Life cycle of Ceratonova shastaCeratonova shasta is a freshwater, myxozoan parasite that is native to the Pacific North West of North America. It causes enteronecrosis in juvenile salmonids and is associated with population-level impacts in the Klamath River. Transmission occurs through waterborne stages: actinospores released from polychaete worms infect salmonid fishes and develop into myxospores which then infect polychaetes (see life cycle on right). The parasite proliferates in each host.

In response to the high prevalence and severity of C. shasta-infection in Klamath salmonids, we developed a parasite monitoring program to track the spatial and temporal abundance of C. shasta. The three main approaches are based on the parasite's life cycle and include sentinel fish exposures, polychaete host sampling and molecular quantification of parasite DNA in water samples. These are described in more detail below. Monitoring occurs at established index sites which are shown on the following map.



Klamath River Index Sites with site abbreviations and river kilometers (Rkm).

Iron Gate Dam (Rkm 306) blocks
anadromous salmonid migration.






 Sentinel Fish Exposures

Sentinel fish cages
in the Klamath River
out- of-basin
rainbow trout
Barth Monitoring fish cages Barth Monitoring trout fry

In sentinel fish exposures, fish highly susceptible to the parasite (out-of-basin rainbow trout) are placed in cages alongside fish of interest such as in-basin Chinook and coho salmon at index sites along the river for a three day exposure. All fishes are transported to OSU's John L Fryer Aquatic Animal Health Lab and monitored for infection (~ 60 days). Severity of infection (percent morbidity and mean days to morbidity) are recorded through visual observations and molecular assay (PCR).

The first fish exposure for 2018 is scheduled for: April 19 - 22 at Beaver Creek (KBC) and Seiad Valley (KSV).



DATA UPDATES: summaries of sentinel fish exposures are as follows:  April    May     June   September.



Water Samples

Barth Monitoring filtering
 Barth Monitoring filter paper

 Filtering a water sample
using a vacuum pump

 Folding the filter paper
with captured material

To detect and quantify waterborne stages of C. shasta, river water samples are collected at five mainstem index sites; once a week all year round at two sites (KBC and KSV) and once per week from April through October at three other sites.  Solar-powered automatic samplers (ISCOs) collect 1L water every 2 hours for 24 hours, from which 4 1L samples are manually taken. Each 1L sample is filtered through a nitrocellulose membrane using a vacuum pump, and any captured DNA in 3 of the replicate samples is extracted using a kit. A quantitative PCR (qPCR) specific for C. shasta is used to detect and quantify any parasite DNA present. Cq values generated by the qPCR are converted to numbers of parasite spores per liter of water using reference samples with known quantities of spores. The Karuk and Yurok tribal biologists are integral to the collection and filtration of the ISCO water samples. Water samples are also taken in conjunction with the sentinel fish exposures; manual 'grab' samples are collected on the first and last day of the exposure.

2018 DATA UPDATES: Expedited processing of water samples occurs April through June. Only trace amounts (<1spore/L) of Ceratonova shasta-DNA have been detected in 2018. 

 Density of waterborne Ceratonova shasta in the Klamath River
Density (spores per liter) of Ceratonova shasta in water samples collected at the mainstem longterm index site, near Beaver Creek (KBC), in 2018 (blue data points) compared to 2017 (shaded).


 Density of waterborne Ceratonova shasta in the Klamath River

Density (spores per liter) of Ceratonova shasta in water samples collected at the mainstem index sites in 2018. Note that KMN is sampled only during salmonid outmigration, KBC and KSV year round and remaining sites March through October. KBC = near Beaver Creek, KSV = Seiad Valley, KI5 = near I5 bridge, KTC = Tully Creek, KMN = Kinsman Fish Trap, KOR = Orleans. 



Genotyping: There are multiple genetic types or genotypes of C. shasta simultaneously present in the Klamath River. These differentially disease the various salmonid species. For example, type I causes mortality in Chinook salmon whereas type II can be fatal for coho salmon. Type 0 is found in sympatric Oncorhynchus mykiss (steelhead and redband rainbow trout).

Therefore, we also genotype each water sample using a qPCR that amplifies the variable ITS1 region and then we sequence that amplicon. From the sequencing chromatogram, we can determine the proportion of each genotype present in a sample. We use the total spore density to then determine the number of spores of each genotype in a sample. 


Only samples with 1 spore or greater per liter are genotyped. 


 Polychaete Sampling

many polychaetes in tubes in left photo compared to few worms 5 years later in right hand side image 

diver taking photo of polychaete population on boulder

Comparison of 2012 and 2017 polychaete populations
Scientific diver taking photos at one of the few locations that polychaetes were observed in 2017

To monitor abundance and prevalence of infection in the invertebrate host of C. shasta, polychaete samples are collected annually at seven sites in the Klamath River spanning a discharge gradient. Sites are located in the upper basin downstream from Keno dam, 3 sites are located in the middle basin downstream from Iron Gate Dam, and 2 sites are located in the lower basin downstream from the Scott and Salmon Rivers. Samples are collected once each in fall, winter, spring, and summer, and more frequently if flooding or pulse flow events are scheduled to occur. Samples are processed to determine density, simple demographics, and prevalence of C. shasta infection.


 DATA UPDATES: Polychaete samples were collected March 17, 2018 from all sites except Orleans (flows too high). 

One week after the high flow event of April 6th, opportunistic sampling occurred. We measured the following water temperatures in the field (YSI probe) at the following sites on the Klamath Mainstem during polychaete sampling:

Keno (near gun club)-9.5, JB Boyle bypass-9.0, I5 bridge- 9.0, Tree of Heaven 8.5, Beaver Creek (Fisher’s RV park) 8.6, Seiad Valley 6.8













Bureau of Reclamation Report for 2008

Bureau of Reclamation Report for 2009 

Bureau of Reclamation Report for 2010

Bureau of Reclamation Report for 2011

Bureau of Reclamation Report for 2012

Bureau of Reclamation Report for 2013

Bureau of Reclamation Report for 2014

Bureau of Reclamation Report for 2015

Bureau of Reclamation Report for 2016


 'Tully Creek' Longitudinal Water Sampling

Parasite levels at our lowermost index site, Tully Creek (at ~60 Rkm), have increased over the past several years to surpass those detected at previously high sites, such as Beaver Creek (KBC). To investigate the extent of the high parasite densities at the Tully Creek site, we sampled water downstrea m (beginning at the lowermost road-accessible location, ~38.4Rkm) and upstream of the index site at Orleans (~90Rkm). Link to report.


Data shared here are preliminary and subject to modification.

Page photo credits: S Atkinson, S Hallett & J Alexander

Monitoring Studies are Primarily Supported by the Bureau of Reclamation.