Thesis Defence // Emma Mari

Small artificial waterbodies, such as fishponds, are increasingly recognized as biogeochemical hotspots with disproportionate contributions to greenhouse gas (GHG) emissions relative to their size (Downing 2010; Holgerson & Raymond 2016). Yet their functioning remains overlooked compared to natural lakes for instance, and their role in regional carbon budgets is still poorly constrained (Raymond et al. 2013; DelSontro et al. 2018). This is particularly true for small artificial waterbodies, such as managed pondscapes, where human practices strongly modify hydrology, sediment dynamics, and nutrient inputs. This thesis focuses on the Dombes region (eastern France), one of largest and oldest aquaculture landscapes in Europe, presenting more than one thousand shallow ponds managed through millennia-old fish-farming practices and periodic drying. The objective here is to emphasize GHG fluxes in small artificial waterbodies and their controlling factors ; and how these practices influence CO₂ and CH₄ production, oxidation, and emission throughout the pond hydrological cycle. Using field measurements, laboratory analyses and gas flux monitoring, the first research chapter shows that during the flooded phase (évolage), fish-farming practices (especially feeding, fertilizing and liming) modify sediment and water chemistry, thereby influencing CO₂ and CH₄ concentrations. CO₂ dynamics were strongly linked to dissolved oxygen and pH, while CH₄ patterns reflected complexity linked to shallow depths, consistent with previous findings in small eutrophic systems. The second chapter explores the fate of CH₄ produced in fishponds and how aquaculture practices and pond ecology regulate its oxidation, emission pathways, and incorporation into the food web, using stable carbon isotopes. Stable carbon isotope analysis of dissolved CH₄ has shown that the majority of CH₄ in most fishponds has been oxidized, driven by both oxygen and phosphorus availability. In contrast to chironomids and zooplankton, showing minimal assimilation of CH4-derived carbon, gastropods exhibited strongly depleted δ¹³C values, indicating significant reliance on CH₄-derived biofilms. This demonstrated that CH₄-derived carbon enters the food web primarily through macrophyte-associated periphytic pathways, rather than through sediment or pelagic consumers. These results contrast with patterns observed in some small natural lakes and suggest that in fishponds, most sediment-produced CH₄ bypasses benthic and pelagic food webs, while oxidation occurs predominantly in microhabitats such as the oxic water column or macrophyte surfaces. The third chapter investigates the drying phase (assec), an understudied component of temporary systems. Exposed sediments acted as strong CO₂ sources, with fluxes driven mainly by soil temperature and moisture, while CH₄ emissions were close to zero under oxic conditions. Emissions during the drying period appeared to be comparable to those of the flooded phase, suggesting the importance of intermittency. A fourth explanatory chapter shows the importance of rewetting ponds in carbon fluxes dynamics and carbon cycle.

Overall, this thesis demonstrates that small artificial waterbodies such as fishponds are dynamic but strongly management-influenced sources of GHGs. Their carbon emissions are influenced by hydrological phase and sediment processes, while CH₄ cycling is characterized by spatially variable oxidation but minimal trophic integration. These findings highlight the need to integrate small artificial ponds into regional and global GHG inventories and to consider pond management as a lever for climate mitigation.