Ceratonova Shasta Monitoring Studies in the Klamath River

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
 
 Susceptible
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).

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

The second fish exposure for 2018 occurred: May 21 - 24 at all index sites.

The third sentinel fish exposure occurred June (18 - 21) at all index sites.

The final exposure occurred September (14-17) at Beaver Creek (KBC) and Seiad Valley (KSV).

 

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 (<1 spore/L) of Ceratonova shasta-DNA were detected in 2018 until April 23 when an average of 1 spore per liter was detected at Beaver Creek (KBC).

April 30 - Ceratonova shasta-DNA was detected at all index sites (except KTC, not received) at levels of >1 - < 5 spores/L.

May 7 - Ceratonova shasta-DNA was detected at all index sites at levels of <1 - <5 spores/L; lower than the preceding week and prior to the implementation of the emergency dilution flow on May 8.

May 14 - Ceratonova shasta-DNA was detected at all index sites at levels of <1 - <5 spores/L. This sampling occurred during the 3000 cfs dilution flow event.

May 21 - Ceratonova shasta-DNA was detected at all index sites analysed at levels of <2 spores/L. This sampling occurred during the dilution flow event (final day of 3000cfs/first day of the ramp down).

May 29 (1 day later due to Memorial Day) - Ceratonova shasta-DNA was detected at all index sites analysed at levels of <3 spores/L. This sampling occurred during the dilution flow event (final day of the ramp down to 1175cfs).

June 4 - Ceratonova shasta-DNA was detected at all index sites analysed. Levels were <1 spore/L at all sites except KI5 which was <2 spores/L.

June 11 - Ceratonova shasta-DNA levels at all index sites remain below 5 spores/L. The highest density was measured at KBC which was 3.8 spores/L.

June 18 - Ceratonova shasta-DNA levels in the lower basin were below 5 spores/L. The highest density, 4.8 spores/L, was measured at KBC.

Through July 2 - Ceratonova shasta-DNA levels remained below 5 spores/L at all sites tested.

July 9 - Ceratonova shasta-DNA levels were low (less than 5 spores/L) in the lower basin. The highest density, 2.4 spores/L, was measured at KBC.

July 16 - 1 spore/L or less of C. shasta was detected at index sites in the lower basin.

Aug 6 - fewer than 5 spores/L were detected at any site; the most, 3.1 spores/L, was detected at KBC.

Aug 13 - fewer than 5 spores/L were detected at any site; the most, 1.1 spores/L, was detected at KBC.

August 27 - Ceratonova shasta-DNA levels were less than 1 spores/L in the lower basin; no Cs-DNA was detected at KSV.

September 24 - Ceratonova shasta-DNA levels in the lower basin this week exceded 5 spores/L. Average density at KBC and KOR were the highest detected at any lower river site in 2018.

October 01 - Ceratonova shasta-DNA was detected at all lower river index sites but at lower densities than the previous week; the highest was 3.9 spores/L at KOR.

October 15 - Ceratonova shasta-DNA was detected at all lower river index sites at low densities; the highest was 2 spores/L at KTC.

October 22 - Ceratonova shasta-DNA was detected at three lower river index sites (KI5, KBC & KSV) at <1 - 1 spore/L.

October 29 - Ceratonova shasta-DNA was detected at all four lower river index sites tested at <1 - 2 spores/L.

November 05 - From November through March, water sampling occurs only at KBC and KSV. Less than 1 spore/L of Ceratonova shasta-DNA was detected this week.

November 13 - Average density of Ceratonova shasta-DNA at KBC was 4 spores/L and at KSV <1 spore/L.

 

 

 

 Density of waterborne Ceratonova shasta in the Klamath River upstream of Beaver Creek index site
Density (average spores per liter) of Ceratonova shasta in 24-hour composite 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 at all index sites

Density (average spores per liter) of Ceratonova shasta in 24-hour composite 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 April through October. KBC = near Beaver Creek, KSV = Seiad Valley, KI5 = near I5 bridge, KTC = Tully Creek, KMN = Kinsman Fish Trap, KOR = Orleans. 

 

 Density of waterborne Ceratonova shasta in the Klamath River

Density (average spores per liter) of Ceratonova shasta in 24-hour composite water samples collected at the mainstem index sites Beaver Creek (KBC) and Orleans (KOR) in 2018. 

 

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. 

2018 DATA UPDATES:

April 30: samples from 5 index sites were genotyped. Genotype I was dominant. Genotype 0 was detected at 3 sites and genotype II at only one site, KMN at <1 spore/L.

May 7: samples from 4 index sites were genotyped. Genotype I was dominant at all sites. Type 0 was also detected at all 4 sites. Type II was detected at one site only, KI5, and at <1 spore/L.

 

 Polychaete Sampling

Polychaete sampling

 

Polychaete sampling

Manayunkia tubes from the image on right A high density assemblage sample at TOH

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 in March from all sites except Orleans (flows too high). One week after the high flow event of April 6th, opportunistic sampling occurred at all sites except Orleans and observed a reduction in abundance at Seiad Valley and Beaver Creek. Most notably, infected polychaetes were detected in March samples (all sites), but not in April samples. Samples were collected in late May, mid-July and the final sampling for 2018 will occur Oct 12-14. Density and infection prevalence assays are in progress for these samples.

Polychaete model validation (collaboration with the AFWO) occurred on schedule in July 2018. Density assays are in progress. (photos attached are from 2018 model validation).

 

Polychaete sampling

Model validation sampling

Dr. Alexander collecting a Hess sample at Beaver Creek on SCUBA Field crew 2018 - Ryan Bernstein and Sylvia Gwozdz (USFWS Arcadata office), Robert Predosa (OSU scientific diver volunteer) pictured at Community Center

 

 ANNUAL REPORTS

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

Bureau of Reclamation Report for 2017

B

 '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.