13 Summary concentrations. Here, we defined the Gammaproteobacteria as the most dominant and fluctuating group. The nitrogen reduction processes differed between the two systems: the oligotrophic bioreactor stimulated Dissimilatory Nitrate Reduction to Ammonium (DNRA) whereas denitrification dominated the eutrophic bioreactor. Methanotrophs in the oligotrophic systems (including biofilm growth) consisted of a diverse yet poorly described Methylomonadaceae genus Methylovulum and subgroup KS41 that competed for nitrate with the main driver of DNRA, “Ca. Methanoperedens BLZ2” spp. Moreover, the oligotrophic system selected for the novel MAGs Pseudomonadales IMCC2047 and Rugosibacter with divergent Membranebound MonoOxygenase (CuMMOs) with potential for short alkane degradation. The eutrophic systems selected for better described Methylomonadaceae Methylomonas and Methylobacter species. This investigation highlighted the metabolic versatility of microaerophilic methanotrophs from the family Methylomonadaceae to cope with sulfide, low oxygen, and with potential for denitrification. In Chapter 4, we investigated the flexibility of a stable anoxic co-culture of sulfide oxidizing denitrifiers, anaerobic ammonium-oxidizing (anammox) bacteria, and nitrate/nitrite-dependent anaerobic oxidation of methane (N-DAMO) partners to cope with nitrogen deprivation, and sulfide and nitric oxide stress, mimicking dynamic changes that occur in brackish coastal sediment conditions as described in Chapter 3. Ammonium removal resulted in the disappearance of “Ca. Nitrobium versatile” and anammox bacteria from the initial co-culture. DNRA activity, mainly promoted by “Ca. Methanoperedens”, was unable to sustain anammox activity. Upon ammonium re-introduction, “Ca. Methylomirabilis lanthanidiphila” was replaced by “Ca. Methylomirabilis tolerans” and anammox “Ca. Scalindua rubra” with “Ca. Kuenenia stuttgartienses”. Sulfide and nitric oxide stressors enriched for Thiohalobacteraceae as sulfide oxidizing denitrifiers, and sulfide:quinone oxidoreductase expression was elevated. This research helps to gain insights on the complex microbial community dynamics that can occur coastal ecosystems or engineered ecosystems like wastewater treatment plants. In Chapter 5, we investigated the stress response to sulfide in freshwater anaerobic methanotrophs. We observed a decrease in nitrate-dependent methane oxidation activity after 0.5 mM sulfide exposure to “Ca. Methanoperedens BLZ2” both after
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