Methods – Data Collection
Note: data within the current year’s monitoring season are considered provisional. The monitoring season typically concludes at the end of September.
Rotary screw trap operations
Sampling for juvenile salmonids in Clear Creek (CC) and Battle Creek (BC) is accomplished by using standardized rotary screw trap (RST) sampling techniques using traps manufactured by E.G. Solutions, Corvallis, Oregon. The CC RSTs are located at river miles (RM) 1.7 (lower Clear Creek [LCC]) and 8.4 (upper Clear Creek [UCC]), and the BC RST (upper Battle Creek [UBC]) RST is located at river mile 6.2.
This type of trap utilizes a 5-ft diameter cone-shaped auger covered with a stainless steel screen with one-eighth inch diameter perforations. This cone acts as a sieve, which separates fish from the sampled water. The cone and live-box are supported between two pontoons, and the cone’s auger-type action passes water, fish, and debris to the rear of the trap directly into the live-box. This live-box retains fish and debris while passing water through screens located in its back, sides, and bottom.
Because of the high numbers of Chinook Salmon Oncorhynchus tshawytscha out-migrating from CC, modifications have been made to the RSTs and operations to reduce potential negative effects to juvenile salmonids created by high fish densities in the live-box. A “half-cone modification” has been made by placing an aluminum plate over one of the two cone discharge ports and removing an exterior cone hatch cover. This creates a condition in which 50% of the collected fish and debris are not passed into the live-box but rather are discharged from the cone into the creek, thereby reducing overcrowding of fish in the live-box. Both CC RSTs are operated in the half-cone configuration, while UBC is operated in the “full cone” condition. Other modifications to RST equipment that provided greater protection to collected fish include enlarging the size of the live-box and increasing the size of flotation pontoons (to accommodate the larger live-box). Inside the live-box, a midway fish exclusionary screen made of expanded aluminum is added, dividing the live-box into two halves: fore and aft. This screen prevents large predatory fish from harassing and preying on smaller salmonids. A panel of clear polycarbonate is attached to the rear screen of the live-box to reduce water velocities within the live-box. Modifications to RST operations included day and night sampling during the peak out-migration periods for spring-run and fall-run Chinook to minimize time fish spent in the live-box. To improve JPI computation, attempts are made to fish high flow events when juvenile salmonids are thought to out-migrate and to increase the frequency of mark–recapture trials during those events. Traps are not operated when flows in excess of 2,000 cfs at LCC, 800 cfs at UCC, and 1,000 cfs at UBC are encountered.
Clear Creek RSTs generally start operations in November; and cease operations on June 30; whereas UBC is now operated year-round. Attempts are made to operate the RSTs continually when staffing allows. Methods for access and data collection are identical for all RSTs.
Each RST is attached to a cable high line and positioned instream with a system of ropes and pulleys. The monitoring team typically accesses the RST by wading from the creek bank; however, during higher flows the RST is pulled into shallow water for boarding. After being servicing, the RST is returned to the thalweg as soon as possible to begin operating again. The RST is serviced daily unless conditions (high flows, heavy debris loads, or high fish densities) require more frequent RST checks to avoid mortality of captured fish or damage to equipment. During each RST servicing crews process the collected fish, clear the RST of debris, and provide RST maintenance. Once per day (at the end of the approximately 24-h sampling period) the crew obtains environmental and RST data. Collected data includes dates and times of RST operation, creek depth at the RST, cone operating depth, number of rotations of the cone during the sampling period, the amount and type of debris collected, basic weather conditions, current velocity, and turbidity. Water depths are measured using a graduated staff to the nearest 0.1 ft. The cone operating depth (in) is measured with a gauge that is permanently mounted to the pontoon adjacent to the cone. The rate of rotation (revolutions per min) of the cone is measured with a mechanical stroke counter that is mounted to the RST railing adjacent to the cone. The amount of debris in the RST is volumetrically measured using a 10-gal plastic tub.
Water temperatures are continuously obtained at 30-min intervals with an instream data logger (HOBO(R) Water Temperature Pro v2 Logger; Onset Computer Corp, Bourne, MA) and those data are downloaded weekly. Water velocity is measured from onboard the RST in front of the cone using a mechanical flow meter (Oceanic® Model 2030 flowmeter; General Oceanics, Miami). Water turbidity is measured from a grab-sample with a Hach Model 2100D turbidimeter (Hach(R) Company, Ames, IA). Clear Creek mean daily discharge data are collected at the U.S. Geological Survey’s Igo gage site (Station #11372000), located at Clear Creek near Igo CA, approximately 2.6 river miles upstream of UCC. Battle Creek mean daily discharge data are collected at the Coleman National Fish Hatchery gauging station (#11376550, [BAT]). At the RST site all environmental and biological data is or has been entered into a paper datasheet, or into a Microsoft Access database using a Mesa® tablet (Juniper Systems, Logan, UT), or Survey 123 using an IPad (Apple, Cupertino, CA).
Dip nets are used to remove the contents of the RST live-box (fish, aquatic vegetation, debris) and place them on a sorting table for examination. The RST catch is brought to shore in lidded 5-gal buckets where they are transferred to 10- or 25-gal buckets with aerators. They are then sampled as described below.
Counting and measurement
The monitoring team counts and obtains length measurements (to the nearest 1.0 mm) for all fish taxa, dead or alive, that are collected. However, when large numbers of Chinook are captured, or during intermediate trap clears (not at the end of the 24 h period) no length measurements are taken and the fish are simply identified, counted, and classified to an age-class. Live fish to be measured are anesthetized in a 1-qt plastic tub with approximately 1–3 ml of a 100 g/L solution of Tricaine Methanesulfonate (MS-222; Syncaine®, Syndel, Ferndale, WA) at a concentration of 60–80 mg/L. Fish are measured on a wet measuring board, placed in a 10-gal plastic tub filled with creek water and fish protectant, and allowed to recover from the anesthetic effects before being released back into the creek. Water in the tubs is replaced as necessary with fresh creek water to maintain adequate temperature and oxygen levels.
Chinook Salmon — At the end of the sample period when less than approximately 250 Chinook are collected in the RST, all are counted, measured to FL, and assigned a life stage classification: yolk-sac fry (C0), fry (C1), parr (C2), silvery parr (C3), or smolt (C4). All Chinook that are measured are assigned run designations using length-at-date tables (S. Greene, 1992 memorandum to Randall Brown, California Department of Water Resources, estimated winter-run Chinook Salmon salvage at the State Water Project and Central Valley Project Delta Pumping Facilities). These designations include fall-run, late-fall run, winter-run, and spring-run Chinook. At the UCC and UBC, all Chinook captured that are assigned fall-run Chinook by Greene are considered instead to be spring-run Chinook because at CC we install a picket weir to block fall Chinook from passing upstream of UCC. On Battle Creek the Coleman National Fish Hatchery’s barrier weir provides the same function. There is undoubtedly overlap in the fork lengths of adjoining runs of juvenile salmon that are not accounted for in the dichotomous length-at-date criteria (Harvey et al. 2014).
At the end of the sample period when more than approximately 250 Chinook are collected in the RST, subsampling is conducted. This is accomplished by using a cylinder-shaped, one-eighth inch mesh “subsampling net.” The bottom of the subsampling net is constructed with a metal frame that creates two equal halves. Each half of the subsampling net bottom is built with a mesh bag that is capable of being tied shut. One side of the net is tied shut and the other side is left open. This subsampling net is placed in a 25-gal bucket that is partially filled with creek water. All collected juvenile salmon are poured into this bucket. The net is then lifted resulting in halving of the sample. Approximately one-half of the salmon are retained in the side of the net with the closed mesh bag, and approximately one-half of the salmon in the side with the open mesh bag are left in the bucket. The RST catch is successively subsampled until approximately 150–250 individuals remain. All the fish in the final subsample are then measured. The number of successive splits that are used vary with the number of salmon collected.
O. mykiss — We use the term O. mykiss to refer to both the stream resident (Rainbow Trout) and anadromous (steelhead) life histories because of the difficulties in differentiating the anadromous and resident forms in the field. All O. mykiss that are encountered at the end of the sample period are counted, measured, and classified to life stage in much the same manner as salmon: yolk-sac fry (R1), fry (R2), parr (R3), silvery parr (R4), and smolt (R5). Fish that are found in the live-box during supplemental storm sampling are counted and assigned to a life stage classification. All live juvenile O. mykiss greater than 50 mm FL that are captured during the daytime (measured) sample are weighed to the nearest 0.1 g with an electronic scale (Scout Pro SP601; Ohaus Corp, Parsippany, NJ) for condition factor analysis.
Non-salmonid taxa — All non-salmonid taxa are counted, and up to 20 randomly selected individuals of each species are measured, either FL, or TL for species that do not have a forked caudal fin. Lamprey are recorded by life stage (ammocoetes, macropthalmia, or adult). Fish that are taken from the live-box during supplemental storm sampling are counted, but no length measurements are obtained. Catch data for all fish taxa are consolidated to represent monthly sums.
The LCC and UBC RSTs capture many small (usually < 25 mm), delicate non-salmonid fry. Many of these fish do not survive the extra handling required for measuring. We visually estimate the number of these fish in the live-box and designate them as unidentified fry. Once all the measurable fish are removed from the live-box, the back screen is removed from the RST and the fry are flushed from the live-box.
Sampling weeks are identified by year and number. Week 52 either has either eight or nine days depending on leap year.
Tissue and otolith sampling
Tissue samples are collected from select Chinook for the purpose of run identification. Samples are taken by removing a 1–2 mm^2 tissue sample from the top or bottom lobe of the caudal fin. The samples are divided into two equal parts and placed in duplicate 2-ml vials containing 0.5 ml 100% ethanol, each labeled with the same sample record number. The duplicate samples are taken for USFWS archive and for future analysis. Since 2022 we have switched to collecting dry tissue samples.
Samples at all RSTs are taken when the length-at-date tables designate the Chinook as winter-run Chinook, late-fall run Chinook, or when FL > 99 mm. In addition, at UCC and UBC samples are taken proportionately to the anticipated out-migration distribution of spring-run Chinook. An attempt is made to collect samples from a range of FLs to minimize sampling siblings, which might potentially bias the genetic analysis.
Mark–recapture trials
Since the RST only captures fish from a small portion of the creek cross section, it is necessary to implement a method to project the RST catch numbers to parts of the creek outside of the RST capture zone. Mark–recapture trials are conducted to determine the efficiency of the RST in catching juvenile salmonids moving downstream during a given time period.
Ideally separate mark–recapture trials would be conducted for each species, run, and life stage to estimate species and age-specific RST efficiencies; however, generally, at all RSTs catch rates for O. mykiss and late-fall run Chinook are too low to conduct separate trials. Therefore, all species and life stage passage estimates at all RSTs are calculated from valid mark–recapture trials using either spring-run or fall-run Chinook. Trials on CC are conducted with natural-origin Chinook, while those at UBC are conducted using hatchery-origin fish from Coleman National Fish Hatchery. An attempt is made to mark a minimum of 400 juvenile Chinook for each trial with a goal to recapture at least seven marked individuals in order to generate reliable estimates (Steinhorst et al. 2004). The Red Bluff Fish and Wildlife Office also conducts mark–recapture trials at the Red Bluff Diversion Dam (RBDD) for estimating RST efficiency while monitoring Sacramento River juvenile salmonid populations. Dual marks allows RBDD to distinguish CC and BC-marked Chinook from those marked at the RBDD. The methods used for marking are described below.
Marking procedures — All fish are enumerated, and FL is measured on a minimum of 30 individuals. Single marked fish consist of immersing the salmon in a solution of 1.6 g of Bismarck Brown Y stain in 20 gal of water for a duration of 50 min. This stain can be retained on the fish for up to a week. Dual marked fish are first anesthetized with a 60–80 mg/L solution of MS-222, and surgical scalpels are then used to remove an area of approximately 1–2 mm^2 from the corner of either the upper or lower caudal fin lobe. After the clipping process is complete, the salmon are stained with Bismarck Brown Y stain.
Recovery and release — Marked juvenile salmon are placed in a live-car and allowed to recover overnight in the RST live-box. This overnight retention allows for the detection of salmon with latent injuries and mortalities resulting from the marking procedure. On the following evening weak, injured, and dead fish are removed. The remaining fish are counted and transported for release 0.2 (UCC), 0.4 (LCC), and 1.0 (UBC) river miles upstream of the RST sampling site. The fish are released in batches of less than 50 fish, one batch immediately after another, no earlier than 15 min before sunset. The nighttime releases of marked fish are designed to reduce the potential for unnaturally high predation on the marked fish as they could possibly be experiencing temporary disorientation by the marking and holding procedure and transportation, as well as to imitate the tendency for natural populations of out-migrating juvenile Chinook to move downstream primarily at night (Groot and Margolis 1998; Schraml et al. 2018; Schraml and Chamberlain 2019a). To explore the relationship of RST efficiency to biological and environmental variables, we collect flow, water temperature, and turbidity data at the time of release. Marked Chinook that are recaptured in the RST are counted, measured, and subsequently released downstream of the RST to prevent them from being recaptured again. In most cases when stream flows are predicted to exceed 2,000 cfs, efficiency trials are not conducted to reduce the chance of fish mortalities and to ensure crew-related safety. In those cases, fish being held for a mark–recapture trials are released downstream of the RST.
Further methods and equations
Further methods for calculating Rotary Screw Trap efficiency, interpolated data, hourly proportion of daily catch, juvenile passage indices, mortality, data quality assurance, and references can be found in the PDF attached to the EDI package titled Battle_Clear_Methods.pdf. This file contains equations to support analyses and further information about trapping conditions for each year, including important caveats for interpretation of the data.
