Date of Award

Fall 8-31-2025

Document Type

Thesis: Open Access

Degree Name

MS Marine Science

Department

Environmental and Ocean Sciences

Committee Chair

Nathalie B. Reyns, Ph.D.

Committee Member

Jeffrey Crooks, Ph.D.

Committee Member

Janet Walker, Ph.D.

Abstract

Fish communities are essential to estuarine health, playing key roles in food webs, nutrient cycling, and ecosystem functioning. However, the persistence of native fish populations is increasingly threatened by the cumulative impacts of coastal development, pollution, and climate change. Rapid, effective monitoring of species distributions is a priority, enabling timely conservation and management. However, the study of any ecosystem is limited by time, resources, and the consideration that research of a system can damage the ecosystem under study.

This research aimed to characterize fish species richness and evaluate the benefits and limitations of different estuary monitoring approaches. Specifically, this study compared traditional methods (block net seining, enclosure traps) with contemporary approaches (community science (iNaturalist) and eDNA metabarcoding) to assess species richness and composition in 2023 across five San Diego estuaries: Tijuana River Estuary, San Diego Bay (Sweetwater Marsh, South Bay Salt Ponds), Mission Bay (Kendall-Frost Marsh), Los Peñasquitos Lagoon, and San Dieguito Lagoon. Additionally, long-term traditional sampling data from 2013 to 2023 at Tijuana River Estuary and San Dieguito Lagoon were compared alongside abiotic variables, including salinity, temperature, and dissolved oxygen.

In 2023, iNaturalist reported the highest species richness at most sites, except Los Peñasquitos and San Dieguito Lagoon, where traditional sampling and eDNA, respectively, yielded more detections. Species richness was lowest at Tijuana River Estuary, consistent with evidence of degraded water quality. Despite strict adherence to sampling protocols, only 10 of 89 eDNA samples yielded sufficient sequence reads, likely due to filter clogging and PCR inhibition caused by high organic content. These findings underscore the value of integrating multiple monitoring approaches, highlight the potential of community science to enhance species inventories, and emphasize the need for improved eDNA protocols tailored to the unique challenges of Southern California estuaries.

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