Organic matter and greenhouse gas dynamics across contrasting hydrological states in intermittent rivers.

As intermittent rivers expand globally, understanding how contrasting hydrological conditions relate to organic matter (OM) characteristics and greenhouse gas (GHG) dynamics is important. We investigated CO₂ and N₂O dynamics across contrasting low-flow (LF) and high-flow (HF) campaigns in intermittent rivers. Pore-water GHG concentrations consistently exceeded those in overlying water, suggesting an important internal GHG pool. During the LF campaign, higher chlorophyll-a concentrations coincided with lower overlying-water CO₂ concentrations, whereas the HF campaign showed greater soil-OM contribution, higher DOC, a stronger humic-like/aromatic DOM signature, and higher dissolved CO₂. Multivariate RDA explained substantial joint CO₂-N₂O variation (adjusted R² = 0.720 in LF and 0.668 in HF); nutrients retained large unique fractions in both campaigns, while the OM-associated fraction was larger in HF. Metagenomic profiles linked pore-water CO₂ to multiple carbon-processing and respiratory functions. Pore-water N₂O was less clearly associated with broad microbial-community turnover but showed stronger relationships with substrate balance and denitrification-related functional composition. Higher N₂O coincided with lower WDOC/NO₃⁻-N; CLR-based analyses further showed significant associations between N₂O and denitrification-related gene profiles, with the relative representation of nosZ versus nirK/nirS decreasing as N₂O increased. These patterns were consistent with greater incomplete-denitrification potential under relatively low carbon availability. Across three thin boundary layer (TBL) model parameterizations, estimated CO₂ emissions were consistently higher in the HF campaign, whereas the direction of the N₂O flux contrast varied among models. These findings highlight distinct environmental and microbial associations of CO₂ and N₂O across contrasting hydrological states in intermittent rivers.