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Northeast Oregon-Southeast Washington (NEOR-SEWA

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Northeast Oregon-Southeast Washington (NEOR-SEWA Dr. Craig Busack ii 4.3 Condition of the Action Area ......................................................................................................... 62 4.3.1 Consultations and Conservation Efforts in the Action Area ................................................. 63 4.3.2 Effects of Climate Change in the Action Area ....................................................................... 64 4.4 Conservation Role of the Action Area ........................................................................................... 65 5. Effects of the Proposed Action ........................................................................................... 67 5.1 Locations and Associated Actions Resulting in Insignificant and/or Discountable Effects ......... 67 5.1.1 Adult Collection .............................................................................................................. 68 5.1.2 Hatchery Origin Spring Chinook Adult Outplanting ............................................... 68 5.1.3 Water Diversions .............................................................................................................. 69 5.1.4 Effluent ............................................................................................................................... 71 5.1.5 Facility Operation and Maintenance .......................................................................... 73 5.1.6 Acclimation and Release ................................................................................................ 73 5.1.7 Monitoring and Evaluation ........................................................................................... 74 5.2 Direct Effects to Bull Trout ............................................................................................................ 74 5.2.1 Adult Collection ................................................................................................................ 74 5.2.2 Water Diversions .............................................................................................................. 76 5.2.3 Effluent/Fish Health ......................................................................................................... 79 5.2.4 Facility Operation and Maintenance ........................................................................... 80 5.2.5 Acclimation and Release ................................................................................................. 81 5.2.6 Monitoring and Evaluation ............................................................................................ 81 5.3 Direct Effects to Critical Habitat for Bull Trout ............................................................................ 85 5.4 Indirect Effects ............................................................................................................................... 95 5.5 Interrelated/Interdependent Effects ............................................................................................... 96 6. Cumulative Effects .............................................................................................................. 97 7. Conclusion ............................................................................................................................ 99 7.1 Bull Trout ....................................................................................................................................... 99 7.2 Bull Trout Critical Habitat ............................................................................................................ 99 8. Incidental Take .................................................................................................................... 99 9. Conservation Recommendations ...................................................................................... 112 10. Reinitiation Notice – Closing Statement .......................................................................... 112 LITERATURE CITED ............................................................................................................ 113 Dr. Craig Busack iii ACRONYMS AFS American Fisheries Society BA Biological Assessment BLM Bureau of Land Management BPA Bonneville Power Administration BT Bull Trout CFR Code of Federal Regulations CHU Critical Habitat Unit Corps Army Corps of Engineers CTUIR Confederated Tribes of the Umatilla Indian Reservation CWA Clean Water Act DNA Deoxyribonucleic acid DPS Distinct Population Segment EPA Environmental Protection Agency ESA Endangered Species Act FDA Food and Drug Administration FH Fish Hatchery FMO Foraging, Migrating, and Overwintering FR Federal Register HCP Habitat Conservation Plan IDFG Idaho Department of Fish and Game IGDO inter-gravel dissolved oxygen IHNV Infectious Hematopoietic Necrosis Virus IHOT Integrated Hatchery Operations Team IMW Intensively Monitored Watershed IPCC Intergovernmental Panel on Climate Change IPNV Infectious Pancreatic Necrosis Virus LSRCP Lower Snake River Compensation Program M&E Monitoring and Evaluation mg/L milligrams per liter MHHW Mean Higher High Water MLLW Mean Lower Low Water NE Northeast NOAA National Marine Fisheries Service NOAA National Oceanic and Atmospheric Administration NPDES National Pollution Discharge Elimination System NPT Nez Perce Tribe O&M Operations and Maintenance ODEQ Oregon Department of Environmental Quality ODFW Oregon Department of Fish and Wildlife OHW Ordinary High Water Opinion Biological Opinion OR Oregon PBF Physical or Biological Features PCE Primary Constituent Element PIT Passive Integrated Transponder Dr. Craig Busack iv PNFHPC Pacific Northwest Fish Health Protection Committee Rkm River kilometer SE Southeast SR Spawning and Rearing SRSRB Snake River Salmon Recovery Board USFS US Forest Service USFWS US Fish and Wildlife Service VHSV Viral Hemorrhagic Septicemia Virus WA Washington WDFW Washington Department of Fish and Wildlife WDNR Washington Department of Natural Resources WDOE Washington Department of Ecology Dr. Craig Busack 1 INTRODUCTION This document represents the U. S. Fish and Wildlife Service's (Service) Biological Opinion (Opinion) for the National Oceanic and Atmospheric Administration, National Marine Fisheries Service’s (NOAA’s) issuance of section 10(a)(1)(A) permits for the continued operation and maintenance of the Northeast Oregon and Southeast Washington Spring/Summer Chinook, Steelhead and Rainbow Trout Hatchery Programs funded by the Service’s Lower Snake River Compensation Plan (LSRCP) Office and the Bonneville Power Administration (BPA), and its effects on bull trout (Salvelinus confluentus) and designated critical habitat in accordance with section 7 of the Endangered Species Act (Act) of 1973, as amended (16 U.S.C. §§ 1531 et seq.). The three action agencies jointly prepared and submitted a Biological Assessment (Assessment), dated April 18, 2014; the request for formal consultation was received by our office on April 22, 2014. The Service requested additional information that was provided by LSRCP and BPA on May 13, 2014. The Service sent an email back to LSRCP and BPA initiating consultation on May 21, 2014. Additional information and clarifications regarding the proposed action and potential effects continued to be provided through April, 2016. This Opinion is based on information provided in the April 18, 2014 Assessment, the requested clarifications provided on May 13, 2014, an additional piece of the proposed action provided on April 12, 2016, Hatchery Genetic Management Plans for the 12 programs covered, correspondence with project staff at the BPA and the LSRCP office, and other sources of information. A complete record of this consultation is on file at the Service’s La Grande Field Office in La Grande, Oregon. CONSULTATION HISTORY The LSRCP Office initiated consultation on May 19, 1998 with the Service’s Snake River Basin Office for all LSRCP Programs under a programmatic Assessment. The Service issued an Opinion on Operation of the LSRCP Program (File # 1024.0000, 1-4- 99-F-2) on April 8, 1999. Work at BPA-funded facilities is conducted under Section 10 permits that have been issued to the Confederated Tribes of the Umatilla Indian Reservation (CTUIR) (permit TE844468-10) and the Columbia River Intertribal Fish Commission (permit TEOO1598-5). LSRCP requested the Service review a draft Assessment on May 6, 2013. The Service provided comments to the draft Assessment on July 30 and August 12, 2013. The Service, BPA, LSRCP, and National Marine Fisheries Service (NOAA) had a conference call to discuss Service comments on the draft Assessment and combining BPA and LSRCP funded programs into a single Assessment on September 20, 2013. BPA and LSRCP requested a review of the combined draft Assessment on January 8, 2014. The Service provided comments to the January 8, 2014 draft Assessment on January 29, 2014. The Service, NOAA, BPA, and LSRCP had a conference call to discuss multiple hatchery consultations on February 11, 2014. Dr. Craig Busack 2 There was a follow-up meeting on March 21, 2014, in which the draft Assessment at that date was deemed by all parties to be complete. The Service received a request from NOAA for consultation on the project and final Assessment on April 22, 2014. The Service requested additional information that was provided by LSRCP and BPA on May 13, 2014. The Service sent an email back to NOAA (and LSRCP and BPA) initiating consultation on May 21, 2014. The Service sent a draft Opinion to NOAA, BPA, and LSRCP for review
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