105 Unraveling nitrogen, sulfur and carbon microbial bioreactor responses to stress INTRODUCTION Microorganisms drive and link the biogeochemical cycles of carbon, nitrogen and sulfur by a variety of redox reactions (Madsen, 2011). Anthropogenic nutrient inputs from land into the ocean constitute a major impact on marine ecosystems, altering seawater and sediment biogeochemistry and leading to increased primary production that can result in toxic algal blooms and oxygen depletion (Wallenius et al., 2021). Such impacts, combined with ocean warming and consequent seawater stratification and deoxygenation, can further stimulate the production of methane and nitrous oxide, potent greenhouse gases, as well as sulfide and nitric oxide, toxic products of sulfate reduction and denitrification (Van Helmond et al., 2019; Malone and Newton, 2020; Wells et al., 2020; Wallenius et al., 2021). In coastal sediments, ammonium and nitrate can be introduced via agricultural runoff, while sulfide, nitrogen oxides, methane, and ammonium are generated in situ via sulfate reduction, partial denitrification, methanogenesis, and organic matter decomposition, respectively (Egger et al., 2018). Therefore, characterizing microbial communities, interactions and reactions performed by microorganisms that couple methane, nitrogen and sulfur cycling is fundamental for understanding biogeochemical cycling and linked greenhouse gas emissions in dynamic coastal ecosystems impacted by anthropogenic activity. Modeling efforts suggest links between future environmental changes, biogeochemical cycles and ecosystem functions (Treseder et al., 2012; Nazaries et al., 2013). However, given that most microorganisms are widespread and functionally redundant, they are frequently treated as a “black box” in models - preventing the effective modeling of their reactions and responses. Additionally, recent efforts with laboratory cultures and engineered systems have provided insights about impacts of substrate availability changes on environmentally and economically relevant microbial communities (Chen et al., 2017; Saad et al., 2017; Caffrey et al., 2019; Delgado Vela et al., 2021; Deng et al., 2021; Nie et al., 2021). Yet, few studies have examined microbial community responses to prolonged periods of substrate scarcity or environmental stresses in controlled systems (Bürgmann et al., 2011; Shade et al., 2012). However, these are highly relevant disturbances in coastal ecosystems, where, for instance, nitrogen limitation is a major control 4
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