Soos Creek. Juvenile Out-Migrant Evaluation 2014 Annual Report Annual Report. Prepared by: Curtis M. Nelson

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1 Soos Creek Juvenile Out-Migrant Evaluation 2014 Annual Report Prepared by: Curtis M. Nelson Page 1

2 Table of Contents Acknowledgements... 5 Executive Summary Introduction Watershed Description Soos Creek Hatchery and Screw Trap Location Methods Trapping Equipment and Operation Biological Sampling Mark-Recapture Trails Data Analysis Results Dates of Operation Daily catch and biological sampling Chinook Coho Trout Other Salmonids Fish health Trap Efficiency and Population Estimates Chinook Coho Discussion Chinook Coho Comparable Production Estimates Comparable egg-to-emigrant survival rates Fish Condition and Health References Page 2

3 List of Tables Table 1. Number and Species Composition (% by number) of fish captured in the Soos Creek rotary screw trap in Table 2. Summary of length, weight and condition factor for NOR Chinook captured at the Soos Creek screw trap in Table 3. Mean fork length (mm), standard deviation (St.Dev.) range, and sample size of 0+ Chinook caught in the Soos Creek screw trap in Table 4. Summary of length, weight and condition factor for NOR yearling coho captured at the Soos Creek screw trap in Table 5. Mean fork length (mm), standard deviation (St.Dev.) range, and sample size of 1+ coho caught in the Soos Creek screw trap in Table 6. Summary of length, weight and condition factor for NOR sub-yearling coho captured at the Soos Creek screw trap in Table 7. Mean fork length (mm), standard deviation (St.Dev.) range, and sample size of 0+ coho caught in the Soos Creek screw trap in Table 8. Summary of length, weight, and condition factor for all trout species captured at the Soos Creek screw trap in Table 9. Summary of length, weight, and condition factor for pink, and chum salmon captured at the Soos Creek screw trap in Table 10. Morbidity of Soos Creek salmonids captured showing visible abnormalities common with Nanophyetus salmincola Table 11. Outmigration and movement abundance estimates for Chinook and coho from the Soos Creek screw trap in Table includes juvenile fish abundance, 95% confidence intervals (CI) and coefficients of variation (CV) Table 12. Trap efficiency trials conducted with sub-yearling Chinook (BY 2013) at the Soos Creek screw trap in Table 13. Estimated egg-to-emigrant survival and emigrants per spawner for Soos Creek Basin Chinook Table 14. Trap efficiency trials conducted with yearling coho (BY 2012) at the Soos Creek screw trap in Table 15. Estimated egg-to-emigrant survival and emigrants per spawner for Soos Creek Basin Yearling Coho Table 16. Trap efficiency trials conducted with sub-yearling coho (BY 2013) at the Soos Creek screw trap in Table 17. Comparison between MIT and WDFW analysis methods used to determine subyearling Chinook and yearling coho abundance for the Soos Creek Screw Trap, Table 18. Comparison between MIT and WDFW analysis methods used to determine subyearling Chinook egg-to-emigrant survival for the Soos Creek Screw Trap, Page 3

4 List of Figures Figure 1. Map of the Soos Creek basin including the location of the Soos Creek screw trap and Muckleshoot Reservation... 9 Figure 2. Mean weekly stream discharge (cfs) at the Soos Creek USGS stream gage # from statistical week 3 27 for 2014, , and juvenile Salmonid out-migrant period Figure 3. Soos Creek mean daily stream discharge (cfs) from January to July for 2014, including median, 90% exceedance, and 10% exceedance discharge for years (collected at USGS stream gage # ) Figure 4. Daily mean water temperature at the mouth of Soos Creek (King County s Hydrologic Monitoring Site 54a) from January - June for the 2014 juvenile outmigration period, including a twenty-year mean Figure 5. Weekly catch of sub-yearling Chinook (BY 2013) with mean weekly stream discharge (cfs) at the Soos Creek screw trap. Discharge data are mean, minimum, and maximum values by statistical week Figure 6. Weekly catch of sub-yearling Chinook (BY 2013) with fork lengths (mm) at the Soos Creek Fork length data are mean, minimum, and maximum values by statistical week Figure 7. Weekly catch of yearling coho (BY 2012) with mean weekly stream discharge (cfs) at the Soos Creek screw trap. Discharge data are mean, minimum, and maximum values by statistical week Figure 8. Weekly catch of yearling coho (BY 2012) with fork lengths (mm) at the Soos Creek Fork length data are mean, minimum, and maximum values by statistical week Figure 9. Weekly catch of sub-yearling coho (BY 2013) with mean weekly stream discharge (cfs) at the Soos Creek screw trap. Discharge data are mean, minimum, and maximum values by statistical week Figure 10. Weekly catch of sub-yearling coho (BY 2013) with fork lengths (mm) at the Soos Creek Fork length data are mean, minimum, and maximum values by statistical week Figure 11. Weekly migration of estimated sub-yearling Chinook out-migrants at the Soos Creek The out-migration is separated into two freshwater rearing strategies Fry and Parr Figure 12. Estimated weekly migration of yearling coho at the Soos Creek trap Page 4

5 Acknowledgements Evaluation of 2014 juvenile out-migration from the Soos Creek basin was made possible by multiple agencies, personnel, and individuals. Funding was provided by an Environmental Protection Agency sponsored grant by the Northwest Indian Fisheries Commission (NWIFC). Bruce Stewart (NWIFC) provided a fish pathology report, Bill Patton provided take permit support, and Tiffany Waters provided grant support. The Washington Department of Fish and Wildlife s (WDFW) Soos Creek Hatchery provided 24- hour access to the trapping location and power to the screw trap. WDFW hatchery staff graciously provided hatchery surrogates for efficiency trials and providing historic information on fecundity and adult passage at the hatchery weir. We would like to thank WDFW personnel for sharing their regional expertise, and trapping experience. Thanks to Mike Wilson, Joe Rankin, and Pete Topping. Success of this project relied on the hard work of the s (MIT) field members including Dick Bevins, Moon Martin, Bob Spencer, Matt Jones, William Bachel, Justin Moses, Richard Hamilton, and Dewayne Ross Senior who maintained and operated the screw trap during all hours, day or night. MIT personnel provided endless support and leadership. Thanks to Mike Mahovlich, Jason Schaffler, Sean Hildebrandt, Eric Warner, Jesse Nitz, Erin Slaten, Holly Coccoli, Carla Carlson, Karen Walter, Martin Fox, Nancy Rapin, Ava Fuller, and Lena Chavez. Thanks to Will Markey for providing access to and from their property for releasing marked fish for trap efficiency trials 0.2 miles upstream of the screw trapping location. Page 5

6 Executive Summary The Soos Creek basin has the potential to be a major producer of Puget Sound Chinook salmon within the Green-Duwamish river system. Puget Sound Chinook, and Steelhead have been listed as threatened under the Endangered Species Act (EPA) by the National Marine Fisheries Service (NMFS). The primary objective of the Soos Creek Juvenile Outmigration Monitoring is to estimate juvenile abundance and productivity of natural origin juvenile Chinook and coho salmon emigrating from the basin. Data collected in this study will help managers better understand emigration timing, abundance, health, survival, and condition of salmonids in the Soos Creek basin. In 2014, the conducted its third consecutive year of a juvenile outmigrant evaluation on lower Soos Creek Soos Creek juvenile out-migrant evaluation is funded by Environmental Protection Agency (EPA) Puget Sound Partnership Implementation grant, from the Northwest Indian Fisheries Commission. The first two years ( ) of Soos Creek Juvenile out-migrant evaluation was funded by Pacific Coastal Salmon Recovery Funding. A rotary screw trap, located upstream of the Soos Creek Hatchery (at approximately RM 1.1), was used to collect, sample, and quantify juvenile salmonids from January 13 to June 30. Markrecapture trials were used to establish trap efficiency and expand daily catch. Juvenile abundance observed during the 2014 trapping period was estimated to include 101,748 ± 19,357 (95% CI) sub-yearling Chinook (BY 2013) and 19,020 ± 8,553 (95% CI) yearling coho (BY 2012). This estimate is based on a total catch of 7,349 sub-yearling Chinook and 1,077 yearling coho. Sub-yearling Chinook fork length (FL) increased from a weekly average of 37 mm to 76 mm by the end of the 2014 trapping period. Yearling coho had weekly average FLs that increased from 77 mm to 91 mm. Incidental catch at the Soos Creek screw trap included chum salmon, steelhead trout, pink salmon, cutthroat trout, western brook lamprey, lamprey ammocoetes, sculpin, stickleback, Largemouth bass, yellow perch, bluegill, Pumpkinseed, longnose dace, and brown bullhead. Chinook and coho daily catch showed physical signs of stress and external abnormalities (or impairments) from the start of the out-migration period for yearling salmonids, and in early-april to mid-june for sub-yearling salmonids. A pathologist report identified Nanophyetus salmincola (N. salmincola) as the primary pathogen responsible for compromising the health of the Soos Creek fish. This pathogen, as with other fish diseases, is possibly linked to poor water quality and environmental stress. Questions pertaining to the link between juvenile fish health and habitat quality within the Soos Creek basin will require continued research and monitoring. A fourth year of trapping is planned for Additional juvenile out-migrant data will provide refined status and trend information on ESA listed Chinook in the Soos Creek basin while providing detailed stock information about other Soos Creek salmonids. Page 6

7 1 Introduction Rotary screw traps have long been used by biologists to capture downstream migrating juvenile anadromous salmonids from medium- and large-sized rivers (Schoeneman et al. 1961; Seiler et al. 1981) and from small tributary streams (Solazzi et al. 2000). While estimating smolt abundance is the most common reason for operating a screw trap, the collection of downstream migrants has broader utility. Trapping information can be used to validate assumptions about the effect of watershed restoration programs and land use policies on fish populations, and to assess survival between life stages, such as egg-to-smolt survival or parr-to-smolt over-winter survival (Seiler and Volkhardt, 2002). The number, timing, size, and health of salmon spawners and juvenile out-migrants are important metrics used in salmon management and salmon recovery efforts. The 2012 Puget Sound Action Agenda, D.4.1.1, notes that juvenile abundance and productivity are key measures of ecosystem status and the effectiveness of recovery actions, and serve as ecosystem indicators. However, the contribution naturally-spawning Chinook and coho salmon in the Soos subbasin to the overall salmon production in the Green-Duwamish River is not well understood. Annual juvenile migrant monitoring (often called smolt trapping) has occurred on the mainstem Green River just upstream of the Soos Creek mouth since Chinook spawning data in the subbasin are also scarce. As a result, in 2012, MIT began a multiyear juvenile migrant trapping project on Big Soos Creek to answer questions about natural production of Chinook and coho in the subbasin. In addition, Chinook spawning surveys were conducted in 2012 and 2013 along with a Chinook habitat inventory in Big Soos, Covington, and Jenkins creeks. The (MIT) operated a rotary screw trap on Soos Creek (also referred to as Big Soos Creek) in was the third consecutive year MIT operated a juvenile out-migrant trap on Soos Creek. Funding for this project was provided by an Environmental Protection Agency (EPA) grant, from the Northwest Indian Fisheries Commission (NWIFC). Trap operation was conducted in collaboration with the WDFW s Soos Creek Hatchery. Hydraulic Project Approval (HPA) has been granted for this project through February 12, 2017, and the Endangered Species Act (ESA) Section 10 (incidental take permit) was covered under the NWIFC s long-term 4d take permit, for tribal research in Puget Sound by National Marine Fisheries Service (NMFS). The objectives of this project are to: Estimate juvenile abundance and productivity of natural origin out-migrant Chinook and coho salmon in the Soos Creek basin. Describe emigration timing, health, and condition of out-migrant salmonids in the Soos Creek basin. Obtain baseline data to help assess the cumulative effects of habitat trends and recovery actions on juvenile salmon abundance, health, and productivity over time. Complete an inventory of the spawning habitat available for Chinook in the Soos Creek sub-basin and complete a Chinook spawning survey in Page 7

8 This project will produce estimates of natural coho and Chinook salmon production within the Soos Creek subbasin for the 2014 outmigration year, document migration timing and fish condition, and eggto-migrant survival for BY 2013 Chinook and BY 12 coho. The project includes the completion of a stream habitat inventory initiated on Jenkins Creek, a tributary of Soos Creek, in The habitat inventory will assess Chinook spawning capacity, document baseline instream and riparian conditions in areas utilized by Chinook salmon spawners to facilitate monitoring of habitat trends. Chinook spawning surveys were conducted to estimate spawning abundance, document pre-spawning mortality, and determine the temporal and spatial distribution of redds in fall of State and tribal fisheries co-managers will consider the information resulting from this project to optimize Chinook spawner abundance upstream of the Soos Creek Hatchery weir; identify trends in juvenile salmon abundance, health, and productivity over time; and monitor habitat trends in Chinook spawning habitat in the Soos Creek subbasin. 1.1 Watershed Description The Green-Duwamish watershed is located in King County in Water Resource Inventory Area (WRIA) 9. The watershed area is approximately 484 square miles, extending from the Cascade Mountains at the headwaters of the Green River, west to the mouth of the Duwamish River in the City of Seattle. Of the many small tributaries that enter the Green River below Howard Hanson Dam, Big Soos Creek (Soos Creek) is the largest (Figure 1). Soos Creek is located in south King County, southeast of Renton and east of Kent. The Soos Creek basin lies within the MIT s Usual and Accustomed (U&A) fishing grounds. The drainage basin includes mainstem Soos Creek and 25 tributary streams (King County, 2000). Four major tributaries include Little Soos, Jenkins, Covington, and Soosette Creeks. In total, the Soos Creek basin drains approximately 70 square miles. This basin also includes several lakes: Shadow Lake, Lake Meridian, Lake Sawyer, Morton, Pipe/Lucerne and Wilderness Lakes. In its entirety, the Soos Creek basin is an extensive system of interacting lakes, wetlands, and infiltrating soils that drains into the Green River at river mile (RM) Total impervious area was estimated at 34% in Land development and human population continue to grow, effective fish habitat protection, restoration, and fisheries management practices will be needed to sustain salmonid production and the water supply to the Soos Creek Hatchery. Page 8

9 Figure 1. Map of the Soos Creek basin including the location of the Soos Creek screw trap and Muckleshoot Reservation. Current land use in the Soos Creek basin consists of rural residential, agriculture, and highly urban commercial and residential areas (Herrera 2005). In 1990, much of the Soos Creek basin was considered rural and in good condition (King County 1990). Today, WRIA 9 is considered to be highly urbanized and impacted (NWIFC 2012). Groundwater extractions and increased impervious surface area in the Soos basin have contributed to reduced summer and fall flows (by an estimated 52%) and increases in winter storm water flows (King County 1990). Low streamflow is one of the many factors that contribute to low productivity and abundance of Chinook and other salmon (NWIFC 2012). In 2014, mean daily discharge for Soos Creek during the juvenile outmigration period, from January to July, was 239 cubic feet per second (cfs) (Figure 2). Peak daily discharge was Page 9

10 recorded at 710 cfs on March 6. In relation to the 10-year mean, 2014 stream discharge was generally higher with multiple peaks. Mean daily discharge in 2014 was similar to the 10% historical exceedance discharge for Soos Creek (from water year 1961 to 2013), Overall, 2014 was a wetter than normal year (Figure 3). Soos Creek experienced high water events (>500cfs) in the middle of February through late March, which caused some redd scouring during the incubation and pre emergence period for several salmonids. For example salmonid eggs and alevins were found in the screw trap during these high discharge periods. Soos Creek is a flashy system due to the amount of impervious area that makes up its basin, causing rapid spikes in discharge. Mean daily stream temperatures ranged from 3.0 C to 15.5 C during the outmigration period (Figure 4). Soos Creek was warmer in 2014 during the juvenile out-migration period January to July, with a mean water temperature of 9.82 C, compared to the 20-year mean water temperature of 9.42 C. Figure 2. Mean weekly stream discharge (cfs) at the Soos Creek USGS stream gage # from statistical week 3 27 for 2014, , and juvenile Salmonid out-migrant period. Page 10

11 Daily water temperature ( C) Stream Discharge (cfs) 2014 Annual Report Statistical Week Year Historic Median 90% Historic Exceedance 10% Historic Exceedance Figure 3. Soos Creek mean daily stream discharge (cfs) from January to July for 2014, including median, 90% exceedance, and 10% exceedance discharge for years (collected at USGS stream gage # ) Year Mean Figure 4. Daily mean water temperature at the mouth of Soos Creek (King County s Hydrologic Monitoring Site 54a) from January - June for the 2014 juvenile outmigration period, including a twenty-year mean. Page 11

12 1.2 Soos Creek Hatchery and Screw Trap Location In 1901, WDFW began operating a salmon hatchery along lower Soos Creek at RM 0.9. The Soos Creek Hatchery produces fall Chinook (Green River stock), coho, and both winter and summer run steelhead. As part of hatchery operations, a weir acts as a fish barrier for broodstock collection when in place from mid-august through late November, or when coho broodstock requirements are met. Large storm events or unforeseen occurrences that compromise the weir are the only events that allowed volitional upstream passage during this period. Chinook and coho escapement upstream of the hatchery weir is tightly regulated by hatchery staff and only occurs after broodstock goals are met. The Soos Creek rotary screw trap, operated by MIT, is located upstream of the hatchery at RM 1.1 (N , W ). The location of the screw trap is ideal for catching naturally produced salmonids in the Soos Creek basin (Error! Reference source not found.1). Adult salmon returning to the Soos Creek Hatchery play a crucial role in providing salmon for tribal treaty and other harvest, and in maintaining abundant naturally spawning fish (NWIFC, 2012). 2 Methods 2.1 Trapping Equipment and Operation The Soos Creek rotary screw trap is equipped with a 5-ft diameter cone to collect downstream migrants at RM 1.1. This cone has a sampling depth of 2.5-ft. below the water surface where actively migrating fry, parr, and smolts swim and are subject to capture. Captured fish were retained in a live box until they were dipped out for sampling. The live box was checked a minimum of two times per day, at dawn and dusk. A rotating drum-screen removed small debris from the live box. The trap was secured by cables along both the left and right banks. These cables were secured to 3 polyester tow straps that have a load rating of 35,000lbs via 0.75 inch D-ring shackles. The D-ring shackles have a load rating of 9,500 lbs. The tow straps help distribute the load of trap around the base of the tree preventing girdling or damage to load bearing riparian trees. The rotary screw trap was positioned laterally in the thalweg for optimum catch efficiency. Additionally, stern ropes were utilized to further stabilize the trap. 2.2 Biological Sampling All fish were enumerated by species and size class. Sampled fish were anesthetized in a 60mg/L solution of MS-222, weighed with an electronic scale, and measured in a wetted trough-type measuring board. Anesthetized fish received oxygen through aquarium bubblers and were allowed to fully recover before being either released downstream of the trap or used in trap efficiency trials. Fork length (FL) and weight were recorded for a sub-sample of at least 10 fish of each species and size class every time the live box was checked. Developmental stages (or size classes) were visually classified as fry, parr, or smolt. Age of emigrants was classified as sub-yearling 0+, and yearling 1+. Fish that were not measured and weighed were tallied and Page 12

13 recorded as part of the daily total catch. FL was recorded to the nearest millimeter (mm) and weight to the nearest 0.1 gram (g). This data was used to calculate a Fulton-type condition factor (K-factor) using the formula: K = (W/L 3 ) x 100,000 Where K = Fulton-type condition metric, W = weight in grams, L = fork length in millimeters and 100,000 is a scaling constant. All salmonids were visually inspected for an 1) adipose fin clip to classify their origin as either natural (NOR) or hatchery (HOR) origin; and 2) marks used in trap efficiency trials (Bismarck Brown and caudal fin clip) that would classify those fish as recaptures. Additionally, fish were visually inspected for health and/or growth deformities that may be caused by pathogens, or poor water quality in the basin. 2.3 Mark-Recapture Trails Trap efficiencies for the Soos Creek screw trap were determined for Chinook and coho outmigrants from recaptures of marked fish released above the trap. Efficiency trials were conducted for each species over a range of stream discharges. A minimum sample size of 30 fish was used for each mark-recapture trial, as trap efficiency can be greatly biased if mark groups are small (AFS, 2007). Pooling mark-recapture trials and maintaining a minimum number of recaptures per strata (or pooled group) will minimize biases (Schwarz and Taylor, 1998). Mark-recapture trials were conducted with HOR surrogates when a mark group of 30 NOR Chinook was not achievable. HOR surrogates used in these trials were measured and weighed to compare with NOR Chinook actively emigrating from the basin. Each mark-recapture trial was conducted over at least a three-day period to allow time for passage or capture. Trials were considered invalid if no marked fish were recaptured or if there were significant interruptions to trap operation during the three-day period (i.e. debris/flood). During periods when the trap was not operating (e.g. high discharge, high debris, mechanical problems), the number of target species captured was estimated. The estimated number of fish was calculated using the average number of fish captured three days prior and three days after the break in operation. This estimate was incorporated into the overall emigration estimate. Catch was saved and combined for up to 72 hours to provide the largest mark group possible. Fry and parr used for efficiency trials were marked in a solution of Bismarck Brown dye (21 mg/l for 40 minutes). Larger parr ( 45 mm) and smolt were anesthetized in a solution of MS-222 (60 mg/l) and marked with alternating upper and lower partial-caudal fin clips. Fish being held for mark-recapture trials were kept in either a: 1) submerged five-gallon bucket weighted down inside the screw trap live box; 2) holding box with circulated ambient river water; or 3) instream floating release box. On the evening of efficiency trial, marked fish were released at dusk 0.2 Page 13

14 RM upstream of the screw trap. Only mark groups consisting of 30 fish of a single size class and species were used in pooled efficiency estimates. 2.4 Data Analysis Using the mark-recapture data, trapping efficiency was calculated with the following formula: Trap efficiency = e i = m i M i Where e i is the trap efficiency during time period i; m i is the number of marked fish recaptured during time period i; and M i is the number of marked fish released during time period i. A linear regression is used to test how well trap efficiency from individual efficiency trials correlated with discharge (cfs). If the results of the regression are significant (p < 0.05; r 2 > 0.50), the regression and associated variance equations would be used to estimate daily trap efficiency. When a relationship between discharge and trap efficiency is not present (i.e. p > 0.05; r 2 < 0.50), pooled trap efficiencies (or the sum of all mark-release groups and associated recaptures for time period i) are used to estimate emigration using the following equation: Estimated Out-migration = U i = u i (M i + 1) (m i + 1) where U i is the estimated number of unmarked downstream migrants during time period i; u i is the number of unmarked fish captured during time period i; M i is the number of marked fish released during time period i; and m i is the number of marked fish recaptured during time period i. Variance for the estimated out-migration using pooled trap efficiencies was calculated with the formula: Variance for estimated out-migration = V(U i ) = (M i + 1) (u i + m i +1) (M i m i ) (u i ) (m i + 1) 2 (m i + 2) The total juvenile abundance estimate and total variance of the abundance estimate is the sum of estimated out-migration ( U i ) and sum of pooled variance ( V(U i ) ), respectively. Confidence intervals and coefficient of variation associated with the abundance estimate was calculated from the total variance using the following formulas: 95% confidence interval = 1.96 x ( V(U i ) ) ½ Coefficient of Variation (CV) = U i ( V(U i ) ) ½ The following assumptions regarding efficiency trials must be made for the abundance estimate to be valid (Everhart and Young 1981): 1. Population is closed with no immigration or emigration. Note: the no emigration assumption is technically violated because the trap catches fish that are emigrating from the creek. However, we assume that the entire cohort leaves the system within Page 14

15 a defined period and that the abundance of juveniles can be estimated at a fixed station during this migration and no births or deaths occur. 2. All marked fish passed the trap or were recaptured during time period i. 3. The probability of capturing a marked or unmarked fish is equal. 4. Marking does not affect catch ability. 5. Marks were not lost between the time of release and recapture. 6. Marked fish mix at random with unmarked fish. Stratification of the mark-recapture data was necessary to accommodate for changes in trap efficiency over the season. These changes result from a number of factors including stream discharge, time (fish size), turbidity, diel period, and avoidance behavior. Pooling a series of trap efficiency trials increases overall sample sizes and improves statistical validity. It can also be a good alternative to trap efficiency-discharge regression models when fish abundance is limited, sample sizes are small, and a lack of correlation is determined. Pooling trapping efficiencies was achieved by conducting a G-test, which pools statistically similar trapping efficiencies together (Sokal and Rohlf, 1981; Kiyohara and Zimmerman, 2011a, 2011b, 2012). Efficiency trials that were not different were pooled, and then pooled groups were compared to the next adjacent efficiency trial. Once a significant difference was identified, the pooled trials were placed into one stratum with the significantly different trial at the beginning of the next stratum. 3 Results This section summarizes the results of the 2014 trapping period. 3.1 Dates of Operation The trap was operated continuously for 169 days, with no outages. The 2014 trapping period ran from January 15 to June 30. Throughout this active trapping period the trap operated continuously 24 hours a day, for a total of 4054 hours. Throughout this active trapping period, there was one period where the trap was not fishing properly, due to a broken live box seal, on February 20. During this period when the trap was not operated properly, the estimated number of fish captured on February 20 was calculated using the average number of fish captured three days prior and three days after the break in operation. This estimate was incorporated into the overall emigration estimate. 3.2 Daily catch and biological sampling Chinook (Oncorhynchus tshawytscha), coho (O. Kisutch), chum (O. Keta), pink (O. gorbuscha), steelhead (O. mykiss), and cutthroat trout (O. clarkia) were salmonid species captured at the Soos Creek trap. Sculpin (Cottus spp.), three spine stickleback (Gasterosteus aculeatus), longnose dace (Rhinichthys cataractae), bluegill (Lepomis macrochirus), brown bullhead (Ameiurus nebulosus), pumpkinseed (Lepomis gibbosus), largemouth bass (Micropterus salmoides), redside shiner (Richardsonius baltertus), and Lamprey ammocoetes (Petromyzontidae) were bycatch species encountered during the 2014 trapping season (Table 1). Page 15

16 Table 1. Number and Species Composition (% by number) of fish captured in the Soos Creek rotary screw trap in Species Composition bluegill % bullhead % Chinook % chum % Coho % Coho % crayfish % cutthroat % dace % lamprey % lamprey % LMB % pink % pumpkinseed % redside % sculpin % steelhead % stickleback % Chinook Yearling Chinook (BY 2012) Out-migrant No natural-origin yearling Chinook were captured during the 2014 out-migration season. Sub-Yearling Chinook (BY 2013) Out-migrant A total of 7,349 sub-yearling Chinook were captured during the 2014 trapping period, of which 1,738 sub-yearling Chinook were sampled. The peak catch of sub-yearling Chinook was observed during statistical week 8 (February 16-22), with a weekly catch total of 2,416 (Figure 6). The Mean FL and weight for sub-yearling Chinook was mm (n=1,738; SD = 7.58) and 0.90 g (n=1,738; SD = 0.80), respectively (Table 2). Weekly average FLs for sub-yearling Chinook ranged from 36.8 mm to 76.0 mm (Figure 7). Fulton-type condition factor for subyearling Chinook had a mean of % of the sub-yearling Chinook were fry emigrants ( 45 mm), and 11% emigrants were parr (>45 mm). Emigration was 25%, 50% and 75% completed by February 18, February 26, and March 6. Although the emigration was dominated by fry, there were distinct peaks associated with both fry and parr. Fry emigration peaked during statistical week 8 (2,416 fry out-migrants February 16 to February 22), which was also the peak average discharge of 469 cfs (Figure 6). Parr emigration peaked during statistical week 13 (334 Page 16

17 Chinook Catch Fork Length (mm) Chinook Catch Stream Discharge (cfs) 2014 Annual Report parr/smolt out-migrants March 23 to March 29), which was the fifth highest average discharge of 323 cfs (Figure 7) Soos Creek Figure 5. Weekly catch of sub-yearling Chinook (BY 2013) with mean weekly stream discharge (cfs) at the Soos Creek screw trap. Discharge data are mean, minimum, and maximum values by statistical week Figure 6. Weekly catch of sub-yearling Chinook (BY 2013) with fork lengths (mm) at the Soos Creek Fork length data are mean, minimum, and maximum values by statistical week Statistical Week 2014 Sub-Yearling Chinook Statistical Week Page 17

18 Table 2. Summary of length, weight and condition factor for NOR Chinook captured at the Soos Creek screw trap in Brood Year Age Class/ Stage Total Sample Fork Length (mm) Weight (g) Mean Median SD Mean Median SD K- Factor 2013 Sub-yearling Fry/Parr 1, Table 3. Mean fork length (mm), standard deviation (St.Dev.) range, and sample size of 0+ Chinook caught in the Soos Creek screw trap in Statistical Week Range Number Percent Number Begin End Average St.Dev. Min Max Sampled Caught Sampled 3 01/13/14 01/18/ % 4 01/19/14 01/25/ % 5 01/26/14 02/01/ % 6 02/02/14 02/08/ % 7 02/09/14 02/15/ % 8 02/16/14 02/22/ % 9 02/23/14 03/01/ % 10 03/02/14 03/08/ % 11 03/09/14 03/15/ % 12 03/16/14 03/22/ % 13 03/23/14 03/29/ % 14 03/30/14 04/05/ % 15 04/06/14 04/12/ % 16 04/13/14 04/19/ % 17 04/20/14 04/26/ % 18 04/27/14 05/03/ % 19 05/04/14 05/10/ % 20 05/11/14 05/17/ % 21 05/18/14 05/24/ % 22 05/25/14 05/31/ % Coho Yearling coho (BY 2012) Out-Migrant A total of 1,077 yearling coho (parr and smolt) were captured at the Soos Creek screw trap during the 2014 trapping period, of which 1,006 yearling coho were sampled. Yearling coho were observed from February 1 to June 22, with the peak count of 56 on May 6 (Figure 8). The mean FL and weight for yearling coho was mm (n = 1,006; SD =12.3) and g (n = 1,006; SD = 6.06), respectively (4). Weekly average FLs ranged from 63 mm to 105 mm (Figure Page 18

19 Yearling coho Fork Length (mm) 2014 Annual Report 9). Fulton-type condition factor for yearling coho had a mean of 1.13, which will assist in comparing condition of 2014 Soos Creek yearling coho to other basins, and different years of yearling coho monitoring on Soos Creek. Emigration was 25%, 50% and 75% completed by April 22, May 1 and May 8. Figure 7. Weekly catch of yearling coho (BY 2012) with mean weekly stream discharge (cfs) at the Soos Creek screw trap. Discharge data are mean, minimum, and maximum values by statistical week Figure 8. Weekly catch of yearling coho (BY 2012) with fork lengths (mm) at the Soos Creek Fork length data are mean, minimum, and maximum values by statistical week Statistical Week 20 0 Page 19

20 Table 4. Summary of length, weight and condition factor for NOR yearling coho captured at the Soos Creek screw trap in Brood Year Age Class/ Stage Total Sample Fork Length (mm) Weight (g) Mean Median SD Mean Median SD K- Factor 2013 yearling Parr/Smolt 1, Table 5. Mean fork length (mm), standard deviation (St.Dev.) range, and sample size of 1+ coho caught in the Soos Creek screw trap in Statistical Week Range Number Percent Number Begin End Average St.Dev. Min Max Sampled Caught Sampled 5 01/26/14 02/01/ % 6 02/02/14 02/08/ % 7 02/09/14 02/15/ % 8 02/16/14 02/22/ % 9 02/23/14 03/01/ % 10 03/02/14 03/08/ % 12 03/16/14 03/22/ % 13 03/23/14 03/29/ % 14 03/30/14 04/05/ % 15 04/06/14 04/12/ % 16 04/13/14 04/19/ % 17 04/20/14 04/26/ % 18 04/27/14 05/03/ % 19 05/04/14 05/10/ % 20 05/11/14 05/17/ % 21 05/18/14 05/24/ % 22 05/25/14 05/31/ % 23 06/01/14 06/07/ % 24 06/08/14 06/14/ % 25 06/15/14 06/21/ % 26 06/22/14 06/28/ % Sub-Yearling coho (BY 2013) A total of 17,860 sub-yearling coho (fry and parr) were captured at the Soos Creek screw trap during the 2014 trapping season (Figure 10), of which 2,498 sub-yearling coho were sampled. The greatest catch of sub-yearling coho was observed on April 6, with a daily total of 627. The mean FL and weight was 35.3 mm (n = 2,498; SD = 3.97) and 0.5 g (n = 2,498; SD = 0.96), respectively (Table 6). Weekly average FLs ranged from 33.0 mm to 41.0 mm (Figure 11). Fulton-type condition factor for sub-yearling coho had a mean of 1.0. Page 20

21 Sub-Yearling coho Out-Migrants Fork Length (mm) 2014 Annual Report Figure 9. Weekly catch of sub-yearling coho (BY 2013) with mean weekly stream discharge (cfs) at the Soos Creek screw trap. Discharge data are mean, minimum, and maximum values by statistical week Soos Creek Statistical Week Figure 10. Weekly catch of sub-yearling coho (BY 2013) with fork lengths (mm) at the Soos Creek Fork length data are mean, minimum, and maximum values by statistical week. Page 21

22 Table 6. Summary of length, weight and condition factor for NOR sub-yearling coho captured at the Soos Creek screw trap in Brood Year Age Class/ Stage Total Sample Fork Length (mm) Weight (g) Mean Median SD Mean Median SD K- Factor 2013 Sub-yearling Fry/Parr 2, Table 7. Mean fork length (mm), standard deviation (St.Dev.) range, and sample size of 0+ coho caught in the Soos Creek screw trap in Statistical Week Range Number Percent Number Begin End Average St.Dev. Min Max Sampled Caught Sampled 4 01/19/14 01/25/ % 5 01/26/14 02/01/ % 6 02/02/14 02/08/ % 7 02/09/14 02/15/ % 8 02/16/14 02/22/ % 9 02/23/14 03/01/ % 10 03/02/14 03/08/ % 11 03/09/14 03/15/ % 12 03/16/14 03/22/ % 13 03/23/14 03/29/ % 14 03/30/14 04/05/ % 15 04/06/14 04/12/ % 16 04/13/14 04/19/ % 17 04/20/14 04/26/ % 18 04/27/14 05/03/ % 19 05/04/14 05/10/ % 20 05/11/14 05/17/ % 21 05/18/14 05/24/ % 22 05/25/14 05/31/ % 23 06/01/14 06/07/ % 24 06/08/14 06/14/ % 25 06/15/14 06/21/ % 26 06/22/14 06/28/ % 27 06/29/14 06/30/ % Page 22

23 3.2.3 Trout Life history strategies used by trout in the Soos Creek basin include anadromous, fluvial, and resident forms. Both summer and winter steelhead are present throughout the basin. No attempt was made to distinguish between resident and anadromous steelhead/rainbow trout that were captured at the Soos Creek screw trap, therefore they were counted as steelhead. Emergent fry/parr less than 40 mm in length were not identified to species, rather grouped collectively as trout, as characteristics are difficult to distinguish in the field at this life stage. For simplicity, trout catch includes fish visually identified as either Oncorhynchus clarki (cutthroat trout) or O. mykiss (steelhead/rainbow trout). A summary of catch, length, weight and condition factor (K) for all trout species encountered at the Soos Creek screw trap is found in Table 8. A total of 42 NOR and 2 HOR steelhead were captured in the screw trap. Catches were too few to develop migration estimates. HOR steelhead were visually identified by the presence of an adipose fin clip. NOR steelhead ranged from 58 mm to 208 mm and were captured at the screw trap from January 15 to June 19. HOR steelhead ranged from 145 mm to 185 mm and were captured from April 4 to April 28. A total of 44 cutthroat trout were captured in the screw trap from January 20 to June 14. Cutthroat FLs ranged from 86 mm to 227 mm. A total of 1,804 trout fry were captured at the screw trap from May 16 to the final day of trap operation (peaking on May 30), and had fork lengths that ranged from 21 mm to 50 mm. Table 8. Summary of length, weight, and condition factor for all trout species captured at the Soos Creek screw trap in Species Origin/ Stage Total catch/ Sample (N) Fork Length (mm) Weight (g) Mean Median SD Mean Median SD K- Factor Steelhead NOR Parr/Smolt 42/ Steelhead HOR Parr/Smolt 2/ Cutthroat HOR Trout Parr/Smolt 44/ Trout NOR Fry 696/ Page 23

24 3.2.4 Other Salmonids 1,108 Chum salmon and 127 Pink Salmon were captured at the screw trap in 2014, and lengths and weights were recorded. A summary of catch, length, and weight for sampled incidental species is found in Table 9. Table 9. Summary of length, weight, and condition factor for pink, and chum salmon captured at the Soos Creek screw trap in Species Origin/ Stage Total catch/ Sample (N) Fork Length (mm) Weight (g) Mean Median SD Mean Median SD K- Factor Pink Fry 110/ Chum Fry 601/ Fish health Chinook and coho daily catch showed physical signs of stress and external abnormalities (or impairments) from January to June (Table 10). Common impairments included: fungus, hemorrhage in the eye(s), hemorrhage on the fins (especially the caudal fin), and fin erosion (caudal and dorsal). NWIFC fish pathologist, Bruce Stewart, sampled multiple yearling coho (BY 2012) during an onsite fish health investigation at the Soos Creek screw trap and identified Nanophyetus salmincola as the primary pathogen responsible for compromising the health of the Soos Creek fish. This pathogen, as with other fish diseases including bacterial kidney disease (BKD), was found to be strongly linked to poor water quality and environmental stress. These poor fish health indicators demonstrated a potential link to a larger scale water quality, habitat quality or environmental issues present throughout the Soos Creek basin. The heavy load of N. salmincola is contributing to the poor health of fish captured at the Soos Creek screw trap, thus effecting fitness and overall survival of Soos Creek salmonids. N. salmincola, is only found in salmonids from the U.S. Pacific Northwest because of the limited range of its intermediate host, the snail Juga Picifera (Dalton 1991). Within the Green River Basin the Juga snail is only known from Soos Creek Basin and Mill Creek (King County department of Natural Resources and Parks. 2012). N. salmincola is a parasitic fluke worm which has a complex life cycle in which the fish is only one of a series of hosts necessary for the maturation and perpetuation of the parasite. The life cycle of N. salmincola starts as an egg in mammal or bird feces, of which a miracidium hatches from each egg and burrows into a snail (Juga sp.) its first intermediate host. The parasite s range is controlled by that of its obligatory first intermediate host, snails of the genus Juga (Quinn, 2005). Multiple miracidia are known to infect one single Juga snail. Intensity of infection is pretty much a factor of age when you're talking about snails in the wild, where repeated exposure to infection results in higher numbers of transmitted parasites. In the snail the miracidium Page 24

25 develops into a redia, which produces and shed many cercariae (parasitic larvae). In a laboratory setting manipulating factors of light, temp, and ph, can get infected snails to shed a max average of 5570 cercariae per snail in a 24 hour period with temperatures around 20 degrees Celsius (Law, 1968). So, if a snail continues to become infected with new miracidia, it will continue to produce cercariae (at differing rates and cycles depending on conditions) its entire life. The cercariae swim/drift in the water for a short time until they come in contact with a salmonid (second intermediate host) penetrating the fins, skin, eyes, and gills. The cercaria will migrate through the circulatory system to carious tissues such as the gill, heart, liver, muscle, optic nerve, and kidney (Foott et al. 1997). The parasite (now referred to as metacercaria) tends to concentrate in the posterior kidney (Milleman and Knapp 1970). Once in the fish the cercariae make their way to the kidney or muscle tissue becoming encysted forming into metacercaria (Bennington, E. et al. 1960). The metacercaria go dormant as the salmonid out-migrates to the ocean, and one juvenile salmonid can have upwards of 60,000 encysted metacercaria (Personnel communication, Martin Chen NWIFC pathologist). Once the salmonid completes its seaward migration and returns years later as a spawning adult the fish will spawn and or die, and potentially being consumed by a mammal or pisicorous bird (third host) which would become infected, maturing the metacercariae into an adult fluke. Once the fluke has infected the intestine of the third and final host each metacercaria will hatch out an adult, which then reproduces sexually. Most trematodes are simultaneous hermaphrodites, possessing both male and female sex organs, and will sexually reproduce in both forms. So, in theory, each metacercariae should eventually produce eggs. Adult fluke develops eggs which are passed in the feces of the third host ultimately hatching a miracidia from each egg completing the lifecycle. It is unknown exactly how many eggs are shed from an adult N. salmincola Fluke, but if compared to a similar trematode Fasciola hepatica, on single adult fluke can produce 20,000-50,000 eggs per day and can live for years within the final host (Personal communication, Bonnie Besijn, USGS Research biologist). Yearling coho captured in early February showed visible abnormalities common with N. salmincola infection (saprolegnia, hemorrhage on fins and eyes, bulging eyes, and fin erosion), and sub-yearling Chinook and coho didn t show signs until early April. N. salmincola is known to have a spring and fall pulse when the juga snail sheds the cercariae, which has been theorized to be related to water temperature and duration of daylight. Based on the data (Table 10) yearling coho are showing signs much earlier than the sub-yearlings, pointing towards infection from the fall pulse in 2013, whereas sub-yearling salmonids are susceptible to the spring pulse which seems to occur in early April based on the data obtained in The majority (90% + of emigrants) of sub-yearling Chinook, chum, and pink salmon emigrate Soos basin before the spring pulse of the shed cercariae, increasing their chances of survival on their seaward migration. This juvenile life history strategy of emigrating Soos Basin as sub-yearlings should increase survival opposed to salmonids that rear in Soos basin for at least a year (coho, and Page 25

26 steelhead). Juvenile fish health and habitat quality within the Soos Creek basin will require ongoing research and monitoring to understand this trematode endemic in Soos Basin. Table 10. Morbidity of Soos Creek salmonids captured showing visible abnormalities common with Nanophyetus salmincola. Stat Week Sum of QUANTITY Max. Daily Average temp (C ) Average of LENGTH (mm) Average of WEIGHT (g) Impairment common with Nanophyetus % impaired of weekly catch % % % % % % % % % % % % % % % % % % % % Stat Week Sum of QUANTITY Max. Daily Average temp (C ) Sub-Yearling Chinook 2014 Soos Creek summary Sub-Yearling Coho 2014 Soos Creek summary Average of LENGTH (mm) Average of WEIGHT (g) Impairment common with Nanophyetus % impaired of weekly catch % % % % % % % % % % % % % % % % % % % % % % % % Page 26