Authorizations and Permits for Protected Species (APPS)

ESA LISTING STATUS:  Listed as threatened on Mar. 19, 1998; threatened status reaffirmed on Jan. 5, 2006. NOAA Fisheries issued results of a five-year review on Aug. 15, 2011, and concluded that this species should remain listed as threatened.*

DESCRIPTION:  The DPS includes all naturally spawned anadromous O. mykiss (steelhead) populations below natural and manmade impassable barriers in the Sacramento and San Joaquin Rivers and their tributaries, excluding steelhead from San Francisco and San Pablo Bays and their tributaries, as well as two artificial propagation programs: the Coleman NFH, and Feather River Hatchery steelhead hatchery programs.*

*(NMFS, http://www.nwr.noaa.gov/ESA-Salmon-Listings/Salmon-Populations/Steelhead/STCCV.cfm)

Sampling Method 1:  Raft Mounted Electroshocker
Electrofishing is a common method used in monitoring steelhead population (e.g., Mill and Deer creeks, and Feather, American, Mokelumne, Stanislaus, and Merced rivers).  One potential drawback for using electrofishing in rivers involves the difficulty in obtaining permits due to the possibility of injuring fish in anadromous salmonid waters.  However, electrofishing effectiveness and safety have improved over time. Sampling frequency will be monthly from December through March of the following year.  Capture of the same fish multiple times is to be anticipated, thus monthly sampling is important to ensure fish recovery from stress between capture.  Raft mounted electroshockers will be used in order to navigate through shallow waters of the sampling locations (i.e., Mud Slough, Salt Slough, Newman Wasteway, Eastside Bypass, Mariposa Bypass, Sand Slough Control Structure, and base of Sack Dam).  This is a three person task.  One person to operate the boat and the main controller of the eshocker's generator.  Then two netters. One of the two netters will have control of the pedal to turn the electricity on (push down) and off (release) for safety of the crew and the fish.  Electrofishing methods would refer to the NMFS guidelines for sampling waters with anadromous fish (Guidelines for Electrofishing Waters Containing Salmonids Listed Under the Endangered Species Act. June 2000. http://www.nwr.noaa.gov/ESA-Salmon-Regulations-Permits/4d-rules/upload/electro2000.pdf).  However, the guidelines are for backpack electrofishing, but researchers are not precluded from using other techniques or equipments as long as NMFS are given substantial proof that proposed techniques or equipments are necessary for the study and that listed species are safeguarded.  Additional permitting is necessary under this method.  This technique has a high potential to be successfully implemented during 2012 spring interim flows. The significant constraints to this method are permitting and access to appropriate sampling locations.  The only difference between a boat-mounted electroshocker and a raft-mounted electroshocker is that a raft-mounted electroshocker can access shallow water habitats.  We will use raft mounted electroshocker to have access to both deep and shallow water habitats. A boat electroshocker may be limited to only deeper water habitats.  Backpack electroshocker will not be used due to the enormous size of the Restoration Area.  Electroshocking raft can access the same habitat as a wading backpack electroshocker.  Backpack electroshocker is limited by the wading individual.  The same guidelines for initial and maximum settings for backpack electroshocking will be followed in raft-mounted electroshocking.  We will only do one pass per month at each site due to the sensitivity of the species.  Captured steelhead will be measured, pictured, catalogued, and translocated to a more suitable habitat (i.e., San Joaquin River at the Merced River Confluence). 

Sampling Method 2:  Fyke nets with wing walls and fish traps
Migrating adult steelhead are difficult to monitor using techniques commonly used (e.g., carcass surveys, snorkel surveys, redd counts) to assess salmon populations due to their unique life-history traits.  Steelhead, unlike salmon, may not die after spawning.  Therefore, carcasses may not be available for a mark-recapture survey.  In addition, steelhead migrate and spawn during the late-fall, winter, and spring months when rivers have periods of pulse flows (e.g., VAMP), high flows (e.g., flood releases), and turbid water conditions.  A fyke net with wing walls and traps is the proposed sampling method to overcome difficulty of monitoring adult steelhead. 

Fyke nets have long been used to capture migrating fish to monitor their yearly changes and abundances.  This net tends to be the most useful in capturing fish that follow the shorelines at different times of the day during fish migration season.  These nets are constructed of 3.7-cm mesh formed over a 1.5 m x 0.5 m rectangular lead hoop with 0.95 cm diameter solid round stock and three 1.5-m diameter hoops.  The traps contain two 5 m long throats with 15 or 25 cm diameter throats, and have a zipper for easy fish removal. Wings will be 1.8 m deep and 48.8 m long.  A buoy will be affixed with a 10-m length of rope.  Nets will be held in place with 22-kg anchors and will be deployed in sampling locations (i.e., upstream of the confluence of the Merced River, the mouths of Mud, Slough, Salt Slough, Newman Wasteway, and existing structure at Sack Dam).  This proposed technique will be implemented once the Hills Ferry Barrier is removed around mid-December and will remain deployed at the sampling locations until March 15. The traps will be checked daily so the likelihood of fish being physically injured is low.  Adult steelhead that get captured will be sampled, tagged, and released.  Data from this trap will give an actual count of steelhead abundance migrating in the upper reaches of the SJR.  

Fyke nets will be used in lieu fyke traps for several reasons: fyke nets are relatively inexpensive and easy to install, are not a boat passage impediment (can be pushed down in the water column for boat passage), easily replaced if damaged, easy to transport, and no permitting required to transport.  Although, California Department of Fish and Game wire fyke trap can catch fish in high flows, it will require a crane to remove the trap out of water under increased hydraulic pressure and in the event that the trap becomes silted.

Sampling Method 3:  Steelhead specific trammel nets
Trammel nets are most common as stationary gear to block off channels with low velocities or no flows.  However, they can also be used to drift in short durations (e.g., 20 min) on high velocity water.  A short duration drifting of trammel net is necessary to prevent fish from being entangled for a long period of time.  Trammel nets are advantageous and relatively efficient in turbid waters.  This net consist of three parallel vertical layers of netting, the inner net has a very small mesh size, while the outer nets have mesh size large enough for fish to pass.  The larger and smaller mesh size nets form a pocket when fish try to swim through.   Similar to seine nets, trammel nets are equipped with floats attached to the head rope and lead weights along the ground rope.  For safety reasons, brightly colored floats will be used to attach to the head rope so boaters and other recreationists can avoid entangling themselves, their boats, and/or their fishing gears with the nets while floated.  To ensure safety of steelhead, fisheries biologists tending the nets follow at a close distance to observe, reduce risk of entanglement, and retrieve nets in short time intervals.  Sampling time will depend on the number of fish and bycatch caught at each location.

Sampling will begin during adult steelhead migration (mid-December until mid-March) on a number of habitats on the SJR where steelhead may be present.  Additional permitting is necessary under this method.

Fish Handling and Relocation
For all sampling methods listed above, captured adult CV steelhead will be subject to standard handling and transporting procedures.  Captured steelhead will be recorded, measured (i.e., fork length and total length), sexed (if possible), sampled for scales and tissues, and checked for injuries and presence of tags.  Additionally, fish will be Floy tagged with a unique identification number to document any recaptures that may occur in the study area.  

Captured steelhead would be transported downstream of the mouth of the Merced River in transport tanks following proposed transport protocols.  The transport tanks will be immediately filled with river water prior to transport using a portable screened water pump.  Captured steelhead will be moved in and out of the transport truck using a water-filled vessel to help minimize stress and loss of slime.  Oxygen gas will be supplied to the transport tanks using compress oxygen gas cylinders and micro-bubble diffusers to maintain dissolved oxygen levels at near saturation during transport.  Transport water will be supplemented with sodium chloride to decrease ionic gradient as another way to minimize stress.  The truck will be stopped after 30 minutes of transportation and each hour thereafter for visual inspection of the life-support system and fish wellbeing.  Water will be tempered to the receiving water at the predetermined release location before transferring fish, by pumping receiving water directly into the transport tank until the temperature reaches that of the release water.

Hills Ferry Barrier (HFB) has been operated every fall by DFG on the SJR since 1992.  CV steelhead have not yet been captured or identified.  However, the HFB has not been operated in the spring when steelhead are emigrating from the downstream tributaries. The opportunity for these fish to access the SJR upstream of the Merced River has been extremely low due to inhospitable water flow and water quality conditions. Although Interim Flows may provide conditions that could allow steelhead to stray upstream of the Merced River, the likelihood of finding CV steelhead in the SJR upstream of the Merced River is low and lethal take is not anticipated for this study.

Effects associated with monitoring from utilization of the raft mounted electroshocker may occur and result in potentially non-lethal effects.  Staff involved in implementation of the SMP will use caution in electroshocking techniques.  The sampling frequency will be monthly in order to reduce the likelihood of capturing the same fish multiple times and to allow ample recovery time.  The potential lethal take is described in "Lethal Take", above.  Electroshocking also has a potential to harm or harass CV steelhead, if present, through capture and study activities.  However, these effects are temporary.

Effects associated with the capture of fish with fyke nets and fish traps are anticipated to be non-lethal.  The traps will be checked daily to reduce the risk of fish sustaining physical injury.  Any CV steelhead that are captured will be sampled, tagged, and realeased.  The trapping, sampling, and tagging of fish could result in a small amount of harm of harassment.  However, the effects are expected to be temporary, minimal, and non-lethal.

Effects associated with the placement and use of trammel nets would be similar to the effects to CV steelhead from the use of fyke nets.  The nets would be drifted and fisheries biologists would be present on-site during their placement to ensure that species collected would be expeditiously sampled and released.  The effects from the use of trammel nets is expected to be temporary, minimal, and non-lethal.

There could be potential effects to steelhead in fish handling and relocation.  Care will be taken to ensure that stress to the fish is minimized.  Fish transport tanks with water pumps, gas cylinders, diffusers, and sodium chloride will be used to minimize stress.  However, some effects could occur as CV steelhead could be harmed or harassed through this process.

The use of fyke nets and trammel nets will be implemented and monitored frequently.  The fyke nets will be checked at least daily and the trammel nets will be manned during the entire time of their deployment.  As biologists will be present during these activities, this is expected to minimize negative effects as staff would be present to collect and release fish in a reasonable period of time.

Raft mounted eletroshockers will be utilized in coordination with suggested NMFS guidelines for electroshocking and in coordination with NMFS staff before and during monitoring activities.  All staff will be trained in the use of electroshocking and the sampling frequency will be limited to once per month in specific locations to avoid stress to the species and allow for adequate recovery time as it is expected that the same fish could be captured multiple times.

The transporation and handling of fish will occur quickly and any CV steelhead caught will be transported downstream of the Merced River confluence with the SJR.  Captured steelhead would be transported downstream of the mouth of the Merced River in transport tanks following proposed transport protocols.  The transport tanks will be immediately filled with river water prior to transport using a portable screened water pump.  Captured steelhead will be moved in and out of the transport truck using a water-filled vessel to help minimize stress and loss of slime.  Oxygen gas will be supplied to the transport tanks using compress oxygen gas cylinders and micro-bubble diffusers to maintain dissolved oxygen levels at near saturation during transport.  Transport water will be supplemented with sodium chloride to decrease ionic gradient as another way to minimize stress.  The truck will be stopped after 30 minutes of transportation and each hour thereafter for visual inspection of the life-support system and fish wellbeing.  Water will be tempered to the receiving water at the predetermined release location before transferring fish, by pumping receiving water directly into the transport tank until the temperature reaches that of the release water.

The staff that will be involved in these monitoring activities will be trained staff with specialized skills in collection and sampling techniques.  Fisheries biologists, out of Reclamation's Technical Services Center, DFG, and U.S. Fish and Wildlife Service, implementing the monitoring activities are trained and have experience in the use of nets, traps, and electroshockers.  

Reclamation shall purchase and supply all required equipment, including vehicles, nets, gloves, traps, the raft electroshocker,  and any other required equipment.

Samples will be surrendered to the California Department of Fish and Game at the conclusion of sampling for testing and disposition.

An annual project report for Steelhead Monitoring will be submitted to the Bureau of Reclamation SJRRP and the SJRRP Fisheries Management Work Group by June 1 of each year.  Once reviewed and finalized, this report will be provided to the public via the SJRRP web site at:  www.restoresjr.net.