98 Chapter 3 subunits, due to a variation in the protein family level annotation. Another shared feature of the Pseudomonadales IMCC2047 and Rugosibacter MAGs is the lack of known CO2 fixation or formaldehyde-derived C1-assimilation pathways (serine and RuMP) characteristic for AOBs or MOBs (Kalyuzhnaya et al., 2019), and therefore are apparent heterotrophs with unknown function(s) of their Cu-MMO. A third common shared unusual observation in these two genomes is the presence of PQQdependent ADHs (Figure 5C, Supplementary Figure 14 and Supplementary Table 6). MOBs and methylotrophs employ PQQ-ADH-like lanthanide (xoxF) or calcium dependent (mxaF) methanol and related ADHs to oxidize alcohols to aldehydes, a genetic repertoire that AOBs do not have (Kikuchi et al., 2023; Kuypers et al., 2018). Neither of the new PQQ-ADHs clusters near methanol dependent dehydrogenases (Supplementary Figure 14) but seem to be more affiliated to alcohol/ethanol dehydrogenases (Keltjens et al., 2014). Therefore, rather than methanol, the PQQ-dependent-ADH may be oxidizing short-chain alcohols that are possibly fermentation products of other community members. One clear genetic feature that distinguished Pseudomonadales IMCC2047 from Rugosibacter was the presence of a hydroxylamine oxidoreductase haoA with a cytochrome c-544 (cycB) encoded in the same operon (Supplementary Table 6). It is known that MOB can use Hao to detoxify hydroxylamine under high ammonium loads (Poret-Peterson et al., 2008). In contrast, AOB can conserve energy from hydroxylamine oxidation by employing two cytochromes in the same operon (haoAB, cycAB), funneling electrons to the quinone pool and generating a proton motive force. Some exceptions to the classic AOB operon organization include “Ca. Nitrosacidococcus tergens” sp. RJ19, which has a haoAB-cycB structure (Picone et al., 2021). Additionally, quite often AOB genomes encode multiple copies of hydroxylamine oxidoreductases genes compared to MOB (Kikuchi et al., 2023). Moreover, Pseudomondales IMCC2047 lacks the haoB subunit, the signature catalytic subunit of Hao in AOBs (Kikuchi et al., 2023). Still, some MOB like M. capsulatus Bath also harbor Hao homologs haoA and haoB subunits together (Poret-Peterson et al., 2008).These contrasting AOB and MOB genetic signatures all together highlight the atypical nature of Pseudomonadales IMCC2047 (p/a)moCAB gene operon-like and haoA-cycB operon structures and metabolic capabilities.
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