123 Unraveling nitrogen, sulfur and carbon microbial bioreactor responses to stress (T4), transcripts for 161 genes were detected, including norC and phsA but not sqr or norB, while by the end of the experiment (T5), still transcripts for 130 genes were found (Supplementary Table 2). Interestingly, in MAG 39 Nitrobium versatile, several other functional genes were transcribed at low levels: membrane-bound and periplasmic nitrate reductase genes (narGHI and napA), ammonium-forming cytochrome c552-nitrite reductase (nrfA), and anaerobic dimethyl sulfoxide reductase (dmsABC). Although previously identified (Arshad et al., 2017), napB and nirBD were absent in the genome, and nrfH was present in the genome but no transcription was detected. All genes encoding subunits of electron transport chain proteins were transcribed (Figure 4). Two genes encoding complexes with homology caa3-type low affinity cytochrome c oxidase proteins in Acidobacteria were identified: (i) ctaCFED, which was followed by a downstream sco assembly protein-encoding gene and a cytochrome c6 (homologous to petJ, K08906), which we have putatively denominated ctaX, for it could be part of the complex, and (ii) sco followed by a downstream ctaDEFC. All these subunits were transcribed, except for ctaF of the latter complex. A Rieske bc1 complex was encoded by petBCD, which was preceded by a cytochrome c protein-encoding gene immediately upstream. Two other copies of petBC were present in the genome. All these subunits were transcribed except for the first petB (Supplementary Table 4). Finally, the MAG 39 Nitrobium versatile had two ammonium transporter-encoding genes (amtB-type), of which only the second was transcribed, solely in T0 (Supplementary Table 4). The gammaproteobacterial MAG 65 Thiohalobacteraceae, representing an organism that seemed enriched over the sulfide and NO toxicity experiment (Figure 3), was estimated to be a 98.1% complete genome with 0.3% contamination (Figure 2). Based on metatranscriptomic analyses, we infer that the most likely metabolism performed by this organism was sulfide oxidation coupled to denitrification (Figure 4). A sulfide:quinone oxidoreductase-encoding sqr gene was among the functional genes with highest transcription by the end of the sulfide and NO toxicity experiment (T5; TPM = 0.43 ± 0.36; Supplementary Table 2, Supplementary Table 4). Also highly transcribed were the genes dsrA (TPM = 1.07 ± 0.78), dsrB (TPM = 0.95 ± 0.5), dsrC (TPM = 4.3 ± 1.1), as well as additional dsrABC copies. Sulfite 4
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