Biological Opinions - Bureau of Reclamation

similar to Chinook salmon infection rates since coho salmon have similar susceptibility to C.
shasta as Chinook salmon (Stone et al. 2008). In 2008, 46 percent of the Chinook salmon
sampled from the mainstem Klamath River between the Shasta River and Scott River in May and
June were infected and up to 37 percent showed clinical infections (e.g., inflammatory tissue in
>33% of the intestine section; Nichols et al. 2009).
As previously discussed in the Hydrologic Effects section (i.e., section 11.4.1.1), the proposed
action generally reduces spring flows in the mainstem Klamath River downstream of IGD. By
reducing spring flows, the proposed action will result in drier hydrologic conditions in the
mainstem Klamath River relative to the natural hydrologic regime. Summer base flow
conditions occur earlier than historically, with spring flows now receding precipitously in May
and June, whereas the spring snow-melt pulse and the vast amount of upper Klamath Basin
wetland historically attenuated flows in the Klamath River much more slowly into August or
September. Therefore, when environmental conditions are conducive to actinospore release in
the spring (e.g., elevated water temperature), the proposed action will likely result in hydrologic
conditions in the mainstem Klamath River that contribute to high C. shasta actinospore
concentrations (e.g., ≥5 spores/L actinospore genotype II), which will likely increase the
percentage of disease-related mortality to coho salmon fry in the mainstem Klamath River
between Trees of Heaven (RM 172) and Seiad Valley (RM 129) in May to mid-June (Foot et al.
2008, Hallett et al. 2012, Ray et al. 2012). The proposed action will also likely increase the
percentage of coho salmon fry in the mainstem Klamath River between Klamathon Bridge (RM
184) and Orleans (RM 59) that will experience sublethal effects of C. shasta infections during
April to mid-June. Sublethal effects include impaired growth, swimming performance, body
condition, and increased stress and susceptibility to secondary infections (Hallett et al. 2012).
NMFS notes that Reclamation added a near real-time disease management element to the
proposed action for deviating from the formulaic approach and increasing spring flows when
near-real-time monitoring shows that disease thresholds have been met and EWA surplus volume
is available. Flow increases in the spring to avert potential risks of disease will occur through
close coordination between the Services and Reclamation with consideration to potential effects
to listed suckers. While NMFS cannot specifically predict the full range of hydrologic
conditions when flow increases above the formulaic approach will occur, surplus EWA volume
will likely be available in wet to below average hydrological water years. Because actinospore
densities are likely low during above average and wet years, the proposed increase in spring
flows will help dilute actinospore densities in the mainstem Klamath River below IGD during
average and below average water years. Therefore, the real-time disease management element of
the proposed action may minimize disease risks to coho salmon during average and below
average water years. Note that when EWA surplus volume is used to increase spring flows,
summer flows in the mainstem will be lower than modeled, depending on the amount of EWA
surplus volume used for adaptively minimizing disease risks. However, minimum daily flows in
the summer will not be affected by the near real-time disease management.
During dry water years, the proposed daily minimum flows for April, May and June will provide
at least 1325 cfs, 1175 cfs, and 1025 cfs, respectively, at IGD for diluting actinospores. While
these proposed minimum daily flows are not likely sufficient to dilute actinospore concentrations
to below 5 genotype II spores/L when actinospore concentrations are high, these minimum daily
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