eDNA Monitoring of Ich in the Klamath River

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

Project IDYUROK-2019-2
Recovery Domains -
Start Date04/01/2020
End Date09/30/2021
Last Edited05/28/2020
1 - 1


Project Description: 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, 2016 and 2018 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, only in 2018 was river water sampled for the presence of ich environmental DNA. The YTFP is currently waiting for those samples to be analyzed.
Ich is a fresh-water ciliated protozoan parasite native to Eurasia, but now found throughout the world. It is believed to be ubiquitous in the Klamath River, however in most sampling years it has been at levels below detection threshold using the techniques described below. Ich infections cause damage to the skin and gills of numerous fish species, including salmonids. Large-scale outbreaks occur in rivers and lakes when there is a combination of suitable environmental conditions and susceptible fish. Suitable river conditions for an ich outbreak are low flows and low turnover rates, congregations of susceptible fish, and presence of the disease organism; 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 parasites 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 molecular analysis of water samples. OSU is in the process of applying their expertise with C. shasta to develop a monitoring program for Ich. The project would involve optimization and validation of a quantitative PCR for detection of waterborne stages of the parasite, then application of this method to investigate the spatial and temporal occurrence of Ich in the lower Klamath River.
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 most important aspect of this project.

Project Benefit    

Project Objective: The objective of this project is to monitor levels of the deadly fish parasite Ichthyophthirius multifiliis (ich) in the lower Klamath River using environmental DNA (eDNA) samples that have been extracted from weekly water collections.

Project Benefit: This project will give researchers and managers an enhanced understanding of the ich lifecycle and how it relates to salmonids. Additionally, information gathered during this project could be used as an early warning to identify possible disease outbreaks and/or fish die offs. 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:$20,531

Project Map


Klamath at Blue    

  • Worksite Identifier: Klamath at Blue
  • Start Date: 06/01/2020
  • End Date: 10/30/2020
Area Description
Sites at Klamath River near Blue Creek

Location Information

  • Basin: Klamath
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: California
  • Recovery Domain:
  • Latitude: 41
  • Longitude: -123


  • Upper Klamath / Trinity Rivers Chinook Salmon ESU
  • Southern Oregon/Northern California Coast Coho Salmon ESU
  • Klamath Mountains Province Steelhead DPS




  • 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