Kootenai River Native Fish Restoration and Conservation Aquaculture
Statement of Work and Budget FY2012 and 2013

BPA Project Number:  1988-064-00
BPA Project Title: Kootenai River Native Fish Restoration and Conservation Aquaculture
Contract Number:
Performance/Budget Period: 5/1/12 - 1/31/14

Goal:  Prevent extinction, preserve existing gene pool, and begin rebuilding healthy age class structure of the endangered white sturgeon and burbot in the Kootenai River using conservation aquaculture techniques with wild broodstock.  

Abstract:  Fish and wildlife resources in the Kootenai drainage were historically abundant and were used by the Kootenai Tribe for cultural and subsistence purposes.  Over the past decades, native fish and wildlife populations have declined significantly due to large-scale habitat and ecosystem changes.  Native kokanee from the South Arm of Kootenay Lake are considered “functionally extinct”, burbot from the lower Kootenai River are on the verge of extinction, and the white sturgeon population in the Kootenai River was listed as endangered by the U.S. Fish and Wildlife Service in 1994. The Kootenai Sturgeon Conservation Aquaculture Project was initiated by the Kootenai Tribe of Idaho as a stopgap measure in 1989 to produce fish from wild Kootenai River adults until effective habitat restoration measures could be identified and implemented.  Only the long life span of the sturgeon has forestalled extinction to date.  Natural recruitment has been absent or limited for decades and the current population of large old fish is steadily dwindling.  Continued failure of natural recruitment means that the next generation of Kootenai white sturgeon will come almost entirely from the hatchery.  The Tribe, in cooperation with many agencies and stakeholders, is implementing a native fish restoration program in the Lower Kootenai River for sturgeon, burbot, and kokanee using conservation aquaculture techniques with wild broodstock.  

The project is reflective of and integrated with ESA recovery goals for the white sturgeon outlined in the 1999 USFWS Recovery Plan and the 2006 Biological Opinion for White Sturgeon (RPA Component 4). Implementation is guided by the Conservation Aquaculture Plan for White Sturgeon prepared by the Tribe in cooperation with the USFWS White Sturgeon Recovery Team. Additionally, this project is being implemented as part of the Kootenai River Adaptive Management Program outlined in the Kootenai Subbasin Management Plan (Section 10.3.4 - page 94).

An Environmental Assessment was completed for this project in April 1997 (Kootenai River White Sturgeon Conservation Aquaculture Project - DOE/EA-1169).


Sturgeon Conservation Aquaculture Project Summary
Fish and wildlife resources in the Kootenai drainage were historically abundant and were used by the Kootenai Tribe for cultural and subsistence purposes.  Over the past decades, native fish and wildlife populations have declined significantly due to large-scale habitat and ecosystem changes.  The Kootenai River White Sturgeon Study and Conservation Aquaculture Project was initiated by the Kootenai Tribe of Idaho as a stopgap measure in 1989 to produce fish from wild Kootenai River adults until effective habitat restoration measures could be identified and implemented.  Aquaculture techniques were applied to the Kootenai River white sturgeon population in response to concerns that missing year classes, failed recruitment, and skewed age class structure were threatening this population with extinction. An independently produced conservation breeding plan to preserve the population' s remaining genetic variation was implemented in 1994 (Kincaid 1993). The population was listed as endangered under the Endangered Species Act (ESA 1973) in 1994 (USFWS 1994), due to unmitigated population decline and predominant recruitment failure on a decadal scale.  

A USFWS Recovery Plan for the population was completed during 1999 (USFWS 1999).  Subsequent concerns regarding duration, breadth, and magnitude of Kootenai River ecosystem degradation in Montana, Idaho, and British Columbia, and repeated failure to restore natural recruitment during the past decade suggested that a conservation hatchery program was warranted to preclude extinction. Empirical demographic modeling during 2002 revealed the increasingly imperiled condition of this population.  Model simulations suggested that 90, 75, and 72% reductions in population abundance, biomass, and annually available spawners occurred from 1980 to 2002; population size was estimated to decrease by 50% every 7.4 years (Paragamian et al. 2005).  The 2003 population abundance estimate for Kootenai River white sturgeon was approximately 600 fish (Paragamian et al. 2005).

Without hatchery intervention, population extinction is certain during the next 20-40 years. With intervention, assuming ongoing natural recruitment failure, this hatchery program will contribute to demographic restoration and protection of remaining genetic variability during the next 30 to 50 years, while improvements in the Kootenai River ecosystem occur to collectively reestablish natural production and ecological function.

The Kootenai River White Sturgeon Conservation Aquaculture Program has expanded since the initial implementation of the Kincaid Plan in 1994.  Since then, the Program has: 1) produced, released, and monitored frequent year classes of captive-reared progeny from wild, native brood stock, 2) continued to preserve within-population genetic diversity, 3) minimized disease introduction and transmission, and 4) substantially contributed to the developing field of white sturgeon conservation aquaculture (Anders 1998; LaPatra et al. 1999; Ireland et al. 2002a, 2002b).
The program is designed to preserve the locally adapted Kootenai River white sturgeon genotypes, phenotypes, and associated life history traits and restore age class structure to maximize future population viability and persistence.  The program incorporates an Adaptive Management approach (Walters 1986; Walters 1997) and will be modified as necessary, following collection and analysis of the most recent and most complete empirical datasets.  These datasets will then be used in updated ecosystem, demographic, and genetic models to guide the Program and maximize it's effectiveness and success, in the broader context of Kootenai River ecosystem restoration.

Burbot Conservation Aquaculture Summary
Native burbot (Lota lota) in the Kootenai River in Idaho have been petitioned for ESA listing, are Red Listed in B. C., and are a designated species of Special Concern in Idaho. In Montana, however, burbot are considered common, although they are also listed there as a species of special concern. It is believed that at one time, the burbot fishery in Idaho produced many thousands of fish each winter. Tribal elders report that ling were extremely abundant in the Kootenai River in Idaho and were a main staple for the Tribe in the late winter/early spring months.  The Kootenai Tribe relied heavily upon this important subsistence fishery and tribal members were very adept at using weirs and traps.  Burbot also provided a valuable social, sport, and commercial fishery but the fishery collapsed soon after the completion of Libby Dam (Paragamian et al. 2000). Burbot were once very important to the anglers of Kootenay Lake, as well. Creel data from the West Arm of Kootenay Lake revealed that during some years, the harvest of burbot exceeded 26,000 fish (Paragamian et al. 2000). Just as in Idaho, the Canadian fishery collapsed soon after Libby Dam began operations.

An investigation initiated in 1993 was implemented by IDFG to assess burbot abundance, distribution, size, reproductive success, and movement, and to identify factors limiting burbot in the Kootenai River in Idaho and British Columbia. A total of only 17 burbot were caught in 1993 (CPUE of one burbot/33 net days) and 8 in 1994 (CPUE of one burbot/111 net days).  Only one burbot was captured between Bonners Ferry and the Montana border, with no evidence of reproduction in Idaho. Unspawned females have been caught (post spawn) that were reabsorbing eggs, as have males (one month post spawn) that were in various stages of gonadal maturity. Burbot sampling during the winter of 1993 through 1994 at the mouths of Kootenai River tributaries in Idaho occurred with anticipation of intercepting a spawning run of fish from Kootenay Lake or the lower Kootenai/y River, but no burbot were caught. Cooperative sampling in the British Columbia river reach suggested that burbot were only slightly more abundant in the lower river. Telemetry studies have shown that the population is transboundary (Paragamian 2000).  

Native burbot in the Idaho and Canadian portion of the Kootenai River drainage are at risk of becoming extinct (Paragamian 1996).   Overexploitation of burbot in Kootenay Lake and Kootenai River was a concern for fish managers when it became evident the fishery was at risk of failing.  Measures were taken to reduce exploitation by reduction in creel limits and fishery closures but none of these measures restored the fishery (Paragamian 2000).  Examples of stock rebound in overexploited burbot populations with fishery restrictions or closures have been documented, although habitat was generally intact in such cases (Paragamian et al. 2000).  IDFG has been monitoring the movement, habitat use, and spawning behavior of burbot since 1993 and has not found evidence of successful spawning or recruitment in Idaho.  Operation of Libby Dam for hydropower (including power peaking) and flood control during the winter months has resulted in more erratic flows that are up to 3 fold higher than pre-dam conditions and warmer winter water temperatures. In addition, Lake Koocanusa, the impoundment created by Libby Dam, acts as a nutrient sink and has reduced productivity of the river (Snyder and Minshall 1996; Richards 1996).  Potential threats to the population include: current winter flow management, power peaking, changes in river temperature, loss of slough and side-channel habitat from diking, nutrient loss, and spring management of Kootenay Lake (Paragamian et al. 2000; KRSS 2000).

In 2002, KTOI convened a burbot recovery committee of local stakeholders and scientists from agencies in the Kootenai/y drainage to identify and implement conservation strategies to help alleviate threats to the species (KTOI 2004).  Conservation strategies identified in recovery plan for burbot include: ecosystem recovery, development of a winter flow plan, spring management of Kootenay Lake levels, use of donor stocks, captive broodstock and culture.   As with white sturgeon, conservation aquaculture may play a positive role in the recovery of this species, while efforts to restore habitat conditions necessary for the survival and natural production of burbot continue.  A Memorandum of Understanding signed by the participating management agencies and stakeholders defines the commitment of the participants to implement the conservation strategy to restore burbot in the Kootenai/y drainage. This project will continue to work cooperatively with agencies and the University of Idaho to develop, refine, and implement culture techniques for native burbot.

Kootenai River Native Fish and Conservation Aquaculture Hatchery Step Planning Process
Additionally, we are in a planning process to provide the Kootenai River Native Fish Restoration and Conservation Aquaculture Program for sturgeon and burbot with expanded facilities and support of ongoing operations and maintenance and monitoring and evaluation including:
Upgrading the Kootenai sturgeon production facilities at the existing Tribal Sturgeon Hatchery near Bonners Ferry, Idaho
Developing  a new artificial production facility for Kootenai sturgeon and burbot at the confluence of the Moyie and Kootenai Rivers (Twin Rivers Hatchery)
Collecting native Kootenai sturgeon broodstock from the Kootenai River
Collecting native burbot broodstock from within basin sources (i.e. Moyie Lake stock from British Columbia)
Spawning, incubating, and rearing Kootenai sturgeon and burbot
Refining aquaculture apparatus and techniques for sturgeon and burbot
Releasing Kootenai sturgeon and burbot at appropriate developmental stages to suitable habitat in the Kootenai River
Supporting operations and monitoring at both facilities