134 Chapter 4 experiment (Figure 5). Future studies should further evaluate lateral transfer of nor genes in Methanoperedenaceae, which seem prone to acquire novel metabolic traits via later gene transfer events (Leu et al., 2020b), potentially via recently described Borgs (Al-Shayeb et al., 2021), as well as metabolic flexibility of “Ca. Methanoperedens nitroreducens” under methane deprivation. Hypothetical genes in “Ca. Methanoperedens nitroreducens” identified in this study with high transcription and upregulation in response to stresses could be targets for these future investigations. Sulfide oxidizers had differential resilience to the stresses investigated in this study, dynamically changing in abundance and transcriptional activity across regular and experimental conditions. However, sulfide was completely removed at all time points, likely due to functional redundancy in the microbial community, indicating that sulfide oxidation could also be a relatively stable community function under the investigated stresses. Finally, in our study, denitrification was a dominant nitrogen-cycling pathway, as previously suggested in coastal sediments of the Bothnian Sea (Rasigraf et al., 2019) - particularly, the nitric oxide reduction step, as indicated by norB TPM values (Supplementary Table 2). Anammox activity, as indicated by hzsA TPM values, also had a significant contribution to nitrogen cycling, and dominated at the end of the sulfide and nitric oxide stress experiment (T5). This community function was highly impacted by ammonium deprivation, but was restored when favorable conditions were reestablished. On the other hand, DNRA, as indicated by nrfA TPM values, was a minor nitrogen-cycling pathway, but under ammonium deprivation it became more significant. Future studies should investigate whether anammox and DNRA similarly oscillate in coastal ecosystems under the stresses investigated in this study. In conclusion, this study contributes to the elucidation of metabolic pathways for carbon, sulfur and nitrogen cycling in a bioreactor community mimicking anoxic, brackish coastal sediment conditions, as well as shifts in microbial abundance and transcriptional activity in response to prolonged substrate deprivation and exposure to toxic compounds. Together with follow-up studies, these results will help understanding complex microbial interactions and functions in dynamic
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