Molecular footprint and pathways of DOM biotransformation in the Yangtze River

The biodegradation of dissolved organic matter (DOM) regulates riverine carbon dioxide emissions, yet the specific molecular biotransformation pathways driving dissolved organic carbon (DOC) degradation kinetics remain poorly constrained. Using incubation experiments coupled with FT-ICR MS in the Yangtze River, we show that biodegradation reshapes DOM via a mass-difference-based molecular network dominated by oxidation (26.4%) and carboxylic acid reactions (20.9%), yielding smaller, highly oxidized, and heteroatom-depleted products. These pathways exhibit distinct compositional selectivity, as the specific types of carbon-removal pathways differ significantly between the upstream and downstream of the Three Gorges Dam (TGD) while noncarbon-removal pathways remain spatially consistent. Crucially, hierarchical partitioning identifies mass-derived reactions of carboxylic acids and de-alkyl groups as the primary kinetic drivers, independently explaining 55.45% and 6.36% of the variance in DOC decay rates, respectively, while oxidation primarily serves as a preparatory phase enhancing precursor bioavailability. Spatially, the TGD acts as a biogeochemical boundary, with upstream carbon-removal pathways effectively fueled by agricultural inputs and elevated nutrient levels, whereas downstream noncarbon-removal pathways were predominantly driven by urbanization and autochthonous production. This study elucidates the distinct roles of specific biotransformation pathways in governing DOM decomposition kinetics in regulated large river ecosystems.