eDNA Monitoring of Ich in the Klamath River - Yurok

Salmonid Research, Monitoring, and Evaluation (RM&E)

Project IDYUROK-2022-02
Recovery DomainsN CA - S Oregon
Start Date06/01/2023
End Date09/30/2024
Last Edited05/02/2024
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Project Objective: This project will monitor levels of the fish parasite Ichthyophthirius multifiliis (ich) in the lower Klamath River using environmental DNA (eDNA) in water samples.

Project Description: Following the lower Klamath River fish kill event of 2002, the Yurok Tribal Fisheries Department (YTFD) began monitoring for the prevalence of Ichthyophthirius multifiliis (ich – the primary disease that caused the 2002 fish kill) in fall-run Chinook salmon (Oncorhynchus tshawytscha) in the Lower Klamath River. In 2014, 2015, 2016, 2018 and 2019 ich made a reappearance in the Klamath River. These outbreaks were closely monitored and documented by the YTFD using fish sampling techniques, however due to technological restraints, only in 2018 and 2019 was river water sampled for the presence of ich eDNA.

Ich is a fresh-water ciliated protozoan parasite native to Eurasia, but now found throughout the world. Suitable river conditions for an ich outbreak are low flows and low turnover rates, and congregations of susceptible fish; ich outbreaks may worsen if water temperatures are elevated. Fish become especially susceptible when they are stressed and in high densities.

Researchers at Oregon State University (OSU) have recently developed protocols that allow them to accurately identify and quantify ich eDNA from a given water sample using genetic analysis tools. OSU has done extensive research with a myxozoan parasite of salmonids, Ceratonova shasta. Both C. shasta and Ich have waterborne infectious stages that can be directly quantified through genetic analysis of water samples. OSU is currently applying their expertise with C. shasta to develop a monitoring program for Ich using eDNA from water samples.

The YTFP proposes to collect weekly water samples from 3 locations on the lower Klamath River from May through October using an automated water sampling machine (isco). Once collected, water samples will be taken back to our laboratory to be filtered, frozen, and shipped to OSU for analysis. We will also conduct 2-3 longitudinal sampling events. These events would take place over the course of a single day with multiple sampling locations spread out over the entire lower Klamath River. This sampling strategy assists researchers in identifying any “hot spots” and possible sources of disease epizootics.

Water sampling for ich eDNA will compliment ongoing ich studies and can be utilized as an early warning for disease outbreaks. Working with OSU, we will be able to provide real-time information to water managers regarding the levels of Ich in the Klamath River, providing quantified estimates of ich presence prior to making decisions regarding augmented flows.

Project Benefit    

Information gathered during this project will be used as an early warning to identify possible disease outbreaks and/or fish die offs; such information can be used to inform water managers whether augmented flows are necessary in the late summer/fall to minimize disease risk.


Metric Completed Originally

Funding Details

No Funding data has been entered for this project.

Project Map


klamath river near blue creek    

  • Worksite Identifier: klamath river near blue creek
  • Start Date: 06/01/2023
  • End Date: 11/01/2023
Area Description
klamath river near blue creek

Location Information

  • Basin: Klamath (180102)
  • Subbasin: Lower Klamath (18010209)
  • Watershed: Tectah Creek-Klamath River (1801020910)
  • Subwatershed: Ah Pah Creek-Klamath River (180102091007)
  • State: California
  • Recovery Domain: N CA - S Oregon
  • Latitude: 41.42588415273181
  • Longitude: -123.92984495670132


  • Southern Oregon / Northern California Coastal Chinook Salmon ESU
  • Southern Oregon/Northern California Coast Coho Salmon ESU
  • Upper Klamath / Trinity Rivers Chinook Salmon ESU




  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding .00
    •      . . E.0.b
      Complement habitat restoration project
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
    •      . . E.0.d.1 Number of Cooperating Organizations 1
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
      Oregon State University
    •      . . E.0.e.1 Number of reports prepared 0
    •      . . E.0.e.2
      Name Of Report
    •      . . E.2 ResearchY (Y/N)
      •      . . . . E.2.a Research Funding
      •      . . . . E.2.b.7 Investigating fish health and/or disease/parasitesY (Y/N)
        •      . . . . . . E.2.b.7.a
          Key issues addressed by fish health and/or disease/parasites research