Atmospheric CO2 absorption and counteraction by CH4 emission across contrasting habitats in a large eutrophic lake

[Display omitted] •Atmospheric CO2 absorption and CH4 emission occurred in 4 habitats in Lake Taihu.•Various seasonal fluctuations in CH4 emissions were found in different habitats.•Highest CO2 absorption & CH4 emission occurred at high-density phytoplankton site.•CH4 emissions counteracted 7–69% of CO2 absorption across four lake habitats.•This large eutrophic lake confirmed to be a total CO2-eq sink. Lakes are a crucial component of global carbon cycling and play a key role in the global CO2 and CH4 budgets. Intensified anthropogenic activity contributes to eutrophication, and reduces macrophytes while increasing phytoplankton in shallow lakes. However, the information on how the CO2 and CH4 fluxes at water–air interface temporally varies across habitats dominated by various primary producers in lakes and how CH4 emission counteracts CO2 adsorption is limited. In this study, in situ fluxes of CO2 and CH4 were measured monthly for one year at four sites in Lake Taihu, China. These sites had contrasting habitats dominated by high-density phytoplankton, low-density phytoplankton, floating-leaved macrophytes, and submerged macrophytes. We found that the CO2 fluxes ranged from − 439 ± 385 to − 106 ± 348μmol m−2h−1 and the CH4 fluxes ranged from 1.96 ± 3.79 to 10.7 ± 14.8μmol m−2h−1. The fluxes of CO2 and CH4 were mainly regulated by water pH, phosphorus levels, and sediment organic carbon. All four habitats acted as sinks of atmospheric CO2 and sources of atmospheric CH4, and the habitats with high-density phytoplankton showed the highest CO2 absorption and strongest CH4 emission. Generally, the CH4 emission counteracted 7–69 % of the atmospheric CO2 absorption in the four sites. These results collectively revealed that in a large, shallow eutrophic lake, habitats dominated by various primary producers consistently adsorb atmospheric CO2, even being counteracted by CH4 emission. These findings provide valuable insights for understanding carbon cycling and CO2 and CH4 dynamics across the water–air interface in shallow lakes.