Dissertation Defense: Ashton Bandy

Title: DNA-based marine monitoring reveals carbonate-chemistry-linked zooplankton taxa and depth-region microbial functional states across the California Current Ecosystem

Abstract: Climate-driven change and human pressures are rapidly altering coastal upwelling ecosystems through shifts in carbonate chemistry, nutrient supply, oxygen availability, and food-web structure, yet biological monitoring often struggles to scale from organism condition to community-level impacts. A key unresolved question is whether DNA-based approaches can provide sensitive, transferable indicators of these stressors across diverse taxa and highly dynamic oceanographic gradients. Here, I integrate two omics approaches, metabarcoding of mesozooplankton communities and metagenomics of water-column microbes, to evaluate indicator potential, identify candidate targets, and clarify how spatiotemporal gradients structure coastal biological responses. In the Southern California Bight, mitochondrial cytochrome c oxidase subunit 1 metabarcoding of mesozooplankton (>200 µm) across 20 nearshore locations and four seasons revealed communities dominated by copepods and krill and structured primarily by season, while a subset of taxa tracked carbonate chemistry variability, including Cheilostomatida and the copepods Clausocalanus furcatus and Oncaea scottodicarloi at high aragonite saturation state and Calanus pacificus and Euphausia pacifica at low aragonite saturation state. Routine ocean acidification targets were not uniformly informative in this region; pteropods were rare and detected only in winter, whereas larval stages of benthic calcifiers were more ubiquitous and relatively abundant, supporting alternative candidate indicators for regional monitoring. Across the California Current coastal corridor, analysis of 432 metagenomes collected during five spring surveys recovered functional variation dominated by depth with a secondary regional gradient aligned with the Point Conception transition. Linear mixed-effects enrichment resolved four depth-region community states composed of recurring modules that included organic carbon acquisition, phosphorus, iron, and nitrogen scavenging and recycling, redox and energy metabolism, and particle or surface association. These results show that DNA-based tools can refine ocean acidification biomonitoring toward taxa that are consistently present and tightly linked to carbonate chemistry, while also resolving microbial functional structure relevant to nutrient and redox dynamics. At the same time, this work clarifies practical interpretation needs. Metabarcoding primarily captures presence and relative signal and can be constrained by primer choice and reference database completeness, whereas metagenomic inference requires careful normalization and analysis to separate dominant spatial structure from subtler stress-relevant patterns. Overall, this dissertation provides a scalable framework for mapping coastal “stress landscapes” using DNA-based approaches, prioritizing candidate indicator taxa and gene sets for validation, and supporting evidence-based monitoring and management in dynamic current systems.