127 Unraveling nitrogen, sulfur and carbon microbial bioreactor responses to stress were upregulated, likely to compensate for the ammonium limitation (Figure 5). “Ca. Methanoperedens nitroreducens” accounted for 97.6% of nrfA transcription and 48.2% of amtB transcription 10 weeks after ammonium was completely removed from the medium (T2). Other taxa that shared a large proportion of amtB transcription in T2 were “Ca. Methylomirabilis tolerans” (14.5%), “Ca. Methylomirabilis lanthanidiphila” (9.6%), and “Ca. Kuenenia stuttgartiensis” (3.2%). The hzsA gene of “Ca. Kuenenia stuttgartiensis” had at least 20x higher transcription than hzsA of “Ca. Scalindua rubra” across all time points, although “Ca. Scalindua rubra” had higher genome coverage before experiments were conducted (Figure 3). Finally, minor changes included the upregulation of the periplasmic nitrate reductase napA, nirB, soeA and quinone-thiosulfate dehydrogenase doxD genes. 4
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