DOCUMENTING CHANGE AT UPPER HAMBURG BEND: NEBRASKA\u27S FIRST SIDE-CHANNEL RESTORATION

In 1996 a side channel was excavated on 629 hectares of former agricultural land at Upper Hamburg Bend on the Missouri River in Otoe County, NE. This was the first side channel constructed on the Missouri River in an attempt to restore lost aquatic habitat. The initial design was for an approximately 4,200 m long side channel to be constructed with a 3 m bottom width. Development ofthe site was to be dependent on flows diverted from the main channel of the river with a final projected top width of 61 m. The side channel was completed in the spring, and shortly thereafter the site was subjected to a series of flood events. The side channel has been subjected to periods of both high and low water since opening. We documented physical changes at the site with the aid of aerial photography, acoustic Doppler current profiler (ADCP) surveys, and topographic surveys. By 2010 the side channel was 4,342 m long with a mean top width of89.5 m. Channel development has occurred during periods of high and low water. ADCP surveys established that mean depths and velocities have increased since 2001. An increase in the amount of discharge through the side channel since 2001 has resulted in the loss of some of the shallower and lower velocity habitats. Modifications to the site may be necessary to reverse this loss of shallow, slow water habitat that the side channel was designed to provide. Although new off-channel aquatic habitat has been created, channel development has been impacted by the presence of rock control structures throughout the site. Reducing the number of control structures to the minimum necessary to prohibit the side channel from impacting adjacent properties may allow the continued restoration of lost alluvial processes through the ongoing process of bend development and migration

DOCUMENTING CHANGE AT UPPER HAMBURG BEND: NEBRASKA\u27S FIRST SIDE-CHANNEL RESTORATION

In 1996 a side channel was excavated on 629 hectares of former agricultural land at Upper Hamburg Bend on the Missouri River in Otoe County, NE. This was the first side channel constructed on the Missouri River in an attempt to restore lost aquatic habitat. The initial design was for an approximately 4,200 m long side channel to be constructed with a 3 m bottom width. Development ofthe site was to be dependent on flows diverted from the main channel of the river with a final projected top width of 61 m. The side channel was completed in the spring, and shortly thereafter the site was subjected to a series of flood events. The side channel has been subjected to periods of both high and low water since opening. We documented physical changes at the site with the aid of aerial photography, acoustic Doppler current profiler (ADCP) surveys, and topographic surveys. By 2010 the side channel was 4,342 m long with a mean top width of89.5 m. Channel development has occurred during periods of high and low water. ADCP surveys established that mean depths and velocities have increased since 2001. An increase in the amount of discharge through the side channel since 2001 has resulted in the loss of some of the shallower and lower velocity habitats. Modifications to the site may be necessary to reverse this loss of shallow, slow water habitat that the side channel was designed to provide. Although new off-channel aquatic habitat has been created, channel development has been impacted by the presence of rock control structures throughout the site. Reducing the number of control structures to the minimum necessary to prohibit the side channel from impacting adjacent properties may allow the continued restoration of lost alluvial processes through the ongoing process of bend development and migration

Cross-Sectional Analysis of Sediment and Organic Matter from Transects Across the Lower Unchannelized Missouri River

The United States Army Corps of Engineers, U.S. Geological Survey, and Nebraska Game and Parks Commission cooperated in 1989 to obtain physical data from cross-section transects along the unchannelized Missouri River in northeastern Nebraska. Bed-sediment samples were collected from locations along these transects and taken to the laboratory. Mean particle-size and standard deviation were determined by weighing material retained on seven U.S. Standard sieves after being on a sieve shaker for six minutes. Organic matter content of each sample was obtained by ashing an aliquot in a muffle furnace to remove the organic portion. A new system for coding sediment mixtures was developed, and coded sediment and organic matter content were compared with depth and velocity in a regression analysis. The most common mean particle-size was determined to be medium sand; however, some samples were as coarse as fine gravel. Organic-matter content was less then 3% for the most part; however, it was measured as high as 20%. Sediment and organic matter were related to depth and velocity; however, r-square values were low, suggesting that other factors contribute to the observed variability in the sediment mixtures and organic matter content

Cross-Sectional Analysis of Sediment and Organic Matter from Transects Across the Lower Unchannelized Missouri River

The United States Army Corps of Engineers, U.S. Geological Survey, and Nebraska Game and Parks Commission cooperated in 1989 to obtain physical data from cross-section transects along the unchannelized Missouri River in northeastern Nebraska. Bed-sediment samples were collected from locations along these transects and taken to the laboratory. Mean particle-size and standard deviation were determined by weighing material retained on seven U.S. Standard sieves after being on a sieve shaker for six minutes. Organic matter content of each sample was obtained by ashing an aliquot in a muffle furnace to remove the organic portion. A new system for coding sediment mixtures was developed, and coded sediment and organic matter content were compared with depth and velocity in a regression analysis. The most common mean particle-size was determined to be medium sand; however, some samples were as coarse as fine gravel. Organic-matter content was less then 3% for the most part; however, it was measured as high as 20%. Sediment and organic matter were related to depth and velocity; however, r-square values were low, suggesting that other factors contribute to the observed variability in the sediment mixtures and organic matter content

Survival of Stocked Channel Catfish in Small Ponds

This research was conducted in cooperation with the Fort Sill Fish and Wildlife Branch. The research was conducted on Fort Sill Military Reservation near Lawton, Comanche County in southwest Oklahoma. Our objective was to study survival of stocked channel catfish fry and fingerlings in small ponds and to make management recommendations.Zoolog

Population Genetic Structure of Nebraska Paddlefish Based on Mitochondrial DNA Variation

Eighty-three paddlefish Polyodon spathula that were collected from 1995 to 1999 from the Missouri River Galvins Point Dam tailwater were analyzed for genetic variation in the mitochondrial DNA d-loop region. Additional samples from Montana, South Dakota, and Louisiana were used for comparative purposes. To facilitate the efficient analysis of numerous paddlefish samples, we applied a method that employs polyacrylamide gel electrophoresis (PAGE) to resolve restriction fragment length polymorphisms (RFLPs) amplified by polymerase chain reaction (PCR). DNA sequencing of 10 paddlefish revealed 22 polymorphic sites. Polymerase chain reaction–RFLP analysis of 93 paddlefish using three restriction enzymes detected six of the polymorphic sites and revealed six distinct haplotypes. All of the observed haplotypes were found in the Missouri River Galvins Point Dam tailwater. No temporal differentiation was observed among the 1995, 1998, and 1999 samples from the Missouri River Galvins Point Dam tailwater. Polymerase chain reaction–RFLP, resolved with PAGE, provided an efficient method for population genetic analysis of paddlefish

Population Genetic Structure of Nebraska Paddlefish Based on Mitochondrial DNA Variation

Eighty-three paddlefish Polyodon spathula that were collected from 1995 to 1999 from the Missouri River Galvins Point Dam tailwater were analyzed for genetic variation in the mitochondrial DNA d-loop region. Additional samples from Montana, South Dakota, and Louisiana were used for comparative purposes. To facilitate the efficient analysis of numerous paddlefish samples, we applied a method that employs polyacrylamide gel electrophoresis (PAGE) to resolve restriction fragment length polymorphisms (RFLPs) amplified by polymerase chain reaction (PCR). DNA sequencing of 10 paddlefish revealed 22 polymorphic sites. Polymerase chain reaction–RFLP analysis of 93 paddlefish using three restriction enzymes detected six of the polymorphic sites and revealed six distinct haplotypes. All of the observed haplotypes were found in the Missouri River Galvins Point Dam tailwater. No temporal differentiation was observed among the 1995, 1998, and 1999 samples from the Missouri River Galvins Point Dam tailwater. Polymerase chain reaction–RFLP, resolved with PAGE, provided an efficient method for population genetic analysis of paddlefish

FINAL REPORT -- Missouri River Fish and Wildlife Mitigation Program: Fish Community Monitoring and Habitat Assessment of Off-channel Mitigation Sites

The Missouri River has been developed for flood control, commercial navigation, irrigation, fish and wildlife conservation, municipal water supply, water quality control and hydropower production through a series of congressional acts. However, prior to development, the lower Missouri River was characterized by a highly sinuous to braided channel with abundant log jams, sand bars, secondary channels and cut-off channels. Construction of the Bank Stabilization and Navigation Project (BSNP) converted the lower Missouri River into a narrow, self scouring channel. The active channel downstream of Sioux City, Iowa was as wide as 1.8 km before river modification, but is now confined to a 91.4 m channel. Total river and floodplain habitat altered or destroyed by the BSNP is estimated at 211,246 hectares. The Missouri River Fish and Wildlife Mitigation Project (Mitigation Project) was established to restore fish and wildlife habitat lost by the construction, operation and maintenance of the BSNP. The Water Resources Development Act of 1986 authorized the United States Army Corps of Engineers (COE) to acquire and develop habitat on 12,100 hectares of non public lands and the development of 7,365 hectares of habitat on existing public lands to mitigate habitat losses. The Water Resources Development Act of 1999 authorized an additional 48,016 hectares to the program. The Final Supplemental Environmental Impact Statement (FSEIS) for the expanded Mitigation Project was issued in March of 2003, and it included a preferred alternative proposing the creation of additional shallow water habitat (defined as areas less than 1.5 m deep with a current velocity of less than 0.76 m/s). The preferred action in the FSEIS for the expanded Mitigation Project included creation of 2,833 to 8,094 hectares of shallow water habitat (SWH). In 2005, the Iowa Department of Natural Resources, Nebraska Game and Parks Commission (NGPC), Missouri Department of Conservation and U.S. Fish and Wildlife Service, Columbia Fisheries Resource Office (renamed to Columbia National Fish and Wildlife Conservation Office) were contracted by the COE to monitor and evaluate fish communities of select off-channel aquatic habitat sites that were constructed through the Mitigation Project. Additionally, the NGPC was contracted to collect physical habitat information from the secondary channels that were selected for biological monitoring in the upper channelized section above Kansas City. Sixteen sites selected for monitoring covered a range of aquatic habitats including backwaters and secondary channels with varying levels of engineering and development. Sites from upstream to downstream included Tieville-Decatur Bend (two backwaters), Louisville Bend (backwater), Tyson Island (backwater), California Bend (chute on the Nebraska bank and a chute with connected backwater on the Iowa bank), Tobacco Island (chute), Upper and Lower Hamburg Bends (one chute each), Kansas Bend (two small chutes, treated as one), Deroin Bend (chute), Lisbon Bottom (natural chute), North Overton Bottoms (chute), Tadpole Island (chute) and Tate Island (chute). The study was designed to include three field sampling seasons, but due to delays implementing contracts in 2005 another complete year of sampling was added. Thus, fish community monitoring and habitat assessment of offchannel mitigation sites began in April, 2006 and concluded in October, 2008. The objective of this project was to determine biological performance and functionality of chutes and backwaters and to compare chutes and backwaters in an effort to identify designs most beneficial to native Missouri River fish species. Additionally, this project was designed to help determine if additional modifications are needed at existing mitigation sites, if existing designs are providing a range of habitats, if these habitats are of value to the biological diversity of the Missouri River and if these habitats are of specific value to species of concern or importance, such as pallid sturgeon

Ecology of the Missouri River: Missouri River Creel Survey, Bellevue Bridge to Camp Creek, 3 April through 29 May 2004

The Nebraska Game and Parks Commission\u27s strategic plan has stated the following management goal for the Missouri River: Restore, protect, and maintain the diversity of historic Missouri River habitats, resources, and ecosystem functions in order that present and future generations may enjoy consumptive and non-consumptive outdoor recreational opportunities (NGPC 1996). To accomplish this goal the Nebraska Game and Parks Commission identified the following five objectives: • To restore terrestrial and aquatic floodplain habitat types by 2008. This would include old oxbows, chutes, side channels, sand bars, backwaters, wetlands, and other shallow water habitats. To restore ftows that reflect the natural hydrograph of the Missouri River by the year 2008. • To inform and educate the general public and constituency about Missouri River ecosystem functions and management. To double the number of total recreational use days by the year 2008. To investigate and manage native fish, wildlife, waterfowl, and fur bearers on a sustainable basis. Even though several of these objectives fall outside of NGPC management authority, this project has and will provide the data necessary to plan, implement and evaluate them. This strategic plan is currently being reviewed and updated. Creel surveys on large rivers with numerous public and private access points are difficult and expensive to design and conduct. The first creel survey conducted on the channelized Missouri River in Nebraska was a roving creel during 1972 t01973 (Groen 1973). Segments of the channelized river covered included, Sioux City to Blair, Blair to Nebraska City and Nebraska City to Rulo. These same segments were surveyed again in 1978 and 1979 (Hesse 1980). The Missouri Department of Conservation conducted a recreational use survey on the channelized Missouri River from the mouth to the Iowa-Missouri state line in four segments over a four year period from 1983 through 1987 (Fleener 1989). The segment adjacent to Nebraska was sampled in 1985 and 1986 and extended from the lowaMissouri state line downstream to St Joseph, Missouri. The present project examining several reaches of the channelized Missouri River had several objectives: Develop a creel survey design that when repeated over time would measure changes in recreational fishing activity and success and allow us to estimate the effects of large scale restoration efforts on recreational fishing. Estimate recreational fishing use. Estimate the number and species of fish harvested and released by recreational anglers. Estimate recreational fishing effort on public and private lands and by boating anglers using public and private boat ramps Correlate fishing effort and success with a combination of season, physical habitat variables (location, macrohabitat, microhabitat, water temperature and secchi disk transparency) and fishing methods (bait) Develop recreational fishing educational information based on survey result