with atypical Cu-MMO genes Two high-quality, novel MAGs associated with anoxic coastal sediments were reconstructed from these metagenomes: the MBAE14-like gammaproteobacterial Pseudomonadales IMCC2047 and the betaproteobacterial Rugosibacter (Figure 5A-C). The Pseudomonadales IMCC2047 genome seemed to be a similar species as the described MBAE14 family like Pseudomonadales IMCC2047 (Mori et al., 2019), yet quite different (~ 60% AAI) from the other four Pseudomonadales IMCC2047 genomes available at the GTDB at the time of analysis (Supplementary Figure 11). The Rugosibacter MAG seemed to be quite divergent from the ten available Rugosibacter genomes in the GTDB, sharing only 70% of AAI with the environmental MAG of Rugosibacter GCA.002842395.1 (Supplementary Figure 12). The MBAE-14-like family were only enriched in the oligotrophic bioreactor system from month 5, with varying degrees of abundance that peaked during the last months of monitoring (12 to 15.5) (Figure 5A), with values that ranged from 0.04% (oligotrophic bioreactor month 2) to 8.5% (oligotrophic bioreactor month 12) based on the relative bacterial 16S rRNA gene amplicon sequencing results and matching the Pseudomonadales IMMC2047 MAG abundance (Figure 5A). The Pseudomonadales IMCC2047 coverage accounted for between 0.36% (oligotrophic bioreactor biofilm month 7) and 4.5% (oligotrophic bioreactor month 14.5) of the metagenomic reads (Figure 5A and Supplementary Table 5). The Rugosibacter MAG was found from 0.04% (eutrophic bioreactor month 7) to 0.91% (oligotrophic bioreactor biofilm month 15.5) with markedly increasing coverages in the biofilm of both the eutrophic and oligotrophic bioreactor (Figure 5B and Supplementary Table 5). The annotations of the Pseudomonadales IMMC2047 and Rugosibacter MAGs revealed divergent Cu-MMOs, and PQQ-dependent alcohol dehydrogenases (ADH) (Figure 5C-D). The recovered MAGs showed that both harbored a complete “p(a)moCAB” gene-like cluster, with an additional Open Reading Frame (ORF) that showed low homology to (p)amoD (Figure 5C and Supplementary Table 6). Phylogenetic reconstruction demonstrated that the Cu-MMO proteins sequences from these MAGs were distinct from the homologs encoded by MOB and ammonia monooxygenases (AMOs) of ammonium oxidizing bacteria (AOB) but harbored all
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