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Table 11.5. Modeled suspended sediment concentrations, exposure durations, and likely effects to coho salmon under existing extreme conditions (10 percent exceedance probability), for Klamath River at Seiad Valley (RM 129; USDOI and CDFW 2013). 11.3.8.10 Fish Disease The following baseline information on aquatic diseases is mostly from Synthesis of the Effects to Fish Species of Two Management Scenarios for the Secretarial Determination on Removal of the Lower Four Dams on the Klamath River (Hamilton et al. 2011) and the Klamath Facilities Removal environmental impact statement/environmental impact report (USDOI and CDFW 2013). Existing data and observations in the Klamath River indicate that the most common pathogens of concern can be grouped into four categories: (1) viral pathogens such as infectious haematopoietic necrosis; (2) the bacterial pathogens R. salmoniranrum (bacterial kidney disease), Flavobacterium columnare (columnaris), and Aeromonas hydrophila; (3) external protozoan parasites Ichthyophthirius (Ich), Ichthyobodo, and Trichodina; and (4) the myxozoan 241
parasites Ceratomyxa shasta (causes ceratomyxosis) and Parvicapsula minibicornis. There is a lack of information concerning the presence of infectious haematopoietic necrosis and bacterial kidney disease either above or below IGD (Administrative Law Judge 2006). Columnaris is common worldwide and present at all times in the aquatic environment. Columnaris disease in cold water fishes is generally seen at water temperatures above 15 o C. In natural infections, the disease is often chronic to subacute, affecting skin and gills (CDFG 2004a). Ich infestation of gill tissue results in hyperplasia, a condition that reduces the ability of the fish to obtain oxygen. Death is by asphyxiation. Ich can be found on any fish at any temperature, but typically only causes disease and mortality at water temperatures above 14 o C and in crowded conditions (CDFG 2004a). Other common pathogens are likely present in the Klamath River, but are reported rarely. Ich and columnaris have occasionally had a substantial impact on adult salmon downstream of IGD, particularly when habitat conditions include exceptionally low flows, high water temperatures, and high densities of fish (such as adult salmon migrating upstream in the fall and holding at high densities in pools). In 2002, these habitat factors were present, and a disease outbreak occurred, with more than 33,000 adult salmon and steelhead losses, including an estimated 334 coho salmon (Guillen 2003). Most of the fish affected by the 2002 fish die-off were fall-run Chinook salmon in the lower 36 miles of the Klamath River (CDFG 2004a). Although losses of adult salmonids can be substantial when events such as the 2002 fish die-off occur, the combination of factors that leads to adult infection by Ich and columnaris disease may not be as frequent as the annual exposure of juvenile salmonids to C. shasta and P. minibicornis, as many juveniles must migrate each spring downstream past established populations of the invertebrate polychaete worm host. The life cycles of both C. shasta and P. minibicornis involve an invertebrate and a fish host, where these parasites complete different parts of their life cycle. In the Klamath River, P. minibicornis and C. shasta share the same invertebrate host: an annelid polychaete worm, Manayunkia speciosa (Bartholomew et al. 2006). Once the polychaetes are infected, they release C. shasta actinospores into the water column. Temperature and actinospore longevity are inversely related. In one study, actinospores remained intact the longest at 4°C, but were shortlived at 20°C. Actinospores are generally released when temperatures are above 10°C, and remain viable (able to infect salmon) from 3 to 7 days at temperatures ranging from 11 to 18ºC (Foott et al. 2006). When temperatures are outside of 11 to 18ºC, actinospores are viable for a shorter time. As actinospore viability increases, actinospore distribution may increase, raising the infectious dose for salmon over a larger area of the river (Bjork and Bartholomew 2010). Actinospore abundance, a primary determinant of infectious dose, is controlled by the number of polychaetes and the prevalence and severity of infection within their population. Salmon become infected when the actinospores enter the gills, and eventually reaching the intestines. At that point, the parasite replicates and matures to the myxospore stage. Myxospores are shed by the dying and dead salmon, and the cycle continues with infection of polychaete worms by the myxospores (Bartholomew and Foott 2010). Transmission of the C. shasta and P. minibicornis parasites is limited to areas where the invertebrate host is present. Susceptibility to C. shasta is also influenced by the genetic type of C. shasta that a fish encounters. Atkinson and Bartholomew (2010a, 2010b) conducted analyses of the genotypes of 242
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National Marine Fisheries Service U
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7.4.5 LRS and SNS Population Dynami
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11.1.5 Critical Assumptions .......
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16 APPENDICIES ....................
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Table 8.2 UKL end-of-month elevatio
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LIST OF FIGURES Figure 3.1. The act
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Figure 11.17. Coho salmon fry habit
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ABBREVIATIONS AND ACRONYMS Abbrevia
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Abbreviation/Acronym YTEP WDFW WRIM
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In 2001, the Services issued BiOps
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Findings of Fact and Order of Deter
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proposed changes to the vegetation
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Figure 3.1. The action area for Rec
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4 PROPOSED ACTION Reclamation propo
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4.2 Element Two Operate the Project
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October 1 and March 1. The proposed
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Reclamation incorporated the 1981 t
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Provide Project irrigation deliveri
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Table 4.3. UKL fill rate adjustment
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Table 4.5. Calculation of fall/wint
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Flows below IGD are ultimately the
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The EWA, Project Supply, and UKL Re
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Table 4.8. Environmental Water Acco
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eleases somewhat on the ascending l
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fish disease, die off, entrainment,
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acre-feet when the Project Supply c
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Table 4.11. Monthly maximum Lower K
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4.2.4 Ramp-Down Rates at Iron Gate
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progresses and EWA volumes are upda
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O&M activities are carried out eith
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1. The A Canal has six headgates th
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Therefore, Reclamation proposes to
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coordinate with the NMFS to develop
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the confluence with Omogar Creek at
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though several major improvements t
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Sucker larvae transform into age-0
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units: (1) Clear Lake; (2) Tule Lak
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Figure 7.2. Adult spawning populati
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Table 7.1. Estimated LRS and SNS ad
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1905, Ch. 567, 33 Stat. 714). The P
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Figure 7.4 Modeled April through No
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7.9.2 Klamath Basin The Oregon Clim
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A change in mean precipitation rang
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Table 7.2 Impaired water bodies wit
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Table 7.3 Seasonal comparisons of p
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ammonia that is lethal to 50 percen
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Table 7.4 Estimated external phosph
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examination of juvenile suckers fro
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Evaluation of baseline hydrology in
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2012 1931 through 2012 12.6% 0.24 5
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The overall water year trend (Table
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Figure 7.7 Sprague River trends, wa
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Figure 7.9 Sprague River trends, wa
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Figure 7.12 Williamson River trends
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Figure 7.14 UKL trends, water years
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Figure 7.17 UKL: net inflow departu
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7.10.3.3 Competition and Predation
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By late July, surviving larval suck
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Threat Nature of Threat Life Stage
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2011) and increased adult spawning
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Based on the best available informa
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contrast, water levels began 1.5 ft
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evaporation and seepage estimated a
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prolonged low oxygen conditions if
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The April through September 4,034.6
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8 EFFECTS OF THE ACTION ON LOST RIV
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Although the volume of Project wate
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than 1 m), and fitting one or more
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Figure 8.3. UKL elevations at the e
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Services and Reclamation will deter
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For cumulative net inflow values be
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Figure 8.8. UKL elevations at the e
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Figure 8.10. UKL elevations at the
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Figure 8.12. UKL elevations at the
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natural and man-caused changes in i
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Table 8.1 UKL end-of-month surface
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UKL. Based on best available inform
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larvae in UKL. Annual production of
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Table 8.5 UKL end-of-month elevatio
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Based on our review of the literatu
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into the Pelican Bay water quality
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We assume that UKL surface elevatio
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vary by several orders of magnitude
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survival rates, we know that some o
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populations, and contains the large
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8.3.5.1 Effects to Adult Sucker Spa
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Table 8.8 Clear Lake surface elevat
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occur, especially in the west lobe.
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Table 8.9 End of the month surface
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8.3.7.4 Effects of Entrainment Loss
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The source of the sediment is unkno
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period when they migrate upstream t
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limited LRS and SNS persistence in
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term and localized and because fish
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8.5.1 Canal Salvage Reclamation pro
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high predation rates and failure of
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include the Klamath Basin Rangeland
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Figure 9.1 Designated CHUs for the
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These are discussed in greater deta
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The proposed action will have no ef
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No other spawning habitat exists be
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consulted on. Current monitoring da
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proposed action and this PCE suppor
Page 207 and 208: Because of a multi-decade lack of r
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Page 211 and 212: that juvenile survival is most like
Page 213 and 214: elocation effort in Lake Ewauna to
Page 215 and 216: LRS and SNS population resiliency o
Page 217 and 218: stratum 4 (Interior Klamath) in whi
Page 219 and 220: Pacific salmonids Oncorhynchus spp.
Page 221 and 222: scenario, actions and elements of t
Page 223 and 224: flow prescriptions should mimic pro
Page 225 and 226: 11.2.1 Current Condition of Critica
Page 227 and 228: 11.2.2 Factors Affecting SONCC Coho
Page 229 and 230: e disoriented or displaced downstre
Page 231 and 232: enhancement, and rehabilitative act
Page 233 and 234: Water Temperature Sedimentation Org
Page 235 and 236: Figure 11.1 Longitudinal and season
Page 237 and 238: functioning floodplains that fail t
Page 239 and 240: downstream of IGD, (2) enhance coho
Page 241 and 242: few local ranchers and water distri
Page 243 and 244: in some tributaries, access to and
Page 245 and 246: 11.3.7 Summary of Critical Habitat
Page 247 and 248: these two time periods, the effects
Page 249 and 250: consists of approximately 29,000 ac
Page 251 and 252: The PacifiCorp habitat conservation
Page 253 and 254: IGD, or used in constructed habitat
Page 255 and 256: estoration, watershed planning, sal
Page 257: Table 11.4. Modeled suspended sedim
Page 261 and 262: that become infected is estimated t
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Page 265 and 266: minimizing disease risks, the detai
Page 267 and 268: Figure 11.4. Proposed action, histo
Page 269 and 270: Figure 11.6. Proposed action weekly
Page 271 and 272: Figure 11.9. Regression between EWA
Page 273 and 274: Figure 11.11. Proposed action and o
Page 275 and 276: Figure 11.12. Number of days per wa
Page 277 and 278: Figure 11.14. Monthly coefficient o
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Page 281 and 282: The results from Table 11.7 indicat
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Page 287 and 288: Table 11.9. Daily average mainstem
Page 289 and 290: Table 11.10. Daily average mainstem
Page 291 and 292: 5% 3336 13176 27664 26168 30946 237
Page 293 and 294: The proposed action results in agri
Page 295 and 296: Figure 11.21. Monthly mean of daily
Page 297 and 298: Riparian restoration projects will
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Page 301 and 302: Table 11.13. Annual percent of proj
Page 303 and 304: esource needs as they grow, and 3)
Page 305 and 306: 11.5.2 Klamath River Basin Adjudica
Page 307 and 308: coho salmon within the Klamath Rive
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aspects of a natural flow regime th
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element of coho salmon critical hab
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12.1.1.1 Risk Analyses for Endanger
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ESU DIVERSITY STRATA POPULATIONS IN
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eproduction, and distribution. The
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Figure 12.2. Historic population st
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the average ratio of IP-km to total
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Although long-term data on coho sal
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1980 1981 1982 1983 1984 1985 1986
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maintain viable abundances in many
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12.2.5.5 Viability Summary Though p
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coastal currents and upwelling, kno
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12.2.6.2 Marine Derived Nutrients M
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fisheries south of Cape Falcon, Ore
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12.3 Environmental Baseline of Coho
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water temperatures up to 19 ºC in
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some coho salmon smolts may stop mi
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threshold, all Klamath River coho s
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abundance threshold (Table 12.3). T
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mainstem Klamath and Trinity rivers
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Although there are risks to Klamath
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activities are generally beneficial
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12.4 Effects to Individuals The pro
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12.4.1.2 Response 12.4.1.2.1 Adults
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(2012) believes is representative o
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genotype II density of 5 spores/L w
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flows provide a limit to the increa
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polychaete and sediment disturbance
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which will likely result in a relat
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etween Trees of Heaven (RM 172) and
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action. Reclamation estimated that
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Based on literature, increased comp
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Table 12.6. Summary of risks result
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most juveniles. Stream flow diversi
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at most fish relocation sites, base
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higher, the minimally increased sed
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Small pulses of moderately turbid w
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Boulder faces in the deflector stru
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conditions may fail if those condit
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Adverse effects of the proposed act
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Potential Stressor Habitat Reductio
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Potential Stressor Elevated water t
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12.6.2 Effects of fitness consequen
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13 INCIDENTAL TAKE STATEMENT Sectio
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Table 13.1 Summary of maximum annua
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in fewer larvae and juveniles, and
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Table 13.2 Estimated annual maximum
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1.2.1.8. Incidental Take Caused by
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characteristics of aquatic species,
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Table 13.5 Expected annual Environm
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Cause of Incidental Take Habitat Re
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Clear Lake, Gerber Reservoir, and T
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This term and condition is requirin
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13.4 Mandatory Monitoring and Repor
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Required hydrologic monitoring incl
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Table 13.7. Summary of LRS and SNS
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T&C or Mandatory Monitoring Mandato
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Table 13.9 Summary of reporting and
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Table 13.10 Summary of meetings req
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the above QA/QC procedures describe
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Barry, P.M., E.C. Janney, D.A. Hewi
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Burdick, S.M. and J. Rasmussen. 201
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Dunsmoor, L., L. Basdekas, B. Wood,
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Garen, D. 2011, Upper Klamath Basin
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Janney, E.C., B.S. Hayes, D.A. Hewi
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Laenen, A., and A.P. LeTourneau. 19
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Miller, R.R., and G.R. Smith. 1981.
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Perkins, D.L., and G.G. Scoppettone
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(Deltistes luxatus) in Tule and Cle
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Terwilliger, M. 2006. Physical habi
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USBR [U.S. Bureau of Reclamation].
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Williams, J.E. 2000. Chapter 13. Th
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Arthington, A.H., S.E. Bunn, N.L. P
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Beeman, J., S. Juhnke, G. Stutzer a
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Brommer, J.E. 2000. The evolution o
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Department of the Army Regional Gen
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Chilcote, M. W. 2003. Relationship
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Dunsmoor LK, and Huntington CW. 200
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Foott, J.S., R. Stone, E. Wiseman,
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Habera, J.W., R.J. Strange, B.D. Ca
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Hemstreet, T. 2013. Electronic mail
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Jordan, M. S. 2012. Hydraulic predi
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Kostow, K. E., A. R. Marshall and S
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MacFarlane, R. B., S. Hayes, and B.
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Moyle, P. B. 2002. Inland Fishes of
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PacifiCorp Klamath Hydroelectric Pr
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Oregon Department of Environmental
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Puckridge, J. T., F. Sheldon, K. F.
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Ring, T.E. and B. Watson. 1999. Eff
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Sommer, T. R., M. L. Nobriga, W. C.
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Taylor, R. 1991. A review of local
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USFWS [U. S. Fish and Wildlife Serv
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Ward G, and Armstrong N. 2010. Asse
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Winker, K., J. H. Rappole, and M. A
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77 FR 476. National Marine Fisherie
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UKL Elevation (feet) Active Storage
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16.2 Appendix B: Elevation Flow Dat
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490
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Week of Water Year 1981 1982 1983 1
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Water Year October November Decembe
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16.3 Appendix C: Description of Res
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4. Removal of Small Dams (permanent
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Information regarding consideration
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9. Piping Ditches a. Project Descri
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. Site-Specific Restrictions Restri
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6. Protection Measures The followin
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to enter or be placed where they co
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shall be distributed throughout the
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weed free straw, silt fences) are i
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the project is located, and compris
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2. Post Construction Monitoring and
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Median Seasonal Flow (acre-feet) Me
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Median Seasonal Net Inflow (acre-fe
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16.5 Appendix E: Observed and Model
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Observed and modeled proposed actio
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Observed and modeled proposed actio
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16.6 Appendix F: Analyzing the rela
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Table 1. Paired comparison of the c
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Table 3. The difference in the mean
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