Comparison of carbon budgets and greenhouse gas fluxes in monoculture ponds with milkfish (Chanos chanos) and Taiwanese hard clams (Meretrix taiwanica)

Aquaculture plays a vital role in meeting the growing demand for aquatic food. However, research on carbon fluxes in aquaculture ponds remains limited. This study constructed carbon budgets and determined greenhouse gas (GHG) emissions from monoculture ponds of Taiwanese hard clams ( Meretrix taiwanica ) and milkfish ( Chanos chanos ). Phytoplankton production constituted the major carbon input pathways in the clam (72–85 %) and fish (41–48 %) ponds. However, respiration offset most of the carbon, which turned the fish ponds into heterotrophic systems that emitted an average of 0.21 g C m −2 d −1 . In contrast, the clam ponds remained autotrophic systems, functioning as a carbon sink with an average uptake of 0.06 g C m −2 d −1 , even when accounting for the CO 2 release by biocalcification. The accumulated sediment significantly contributed to the carbon output pathways in the ponds, accounting for 62–77 % of those in the clam ponds and 23–52 % of those in the fish ponds. An unaccounted pathway of carbon input likely contributed to sediment accumulation in the clam ponds caused by the filter-feeding behavior of clams, which induces resuspension or the production of pseudofeces. On the other hand, feed input mainly contributed to sediment accumulation in the fish pond. Methane flux, biocalcification, water exchange, and rainwater accounted for relatively small portions of both carbon budgets. Based on the 100-year global warming potential (GWP 100 ), the GHG emissions during the culture period were 0.46 ± 0.75 g CO 2 e m −2 d −1 in the clam ponds and 1.15 ± 1.15 g CO 2 e m −2 d −1 in the fish ponds. Methane fluxes contribute relatively little to the overall GHG emissions from both ponds, while nitrous oxide fluxes can alter the fish ponds into a greater GHG source. • Fish ponds were heterotrophic systems that emitted an average of 0.21 g C m −2 d −1 . • Clam ponds function as a carbon sink with an average uptake of 0.06 g C m −2 d −1 . • Biocalcification offsets only 4 % of the CO 2 uptake through photosynthesis. • Methane contributes relatively little to the overall GHG emissions from both ponds. • Nitrous oxide could transform the fish ponds into a more significant GHG source.