Tracing The Journey of Dissolved Organic Matter: From Leaf Litter Photodegradation to Microbial Processing in Tropical Streams

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, and controlled experimental approaches to investigate how oxidative pathways influence the molecular composition, lability, and persistence of DOM from source to downstream environments. Across tropical headwater streams in the Río Tempisquito watershed of Costa Rica, DOM composition reflects the interplay between seasonal litter inputs, rainfall-driven transport, and in-stream oxidation processes. Molecular signatures reveal that reduced, bioavailable compounds introduced during dry-season litterfall and wet-season runoff undergo measurable oxidative modification even when bulk carbon concentrations remain relatively constant. Controlled microbial experiments demonstrate that lipid- and protein-like molecules are rapidly consumed and transformed into more oxidized metabolites, some of which persist as newly formed components of the downstream DOM pool. Complementary photochemical analyses of leaf litter leachates show that exposure to simulated solar irradiation produces extensive structural rearrangement and oxygenation, yielding thousands of new molecular formulas and contributing to the generation of partially recalcitrant compounds prior to their entry into stream systems. Overall, these findings establish that oxidative pathways, rather than simply degrading organic matter, also produce recalcitrant molecular structures that enhance the persistence of terrestrial carbon in aquatic networks. By identifying the molecular features that govern DOM oxidation, persistence, and downstream transport, this dissertation advances understanding of carbon processing in tropical watersheds and highlights the importance of early-stage oxidative transformations in shaping the fate of terrestrial organic matter within the global carbon cycle.