Carbonate aquifer promoting a diverse and carbon-active aquatic habitats in a subtropical river system

Riverine aquatic metabolism is a key component of the global carbon cycle, while the regulatory mechanisms of biological processes and their associated carbon fluxes remain poorly understood across river reach water bodies well connected with carbonate aquifers. This study compared the biogeochemical characteristics of several various aquatic environments in a karst headwater river system, highlighting differences in biological community structure and carbon cycling mechanisms among them. The results showed that in the karst water body of ground or underground, the phytoplankton community totally consisted of 132 species belonging to 7 phyla, while the zooplankton community comprised 22 species from 4 phyla, with species richness markedly lower than that in non-karst rivers, reflecting hydrological instability typical of karst waters. The CO₂ degassing rate ranged from 53.74 to 651.66 mmol/(m²·d). Springs and wetlands lacking plankton regulation exhibited higher CO₂ degassing, whereas reservoirs with abundant plankton and fast-flowing rivers or waterfalls showed lower emissions. Moreover, dissolved inorganic carbon (DIC) was significantly positively correlated with FCO₂, suggesting that carbonate weathering and groundwater inputs elevate DIC concentrations and enhance CO₂ degassing in biologically lower active waters. Conversely, DIC and its fertilization effect drive the composition and metabolic functions of plankton-microbial communities, thereby regulating carbon cycling. Overall, variability in karst geomorphology governs groundwater-surface water (GW-SW) interactions, hydrological regimes, and ecosystem metabolism, ultimately controlling spatial patterns of carbon sources and sinks and influencing regional carbon budget estimates.