Water Parasite Sampling in Lower Trinity River - Hoopa Reservation

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

Monitoring Research
Project IDHOOPA-2022-04
Recovery DomainsN CA - S Oregon
Start Date03/01/2023
End Date09/30/2024
Last Edited05/06/2024
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Objective: Determine density of relevant salmonid parasites in river water samples in the Trinity River and in the vicinity of its confluence with the Klamath River.

Project Description: The Hoopa Valley tribe will collaborate with Oregon State University to quantify C. Shasta spore concentration and Ich trophonts at two locations in the Klamath basin as part of a multi year whole basin project. OSU is seeking other funding for running the samples and these funds will be used to cover staff time and equipment that KBAO will not. The sampling will be conducted weekly from March to September coincident with other Klamath sampling and can be used to inform both the existing FASTA team and TRRP staff about conditions in the lower Trinity and Klamath Rivers. The sampling locations Hoopa will be responsible for are the mainstem Trinity in Hoopa and upstream of the confluence with the South Fork Trinity River.

We will determine the density of several waterborne parasites of salmonids in river water samples to include data collection during spring out-migration and fall in-migration. Weekly, 1L river water samples will be collected every 2 hours for 24 hours by an ISCO automatic sampler and pooled. After 24 hours, 4 1L samples will be taken manually from the 12L pool by Hoopa tribal biologists, and filtered within 24 hours. The concentrated captured material will be sent (FedEx or UPS overnight) to OSU for molecular analysis to determine the total parasite DNA in three of the four samples using qPCR (as per Hallett and Bartholomew 2006, Hallett et al. 2012 for C. shasta or Howell et al. 2019 for Ich); the fourth sample will be archived frozen. All water samples are simultaneously tested for assay inhibition. Water sample analysis will be rolling with updates available biweekly, weekly during salmonid outmigration.

Water collection will occur at the following three sites, weekly, March through September:

1. Hoopa Reservation on Trinity River (THR)

2. Mainstem Trinity upstream of South Fork (TBD; TXX)

The water samples will be tested by molecular assay (qPCR) for: Total Ceratonova shasta, C. shasta coho genotype II.

Project Benefit    

Ceratonova shasta is a parasitic diseases found in the Klamath Basin that affect salmon and steelhead. C. shasta can have an enormous negative impact on juvenile salmonid survival. For over a decade there has been consistent monitoring for C. shasta in the mid and upper reaches of the mainstem Klamath but there is only one monitoring site downstream of the confluence with the Trinity River. C. shasta was not detected in the Trinity the last time an investigation was conducted about 10 years ago however, given the low water conditions, lack of geomorphic flows, and observed changes in algae in both the Trinity and lower Klamath, it would be prudent to ensure that is still the case. There were fish with clinical signs of C. shasta caught in the lower Trinity this year but the cause of the abdominal swelling was not confirmed.


Metric Completed Originally
Research and Monitoring
  Stream Miles Monitored 28.70

Funding Details

Report Total:$25,424

Project Map


Lower Trinity River    

  • Worksite Identifier: Lower Trinity River
  • Start Date: 03/01/2023
  • End Date: 12/01/2023
Area Description
Trinity River between Burnt Ranch and Weitchpec.

Location Information

  • Basin: Klamath (180102)
  • Subbasin: Trinity (18010211)
  • Watershed: Horse Linto Creek-Trinity River (1801021112)
  • Subwatershed: Campbell Creek-Trinity River (180102111206)
  • State: California
  • Recovery Domain: N CA - S Oregon
  • Latitude: 41.0493
  • Longitude: -123.67089


  • 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.1 MonitoringY (Y/N)
      •      . . . . E.1.a Monitoring funding
      •      . . . . E.1.b.1 Stream Miles Monitored
      •      . . . . E.1.c.3 Biological instream monitoring (other than salmon)Y (Y/N)
        •      . . . . . . E.1.c.3.a # miles (to nearest 0.01 mile) monitored for Biological indicies (other than salmon)
        •      . . . . E.1.d
          Name Of Comprehensive Monitoring Strategy/Program
      •      . . 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