Evaluating the influence of reef-forming shellfish on nitrogen cycling using a multilevel approach

<p dir="ltr">Reef-forming shellfish such as oysters and mussels can play a crucial role in nitrogen (N) removal from aquatic systems by facilitating nutrient regeneration and denitrification – a microbial process that converts bioavailable N into dinitrogen gas (N₂), which then diffuses into the atmosphere. These organisms harbour denitrifying microbes on their shells and tissues, while also stimulating microbial activities in the surrounding sediments through the release of faeces and pseudofaeces. Yet, there is still a limited understanding about the individual contribution of shellfish and surrounding sediments, as well as their interactions, to support N processes. Additionally, it is unclear how these processes might be influenced by factors such as environmental conditions (e.g. sediment grain size) or other stressors (e.g. increased temperatures) in these habitats. Even though shellfish family lines have been shown to affect associated microbial communities, the effects on shell biofilm function remain unexplored. In this thesis, I have addressed these knowledge gaps using a systematic review and meta-analysis to investigate the impacts of oysters and mussels and their surrounding sediments on N processes across various environmental contexts. I subsequently conducted a large-scale field experiment in oyster reefs at six sites with different environmental conditions to quantify the contributions of oysters, surrounding sediments, and their interactions to N processes. I used both biogeochemical and molecular techniques to estimate biogeochemical fluxes and the microbial genes underlying these processes. Finally, I conducted a laboratory experiment where I applied molecular techniques to investigate the relationships between marine heatwaves and oyster family lines in regulating denitrification in shell biofilms. The review and meta-analysis revealed that shellfish released N₂ and that their presence enhanced nutrient regeneration and denitrification in the surrounding sediments compared to far unvegetated sediments. Denitrification in sediments surrounding shellfish was found to be highest in lagoons, in sandy sediments, and during summer, indicating that environmental context can mediate the effects of shellfish on sediment function. Measurements of biogeochemical fluxes using in-situ incubation chambers, revealed that at siltier sites, denitrification rates from oysters can be higher than from surrounding sediments, but also that interactions between oysters and sediments resulted in lower N removal when compared with oysters. This provides evidence that the contribution of oysters to N removal is dependent on their interactions with sediments and environmental factors. My subsequent gene marker analysis indicated that oyster biofilms have a greater capacity for N removal than microbes in surrounding sediments, although a correlation between gene abundances and respective N fluxes was not established. Finally, results from the laboratory experiment demonstrated the impact of marine heatwaves on denitrification genes in oyster biofilms, but effects were observed only in some family lines, suggesting the importance of oyster genetics in regulating denitrification. Overall, this thesis highlights the crucial role of shellfish in N cycling and denitrification, but rates can vary among shellfish, surrounding sediments and when these two habitats interact, and depend on environmental context and shellfish genetics. Findings provide essential guidelines for shellfish restoration and development of aquaculture farms to facilitate beneficial N cycling in coastal systems.</p>