This dataset supports a manuscript focused on the effects of Tubifex spp. on CH4 and CO2 emissions in three sediments. All raw and processed data, including CH4 and CO2 emissions, sediment bubble volumes, imaging outputs, microbial abundances, and physicochemical analysis, are included. Detailed protocols, custom image annotation scripts (ImageJ), and metadata for each measurement are available in the repository.

Freshwater ecosystems are major natural sources of methane (CH4) and carbon dioxide (CO2), with large amounts of these gases being produced in sediments. Bioturbators such as Tubifex spp. have been proposed to alter the dynamics of both gases as they inhabit the sediment-water interface, where they can mobilize oxygen (O2) and nutrients, thereby shifting microbial communities. Tubifex are also known to tolerate eutrophication that generally leads to strong shifts in the benthic community, yet their role in modulating greenhouse gas emissions requires further elucidation. We used 24 mesocosms to assess the presence of Tubifex spp. on diffusive and ebullitive CH4 and CO2 emissions across three eutrophic sediments: one with clay (C) and two with peat, differing in low and high organic matter content (P- lom and P-hom, respectively). The effects of Tubifex on carbon emissions varied and were modulated by sediment properties. Tubifex reduced diffusive CH4 emissions in P-hom, thereby decreasing 25% of the mean diffusive CH4 emissions. In sediment C, mean ebullitive CH4 emissions were 31% lower compared to the non-Tubifex treatment. Conversely, in P-lom Tubifex spp. increased diffusive mean CH4 and CO2 emissions with 88% and 98% respectively. Tubifex presence exhibited a significant negative effect on ebullitive CH4 and diffusive CO₂ emissions, and altered the maximum sediment bioturbation depth, but we did not find bioturbation to alter O2 levels or the abundance of methanogens and methanotrophs in the sediment. Our findings highlight that although sediment-dependent, the influence of Tubifex spp. on carbon emissions is substantial. Furthermore, more context-dependent insights are needed to incorporate their presence when predicting GHG emissions from aquatic systems.