Biography

Background

I undertook a Ph.D. at the University of Queensland, Brisbane, Australia, with Professor Bob Lester and Peter O'Donoghue on "Myxozoan Parasites of Oligochaetes and Fish". I was then awarded an Alexander von Humboldt Research Fellowship to study with Professor Mansour El-Matbouli at the University of Munich, Germany for two years still focusing on myxozoan parasites. Then I procured a post-doc position with Dr Jerri Bartholomew at Oregon State University, USA, in 2003 where I have been studying myxozoan parasites of the Pacific Northwest.

Courses

• Designed and instruct: MB 480 General Parasitology Ecampus
• Contributed lectures and labs: MB 491/591 Diseases of Fish in Aquaculture and Conservation Biology, and the Salmonid Workshop

Research

I find parasites fascinating organisms and have always been drawn to the aquatic environment. Thus, I am interested in parasites of marine and freshwater fish. Most of my research has focused on one phylum - the Myxozoa and I've never dissected a fish without encountering at least one of these microscopic, spore-forming, endoparasitic metazoans. Over 2000 are found in fish world-wide and most do not harm their host, but there are several that cause serious diseases (Ceratonova shasta, Parvicapsula minibicornis, Myxobolus cerebralis) in the Pacific Northwest of North America. My current research focuses on answering questions about these parasites so that we can make informed management decisions and reduce their impact on native fishes.

Specific Interests

• Discovery and description of novel species
• Taxonomy (morphological & molecular characterization)
• Nomenclature (accurate and unambiguous identification and naming of organisms)
• Discovering life cycles
• Molecular diagnoses and development of detection assays
• Enumeration of waterborne stages
• Ecosystem impacts
• Adaptive management and disease mitigation

Current projects

Klamath River Fish Health Studies: Salmon Disease Monitoring and Research

Funded by: U.S. Bureau of Reclamation; began 2019
Personnel: Jerri Bartholomew, Julie Alexander, Rich Holt, Ryan Craig, Stephen Atkinson, Kristin Kasschau, Denise de Silva, Ruth Milston-Clements, Auden Heitzler, Elliott Cameron (MS student)Hayden Krause (MS student)

We are involved in a long term monitoring and research project that includes sentinel fish studies, annelid sampling and water sampling to describe the distribution and abundance of harmful fish pathogens in the Klamath River (OR/CA). The data we collect informs model development and real time adaptive management to mitigate fish disease in this system. This collaborative effort involves colleagues from the Karuk, Yurok and Hoopa tribes and the USFWS Arcata office.

For more information about this project and our latest data, please visit our monitoring page.

These efforts have contributed to a collaborative review published in Frontiers: Deconstructing dams and disease: predictions for salmon disease risk following Klamath River dam removals

Salmon disease risk in the Klamath River’s hydroelectric project reach, prior to dam removal

Funded by: PacifiCorp; Began: 2021
Personnel: Julie Alexander, Ryan Craig, Stephen Atkinson, Elliott Cameron (MS student), Hayden Krause (MS student), ODFW, CDFW

The freshwater parasites, Ceratonova shasta and Parvicapsula minibicornis can cause disease in salmonids downstream of the dams in the Klamath River. Less is known about these parasites in the hydroelectric reach, the region between the dams, and raises the question of how the project reach and proximal river sections will change following dam removal in 2024. This collaborative project with ODFW and CDFW fish biologists will quantify waterborne parasite densities to document parasite spatial and temporal distribution and to conduct invertebrate host (annelid) studies to document host density and infection in the hydroelectric project reaches.

Detecting and Genetically Verifying Key Aquaculture Viruses Autonomously and Continuously

Funded by: USDA NIFA-SBIR; Began: 2022
Personnel: Jerri Bartholomew, Melissa White (ODFW), Nilanjana Das (MS student)

Viral pathogens can cause disease in wild and cultured fish populations. We are partnering with ODFW fish health specialists and Nucleic Sensing Systems (NS2) to advance the use of a continuous, onsite eDNA detector to include viral RNA, such as IHNV, to provide actionable information in real-time without human intervention.

Laboratory validation of real-time polymerase chain reaction (qPCR) analysis for Myxobolus cerebralis

Funded by: Great Lakes Fishery Commission; Began: 2022
Personnel: Stephen Atkinson

We are working with members of the American Fisheries Society-Fish Health Section, led by Wade Cavendar (Utah) to test the sensitivity and specificity of published qPCR assays to recommend an approach for researchers and fish health professionals.

Emergence of Proliferative Kidney Disease in Salmonids at Oregon Hatcheries

Funded by: Oregon State University Ag Experiment Station Animal Health and Disease Research Program
Personnel: Stephen Atkinson, Nilanjana Das (MS student), Sarah Bjork (ODFW), Aimee Reed (ODFW)

Monitoring and Modeling Pathogen Exposure in Salmon Migrating to the Delta

Funded by: CDFW Proposition 1 Delta Water Quality & Ecosystem Restoration Grant program, Delta Stewardship Council, and U.S. Bureau of Reclamation; began 2019
Personnel: Stephen Atkinson, Kristin Kasschau, Denise Silva

This collaborative effort led by Miles Daniels (NOAA & UCSC), and involving UC Davis aims to characterize the distribution and abundance of fish pathogens in Central Valley Chinook salmon during their outmigration through the Sacramento and Feather Rivers. The approach includes sentinel fish exposures, river water collection and molecular analyses.

Education

Ph.D. at the University of Queensland, Brisbane, Australia

Research areas