Biological Opinions - Bureau of Reclamation

that become infected is estimated to be 10 to 70 percent annually based on surveys of fish
captured in the river (True et al. 2010). High infection rates are apparently resulting in high
mortality of outmigrating smolts. Studies of outmigrating coho salmon smolts by Beeman et al.
(2008) estimated that disease-related mortality rates were between 35 and 70 percent in the
Klamath River near IGD. Their studies suggest that higher spring discharge increased smolt
survival (Beeman et al. 2008). In 2008, mortality rates were as high as 85 percent in May (7-day
exposure for age 1+ coho smolts) and 96 percent (age 0+ coho smolts).
Foott et al. (1999) found that when water temperatures are under 17 °C, Klamath River
salmonids appear to be more resistant to ceratomyxosis. The risk of mortality from
ceratomyxosis was lowest as water temperatures increased from 13 to 15 °C, and was greatest as
temperatures increased from 18 to 21 °C (Ray et al. 2012). In 2010, water temperatures did not
exceed 16 °C until June, which was two to three weeks later than previous years. The delay in
warmer water temperatures may have hindered the development of the polychaete host, the
actinospore stage of C. shasta within the polychaete, or both (Ray et al. 2012). While the water
years between 2007 and 2010 were very similar, coho salmon mortality in 2010 from
ceratomyxosis was low compared with previous years (Ray et al. 2012).
Disease effects are likely to negatively impact all of the VSP parameters of the Interior-Klamath
populations because both adults and juveniles can be affected. In terms of critical habitat,
disease impacts adult and juvenile migration corridors, and juvenile spring and summer rearing
areas.
11.3.8.11 Climate Change
Climate change is likely to have both negative and positive effects on the SONCC coho salmon
populations in the action area. Coho salmon populations in the Klamath basin will have their
freshwater habitat detrimentally affected by alterations in river flows and water temperature as a
result of climate change. However, increased rainfall may increase the duration that intermittent
streams serve as refuges from high mainstem flows.
The hydrologic characteristics of the Klamath River mainstem and its major tributaries are
dominated by seasonal melt of snowpack (NRC 2004). Van Kirk and Naman (2008) found
statistically significant declines in April 1 snow water equivalent since the 1950s at several snow
measurement stations throughout the Klamath basin, particularly those at lower elevations
(