Using environmental DNA metabarcoding to investigate diversity and seasonal variation of fishes in Humboldt Bay, California

Author

Johnathon M. Richardson, Cal Poly HumboldtFollow

Graduation Date

Fall 2025

Document Type

Thesis

Program

Master of Science degree with a major in Natural Resources, option Fisheries

Committee Chair Name

Andrew P. Kinziger

Committee Chair Affiliation

Cal Poly Humboldt Faculty or Staff

Second Committee Member Name

Andre Buchheister

Second Committee Member Affiliation

Cal Poly Humboldt Faculty or Staff

Third Committee Member Name

Jose Marin Jarrin

Third Committee Member Affiliation

Cal Poly Humboldt Faculty or Staff

Keywords

Environmental DNA, eDNA metabarcoding, MiFish 12S, Fish biodiversity, Estuarine fish assemblages, Humboldt Bay, California current, Species richness, Seasonal variation, Community composition, PCR amplification bias, Template masking, Bioinformatics pipeline, Noninvasive monitoring, Estuarine ecology

Subject Categories

Fisheries

Abstract

This study applied environmental DNA (eDNA) metabarcoding to characterize fish diversity and temporal patterns in fish assemblage structure within Humboldt Bay, California. This work advances ecological understanding of Humboldt Bay’s ichthyofauna, regional natural history and ecosystem function. Over one year (February 2023–January 2024), triplicate surface-water samples were collected every two weeks from a fixed site in Humboldt Bay (n = 78). DNA was extracted from filters and amplified using MiFish 12S primers in six replicate PCRs per sample. Amplicon concentrations were normalized, pooled and sequenced on an Illumina MiSeq platform (2×150 bp). Sequences were processed using a custom bioinformatics pipeline, and taxonomic assignments were made using a curated regional 12S reference database. After filtering to a validated list, a total of 97 marine fish species were detected using eDNA metabarcoding, exceeding the diversity reported in four conventional fish surveys conducted between 1960 and 2021, which identified 47–67 ray-finned fishes using traditional methods in Humboldt Bay. Notably, 35 eDNA-detected species were absent from all conventional surveys. Relative to the Guide to California Coastal Marine Fishes of California, which lists 262 species likely to occur in Humboldt Bay, 90 overlapped with the eDNA detections, and seven were unique to the eDNA dataset; the remaining 172 species likely reflect the guide’s accumulation of historical records. Seasonal patterns in species richness showed an ~10% increase in winter and an ~10% decrease in summer relative to fall (generalized Poisson model), contrasting with conventional surveys that often report higher summer richness. Community composition also varied strongly by season; PERMANOVA attributed 28% of among-date variation to season. Collectively, these results indicate that eDNA metabarcoding provides robust biodiversity inventories and resolves seasonal turnover in estuarine fish communities, offering a cost-effective, non-invasive complement to traditional surveys.

Citation Style

APA

Recommended Citation

Richardson, Johnathon M., "Using environmental DNA metabarcoding to investigate diversity and seasonal variation of fishes in Humboldt Bay, California" (2025). Cal Poly Humboldt theses and projects. 2533.
https://digitalcommons.humboldt.edu/etd/2533