UC San Diego

Dissolved organic matter (DOM) sustains microbial activity and structures ecological interactions. The composition of DOM, in terms of quality and quantity, shapes microbial communities, subsequently affecting global biogeochemical cycles. Beyond contributing nutrient, organic molecules can also function as communication signals and, in certain scenarios, engage in chemical warfare. Therefore, a molecular-level study of DOM is necessary for a more thorough understanding of its role in aquatic environments. However, DOM exists as a very complex mixture in seawater, and its individual components' concentrations are extremely small relative to salts. This complicates the analysis of DOM and as a result, the true chemical diversity within DOM has remained elusive. To address this, innovative analytical and data processing techniques are essential. Chapter 2 introduces the analytical framework developed in this thesis. By employing untargeted metabolomics—specifically, liquid chromatography paired with high-resolution tandem mass spectrometry—and utilizing cutting-edge cheminformatic tools, I was able to illuminate the chemical dark matter of DOM. Using molecular networking and in silico annotation tools, I assigned molecular formulas and predicted structures and compound class affiliations for thousands of chemical features, representing most detectable compounds. I then used this established methodological workflow to explore the role of DOM in ecosystems vulnerable to global change, such as harmful algal blooms, coral reefs, and oxygen-deficient zones. Toxin-producing marine microalgae, Pseudo-nitzschia sp. thrive in upwelling coastal ecosystems, and their harmful blooms are increasing in frequency and intensity in the face of ecosystem changes due to global warming and eutrophication. In Chapter 3, I showed that these algae have species-specific microbiomes that appear to be interacting with unique metabolites, particularly compounds containing diverse nitrogen functional groups. This research provides an in-depth cataloging of chemical classes in algal culture, enhancing our understanding of microbial interactions. Oxygen-deficient zones (ODZs) occur naturally in coastal upwelling regions, but studies suggest they may expand due to climate change. In Chapter 4, I examined DOM in the ODZ of the Eastern Tropical North Pacific. I used specific compounds to trace organic matter inputs to the ODZ and highlighted potential reasons for DOM accumulation in these low-oxygen waters. The results suggest selective preservation of DOM, which could lead to carbon sequestration, altering the local carbon cycle. Coral reefs are among the world's most impacted ecosystems, threatened by global warming, ocean acidification, and pollution. In Chapter 5, I investigated the dynamics of DOM, which is critical to coral reefs' health, productivity, and function. Using a Lagrangian sampling approach and following the biogeochemical changes in water flowing over a rapidly flushed reef in Mo'orea, French Polynesia, I was able to provide new insights into nutrient recycling, metabolite production by benthic primary producers, and DOM removal processes over the reef. Together, the chapters of this dissertation establish a robust methodological foundation for molecular-level DOM analysis. By applying this approach to specific environments, I demonstrated the profound impact of DOM on ecosystems vulnerable to global change, underscoring its broader implications for marine biogeochemistry in a changing world.