Abstract
<jats:p>Shallow freshwater ecosystems are significant sources of greenhouse gases, particularly methane, yet the role of bioturbators organisms in shaping these emissions remains poorly understood. This thesis investigates how bioturbators (including rooted macrophytes and benthic animals) influence methane storage, transport, and emissions in shallow freshwater ecosystems through physical and biogeochemical modifications of sediments. Using laboratory and mesocosm experiments combined with a systematic literature review, the thesis shows that rooted macrophytes reduce sediment methane bubble storage through root oxygenation and plant-mediated gas transport, as quantified using a novel cost-effective scanning method. Benthic invertebrates such as Tubifex spp. altered methane and carbon dioxide emissions in a direction and magnitude that depended on sediment organic matter content, while the invasive red swamp crayfish increased CH₄ emissions 2.7-fold by removing macrophytes and disturbing sediments. The overarching finding is that bioturbator effects on greenhouse gas emissions are strongly context-dependent, shaped by the interaction between organism functional traits, bioturbation intensity, and sediment properties. These results highlight the need to explicitly account for bioturbators in freshwater greenhouse gas budgets and ecosystem management strategies.</jats:p>