Biological Opinions - Bureau of Reclamation

of coho salmon fry in the mainstem Klamath River between IGD and Salmon River (RM 66)
from late March to mid-June when IGH salmonids are also in the mainstem.
Conversely, when conditions are favorable (e.g., good water quality, low juvenile abundance,
low disease), the proposed action is likely to have minimal adverse effects to coho salmon fry.
By mid-June, coho salmon fry are likely to have transformed from fry to parr, and coho fry
abundance in the mainstem Klamath River in late June is likely at a level that habitat reductions
resulting from the proposed action are minimal.
Given the abundance of coho salmon fry and juveniles is likely to be greatest in the mainstem
Klamath River from April through June, Reclamation has proposed a precautionary approach to
managing flows during the driest of conditions and has proposed to implement Hardy et al.’s
(2006) recommended ecological base flows as minimums during the April through June period.
During dry hydrologic conditions in the Klamath Basin, the proposed action will minimize
adverse effects to coho salmon fry in April to June by not reducing flows in the mainstem
Klamath River below what Hardy et al. (2006) considers to be acceptable levels of risk to the
health of aquatic resources. Note that Hardy et al. (2006) did not quantitatively assess disease
risks in the ecological base flow recommendation.
12.4.1.2.3.3 Disease
Ceratomyxosis, which is caused by the C. shasta parasite, is the focus for NMFS in the coho
salmon disease analysis because researchers believe that this parasite is a key factor limiting
salmon recovery in the Klamath River (Foott et al. 2009). Coho salmon in the Klamath River
have coevolved with C. shasta and are relatively resistant to infection from this parasite (Hallett
et al. 2012, Ray et al 2012). However, the high mortality of Klamath River salmonids from C.
shasta is atypical (Hallett et al. 2012). Modifications to water flow, sedimentation, and
temperature have likely upset the host-parasite balance in the Klamath River (Hallett et al. 2012).
NMFS believes the high incidence of disease in certain years within the mainstem Klamath River
results largely from the reduction in magnitude, frequency, and duration of mainstem flows from
the natural flow regime under which coho salmon evolved. The proposed action’s effects on
spring flows and channel maintenance flows and their relationship to disease are discussed
below. Research on the effects of C. shasta on coho salmon juveniles is applicable to coho
salmon fry because the parasite targets species not life stages (Hallett et al. 2012).
12.4.1.2.3.3.1 Spring Flows
The likelihood of coho salmon fry to succumb to ceratomyxosis is a function of a number of
variables, such as temperature, flow, and density of actinospores (True et al. 2013). Ray et al.
(2012) found that actinospore density, and then temperature, was the hierarchy of relative
importance in affecting ceratomyxosis for juvenile salmonids in the Klamath River. When
actinospore densities are high, thermal influences on disease dampen (Ray et al. 2012). Recent
studies are further supporting the observation of a threshold for high infectivity and mortality of
juvenile salmonids when the Klamath River actinospore density exceeds about 10 actinospores/L
(Hallett and Bartholomew 2006, Ray et al. 2012). For coho salmon juveniles, actinospore
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