A tiny parasite in the Klamath & Trinity Rivers

What is C. shasta?

Ceratonova shasta (C. shasta) is a microscopic parasite that is native to rivers of the Pacific Northwest, including the Klamath and Trinity Rivers. Infection is most severe for juvenile salmon but can impact returning adults as well. The impact of an infection is highly influenced by water conditions like temperature, flow, and seasonality. If conditions are right for the parasite’s host worm, C. shasta can rapidly proliferate and lead to severe infections that can be devastating to populations. In 2021, after years of drought that impacted river conditions  juvenile salmonid deaths from C. shasta in the lower Klamath reached into the hundreds of thousands [1, 2]. 

To survive, C. shasta needs two hosts

1. A carpet of tiny worms
C. shasta starts its life inside a freshwater worm, called Manayunkia occidentalis. The worm, smaller than an eyelash, lives in mud and on rocks below the surface of a river or reservoir in colonies that can resemble an underwater carpet. Inside the worm, the parasite grows and turns into a new form called an actinospore. Once an actinospore, the worm releases the microscopic parasite to float in the water column and wait for its next host [3].

2. Salmon and Trout
As they swim young salmon breath in the actinospores allowing the parasite to attach to the gills and then enter the fish’s body. The parasite then travels to the fish’s intestines, where it multiplies and causes internal damage. This makes the fish sick and weak, causing many to succumb to the infection. The cycle continues when infected fish (including adults) release more spores back into the water after they die.

Are Adult Salmon Affected?

Adult salmon can be infected with C. shasta however the severity is influenced by other stressors.  Typically, adults encounter the microscopic spores during upriver migration through areas with high spore loads (like the lower Klamath River during spring/summer). If the fish is stressed from high water temperatures, poor conditions or other pathogens, C. shasta could lead to pre-spawn mortality or failure to spawn. Although typically resistant, if infected, adults can act as a carrier of the parasite – shedding spores when they die and decompose. If the spores are shed in a system that does not have adequate flushing flows during the ensuing winter months, juveniles from the area could be affected. While some disease impacts to adult salmon are possible, if conditions in the river are favorable, adults are generally more resistant to effects of the disease than juveniles.

The Klamath River

Salmon health and vitality is of utmost importance for Klamath indigenous groups like the Yurok, Quartz Valley, Karuk, and Hoopa Valley Tribes. For millennia salmon have provided sustenance and are celebrated as integral to the health of people, culture, tradition, and economy. The continued decline of salmon due to C. shasta and other human-enhanced factors are deeply felt by local people and led to the decade’s long advocacy to remove four hydroelectric dams on the Klamath River.

In 2023 and 2024 these dams on the Klamath River were removed, allowing salmon, steelhead and lamprey to reconnect to 400 miles of spawning habitat. It is the largest dam removal project in U.S. history, to date. Ecological goals for dam removal are to improve water quality, restore resources to Klamath River Tribes, restore habitat for salmonid species, and improve the health of salmon and steelhead [5].

The Klamath River is home to several salmon species that are important to Native American tribes, commercial and recreational fishers, and the ecosystem as a whole. Although infections occur in all species of juvenile salmon or trout, if the parasitic worm host is allowed to thrive, results can be devastating for some salmon species. One such species of concern are Coho salmon, which are recognized as “threatened” in the Klamath and the Trinity and are especially vulnerable to population scale impacts from large scale fish kills propagated by parasites.

What made the lower Klamath River a hotspot for C. shasta? Below Iron Gate dam, the primary reasons were twofold. First, scouring events from winter storms were blocked by dams failing to disperse sediment. Second, waters held in several chains of reservoirs warmed. Ultimately these combining factors led to robust habitat conditions for the parasite’s aquatic worm host. Fish heath experts in the Klamath Basin are hopeful that dam removal will mitigate previously favorable growing conditions for the host worm [6]. Removal of JC Boyle, Copco 1 & 2 and Iron Gate dams will allow for a more natural flow of water from tributaries and potentially help to scour growth of the host worm with winter storms.

Hope for Trinity River Fish Populations

The Trinity River joins the Klamath River approximately 44 miles above the ocean, so its fish are subjected to the conditions of the lower Klamath River during their migrations. Beginning in late winter juvenile chinook begin to migrate downriver feeding on drift invertebrates, resting and digesting in warmer slower waters. Once they meet the mild saline waters of the Klamath estuary, they begin a smoltification process where their bodies change and adapt from freshwater to saltwater. Cold temperatures and salinity may reduce progress of disease, but do not eliminate infection [1]. 

Because of their migration paths, Trinity River fish populations were part of the juvenile fish kill on the Klamath River in 2021. This event, along with historic drought conditions that followed, allowed for pathogens like C. shasta to play a significant role in returning adult escapement. Since most Chinook exhibit a 3-5 year life cycle, we’re still experiencing the loss of these juvenile fish today. Historically low returns of adult chinook salmon have prompted recreational fishery managers to close in-river salmon fishing seasons for a third consecutive year [8, 9]. Although the immediate impacts have been devastating for recreational anglers and river enthusiasts, there are many hopes (and also many unknowns still to be learned) following the removal of the dams. The primary hope for Trinity River outmigrant fish to experience less frequent and less severe infections once they reach the Klamath River so that juveniles as well as adults can manage natural stressors and thrive.

Klamath Fish Health Assessment Team

The Klamath Fish Health Assessment Team (KFHAT) is a technical workgroup which formed during the summer of 2003 with the purpose of providing early warning and a coordinated response effort to avoid, or at least address, non-hazardous materials related fish kill events in the anadromous portion of the Klamath River basin [10].

To accomplish this goal, KFHAT created a network of experts and monitoring efforts through which information about current river and fish health conditions in the Klamath Basin can be shared among participants, the general public, and resource managers.

Every year, beginning in late April, members of KFHAT hold meetings to assess Klamath Basin fish health along the Klamath and Trinity Rivers and their main tributaries. The group publishes observations as well as a readiness level map based on those observations on a public facing website: Klamath Fish Health Assessment Team (KFHAT) after each meeting.

How are juvenile populations fairing this out-migration season? The wet winter of 2024/2025 has set the system up with favorable fish health conditions, but our area’s typical hot July weather can lead to stressful lower river environments. Thus far the 2025 monitoring season has seen some irregularities with regards to concentration of C. shasta. Klamath Basin water quality monitoring is implemented annually by a team at Oregon State University and recent monitoring results are showing higher than normal spore counts of C. shasta in geographic areas that are puzzling scientists [10]. In the lower river, screw traps are catching Trinity River hatchery-released yearlings from the fall and spring brood stocks with infections [10]. Although these conditions exist each year, they vary in severity and salmon evolved to this specific weather pattern. The species stay healthy by seeking cold water refugia located in deep stratified pools and cold-water tributary mouths during the hottest weeks of the year.  Also typical to the area, wildfire can aid conditions when smoke sits in drainages, reflecting the sun’s heat back into the atmosphere and therefore cools air and water temperatures.

Although this year’s conditions thus far are concerning (note the yellow readiness levels in the map above), many juvenile salmon are in the last stages of migration to the ocean and are likely in the lower Klamath river undergoing smoltification or learning to live in their new ocean environment. What will conditions be when they return to spawn in our river in 2028, 2029, or 2030? Of course, only time can tell, but with the removal of four Klamath Dams, river managers are hopeful that, when it comes to controlled conditions, Trinity and Klamath run salmonids will have a more favorable environment than what populations have encountered for over six decades, and they might be more favorably armed to withstand what mother nature may bring their way.

Thank you to Dan Troxel, California Department of Fish and Wildlife lead on the Klamath Basin Fish Health Assessment Team and Morgan Knechtle from California Department of Fish and Wildlife for providing detailed edits to this article.

References

1. As massive fish kill continues on Klamath River, Karuk Tribe declares state of climate emergency
2. Serious fish kill consumes the Klamath River | Local News | heraldandnews.com
3. Ceratonova shasta – Wikipedia
4. Benefits of Klamath River Renewal – Klamath River Renewal
5. TRRP: Fish of the Trinity River
6. Dam removals, restoration project on Klamath River expected to help salmon, researchers conclude | Newsroom | Oregon State University
7. Chinook Salmon Fact Sheet – U.S. Fish and Wildlife Service
8. Another Commercial Salmon Season Closure is Expected | News Blog North Coast Journal. April 22, 2025.
9. CDFW News | Limited Chinook Sport Fishing to Reopen in 3 Central Valley Rivers, excludes Klamath Basin and Mainstem Sacramento.
10. KFHAT_2025_Report_5.pdf

Further Reading

1. TRRP: Fish of the Trinity River
2. Trinity River Guage Temperature Readings – at Hoopa, Ca. USGS

Key Parasites of Salmonids in the Klamath and Trinity Rivers

Sun Seekers, Fire Carriers, and Medicine Keepers

Mule’s ears (of the genus Wyethia) and arrowleaf balsamroot (Bupthalmium sagittata) are two flowering plants that to the untrained eye are so similar they are often mistaken for the other. Both herbaceous plants not only look very similar but are a part of the same family, subfamily, tribe and subtribe of plants. Further, genetic testing has confirmed that these two plants are the closest relative to one another. However, distinguishing characteristics do exist. Read on to learn about each plant and their unique place in the northern California biota.

Narrowleaf Mule-Ears (Wyethia angustifolia)

Wyethia is a genus of North American flowering plants in the family Asteraceae, more commonly known as the aster, daisy or sunflower family. Wyethia are commonly referred to as mule’s ears. The genus Wyethia can typically be identified by their leaves that connect to the base of the plant (basal leaves) and 1-2 ft tall flowering stalk with a sun-flower-like head. Most people would probably see this flower and call it a “native sunflower” because of its large yellow radial flower (or inflorescence). Other common names besides “mule’s ears” are “California compassplant” and “black sunflower.” In Yurok language they are called skep’ol, in Hupa they are called sa’liwh. The etymology of the name “compassplant” likely comes from the flower’s ability to track the sunlight through the day. The leaves are fuzzy or velvety and have a lance-shaped blade (long and narrow) which can distinguish it from its closest look-alike.

Photo: Narrowleaf Mule-Ears (Wyethia angustifolia). [Steven Clinton via iNatrualist]

There are several species of Wyethia [1], of these the most commonly found in the Klamath Mountains is Narrow Leaf Mule Ears (Wyethia angustifolia) which grows in stream banks and springs at elevations from 0-5,500 feet. You’ll typically see it flower in the spring to summer depending on its elevation. Mule’s ears also have a characteristically sticky milky sap that can be toxic to the touch when pruned or broken.

Arrowleaf Balsamroot (Balsamorhiza sagittata)

Balsamhoriza, otherwise called arrowleaf balsamroot, is also part of the Aasteracaea family. Arrowleaf balsamroot can be distinguished from mule’s ears when comparing the leaf shape, color and tiny hairs on the underside of the leaf. Arrowleaf balsamroot prefers colder and dryer climates and is found in mountain fields but can also be a common plant in the understory of conifer forests. It ranges from Colorado, west into the Sierra Nevada and north into Canada.

Photo: Arrowleaf balsamroot (Balsamorhiza sagittata). [Simone Groves, Hoopa Valley Tribal Fisheries]

Compare the two leaf systems in the below images.

Similar to a turnip or a carrot, the roots of both mule’s ears and arrowleaf balsamroot have a long branching tap root in which the dormant plant resides during winter. The roots can penetrate over 6ft deep in the soil and spread 3-4 feet out away from the plant. Every year the vegetation dies back completely and will rise again from the earth in spring.

Mule’s ears occupy a range of vegetation types, including many arid and alpine communities whose habitat contains a mixture of dry-climate tree species and native grassland. These plants can handle harsh soil conditions, with very little topsoil and can be an indicator of disturbance activities, as their seeds germinate well in exposed soil. However, if an area is intensively grazed, these plants can be impacted. The young tender leaves of the plant in spring are sought after by ungulates and their populations can be eliminated by persistent grazing. Part of this is because they have dormant buds near the surface of the soil at ground level. If the shoot tips are eaten or damaged, the plant may be impacted.

However, if populations establish, underground roots can be quite large and split multiple times which can allow new plants to form. This can form a circular patch radiating outwards from a central spot. The above ground portion of the plant dies back each summer and fall and the remaining dry material covering the ground can help carry the fire through patches of rock helping to gently move fire through an area. When the material burns, it adds a layer of ash to the soil, slowly accumulating topsoil and allowing new places for grassland to establish.

Shrubs that associate with a mule’s ears or arrowleaf balsamroot typically form fire risk patterns that are classified as a low-growing fuel class with a moderate to occasional high severity fire.  Fires in these communities are often a “Fire Mosaic”  where conditions result in a patchwork of burn severity between low and high severity depending on the fuel loading, and fire weather conditions under which it burns. The concept of a fire mosaic can be applied to much of California’s natural landscapes. Plant species throughout California, and the world, create specific fuel conditions through their physical bodies and life cycle strategies that often set conditions for the plants to return. In the dynamic interplay between life and death, growth and fire, persistent multi-generational patterns throughout history create these plant-and-fire relationships.

Mule’s ear and arrowleaf balsamroot are both very strong medicinal plants and are also used as a food source. Mule’s ear leaves have been used by the Miwok tribe to make a tea that helps to reduce fever and stimulate perspiration. The roots have been used to make a poultice which can reduce swelling, soothe burns, and according to Shishoni tribe – can be an “unfailing cure for syphilis” and wash made with the roots can be used to treat Measles. Today, places where these plants grow are considered medicine places and should be treated with respect. Various tribes document using the roots of the plants as one might eat Jerusalem artichokes, baked in an underground oven with warm rocks for several days.

The large seeds produced by both plants are a favorite for birds and humans and are akin to sunflower seeds. There are several species of insects that use the developing seeds as a host plant and many different native bees such as megachile (leaf-cutter bee) species have a relationship with open pollinated flowers which can be very productive nectar producers. Open pollinated flowers tend to be the most frequently visited flower shapes because they provide a large landing pad and lots of space for pollinators to move around on them.

Photo: Arrowleaf balsamroot seed head and seeds. Photo USDI BLM OR030 SOS.

Mule’s ears and arrowleaf balsamroot are more than just striking wildflowers of the northern California landscape—they are living testaments to the deep interconnection between plant life, fire, wildlife, and human cultures. As food, medicine, and ecological agents, these plants reveal the intricate relationships that have long existed between people and place. Understanding their roles in ecosystem function and traditional knowledge invites us to view the land not as a backdrop, but as a living partner in our shared future. By respecting and learning from these native species, we not only deepen our ecological literacy but also honor the generations of Indigenous stewards that continue to shape the land today.

Resources

1. Wyethia – Wikipedia
2. CalScape – Wyethia
3. Wyethia angustifolia
4. Native American Ethnobotany Database – Wyethia
5. Native American Medicinal Plants: An Ethnobotanical Dictionary by Daniel E. Moreman
6. Natural History Museum Data Portal: Wyethia
7. FEIS USFS Database: Wyethia
8. Reduction of Survival and Growth of Young Pinus jeffreyi by an Herbaceous Perennial, Wyethia mollis
9. Impacts of Predispersal Seed Predation on Seed Production of Wyethia amplexicaulis, Agoseris glauca, and Crepis acuminata
10. Wyethia on iNat
11. Balsamorhiza on iNat
12. Etymology online: Girasole
13. Plant guide for arrowleaf balsamroot (Balsamorhiza sagittata)

Water Year 25 thus far has been a good year for Trinity Reservoir. In October, Trinity Reservoir measured in at 70% full with 1.7 million acre feet. Seasonal storms have recently pushed storage over 2 million acre feet (or 84%). In December, flows were held steady at 1500 cfs through January and increased to 3500 cfs after several atmospheric river systems passed through in early February.

Feb. Forecast – California-Nevada River Forecast Center

The volume of environmental flow releases for the Trinity River Restoration Program’s Wet-Season Baseflow Period (Feb. 15-Apr. 14) are determined by a conservative monthly inflow projection for Trinity Reservoir from the California Department of Water Resources (90% B120) in February, March with the final determination in April.

Prior to the official determination, which is published around the 10th of the month, water managers follow the California-Nevada River Forecast Center Median forecast for Trinity Lake inflow to stay abreast of the water year projections thus far.

The graph (shown in screen shot above) can be a little daunting to read, but when armed with the appropriate information is discernable for any viewer.

The Program’s Water-Year Volume Allocation as specified by the Record of Decision is outlined in the table below. The far left column is the threshold amount of state forecasted inflow in the Trinity Reservoir listed in acre feet which determines the center column, water year type. Then in the right column is listed the allocation to restoration for that water year, which includes baseflows.

Return now to an enlargement of the CNRFC forecast screenshot from Feb 12. Check out the light grey box “WY Vol Fcst 10/90%: 2,190/1,490 kaf” which reads longform as the following;

As of Feb. 12, the 10% of probability for Trinity Lake Inflow is predicted as 2,190,000 acre feet and the 90% of probability is 1,490,000 acre feet. Translated there is a 10% probability that the Trinity Allocation is predicted as “Wet” and a 90% probability is also “Wet”.

As managers track the predicted inflow via CNRFC, the Program’s Flow Workgroup develops hydrograph scenarios to use when the final determination is published by the California Department of Water Resources. The two agencies use different methods when it comes to these prediction tools, the California Department of Water Resources uses data that has a weighted average to compute statewide Snow Water Equivalent (SWE) and is known as a more conservative forecast method when comparing the two.

Wet-Season Baseflow Period (Feb. 15 – Apr. 14)

The next period within the Trinity River Restoration Program environmental flow management is the Wet-Season Baseflow Period, which initiates Feb. 15. The California Department of Water Resources February 90% B120 declaration was published on Feb. 11 as “normal” with the 90% determination at 1,295,000 acre feet.

The hydrograph developed by the Program with the “normal” water allocation does not exceed the current Trinity Reservoir dam releases which have ranged from 1500 cfs to 3500 cfs and are anticipated for the remainder of February because the reservoir is significantly encroached per the safety of dam criteria. For water accounting, the Program will deduct 60,000 acre feet from Reclamation flows during this period (Feb. 15 – Mar. 14), thus saving the reservoir valuable storage in the summer months.

With the river at levels above 300 cfs there are benefits to Trinity River salmonids as wetted areas are providing additional areas to biology within the system. Any reduction in flows would inhibit or halt such production in areas wetted by current flows.

Of course, unexpected flows always come as a shock. This water year has been unique in that maintenance on Clear Creek tunnel has initiated the need to send storage management releases down the Trinity versus to Whiskeytown Reservoir. To remain prepared, river enthusiasts should expect changing flows authorized by Reclamation through the month of March.

Prior to the next period (Apr. 15 – variable), the Program has a check-in on Mar. 15 to adjust flows to the March 90% B120 declaration. In April, the Program implements it’s spring snow-melt and recession hydrograph following the final B120 water year determination by the Department of Water Resources.