Fish Pathogen Monitoring Studies
Fish Pathogen Monitoring Studies
The life cycle of Ceratonova shasta and abiotic and biotic factors that influence the different stages. Published in: Bartholomew JL, Alexander JD, Hallett SL, Alama-Bermejo G, Atkinson SD (2022). Ceratonova shasta: a cnidarian parasite of annelids and salmonids. Parasitology 149, 1862–1875. https://doi.org/10.1017/S0031182022001275
Ceratonova 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 annelids infect salmonid fishes and develop into myxospores which then infect annelids (see life cycle, above). 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, annelid 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.
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.
Sentinel fish exposures
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).
Juvenile fish being placed in a sentinel cage which is then submerged in the Klamath River
2025 data updates
The first sentinel fish exposure occurred May 8-11th at four sites: KBC in the lower basin, and Keno Eddy, Williamson River and Wood River in the upper basin. Out-of-basin rainbow trout were exposed at all four sites and Spring Chinook reared at Klamath Hatchery were exposed at the upper basin sites (in Oregon); there are insufficient Fall Creek Hatchery Fall Chinook available this year.
Their current status can be found at this link.
A second sentinel fish exposure occurred June 5-8th, 2025. Sites included: WDC, WMR, and KED in the upper basin and KI5, KBC, KSV and KOR in the lower basin.
The 60-day post exposure monitoring period in the laboratory has passed and all fish are being assessed for infection status.
The final sentinel fish exposure for 2025 is planned for November to coincide with yearling hatchery releases and their outmigration.
Water samples
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 (see photos below). 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 (see images on right). 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 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. Data are presented as the average spores per liter of three replicate 1 liter water samples collected at each site and time.
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. This is done in two ways. For genotyping type II only, we use a qPCR that amplifies the variable ITS1 region specific to that genotype. Whereas, to determine the overall genotype composition of a sample, we amplify the variable ITS1 region common to all genotypes in a PCR and then 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.
Genotyping commences once we detect greater than 1 spore per liter.
Filtering a water sample using a vacuum pump (left). Folding the filter paper with captured material (right).
2025 data updates
Klamath water sampling and C. shasta spore monitoring is still in its winter phase, with weekly water samples being collected from only two index sites: KBC and KSV. Turbidity levels continue to be much higher than the historic background, so less water can be filtered in every sample (typically < 0.5 L instead of 1 L). As we have seen with previous years, no C. shasta has been detected yet at either KBC or KSV, in the 8 weeks collecting since the New Year.
Klamath water sampling and C. shasta spore monitoring has begun its peak season routine, with weekly water samples being collected at 6 index sites: KSH, KBC, KMN, KSV, KOR (from 03/03) and KTC (from 03/10).
Turbidity levels continue to be much higher than the historic background, so less water can be filtered in every sample (typically < 0.3 L instead of 1 L).
As we have observed with previous years, no C. shasta has been detected yet at any index site through 3/24/2025.
Klamath water sampling and C. shasta spore monitoring is now in its peak season routine, with water samples being collected weekly at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the first week of OSU expediting analysis and reporting of the data.
This is the first week that any C. shasta DNA has been detected, albeit at very low levels.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in every sample (typically < 0.5 L instead of 1 L).
Analysis of samples collected Monday 3/31/2025
KSH 0/3 samples positive; 0.2-0.3L; isco; 0 sp/L
KBC 1/3 samples positive; 0.3L; isco; <1 sp/L
KMN 0/3 samples positive; 0.3L; isco; 0 sp/L
KSV 1/3 samples positive; 0.3-0.4L; isco; <1 sp/L
KOR 0/3 samples positive; 1L; isco; 0 sp/L
KTC 1/3 samples positive; 1L; isco; <1 sp/L
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
ISCO = 24-hour composite collected by an automatic sampler.
Reported values are the estimated spores/L accounting for the sample volume.
Klamath water sampling and C. shasta spore monitoring is in its peak season, with water samples collected weekly at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the second week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in every sample (typically < 0.5 L instead of 1 L).
Findings: No C. shasta DNA was detected at any site this week (in contrast to last week where we saw the first - low - detections of the year).
Details of the analysis of samples collected Monday 4/7/2025:
KSH 0/3 samples positive; 0.3L; isco; 0 sp/L
KBC 0/3 samples positive; 0.2-0.3L; isco; 0 sp/L
KMN 0/3 samples positive; 0.2-0.3L; isco; 0 sp/L
KSV 0/3 samples positive; 0.3-0.4L; isco; 0 sp/L
KOR 0/3 samples positive; 0.3L; grab; 0 sp/L
KTC 0/3 samples positive; 0.5L; isco; 0 sp/L
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume.
Klamath water sampling and C. shasta spore monitoring is in its peak season, with water samples collected weekly at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the third week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in every sample (typically < 0.4 L instead of 1 L).
Findings: low levels of C. shasta DNA were detected at all sites downstream of KSH this week.
Details of the analysis of samples collected Monday 4/14/2025:
KSH 0/3 samples positive; 0.2-0.25L; isco; 0 sp/L
KBC 1/3 samples positive; 0.25-0.35L; isco; <1 sp/L
KMN 3/3 samples positive; 0.25-0.35L; isco; 1 sp/L
KSV 2/3 samples positive; 0.4L; isco; <1 sp/L
KOR 2/3 samples positive; 0.4L; isco; <1 sp/L
KTC 2/3 samples positive; 0.5-0.75L; grab; <1 sp/L
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta.
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its peak season, with water samples collected weekly at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the fourth week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week improving at 0.3 - 1L per sample).
Findings: C. shasta DNA was detected at all sites downstream of KSH this week, in all three replicate samples and at levels higher than last week: to several spores per liter. Now that total C. shasta DNA densities are > 2 sp/L at some sites, OSU will run a second assay to determine if the signal is from the parasite genotype relevant for Coho salmon; these data will be reported from next week.
Details of the analysis of samples collected Monday 4/21/2025:
KSH 0/3 samples positive; 0.3-0.5L; isco; 0 sp/L
KBC 3/3 samples positive; 0.4-0.5L; grab; 3 sp/L
KMN 3/3 samples positive; 0.4L; isco; 3 sp/L
KSV 3/3 samples positive; 0.5L; isco; 1 sp/L
KOR 3/3 samples positive; 1L; grab; 3 sp/L
KTC 3/3 samples positive; 1L; grab; <1 sp/L
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta.
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Update to this week's data: The coho-relevant genotype was detected in only one sample: at a very low level (<<1sp/L) at KOR.
Klamath water sampling and C. shasta spore monitoring is in its peak season, with water samples collected weekly at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the fifth week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was equivalent to last week with 0.3 - 1 L per sample).
Findings: C. shasta DNA was detected at KSH for the first time this week and once again at all other sites this week, at densities similar to last week, up to 2 spores per liter.
Now that total C. shasta DNA densities are at least 2 sp/L at some sites, OSU is running a second assay to determine if the signal is from the parasite genotype relevant for Coho salmon. We detected the Coho-relevant genotype at the uppermost two sites (KSH, KBC) as a small proportion of the total C. shasta density (<1sp/L).
Details of the analysis of samples collected Monday 4/28/2025:
KSH 3/3 samples positive; 0.3-0.5L; isco; 2 sp/L total Cs, <1sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.4-0.5L; grab; 2 sp/L total Cs, <1sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.4L; isco; 2 sp/L total Cs, 0 sp/L Coho-relevant genotype
KSV 3/3 samples positive; 0.5L; isco; 2 sp/L total Cs, 0 sp/L Coho-relevant genotype
KOR 3/3 samples positive; 1L; grab; 1 sp/L total Cs, 0 sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; grab; 1 sp/L total Cs, 0 sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its peak season, with water samples collected weekly at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the 6th week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was slightly better than last week with 0.5 - 1 L per sample).
Findings: C. shasta DNA was detected once again at all sites this week, at much higher levels than last week at 5/6 sites, with densities up to 12 spores per liter (at KSH). We detected the Coho-relevant genotype at all sites except KSV, but only as a small proportion of the total C. shasta density (<1sp/L, except for KOR where it was 1 sp/L).
Notably, total densities reached or exceeded 10 spores per liter at three of the six index sites this week. The majority of the DNA is Chinook type I.
Details of the analysis of samples collected Monday 5/5/2025:
KSH 3/3 samples positive; 0.5L; isco; 12 sp/L total Cs, <1sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.6L; grab; 10 sp/L total Cs, <1sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.6L; isco; 5 sp/L total Cs, <1sp/L Coho-relevant genotype
KSV 3/3 samples positive; 0.6L; isco; 11 sp/L total Cs, 0 sp/L Coho-relevant genotype
KOR 3/3 samples positive; 1L; isco; 8 sp/L total Cs, 1 sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; grab; 1 sp/L total Cs, <1sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its peak season, with water samples collected at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the 7th week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was equivalent to last week with 0.5 - 1 L per sample).
Findings: C. shasta DNA was detected once again at all sites this week, at elevated but slightly lower levels than last week at 5/6 sites, with densities up to 8 spores per liter. Site KTC was the exception - it had its highest spore density of the year so far (6sp/L). We detected the Coho-relevant genotype at all sites, but only as a small proportion of the total Cs density (up to 1sp/L).
Details of the analysis of samples collected Monday 5/12/2025:
KSH 3/3 samples positive; 0.5L; grab; 8 sp/L total Cs, 1sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.6L; isco; 5 sp/L total Cs, <1sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.6L; isco; 4 sp/L total Cs, <1sp/L Coho-relevant genotype
KSV 3/3 samples positive; 0.7L; isco; 5 sp/L total Cs, 1 sp/L Coho-relevant genotype
KOR 3/3 samples positive; 1L; isco; 6 sp/L total Cs, 1 sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; isco; 6 sp/L total Cs, 1sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is still in its peak season, with water samples collected at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC.
This week is the 8th week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was equivalent to last week with 0.5 - 1 L per sample).
Findings: C. shasta DNA was detected once again at all sites this week, with densities similar to last week (some sites higher, some lower and some the same (see graph)), up to 8 spores per liter like last week. We detected the Coho-relevant genotype at all sites, but only as a small proportion of the total C. shasta density (up to 1 sp/L).
Details of the analysis of samples collected Monday 5/19/2025:
KSH 3/3 samples positive; 0.5L; isco; 7 sp/L total Cs, 1 sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.5L; isco; 4 sp/L total Cs, 1 sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.5L; isco; 4 sp/L total Cs, <<1 sp/L Coho-relevant genotype
KSV 3/3 samples positive; 0.5L; grab; 8 sp/L total Cs, 1 sp/L Coho-relevant genotype
KOR 3/3 samples positive; 0.5L; isco; 3 sp/L total Cs, 1 sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; isco; 5 sp/L total Cs, 1 sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is still in its peak season, with water samples collected at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Tuesday this week, given the Memorial Day holiday Monday.
This week is the 9th week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was equivalent to last week with 0.5 - 1 L per sample).
Findings: C. shasta DNA was detected once again at all sites this week, at levels continuing a trend lower over the last several weeks (see graph), with densities only at 5 spores per liter at one site (KSH). We detected the Coho-relevant genotype at 6/7 sites, at generally lower levels than last week, and only as a small proportion of the total Cs density (up to 1 sp/L).
Details of the analysis of samples collected Tuesday 5/27/2025:
KSH 3/3 samples positive; 0.6L; isco; 5 sp/L total Cs, <1 sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.6L; isco; 1 sp/L total Cs, <1 sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.5L; isco; 3 sp/L total Cs, not detected Coho-relevant genotype
KSV 3/3 samples positive; 0.6L; isco; 1 sp/L total Cs, <1 sp/L Coho-relevant genotype
KOR 3/3 samples positive; 1L; grab; 4 sp/L total Cs, <1 sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; isco; 2 sp/L total Cs, 1 sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is still in its peak season, with water samples collected at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Monday June 02.
This week is the 10th and final week of OSU expediting analysis and reporting of the data.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was equivalent to last week with 0.5 - 1 L per sample).
Findings: C. shasta DNA was detected once again at all sites this week, with levels rebounding higher, to have densities 8 -10 sp/L at the three most upstream sites (KSH, KBC, KMN) and half those levels at the three downstream sites (KSV, KOR, KTC). We detected the Coho-relevant genotype at all sites, at only slightly higher levels than last week, despite the higher jumps in density of total Cs sp/L.
Details of the analysis of samples collected Monday 06/02/2025:
KSH 3/3 samples positive; 0.5L; grab; 8 sp/L total Cs, 1sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.7L; isco; 8 sp/L total Cs, 1sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.7L; isco; 10 sp/L total Cs, 1 sp/L Coho-relevant genotype
KSV 3/3 samples positive; 0.7L; isco; 3 sp/L total Cs, 1sp/L Coho-relevant genotype
KOR 3/3 samples positive; 1L; isco; 4 sp/L total Cs, <1sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; grab; 5 sp/L total Cs, 1 sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is still in its peak season, with water samples collected at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Monday June 09.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was slightly better than last week with most samples 0.7 - 1 L).
Findings: C. shasta DNA was detected once again at all sites this week, with levels lower at upstream sites KSH and KMN except KBC (12 sp/L) and similar at the downstream sites. We detected the Coho-relevant genotype at all sites, at similar levels than last week.
Details of the analysis of samples collected Monday 06/09/2025:
KSH 3/3 samples positive; 0.7L; isco; 4 sp/L total Cs, 1 sp/L Coho-relevant genotype
KBC 3/3 samples positive; 0.7L; grab; 12 sp/L total Cs, 1 sp/L Coho-relevant genotype
KMN 3/3 samples positive; 0.7L; isco; 7 sp/L total Cs, <1 sp/L Coho-relevant genotype
KSV 3/3 samples positive; 0.5-0.7L; isco; 2 sp/L total Cs, <1 sp/L Coho-relevant genotype
KOR 3/3 samples positive; 1L; isco; 5 sp/L total Cs, 1 sp/L Coho-relevant genotype
KTC 3/3 samples positive; 1L; isco; 5 sp/L total Cs, 1 sp/L Coho-relevant genotype
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected..
Klamath water sampling and C. shasta spore monitoring is just past its peak season (coinciding with historical Chinook fish outmigration), and we are now outside the period where we run a second assay to detect the Coho-relevant C. shasta genotype proportion of the sample. Given field observations of ongoing juvenile fish movements, we and our collaborators are maintaining weekly collection at the Kinsman (KMN) site, so water samples were still collected at all 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Monday June 16.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week was equivalent to last week with samples 0.6 - 1 L).
Findings: C. shasta DNA was detected once again at all sites this week, with a dramatic rise in spore densities at all sites, reaching the highest levels so far this year (but below peak levels seen in each of the last two years).
Details of the analysis of samples collected Monday 06/16/2025:
KSH 3/3 samples positive; 0.6L; grab; 21 sp/L total Cs
KBC 3/3 samples positive; 0.7L; isco; 16 sp/L total Cs
KMN 3/3 samples positive; 0.7L; isco; 22 sp/L total Cs
KSV 3/3 samples positive; 1L; grab; 28 sp/L total Cs
KOR 3/3 samples positive; 1L; grab; 11 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 16 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring involved water sample collection at 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Monday June 23.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (this week had samples 0.7 - 1 L).
Findings: C. shasta DNA was detected once again at all sites this week, with levels slightly lower at all sites except KOR.
Details of the analysis of samples collected Monday 06/23/2025:
KSH 3/3 samples positive; 0.7L; isco; 10 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 10 sp/L total Cs
KMN 3/3 samples positive; 1L; isco; 17 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 7 sp/L total Cs
KOR 3/3 samples positive; 0.9L; grab; 20 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 15 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is into its summer season. However, given field observations of ongoing juvenile fish movements through June, we and our collaborators are maintaining weekly collection at the Kinsman (KMN) site, so water samples were still collected at all 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Monday June 30.
Turbidity levels continue to be higher than the historic background, so less water can be filtered in most samples (however, this week was the first week this year where 1-L samples could be filtered at all sites (but still using 2 filters).
Findings: C. shasta DNA was detected at all sites this week, with a mix of some sites having lower spore densities and some sites higher than last week, and reaching the highest levels so far this year of 32 sp/L at KMN (which was still below peak levels seen in each of the last two years).
Details of the analysis of samples collected Monday 06/30/2025:
KSH 3/3 samples positive; 1L; isco; 5 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 15 sp/L total Cs
KMN 3/3 samples positive; 1L; isco; 32 sp/L total Cs
KSV 3/3 samples positive; 1L; grab; 18 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 5 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 15 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its summer season, with weekly collection but a reduced rate of reporting (every 2 weeks or so). However, given field observations of ongoing juvenile fish movements through June, we and our collaborators have been maintaining weekly collection at the Kinsman (KMN) site.
Water samples were collected at all 6 index sites: KSH, KBC, KMN, KSV, KOR and KTC on Monday July 7 and 14.
Turbidity levels continue to be higher than the historic background, however by using 2 filters, most sites have 1-L water filtered again these 2 weeks, which is an improvement on most early 2025 dates.
Findings: C. shasta DNA was detected at all sites both weeks. 7/7 saw some of the highest levels detected this year, with the highest level of 45 sp/L at KMN (which was still below peak levels seen in each of the last two years). These levels decreased by more than half by 7/14.
Details of the analysis of samples collected Monday 07/07/2025:
KSH 3/3 samples positive; 1L; isco; 11 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 19 sp/L total Cs
KMN 3/3 samples positive; 1L; grab; 45 sp/L total Cs
KSV 3/3 samples positive; 1L; grab; 20 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 7 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 11 sp/L total Cs
Details of the analysis of samples collected Monday 07/14/2025:
KSH 3/3 samples positive; 1L; isco; 3 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 39 sp/L total Cs
KMN 3/3 samples positive; 1L; isco; 21 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 3 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 2 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 8 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its summer season, with weekly collection but a reduced rate of reporting (every 2 weeks or so). Kinsman site (KMN) has now concluded sampling for the season (after an additional month to monitor during extended out-migration).
Water samples were collected at 5 index sites: KSH, KBC, KSV, KOR and KTC on Monday July 21 and 28.
Turbidity levels continue to be higher than the historic background, however by using 2 filters, most sites have 1-L water filtered again these 2 weeks, which is an improvement on most early 2025 dates.
Findings: C. shasta DNA was detected at all sites both weeks, but with a distinct shift in spore density from week-to-week: on 7/21 levels of about 10 sp/L were measured at the upper river sites (KSH, KBC, KSV) with much lower densities (<1 sp/L) downriver. A week later densities at the upper sites had decreased to 1-3 sp/L, whereas densities at the lower river sites had increased to 5+ sp/L.
Details of the analysis of samples collected Monday 07/21/2025:
KSH 3/3 samples positive; 0.8-1L; grab; 10 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 11 sp/L total Cs
KMN no further sampling this season
KSV 3/3 samples positive; 1L; grab; 8 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; <1 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 1 sp/L total Cs
Details of the analysis of samples collected Monday 07/28/2025:
KSH 3/3 samples positive; 0.8-1L; isco; 1 sp/L total Cs
KBC 3/3 samples positive; 1L; grab; 3 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 7 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 5 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its summer season, with weekly collection but a reduced rate of reporting (~every 2 weeks). Kinsman index site (KMN) has now concluded sampling for the season (after an additional month to monitor during extended out-migration).
This week, water samples were collected at 5 index sites: KSH, KBC, KSV, KOR and KTC, on Monday August 04, 2025.
Turbidity levels continue to be higher than the historic background, however by using 2 filters, most sites have 1-L water filtered (except for KSH and KBC), which is an improvement on most early 2025 dates.
Findings:
C. shasta DNA was detected at all sites. The highest density was at or above 10 sp/L at upper sites KSH and KSV, with KBC being the outlier and only site <5 sp/L.
Note that we also updated KBC data for 07/14/2025 as the samples required re-running due to PCR inhibition in the original sample analysis (density = 39 sp/L).
Details of the analysis of samples collected Monday 08/04/2025:
KSH 3/3 samples positive; 0.5L; isco; 13 sp/L total Cs
KBC 3/3 samples positive; 0.5-0.8L; isco; 2 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 10 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 6 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 9 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring is in its summer season, with weekly collection but a reduced rate of reporting (every 2 weeks or so).
In this update: the water samples that were collected at 5 index sites: KSH, KBC, KSV, KOR and KTC, on Monday August 11 and 18, 2025.
Turbidity levels continue to be higher than the historic background, however by using 2 filters, most sites have 1-L water filtered (except for KSH and KBC 8/11), which is an improvement on most early 2025 dates.
Findings: C. shasta DNA was detected at all sites. Spore levels rose at the three upper sites (KSH, KBC, KSV) with the grab samples taken at KSV on 11/18 returning the highest C. shasta spore densities of the year (and similar to the highest level detected in 2024). Spore levels at 4/6 sites were above 10sp/L 08/18.
Details of the analysis of samples collected Monday 08/11/2025:
KSH 3/3 samples positive; 0.5L; isco; 14 sp/L total Cs
KBC 3/3 samples positive; 0.6L; isco; 23 sp/L total Cs
KSV 3/3 samples positive; 1L; grab; 60 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KTC 3/3 samples positive; 1L; grab; 10 sp/L total Cs
Details of the analysis of samples collected Monday 08/18/2025:
KSH 3/3 samples positive; 1L; isco; 16 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 17 sp/L total Cs
KSV 3/3 samples positive; 1L; grab; 11 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 8 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 4 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring continues in its summer season, with weekly collection but a reduced rate of reporting. While wildfires prevented collections at some sites 09/02/2025, all other weeks water samples were collected at the 5 index sites: KSH, KBC, KSV, KOR and KTC. Turbidity levels continue to be higher than the historic background, however by using 2 filters, most sites have 1-L water filtered most weeks now.
Findings: C. shasta DNA continues to be detected at all sites, with a general tapering downward trend in late summer. Over these 4 sample weeks, average spore levels did not exceed 10sp/L at any site.
Details of samples collected 08/25/2025:
KSH 3/3 samples positive; 1L; grab; 6 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 2 sp/L total Cs
KSV 3/3 samples positive; 1L; grab; 3 sp/L total Cs
KOR 3/3 samples positive; 1L; grab; 2 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 1 sp/L total Cs
Details of samples collected 09/02/2025:
KSH 3/3 samples positive; 0.9L; isco; 6 sp/L total Cs
KBC 3/3 samples positive; 0.9L; isco; 9 sp/L total Cs
KSV wildfire prevented collection
KOR 2/3 samples positive; 0.5L; isco; 2 sp/L total Cs
KTC wildfire prevented collection
Details of samples collected 09/08/2025:
KSH 3/3 samples positive; 1L; grab; 4 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 3 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 2 sp/L total Cs
KOR 2/3 samples positive; 1L; isco; 2 sp/L total Cs
KTC 2/3 samples positive; 1L; isco; <1 sp/L total Cs
Details of samples collected 09/15/2025:
KSH 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 3 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 1 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected.
Klamath water sampling and C. shasta spore monitoring has progressed into its Fall season, with weekly collection at all sites except KMN, but a reduced frequency of reporting (every 2 weeks or so).
On Monday, September 22 and 29, water samples were collected at 5 index sites: KSH, KBC, KSV, KOR and KTC.
Turbidity levels continue to be higher than the historic background, however by using 2 filters, all sites these weeks had 1-L water filtered, which is an improvement on most early 2025 dates.
Findings: C. shasta DNA was detected at all sites, but with levels at the two upriver sites (KSH and KBC) higher than the lower river sites: 4-9 sp/L versus <1-1 sp/L total C. shasta.
Details of the analysis of samples collected Monday 09/22/2025:
KSH 3/3 samples positive; 1L; isco; 8 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 9 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KOR 1/3 samples positive; 1L; isco; <1 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 1 sp/L total Cs
Details of the analysis of samples collected Monday 09/29/2025:
KSH 3/3 samples positive; 1L; isco; 5 sp/L total Cs
KBC 3/3 samples positive; 1L; isco; 4 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; <1 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; <1 sp/L total Cs
Notes:
Data: Site code; analysis; sample volume; collection method; average spores/L total C. shasta
Samples are 24-hour composite by isco automatic sampler or manual grab.
Reported values are the estimated spores/L accounting for the sample volume, and averaged over the three samples collected..
Klamath water sampling and C. shasta spore monitoring has moved into the fall season, with continued weekly collection but a reduced rate of analysis and reporting. Both weeks, water samples were collected at the 5 index sites: KSH, KBC, KSV, KOR and KTC. Turbidity levels continue to be higher than the historic background, however by using 2 filters, all sites had 1-L water filtered both weeks.
Findings: C. shasta DNA continues to be detected at all sites, with a general tapering downward trend into fall. Over these two sample weeks, average spore levels reached 10 sp/L at only one site (KSH) one week. And both weeks the two upstream sites (KSH, KBC) had higher total C. shasta levels than the three downstream sites (KSV, KOR, KTC).
Details of samples collected 10/06/2025:
KSH 3/3 samples positive; 1L; isco; 10 sp/L total Cs
|KBC 3/3 samples positive; 1L; grab; 6 sp/L total Cs
KSV 2/3 samples positive; 1L; isco; 1 sp/L total Cs
KOR 2/3 samples positive; 1L; isco; <1 sp/L total Cs
KTC 2/3 samples positive; 1L; isco; 1 sp/L total Cs
Details of samples collected 10/13/2025:
KSH 3/3 samples positive; 1L; grab; 3 sp/L total Cs
KBC 3/3 samples positive; 1L; grab; 3 sp/L total Cs
KSV 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KOR 3/3 samples positive; 1L; isco; 1 sp/L total Cs
KTC 3/3 samples positive; 1L; isco; 1 sp/L total Cs
Density (average spores per liter) of Ceratonova shasta in 24-hour composite water samples collected at the mainstem long term index site, near Beaver Creek (KBC) in 2025 (blue data points) compared to the previous years (2020-2024).
Density (average spores per liter) of Ceratonova shasta in 24-hour composite water samples collected at the mainstem index sites in 2025. 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, KSH = near Shasta River, KTC = Tully Creek, KMN = Kinsman Fish Trap, KOR = Orleans. The line denotes 10 spores per liter which corresponds with 40% mortality threshold in Chinook salmon.
Density (average spores per liter) of Ceratonova shasta in 24-hour composite water samples collected at the mainstem index sites in 2024. 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, KSH = near Shasta River, KTC = Tully Creek, KMN = Kinsman Fish Trap, KOR = Orleans. The line denotes 10 spores per liter which corresponds with 40% mortality threshold in Chinook salmon.
Manual water sampling by Karuk Tribal Biologist Larry Alameda at index site K-I5
Solar powered automatic sampler at the Kinsman index site. An ISCO is used at all index sites but manual sampling provides a backup.
Collection of 4 1L technical replicate water samples from the larger 12L composite collected over 24 hours at KSV
Manual water sampling at Orleans index site.
Photos courtesy of Karuk Tribal Biologist Larry Alameda
Annelid sampling
To monitor abundance and prevalence of C. shasta infection in the invertebrate annelid host, Manayunkia occidentalis, benthic samples are collected at seven sites in the Klamath River in fall, winter, spring, and summer. Sites span a discharge gradient; 2 are located in the upper basin downstream from Keno Dam, 2 are located in the hydroelectric reach, 3 are located in the middle basin downstream from Iron Gate Dam, and 2 are located in the lower basin downstream from the Scott River. Although samples are routinely collected in fall, winter, spring, and summer, they are also scheduled to occur prior to and after flooding or pulse flow events (when possible). Samples are processed to determine density, simple demographics, and the prevalence of myxozoan infections including C. shasta and P. minibicornis.
2024 Update: Annelids were sampled in March, May, June (intensive work in mid basin with USFWS) and July in 2024. The fall sampling is planned for early November 2024. In 2024, annelids were most abundant at upper and middle basin sites in March, which contrasts with other years- when annelids are most abundant in warmer months from late spring to fall. Although the mechanism has not yet been determined, we hypothesize that sediment associated with dam deconstruction activity and fire disrupted annelid populations leading to the lower abundance in warmer months. Density and infection assays are in progress.
Manayunkia occidentalis tubes from the image on right
A high density assemblage sample at TOH
Diver collecting a benthic sample from boulder substrate at the TOH reach. We use a modified Hess sampler fitted with 80um Nytex mesh netting and a 500mL Nalgene collection bottle. Samples are preserved in ethanol until processing.
Benthic samples are fractioned prior to sorting.
Dr. Alexander photographing annelids on riprap substrate at the KBC monitoring site.
Annelid sampling at the KI5 reach. Foreground diver measures depth and velocity, while background diver measures substrate grain sizes.
Annual reports
Annual reports for Bureau of Reclamation funded studies for 2015 onwards are available. Please contact Sascha Hallett ([email protected]). Annual reports are submitted June 1 the year after the research year.
Annual Klamath River Fish Health Workshop
We are planning the 2025 Annual Klamath River Fish Health Workshop. This will likely be remote format this year in response to the travel restrictions on our Californian partners and all federal colleagues.
Details coming soon!
