Uncovering the role of chemically dark dissolved organic matter across sediment-water interface along river-to-ocean...

Benthic-pelagic exchange of dissolved organic matter (DOM) plays a critical role in coastal carbon cycling. Yet conventional ultrahigh-resolution mass spectrometry analyses routinely discard a substantial fraction of unassigned mass peaks, termed dark DOM (DDOM), leaving its contribution to carbon exchange unresolved. Here, we characterized the chemical fingerprints and exchange dynamics of DDOM across the sediment-water interface along the Yangtze River Estuary-to-Ocean continuum. Our results reveal that surface sediments act as a large, selective reservoir for DDOM, containing 8542 unique DDOM features compared to 6969 in the water column, of which 2433 were shared between these compartments. These shared, cross-interface DDOM features accounted for approximately 40% of the DDOM signal intensity in the water-column samples, indicating substantial compositional overlap between sediment and water-column DDOM pools. Isotope-association tracking further identifies distinct biogeochemical patterns: terrestrial- linked DDOM extends farther offshore, whereas ¹⁴C-depleted, older-carbon-associated DDOM is preferentially enriched near the mouth of the estuary. Together, these findings demonstrate that DDOM is not analytical noise, but rather a previously underappreciated DOM fraction that provides complementary molecular evidence of connectivity across the sediment-water interface in river-dominated coastal margins.