Dalbey Bottoms Pallid Sturgeon Habitat Rehabilitation Monitoring Project

Dalbey Bottoms Pallid Sturgeon Habitat Rehabilitation Monitoring Project 2009 Field Season Pre-Construction Phase Annual Report Dalbey Bottoms Prepared By Clayton J. Ridenour and Tracy D. Hill E-mail contact: clayton_ridenour@fws.gov tracy_hill@fws.gov U.S. Fish and Wildlife Service Columbia Fish and Wildlife Conservation Office 101 Park DeVille Drive Columbia, Missouri (573) 234-2132 March, 2010 1

BACKGROUND Pallid sturgeon (Scaphirhynchus albus) are long lived large bodied fish that adapted to the turbid and turbulent pre-regulated Missouri River. Pallid sturgeon were listed as federally endangered in 1990 and species recovery is a priority of federal and state natural resource agencies, and many non-government organizations (Dryer and Sandvol 1993). Habitat restoration is identified as an important component to species recovery (USFWS 2003; Bergman et al. 2008). Off-channel and backwater areas adjacent to the main river channel were once a common feature on Missouri River and many existing areas provide important nursery habitat for young fishes (Tibbs and Galat 1997; Whitledge et al. 2005; Ridenour 2007; Ridenour et al. 2009a). Restored secondary channels create shallow-water habitat in other large rivers that benefit native species (Langler and Smith 2001) and many young sturgeon have been found in reclaimed chutes on lower Missouri River (Utrup et al. 2008; Ridenour et al. 2009b). Monitoring fish response to created off-channel areas informs and benefits ongoing and future habitat restoration efforts and provides a measure of success for habitat creation projects. OBJECTIVES Collect fisheries data to evaluate pre- and post-construction impact on the fish community at the Dalbey Bottoms site to assess the ecological impact of a constructed chute on pallid sturgeon and other native Missouri River fishes. This annual report summarizes fish data collected during the pre-construction phase (2009) of the project. STUDY SITE Dalbey Bottoms is located on the Missouri River between northwest Missouri and northeast Kansas near river mile (RM) 417. The constructed chute is proposed to extend from RM 419.1 at the most upstream entrance to RM 415.1 at the most downstream exit, and have two additional entrance and exit connections with the main channel. The study site will extend to one mile above the most upstream and below the most downstream connection between the chute and main-channel Missouri River; between RM 420 and 414 as the chute is currently planned for construction (Figure 1). 2

Figure 1. Map of Dalbey Bottoms study area (yellow) between river mile 415 and 420 on Missouri River. METHODS Sampling targeted adult and juvenile pallid sturgeon and other native fishes using trotline (adult) and trawling (all ages) gears in the main-channel at Dalbey Bottoms. We sampled with small mesh otter trawls (push trawl POT02; stern trawl OT04; see Sampson and Drobish 2008 for details about sampling gears) to assess young and small-bodied fishes during the weeks 29 June and 3 August and with trotlines (TLC2) to assess pallid sturgeon and other large bodied fishes during the week of 19 October. Trawl samples were adjusted to account for variation in sampling effort among trawls to catch-per-unit-effort (CPUE) as the number of fishes (accounting for species as well) per square-meter trawled for each trawl. The sum of all species specific CPUEs of a trawl represented the overall CPUE for that trawl sample. Trotline samples were adjusted to a standard effort of 40 hooks per 200 ft. line so that CPUE was the number of fish per 40 hook line. Our goal was to set and retrieve exactly 40 hooks on each 200 ft. line. However, we found it necessary to standardize catches because occasionally 1) more or fewer hooks were set and 2) hooks were lost (i.e., not retrieved) and thus not included in our assessment. Our target sampling intensity in shallow areas (<1.5m deep) with our push trawl 3

was six runs per river mile, four runs per river mile in deep areas (1.5-5.0m deep) with our stern trawl, and five 40 hook lines per river mile with trotlines. RESULTS & DISCUSSION River stage was between 8 and 12 ft during our three sampling events in 2009 (Figure 2). To minimize the effect of river flow on interpretation of differences in fisheries data before and after chute construction, we attempted to only sample while stage was within a normal range and relatively stable. However, the flashy nature of Missouri River near Dalbey Bottoms presented little opportunity to sample at stable flows during our target sampling periods (especially June). 18 16 USGS 06818000 14 Stage (ft) 12 10 8 June 6 4 2 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 2009 Figure 2. Stage hydrograph of Missouri River at USGS St. Joseph, MO gage upstream of Dalbey Bottoms during 2009. Vertical dashed lines indicate when fish were sampled at Dalbey Bottoms. We captured 839 fish in 62 trawls between river miles 420.1 and 414.1 during June. We identified 601 individuals to 25 unique species, and 228 were only identifiable to 11 family or genus groups (Table 1); most unidentifiable fish were too small (i.e., young) for specific identification. No pallid sturgeon were collected, however, four species were globally listed as vulnerable. Fish densities were highest behind kicker dikes (Figure 3, top). However, young of year sturgeon (i.e., USG) were in the top ten most abundant fish collected (Figure 3, bottom) and found most frequently behind wing dikes (Figure 4). Most fish (all species; 87%) were found in water less than 5-ft (1.5-m) deep. 4

Table 1. Species, global status, and number of each species collected at Dalbey Bottoms during 2009 by month. Status as reported from NatureServe.org (Oct 2009). Species Count Common name Scientific name code Status Jun Aug Oct bullhead minnow Pimephales vigilax BHMW G5 76 1 - blue catfish Ictalurus furcatus BLCF G5 2 276 26 bluegill Lepomis macrochirus BLGL G5 7 1 - bluntnose minnow Pimephales notatus BNMW G5-1 - blue sucker Cycleptus elongatus BUSK G3-G4 2 2 1 common carp Cyprinus carpio CARP G5 3-2 channel catfish Ictalurus punctatus CNCF G5 64 177 49 emerald shiner Notropis atherinoides ERSN G5 84 198 - fathead minnow Pimephales promelas FHMW G5-2 - freshwater drum Aplodinotus grunniens FWDM G5 54 245 9 goldeye Hiodon alosoides GDEY G5 8 1 - goldfish Carassius auratus GDFH G5-1 - green sunfish Lepomis cyanellus GNSF G5 2 - - gizzard shad Dorosoma cepedianum GZSD G5-41 - Hybognathus spp. Hybognathus spp. HBNS G4-G5 1 58 - lake sturgeon Acipenser fulvescens LKSG G3-G4 - - 1 largemouth bass Micropterus salmoides LMBS G5 4 - - longnose gar Lepisosteus osseus LNGR G5 1 1 - mimic shiner Notropis volucellus MMSN G5 3 - - Western mosquitofish Gambusia affinis MQTF G5-1 - oragespotted sunfish Lepomis humilis OSSF G5-1 - paddlefish Polyodon spathula PDFH G4 3 - - pallid sturgeon Scaphirhynchus ablus PDSG G2-1 14 red shiner Cyprinella lutrensis RDSN G5 80 45 - river carpsucker Carpiodes carpio RVCS G5-12 - river shiner Notropis blennius RVSN G5 8 57 - sicklefin chub Macrhybopsis meeki SFCB G3 3 6 - sturgeon chub Macrhybopsis gelida SGCB G3 2 - - Sauger Sander canadensis SGER G5 4 7 - speckled chub Macrhybopsis aestivalis SKCB G3-G4 72 22 - smallmouth buffalo Ictiobus bubalus SMBF G5 1-4 suckermouth minnow Phenacobius mirabilis SMMW G5 7 9 - shortnose gar Lepisosteus platostomus SNGR G5-1 - shovelnose x pallid hybrid S. platorynchus x S. albus SNPD - 1 - shovelnose sturgeon Scaphirhynchus platorynchus SNSG G4 25 64 140 sand shiner Notropis stramineus SNSN G5 5 15 - silver chub Macrhybopsis storeriana SVCB G5 80 208 - unidentified bu ffalo Ictiobus spp. UBF 2 - - unidentified catfish not Ictalurus spp. UCF - 1 - unidentified carpsucker Carpiodes spp. UCS - 6 - unidentified minnow Cyprinidae spp. UCY 131 7 - unidentified gar Lepisosteus spp. UGR 4 - - unidentified herring (shads) Clupiedae UHR - 3 - unidentified chub Macrhybopsis spp. UHY 11 13 - unidentified Ictalurus Ictalurus spp. UIC 11 20 - unidentified Ictalurus (catfish) Ictalurus spp. UIC 11 20 - unidentified Lepomis Lepomis spp. ULP 3 10 - unide ntified Unide ntified UNID 1 - - unidentified shiner Notropis spp. UNO 19 106 - unidentified sturgeon Scaphirhynchus spp. USG 40 57 - unidentified temperate bass Morone spp. UTB 5 Status Global-rank: G1=critically imperiled, G2=imperiled, G3=vulnerable, G4=apparently secure, 1-5 G5=secure, Gx-Gx=uncertian

August Sampling crews captured 1,699 fish in 67 trawls between river mile 420.1 and 414.1. We identified 1,397 individuals to 29 unique species, 302 were only identifiable to 10 family or genus groups (Table 1); most unidentifiable fish were too small (i.e., young) for specific identification. One pallid sturgeon and one shovelnose-pallid sturgeon hybrid were collected, and three other species collected are globally listed as vulnerable. Fish densities were highest behind kicker-dikes and along bank lines (Figure 3, top). However, young-of-year sturgeon (i.e., USG) were in the top ten most abundant fish collected (Figure 3, bottom) and were found most frequently behind wing dikes (Figure 4). June August OTHER 14% UCY 15% SNSG 3% RDSN 3% Other 11% BLCF 18% USG 5% FWDM 7% CNCF 8% SKCB 9% BHMW 9% RDSN 10% ERSN 10% SVCB 10% USG 3% RVSN 3% HBNS 3% SNSG 4% UNO 6% CNCF 10% ERSN 12% FWDM 15% SVCB 12% Figure 3. (Top) Mean fish (all species) CPUE ± SE (red) and number of small mesh trawl deployments (blue) by habitat type on main-channel Missouri River at Dalbey Bottoms during June (left) and August (right) 2009. (Bottom) Relative abundance of fishes collected on main-channel Missouri River at Dalbey Bottoms during June (left) and August (right) 2009. See Table 1 for species code definitions. 6

Figure 4. Distribution of sampling effort and young of year sturgeon catch-per-unit-effort (CPUE; see legend) on Missouri River at Dalbey Bottoms during June (left) and August (right) 2009. Flow is from top left to bottom right; each dot represents a small mesh trawl deployment. 7

October Our crews captured 246 fish from 29 retrieved trotlines between river mile 420.1 and 414.1; one trotline was severely snagged and broke before we could retrieve any fish from it. Three trotlines yielded no fish. There were nine species collected (Table 1) ranging in length from 1,055 mm FL (pallid sturgeon) to 138 mm TL (channel catfish). We caught 14 pallid sturgeon and two other species globally listed as vulnerable (Table 1). Fish densities were highest behind kicker-dikes and catches were dominated by shovelnose sturgeon (Figure 5). However, pallid sturgeon were found exclusively in habitats behind wing dikes (Figure 6). Mean (± 2 SE) water depth (m) where pallid sturgeon were found was 2.24 ± 0.36 and 2.72 ± 0.30 where they were not found. Bottom water velocity ranged from 0.23 to 1.35 m/s (mean ± 2 SE = 0.54 ± 0.28) where pallid sturgeon were collected; only one pallid sturgeon was collected in water faster than 0.55 m/s at the bottom. Mean CPUE (#/40 hook line) 16 14 12 10 8 6 4 2 0 CPUE # Trotlines Not accessible with trotlines 14 PDSG 0 PDSG 0 PDSG L-dike Wing-dike Kicker-dike Ch Sandbar Habitat Type 30 25 20 15 10 5 0 # Trotlines BLCF 9% PDSG 6% CNCF 22% FWDM 4% Other 3% SNSG 56% Figure 5. (Left) Mean fish catch-per-unit-effort (CPUE) ± SE (red), number of trotlines (blue), and number of pallid sturgeon by habitat type on main-channel Missouri River at Dalbey Bottoms during October 2009. (Right) Relative abundance of fishes collected with trotlines on main-channel Missouri River at Dalbey Bottoms during October 2009. See Table 1 for species code definitions. 8

Figure 6. Distribution of trotline sampling effort (dots) and pallid sturgeon catch (color of dots, see legend) on Missouri River at Dalbey Bottoms during October 2009. Flow is from top left to bottom right. 9

Annual Summary Average depth sampled with the push trawl was 0.8 m (±0.3 st.dev.), 3.0 m (±0.8) with the stern trawl, and 2.4m (±0.8) with trotlines. Most (96%) of the fish sampled with our small mesh trawls were <100 mm long. Wing-dikes were the dominate habitat structure at Dalbey Bottoms during pre-construction monitoring, but CPUE of many non-scaphirhynchus age-0 fish (e.g., <40 mm) was highest in habitats associated with kicker-dikes and bank lines that were not immediately associated with a dike (Figure 7). Kicker-dikes are typically associated with a channel crossover and promote slow velocity habitats (e.g., <0.3 m/s) with fine substrates (i.e., silt). Bank lines are generally characterized by slow velocity near the immediate shoreline, but velocity rapidly increases riverward. In contrast, 100% of age-0 sturgeon were found in habitats associated with wing-dikes where velocity was faster (e.g., 0.5-0.8 m/s) and substrate was coarser (i.e., sand). Among wing-dikes, age-0 sturgeon were most frequently found in bar (<1.2 m deep) and open water (>1.2 m deep) microhabitats away from the shoreline where velocity is generally swift, and never found in bank microhabitats near the shoreline where velocity is generally slow (Figure 8). Figure 7. Distribution of CPUE by length class (10 mm groups, narrow black bars, left axis) among habitat type of all fishes collected with small mesh trawls at Dalbey Bottoms during 2009. Grey bars (right axis) are number of trawl deployments by habitat type. 10

Figure 8. Mean (±95%) age-0 sturgeon CPUE among microhabitats at wing-dikes. Bar is <1.2 m deep, open water is >1.2 m deep, bank is shoreline not associated with a sandbar, Bar/OW is a combination of bar and open water (depth ranged above and below 1.2 m deep). Results from the first year of pre-construction monitoring indicate that nursery habitat in the main-channel Missouri River at Dalbey Bottoms may be a limiting resource to age-0 fish. Constructing the chute to address early life habitat needs of fish that use backwaters (e.g., group of fishes represented by high CPUE at kicker-dikes) and fish that use swifter water (e.g., age-0 sturgeon in bar and open water microhabitats) may benefit native species. Age-0 sturgeon were relatively abundant in the main channel at Dalbey Bottoms, but limited to a relatively narrow band of available habitat downstream of relatively short wing-dikes between the river bank and navigation channel. Finally, increasing the number of connections between the chute and mainchannel (e.g., tie channels, multiple inflows) may improve access to the chute to support early life stage survival of native species like Scaphirhynchus sturgeon (Ridenour et al. 2009b). 11

LITERATURE CITED Bergman, H.L., A.M. Boelter, K. Parady, C. Fleming, T. Keevin, D.C. Latka, C. Korschgen, D.L. Galat, T. Hill, G. Jordan, S. Krentz, W. Nelson-Stastny, M. Olson, G.E. Mestl, K. Rouse and J. Berkley. 2008. Research needs and management strategies for pallid sturgeon recovery. Proceedings of a workshop held July 31 August 2, 2001, St. Louis, Missouri. Final report to the U.S. Army Corps of Engineers. William D. Ruckelshaus Institute of Environmental and Natural Resources, University of Wyoming, Laramie, WY. 38 p. Sampson, S.J. and M.R. Drobish, (Editors). 2008. Pallid Sturgeon Habitat Assessment and Monitoring Project, Version 1.0. U.S. Army Corps of Engineers, Omaha District, Yankton, SD. Dryer, M.P. and A.J. Sandvol. 1993. Recovery plan for the pallid sturgeon (Scaphirhynchus albus): U.S. Fish and Wildlife Service, Bismarck, ND. 55 p. Langler, G.J. and C. Smith. 2001. Effects of habitat enhancement on 0-group fishes in a lowland river. Regulated Rivers: Research and Management 17:677-686. Ridenour, C.J., A.B. Starostka, W.J. Doyle and T.D. Hill. 2009a. Habitat used by Macrhybopsis chubs associated with channel modifying structures in a large regulated river: implications for river modification. River Research and Applications 25: 472-485. Ridenour, C.J., J.A. McMullen and T.D. Hill. 2009b. Assessment of connected side-channel chutes as habitat restoration for age-0 sturgeons in lower Missouri River. U.S. Fish and Wildlife Service, Region 3 Fisheries Data Series: FDS-2009-1. Tibbs, J.E. and D.L. Galat. 1997. Larval, juvenile, and adult small fish use of scour basins connected to the lower Missouri River. Final Report to Missouri Department of Conservation, Columbia, MO. 133 p. USFWS (U.S. Fish and Wildlife Service). 2003. Amendment to the 2000 biological opinion on the operation of the Missouri River main stem reservoir system, operation and maintenance of the Missouri River bank stabilization and navigation project, and operation of the Kansas River reservoir system: Minneapolis, MN., U.S. Fish and Wildlife Service. 308 p. Utrup, N.J., Z. Beussink, J. McMullen, J. Finley, and T.D. Hill. 2008a. Evaluation of fish use of the side-channel chutes at Lisbon Bottom, North Overton Bottoms, Tadpole Island, and Tate Island. 2007 Annual Report of the Missouri River Mitigation Project. U.S. Fish and Wildlife Service, Columbia National Fish & Wildlife Conservation Office, Columbia, MO. 146 p. Whitledge, G.W., D.L. Galat and G.T. Gelwicks. 2005. Habitat use by fishes in periodically and continuously connected lower Missouri River floodplain water bodies. Final Report to Missouri Department of Conservation, Columbia, MO. 68 p. 12