77 Contrasting methane, sulfide and nitrogen regimes in coastal sediment bioreactors INTRODUCTION By bridging freshwater and seawater bodies, coastal ecosystems are kinetic drivers of microbial carbon, nitrogen, and sulfur cycling (Siefert & Plattner, 2004). Methane is becoming a greenhouse gas of increasing concern in these anthropogenically and climate-change exposed environments (Howarth et al., 2011; Rosentreter et al., 2021; Saunois et al., 2016; Saunois et al., 2020). Methane is produced by methanogenic archaea using a limited number of substrates, whereas the consumption of methane in the sediment is mostly attributed to consortia of sulfate-reducing bacteria and anaerobic methane-oxidizing archaea, or to aerobic methane-oxidizing bacteria (MOB) in the oxygenated sediment layers or water column (Kalyuzhnaya et al., 2019; Venetz et al., 2023; Wallenius et al., 2021; Welte et al., 2016). There is growing evidence that oxidized nitrogen compounds and metalloids could be used as electron acceptors by methanotrophs (Glodowska et al., 2022; He et al., 2019). Still, methane oxidizers share the same niche and compete for electron acceptors in coastal sediments with other microbial guilds such as nitrifiers (oxygen), anaerobic ammonium oxidizers (nitrite) and denitrifiers (NOx), or sulfide oxidizers (oxygen, NOx) (Kuypers et al., 2018; Wu et al., 2021). We currently lack detailed knowledge on how coastal microbial communities could be affected by long-term nutrient loading or salinity increase. Likewise, we do not yet know how the methane-oxidizing communities cope with or adapt to such challenges. Coastal microbiomes, including the methane-oxidizers, are subjected to various stressors, such as deoxygenation leading to high ebullitive methane fluxes (Żygadłowska et al., 2024), eutrophication due to agricultural runoff and human sewage release (Tuholske et al., 2021), sulfide toxicity that is compromising the microbial methane filter (Dalcin Martins et al., 2024, Chapter 2), and salt intrusion leading to Freshwater Salinization Syndrome (Kaushal et al., 2021). Fortune et al. (2024) investigated eutrophication-derived shifts in key nitrogen functional marker genes in tidal systems, and observed a negative correlation between the nitrous oxide reduction gene nosZ involved in denitrification and excess nutrient load, suggesting that microbial marker genes could be used as monitoring tool for the trophic status of the ecosystem (Fortune et al., 2024). Laboratory-scale bioreactor 3
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