129 Unraveling nitrogen, sulfur and carbon microbial bioreactor responses to stress norB (average TPM = 5.22) TPM values were similarly low. “Ca. Methylomirabilis tolerans” accounted for 43% of norB transcription at T5, which included NOD-1 (18%), NOD-2 (19%), and qNOR (6%)-encoding genes, followed by “Ca. Methanoperedens nitroreducens” (21%, with the qNOR-encoding gene accounting for 13% and cNOR-encoding gene for 8%), “Ca. Methylomirabilis lanthanidiphila” (10%) and MAG 65 Thiohalobacteraceae (9.6%). The transcription of several other genes encoding proteins involved in denitrification (narG, napA, nirS, and nirB) was downregulated. However, nirK had a 12-fold increase in transcription, and nosZ had a minor increase. Methane oxidation marker genes were downregulated, as indicated by a 19-fold decrease in mcrA transcription and 21-fold decrease in pmoA transcription. Transcription of the anammox marker gene hzsA decreased 2.7 fold. RT-qPCR of mcrA, pmoA, and hzsA confirmed these trends (Supplementary table 3). Carbon fixation via CODH/ACS was downregulated, but CO2 fixation via ribulosebisphosphate carboxylase-oxygenase was upregulated. DISCUSSION In this study, we conducted metagenomic and metatranscriptomic analyses in order to unravel metabolic pathways, microbial dynamics, and responses to stresses in a bioreactor community mimicking anoxic, brackish coastal sediment conditions. Microbial interactions and resiliency were tested by removal and addition of key substrates. Removal of ammonium from the medium had major effects on microbial activity and community structure: “Ca. Methanoperedens nitroreducens” dominated DNRA activity (Figure 5), and, after ammonium was reintroduced in the medium, became the most abundant community member (Figure 3). “Ca. Kuenenia stuttgartiensis” replaced “Ca. Scalindua rubra” as the most abundant anammox bacterium, several sulfide oxidizers replaced “Ca. Nitrobium versatile”, and “Ca. Methylomirabilis tolerans” dominated over “Ca. Methylomirabilis lanthanidiphila” (Figure 3 and 5). These results suggest strong microbial cooperation between “Ca. Methanoperedens nitroreducens” and “Ca. Methylomirabilis” species for the exchange of nitrite under the abundance of methane. Before the ammonium removal experiment, TPM values indicate that “Ca. Methanoperedens nitroreducens” reduced nitrate to nitrite, which was reduced to nitric oxide mostly by “Ca. Methylomirabilis lanthanidiphila”. Nitric oxide was 4
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