eDNA Monitoring of Ich in the Klamath River 2019

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

Project IDYUROK-2018-4
Recovery DomainsN CA - S Oregon
Start Date04/01/2019
End Date09/30/2020
Last Edited04/16/2020
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Following the lower Klamath River fish kill event of 2002, the Yurok Tribal Fisheries Program (YTFP) began monitoring in September 2003 for the prevalence of Ichthyophthirius multifiliis (ich) in fall-run Chinook salmon (Oncorhynchus tshawytscha) in the lower Klamath River as well as an associated organism Flavobacterium columnare that causes the disease columnaris. In 2014, 2015, and 2016 ich made a reappearance in the Klamath River. These outbreaks were closely monitored and documented by the YTFP using fish sampling techniques, however due to technological restraints, river water was not sampled for the presence of ich environmental DNA.

The YTFP proposes to collect water samples from 3 locations on the lower Klamath River. These sites will be selected based on their proximity to past ich outbreaks and ease of accessibility. Sampling would occur from May through October with water samples collected on a weekly basis using an automated water sampling machine (isco). Once collected, water samples will be taken back to our laboratory to be filtered and the filtrate will be frozen and shipped to OSU for analysis. We would 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. Ideally, longitudinal sampling would take place before, during, and after any potential outbreak of ich. This sampling strategy assists researchers in identifying any “hot spots” and possible sources of disease epizootics.

Currently, the YTFP ich monitoring program is through direct, lethal sampling of fish which can insensitive to early or light infections. Sentinel fish exposures are not possible during periods of high water temperature typically associated with Ich outbreaks. Water sampling for ich eDNA will provide valuable insight and compliment any ongoing ich studies and can be utilized as an early warning for disease outbreaks. This is the the most important aspects of this project. Working with OSU, the YTFP has the ability to relay specific real time information to water managers regarding the levels of Ich in the Klamath River. This tangible result can be invaluable when dealing with disease issues on the lower Klamath River.

Project Benefit    

Outcomes & Benefits

• This project will give researchers and managers an enhanced understanding of the ich lifecycle and how it relates to salmonids.
• Information gathered during this project could be used as an early warning to identify possible disease outbreaks.
• This project will also provide data so that management actions (primarily water management related to the operation of the federally owned Klamath Irrigation Project and the Trinity Division of the Central Valley Project) can be improved with respect to their effect on anadromous fish in general, and particularly with respect to ESA-listed SONCC coho salmon and Chinook salmon important to the Yurok Tribe’s subsistence and commercial fisheries.


Metric Completed Originally

Funding Details

Report Total:$30,000

Project Map


Klamath near Blue Creek    

  • Worksite Identifier: Klamath near Blue Creek
  • Start Date: 04/01/2019
  • End Date: 09/30/2020
Area Description

No Area Description data was found for this worksite.

Location Information

  • Basin: Klamath
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: California
  • Recovery Domain: N CA - S Oregon
  • Latitude: 41.42926750579577
  • Longitude: -123.93173217773159


  • Upper Klamath / Trinity Rivers Chinook Salmon ESU
  • Southern Oregon / Northern California Coastal Chinook Salmon ESU
  • Southern Oregon/Northern California Coast Coho Salmon ESU
  • Northern California Steelhead DPS
  • Un-Named ESU Chinook




  • 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
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
    •      . . E.0.e.1 Number of reports prepared
    •      . . 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