124 Chapter 4 oxidation to sulfate could proceed via proteins encoded by sorA, soeABC (quinonesulfite dehydrogenase), as well as aprAB and sat, which were all transcribed. Sulfur oxidation system soxBAZYX genes for thiosulfate oxidation and a thiocyanate dehydrogenase tcdh gene were transcribed, indicating that these substrates could also be oxidized, although they were not provided to the reactor. No soxCD gene was identified in the genome. A cytochrome cd1-nitrite reductase nirS gene was highly transcribed (TPM = 1.74 ± 0.78), along with all other genes in the denitrification pathway, including a nirK gene encoding a copper-containing nitrite reductase. Ribulose-bisphosphate carboxylase cbbSL genes were among the most highly transcribed in the genome, and all genes encoding subunits of the electron transport chain were transcribed. MAG 36 (Methanoperedens nitroreducens) was 99.4% complete with 4.6% contamination, and had all genes in the reverse methanogenesis pathway (Figure 4, Supplementary Table 4) as well as potential for carbon fixation via the Wood– Ljungdahl pathway with carbon monoxide dehydrogenase/ acetyl-CoA synthase (CODH/ACS)-encoding genes and acetate production or assimilation via an acetylCoA synthetase-encoding acs gene. All these genes were transcribed by the end of the sulfide and NO toxicity experiment (T5), as well as electron transport chainencoding genes (Figure 4). The succinate dehydrogenase sdhC subunit was not present in the genome. Remarkably, the genome had genes encoding two copies of the membrane-bound nitrate reductase (narGHI), an ammonium-forming nitrite reductase (nrfAH), a non-electrogenic cytochrome c-oxidizing (cNOR) nitric oxide reductase (norBC), and an electrogenic quinone-oxidizing (qNOR) nitric oxide reductase (norZ). Methyl-coenzyme M reductase genes mcrBDGA had TPM values around ~ 200-400 before the sulfide and NO toxicity experiment (T4), and ~ 20-40 after (T5, Supplementary Table 2), indicating that, although “Ca. Methanoperedens nitroreducens” was still abundant by the end of the experiment (Figure 3), it suffered a degree of inhibition. Three hypothetical genes had highest transcription at T5 and were upregulated relative to T4 (Supplementary Table 2). A second key methane oxidizer was represented by MAG 38 (“Ca. Methylomirabilis tolerans”), 94.5% complete with 2% contamination. This genome had all genes for carbon fixation via the Calvin cycle and for the methane oxidation via particulate
RkJQdWJsaXNoZXIy MTk4NDMw