240 Chapter 8 Culturing in bioreactor vs. batch When comparing the bioreactor and batch culturing approach, in line with the observations in Chapter 3, we observed that the microbial community complexity was directly linked to low substrate amendments (oligotrophia). While batch cultures remain a good approach for enrichment of processes and enhanced replicability of conditions (Chapters 2 and 7), the environmental relevance of the microorganisms and processes decreases. For instance, in Chapter 7, the in situ sediment “Ca. Methanoperedens” disappeared from the microbial community. Another advantage of batch incubations over non-pressurized bioreactors is the possibility to avoid oxygen leakage derived from non-fully airtight connectors or medium in bioreactor systems. However, bioreactors enable increased biomass and continuous controlled culturing, maintaining a constant steady state in the bioreactor enrichments, with operational times lasting for years (Chapters 4 to 6). Furthermore, some microorganisms with low oxygen requirements are hard to obtain in batch, since frequent oxygen re-adjustments and nitrate limitation need to be ensured, such as for the Methylomonadaceae microaerophilic methanotrophs (Chapter 3). Still, for specific responses such as “Ca. Methanoperedens” morphotype shifts, employing batch systems over bioreactors would likely enhance the measured stress signals since cells remain in the system, as successfully demonstrated in the first “Ca. Methanoperedens” morphotypes description paper (McIlroy et al., 2023). IMPROVED BIOGEOCHEMICAL MODELLING EFFORTS THROUGH TOXICITY THRESHOLDS COUPLED TO FUNCTIONAL MARKER VALIDATION (CHAPTER 2) Biogeochemical models have attempted to model functional marker gene-based reactions and key microbial processes. Some of these models study processes in systems such as the Arabian Sea oxygen minimum zone (OMZ) (Reed et al., 2014), the seasonally anoxic fjord of Saanich Inlet in Vancouver (Louca et al., 2016), and the Öre Estuary in the Bothnian Sea (Lenstra et al., 2023). All these modelling efforts rely on Michaelis-Menten kinetics to model key processes such as the relative contribution of nitrogen and sulfur cycling in OMZ (Reed et al., 2014) or the drivers of methane oxidation (Lenstra et al., 2023) (Figure 1).
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