Our research investigates how pathogens affect the health and performance of aquatic organisms, with particular emphasis on fish species of conservation concern. By combining molecular approaches, pathogen detection, and physiological assessments, we examine the consequences of infection and how environmental conditions influence disease dynamics. Our goal is to better understand the role of pathogens in aquatic ecosystems and provide scientific knowledge to support fish health, conservation, and management.
Pathogens & Fish Health
We combine molecular pathogen screening with physiological assessments to investigate the potential consequences of infection for fish species of conservation concern.
Selected Research Findings
Delta Smelt — Pathogen Detection & Surveillance: Our collaborative research evaluated molecular methods for detecting pathogens in cultured and wild Delta Smelt. The findings highlighted the potential of molecular screening as an early warning tool for pathogen surveillance, supporting disease management and conservation supplementation programs (Gille et al., 2022).
Chinook Salmon — Pathogen Exposure & Physiological Responses: We investigated pathogen exposure and physiological responses in juvenile Chinook Salmon deployed in the Sacramento River. Field-exposed fish were detected with two myxozoan parasites and exhibited reduced body mass, depleted liver glycogen reserves, and altered expression of immune- and stress-related genes. However, acute thermal and hypoxia tolerance remained unaffected. These findings highlight the importance of integrating molecular and physiological endpoints when evaluating fish health (Mauduit et al., 2022).
Mucosal Defenses & Experimental Infection
Fish mucus provides an important first line of defense against pathogens and environmental stressors. Our research investigates how pesticide exposure and bacterial infections may interact to affect mucosal defenses and fish health. Through experimental exposures, we examine changes in gill condition, mucus secretion, microbial communities, metabolic rate, growth, and survival. In collaboration with Dr. Soto at UC Davis, we conducted preliminary experiments exposing salmon to the insecticide bifenthrin followed by a bacterial challenge with Flavobacterium columnare, exploring potential interactions between chemical exposure and pathogen susceptibility.
Here Salmon were preliminary exposed to an insecticide (Bifenthrin) followed by an bacterial challenge using Flavobacterieum columnare in the Aquatic Pathology Lab at the Center for Aquatic Biology and Aquaculture (CABA) (collaboration with Dr. Soto).
Disease Ecology & Conservation
Understanding how environmental conditions influence pathogen occurrence and infection risk is important for managing fish populations of conservation concern. Our research combines field-based monitoring, molecular pathogen detection, and environmental assessments to investigate patterns of infection and their implications for conservation and management.
Winter-Run Chinook Salmon Reintroduction — McCloud River: As part of a collaborative project with academic, agency, and Tribal partners, we investigated pathogen occurrence and infection status in winter-run Chinook Salmon during their reintroduction to the McCloud River. By examining environmental factors associated with infection, this research aims to improve our understanding of disease risks and support monitoring and management strategies for salmon reintroduction programs.
Emmy and Louise collect samples from Chinook Salmon involved in a behavioral study near the McCloud River. The behavioral study was conducted by Leanne Pearl in the Fangue Lab, while samples collected by the Segarra Lab were used for pathogen screening.
Pathogen Surveillance in Migrating Adult Chinook Salmon: In collaboration with Dr. Miles Daniels at NOAA Fisheries and UC Santa Cruz, we investigate pathogen exposure in adult Chinook Salmon before they enter freshwater to begin their spawning migration. Using gill samples collected from ocean-caught adult Chinook Salmon, we screen for 47 bacterial, viral, and parasitic pathogen targets using high-throughput quantitative PCR (Fluidigm). This research contributes to a broader understanding of pathogen occurrence and its potential relationships with environmental conditions and the energetic demands of salmon migration, with implications for fisheries conservation and management.
Segarra Lab members processing samples for molecular pathogen screening.
Fluidigm microfluidic array used for high-throughput pathogen screening.
Molecular Mechanisms of Host–Pathogen Interactions
Our earlier research investigated the molecular mechanisms of host–pathogen interactions and immune defenses in marine bivalves. In Pacific oysters (Crassostrea gigas), we examined ostreid herpesvirus 1 (OsHV-1) replication, host gene expression, and differences in disease susceptibility (Segarra et al., 2014; Segarra et al., 2014). Complementary research focused on mucosal immunity and microbial homeostasis in oysters (C. gigas and C. virginica) and hard clams (Mercenaria mercenaria), using proteomic and metagenomic approaches in collaboration with the Marine Animal Disease Laboratory at Stony Brook University.
C. virginica prior a bacterial injection in the adductor muscle using recombinant Vibrio parahaemolyticus, pathogen for human.
GFP and RFP recombinant Vibrio parahaemolyticus incubated at 37C