Date

Summer 2025

Document Type

Master's Thesis (Open Access)

Degree Name

Master of Science (M.S.)

Department

Moss Landing Marine Laboratories

Abstract

This thesis investigates the fine-scale dynamics of the Monterey Bay upwelling shadow front by integrating autonomous underwater vehicle (AUV) observations with environmental DNA (eDNA) analysis. Using a clustering technique on temperature-salinity profiles from 29 missions, I identified distinct water masses that consistently reflected seasonal and spatial hydrographic structure. Phytoplankton communities, resolved via eDNA and robust Aitchison Principal Component Analysis (PCA), exhibited clear seasonal transitions-from diatom-dominated assemblages during peak upwelling to dinoflagellate-enriched communities in warm, stratified shadow waters in the fall. Case studies during sustained upwelling revealed front-associated differences in community composition, supported by ordination and statistical testing. Notably, t-tests comparing taxonomic correlation matrices show significant divergence in internal community structure between water masses, with transitional clusters exhibiting distinct co-occurrence patterns. These findings underscore the tight coupling between ecological structure and hydro graphic gradients, and highlight the value of integrating physical clustering with eDNA to inform real-time ecosystem monitoring and Harmful Algal Bloom (HAB) forecasting. This work advances our understanding of upwelling systems and contributes to the development of scalable, high-resolution tools for coastal ocean management.

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