Field Manual
Okanogan Monitoring and Evaluation Program
Biological Protocols
DRAFT
September 1, 2005
Prepared by
The Colville Confederated Tribes
John Arterburn
Keith Kistler
KWA Ecological Sciences, Inc.
Paul Wagner
Rhonda Dasher
Table of Contents
Introduction 3
Acknowledgements 4
Section 1. Method For Detecting Fish Species Assemblages Using Snorkeling 4
Purpose 4
Equipment 4
Site Selection 4
Sampling Duration 4
Permits 4
Snorkeling Sampling Procedures 5
Section 2. Smolt Trapping 7
Summary 7
Purpose 7
Background 10
Safety 11
Equipment 11
Site Selection 11
Preparation and Installation 13
Sampling Duration 14
Procedure 14
Data Analysis 17
Estimating Total Migration 17
Literature Cited 22
Section 3. Adult Enumeration 25
Purpose 25
Procedure 26
Section 4. Benthic Macro-Invertebrate Assessment 26
Purpose 26
Equipment 26
Site Selection 26
Sampling Duration 26
Procedure To Collect Kick Net Samples 26
Procedure For Preparing Composite Samples for Identification 28
Multi-Metric Index Development 29
Definition of Terms 32
References Cited 32
Section 5. Method For Detecting Steelhead Redds 32
Purpose 32
Site Selection 33
Sampling Duration 34
Equipment 35
Anatomy of a Redd 35
Multiple Pass Marked Redd Survey Method 36
Peak Redd Count Method 37
Foot Surveys 37
Boat /Raft Surveys 37
Fish Observation 37
Carcass Surveys 37
QA/QC Procedures 38
Removal Of Flagging 38
Estimating Total Redds and Escapment 38
Literature CIted 40
Introduction
This Field Manual was developed by the Colville Confederated Tribes to provide specific guidance in the evaluation and monitoring of fish populations in the Okanogan Subbasin for the 2005 Okanogan Baseline Monitoring and Evaluation Program (OBMEP). The OBMEP is long-term status and trend monitoring program subject to future adaptation management. Therefore, this Field Manual should be considered to be a "living document" with the following protocols potentially subject to some level of modification over time as new information becomes available.
The protocols contained within this Manual are closely aligned with the Environmental Monitoring and Assessment Program (EMAP) developed by the Environmental Protection Agency (EPA) as adopted into the Upper Columbia Monitoring and Evaluation Strategy. These protocols were further refined to address specific program needs and for compatibility with the Ecosystems Diagnosis and Treatment (EDT) Model developed by Mobrand Biometrics Incorporated. EDT is the primary assessment tool used by subbasin planners throughout the Columbia Basin and specifically within the Okanogan Subbasin and periodic updating of EDT input fields with compatible data will be necessary to assess changes that may occur within the subbasin over time.
Acknowledgements
Ken MacDonald (USFS) provided valuable information pertaining to the snorkeling protocols in use in the Wenatchee Subbasin Monitoring and Evaluation Program. Andrew Murdock (WDFW) and Greg Volkhardt (WDFW) provided essential material and advice used in the development of the smolt trapping protocols.
Section 1. Method For Detecting Fish Species Assemblages Using Snorkeling
Modified Protocol taken from: Rodgers (2002), Thurow (1994), and
Peck et al. (Unpubl.)
Purpose
Estimating the density of juvenile salmonids with a primary emphasis on summer steelhead allows the investigator to obtain a sample over time of the change in abundance of rearing juvenile salmonids produced in the Okanogan River basin. Collection of information pertaining to salmonids and other species of fish may be collected but is ancillary to the goal of estimating juvenile summer steelhead production in the Okanogan subbasin. In addition, information pertaining to the presence of salmonids and non-salmonids can be used to provide input for the Ecosystem Diagnosis and Treatment Model in the Predation Risk, Fish Community Richness, and Fish Species Introductions attribute fields.
Equipment
Persons conducting snorkel counts should be equipped with dry suits or wet suits, masks, snorkels, rubber soled boots, hand held thermometer, field forms/data logger, and a stopwatch. Additional equipment such as hand counters, underwater white boards, and measuring rods are helpful for enumerating fish and determining fish lengths. A submersible halogen light may be useful to search for fish in shaded locations.
Site Selection
The sample reach is laid out according to Section 1 of the Physical Habitat Field Manual.
Sampling Duration
Sampling for fish species should occur during the low flow period in late summer when water temperatures exceed 90C.
Permits
Be sure that all necessary collection permits and ESA clearances are obtained and copies of required permits are with you while in the field.
Snorkeling Sampling Procedures
Step 1: After team members don their wetsuits, a quick equipment check will ensure that all members have the necessary tools to complete their survey. Team members need to designate one person as the data recorder for each group in the survey. All members in the group report fish observations to the recorder after each transect.
Step 2: Measure the visual distance to determine the number of snorkelers needed to survey a given reach on a given day. A snorkeler should take one end of a measuring tape and back away from the bank while another person holds the tape. Once the snorkeler can no longer clearly see detail along the bank. The person on shore will take a measurement of this distance. On small streams this distance will be used to determine the number of snorkelers needed to survey a reach. On larger streams with maximum depths greater than 3 meters the visual distance will be measured by visual depth. A snorkeler will enter the deepest area of the stream and drop a small unpainted lead weight attached to a string toward the bottom until it can no longer be seen then slowly begin raising the weight, marking the string at the depth where it first becomes visible again. The string can be measured on shore to determine the visual distance for the reach. Once the visual distance is determined, the number of persons needed is calculated by dividing the average width of the reach by two times the visual depth. Snorkel surveys of large stream reaches should be conducted during periods of maximum visibility to minimize the number of staff required.
Step 3: Before starting a survey, record the weather conditions and water temperature (clear, overcast, rainy, etc). In all wadeable and most non-wadeable stream reaches, snorkeling should involve only a single pass through areas that are deep enough to survey. Record weather conditions, temperature, and total time required at the beginning and end of the entire reach.
Note: Team members need to look downstream periodically and read the water for areas of increased flow or change of gradient (riffles, falls, or rapids). Before making a pass through an area of increased flow, consider possible safety issues. Objects such as boulders and woody debris can pose a significant hazard, if team members are not prepared. Studying the reach, before a survey, will alert team members to possible hazards so that they can develop a plan for working through difficult areas.
Step 4: .
Wadeable Streams: Begin at the downstream boundary (Transect A) of the sample stream reach and proceed upstream through the pools and riffles. All movements in the water need to be slow and careful so as not to create a flight response in fish observed (Thompson 2000) or reduce the visual distance by disturbing fine sediments. Members will slowly proceed upstream with team members keeping each other in their line of sight. Where possible, members should float, to avoid stirring up sediment with their feet or hands. If there are multiple groups within a reach, each group should minimize disturbance so that visibility downstream is not compromised.
Non-wadeable Streams and Rivers: Begin at the upstream boundary (Transect K). Depending on flow conditions group members can stay in line by keeping each other within the visual distance or by using a section of rope with floats on it that everyone holds onto. Members will proceed downstream with the current, controlling their movement enough to keep within the visual distance to the other group members. If the number of snorkels available is less than those needed as outlined in Step 2 but visibility is considered good for the site, a second pass maybe used. If conducting the 2-pass strategy, have snorkelers spread from the right bank to the mid-point of the stream and conduct the survey through all transects. Proceed to the top of the stream reach and spread out from the left bank to the mid-point in the stream and conduct the second survey. Sum all counts for each transect for a complete survey.
Step 5: A minimum of two persons should be present during snorkel surveys. A two person snorkeling crews can conduct snorkel surveys in many wadeable streams. In wadeable stream reaches, one crew member should snorkel each transect while the other crew member records the counts as they are given by the snorkeler. In non-wadeable areas, crew members should snorkel side by side and sum their individual counts. Using an arm chart, white board, or hand counter. Each snorkeler counts the fish to the immediate front and to the sides opposite the other snorkeler or as designated by the team leader to avoid duplication of counts. Each individual snorkeler should maintain a spacing of 2-times the visual distance from the nearest snorkeler and observe fish both to the right and left. The designated team leader will control spread as the stream channel changes width according to pre-snorkeling instruction.
Step 6: Counts of the number of fish should be recorded along entire transect area (A-B, B-C, etc.). When enumerating and identifying fish three levels of identification are possible. First, All fish encountered during the snorkel survey should be identified to species this is especially critical for salmonid species. Second, non –salmonid species can be enumerated into major taxa if species identification is not possible as may be the case of some non-salmonids (i.e..sculpin, bass, sunfish, suckers, trout, salmon, char, whitefish). Lastly, every effort should be made to at least classify fish as salmonids or non-salmonids. The unidentified column on the data sheet should rarely be used.
Step 7: In addition to enumerating all fish, salmonids should be lumped into the following length categories: 1) young of the year (<100 mm), 2) juveniles (100-300mm), and 3) adults (>300mm).
Step 8: After snorkeling, the underwater visibility of each study reach is ranked on a scale of 0 to 3 where 0 = not snorkelable due to an extremely high amount of hiding cover or zero water visibility (No snorkel survey should be conducted, <25% visibility); 1 = high amount of hiding cover or poor water clarity (25%-50% visibility); 2 = moderate amount of hiding cover or moderate water clarity, neither of which were thought to impede accurate fish counts (50%-75% visibility); and 3 = little hiding cover and good water clarity (>75% visibility).
Step 9: To calculate fish densities (fish/m2), determine the area for each reach by utilizing the physical habitat data collected (previously described in Section 2 of the Physical Habitat Protocols Field Manual) for average width and multiplying this by reach length to get the area sampled. Then divide the total number of fish along with the total number of all identified categories by the area sampled. Total salmonids, and total O. mykiss should also be calculated.
Step10: Consult Thurow (1994) for additional information.
Section 2. Smolt Trapping
Protocol adapted from; Seiler and Volkhardt 2005, and Murdock et al. 2001.
Summary
Investigators will use floating screw traps (or other appropriate traps depending on stream conditions) to collect downstream migrating smolts to estimate the total number (abundance) of smolts produced within a watershed or basin. Traps will operate for at least the entire period of the smolt migration. Trapping efficiency, based on mark/recapture will be estimated throughout the trapping period. Methods for operating the trap, estimating efficiency, and the frequency at which efficiency tests are conducted are described in Murdoch et al. (2000). Numbers of smolts will be reported for populations or subpopulations. The Fulton-type condition factor will be estimated from length and weight measurements to describe the well-being of smolts within a population or subpopulation. Genetic samples will also be collected to characterize (via DNA microsatellites) within- and between-population genetic variability of smolts.
Purpose
Operating a downstream migrant trap allows the investigator to sample the wild salmonids produced in a watershed or tributary over time. The sample in itself is valuable because it documents the presence/absence of migrating juveniles, enables determination of age at migration, condition, timing, species, and genetic characteristics. Furthermore, if the location of the trap, its placement, and hours of operation are sufficient and held reasonably constant from year to year, catch of a given species or catch per unit effort can be used as an index of downstream migrant production (Seiler and Volkhardt, 2005).
More importantly, trapping information can also be used to create estimates of the total freshwater production by using a simple mark-recapture population estimation methodology. The rationale is simply that the proportion of marked fish appearing in a random sample provides an estimate of the proportion marked in the total population. The proportion captured (trap efficiency) is estimated by conducting a series of trap efficiency experiments over the trapping season (Seiler and Volkhardt, 2005).
This protocol describes methods used to achieve estimates of wild downstream migrant salmonid production using a rotary screw trap. Since the traps strain the upper portion of the water column, they are generally not very useful for capturing species that migrate along the bottom of the river (e.g., lamprey). The traps can be scaled to operate in various sized streams, but are most commonly used in streams that are too large or powerful to employ a fence weir (e.g., ~10 to 15-m or larger channels) (Seiler and Volkhardt, 2005).
The rotary screw trap is used in medium to large rivers. The screw trap consists of a cone covered in perforated plate that is mounted on a pontoon barge (Figure 1). Within the cone are two tapered flights that are wrapped 360-degrees around a center shaft. The trap cone is oriented with the wide end facing upstream and uses the force of the river acting on the tapered flights to rotate the cone about its axis. Downstream migrating fish are swept into the wide end of the cone (typically either 1.5-m or 2.5-m in diameter) and are gently augered into a live box at the rear of the trap. Typically one or more winches are used to adjust the fore and aft elevation of the trap. A small drum screen, powered by the rotating cone, is located at the rear of the live box and removes organic debris (Seiler and Volkhardt, 2005).