PIT-tagging large numbers of salmonids at Snake River juvenile collection facilities presents the researcher with many questions.  Chief among the questions are how to collect the large numbers of fish needed and where to conduct the tagging.  While the Smolt Monitoring Program (SMP) can serve as a source of fish, and the facility's juvenile laboratory can provide a location for tagging, both are limited.  The SMP is limited in the number of fish that can safely be handled in a day, especially if the fish must be processed prior to a transport barge or truck leaving the facility.  The laboratories at the facilities are not designed for more than 2-3 tagging stations.  If a researcher needs more than can be provided by the SMP or laboratory, they must create a different source of fish and either bring in a dedicated tagging facility or build one on-site.

In 2005, NOAA Fisheries built a two-story tagging facility along the south side of the east bank of raceways at the Lower Granite Dam juvenile fish facility (JFF) (Marsh et al. 2006).  This tagging facility, which includes a separate, two-story pre-anesthetic tower, replaced a semi-permanent facility that had been in place since the 1980s.  

The upper story of the tagging facility is one long room containing two sorting stations and 10 PIT-tagging stations.  The bottom story is split into a break/lunch room and a mechanical room, which contains all the equipment necessary to operate three separate re-circulating anesthetic systems.  There are also two holding tanks located east of the tagging facility, each plumbed to release fish to the dam's tailrace.

The tagging facility obtains research fish from two raceways in the east bank of raceways.  These fish are collected by diverting the general population of fish bypassed into the juvenile fish facility to one of the two raceways each day prior to tagging.  Because the general population of fish contain fish that were PIT-tagged by researchers located above Lower Granite Dam, NOAA Fisheries, the U. S. Army Corp of Engineers (COE) (the owners and operators of the dam), and Pacific State Marine Fisheries Commission staff (who are responsible for the maintenance and operation of PIT tag detectors at the dams) worked together to develop a PIT-tag diversion system in the flume leading to the NOAA collection raceways.  This diversion system can divert previously PIT-tagged fish either to a general collection raceway or to the river.  This reduces NOAA's impact on other researchers' studies.

All fish movement employs water-to-water transfer methods.  Fish collected in the NOAA raceways are sent from the raceway to the pre-anesthetic tower using an Aqualife fish transfer device, similar to devices used at hatcheries throughout the Columbia River basin.  Once fish enter the tagging facility, they can be sent via pipes to raceways, holding tanks, or even trucks in parking areas around the facility.  Fish sent to the holding tanks located east of the tagging facility are released to the river at the same location used by the juvenile fish facility for returning fish to the river.  This is accomplished via a pipe fastened along the top of the JFF's outfall pipe.

Each re-circulating anesthetic system consists of a collection box, one or two pumps, three filters (macro, 100 micron, 25 micron), a UV-sterilization system, and a chiller.  One system is used solely for the sorting lines, while the other two systems can be split between the 10 tagging stations as needed (Marsh et al. 2001).

Using this tagging facility, NOAA researchers have tagged over 21,000 salmonids (out of 30,000 fish processed through the facility) in an 8-hour day.  The large number of tagging stations and the ability to route pipes to several destinations allow multiple studies to use the same collection of fish, reducing the overall impact of research in general.

Daily setup prior to tagging:

1.  Collecting fish for tagging - 24 hours prior to tagging, we provide the COE with the number of fish we need to collect and what time of day to perform the collection.  At the designated start time, the COE activates the PIT-tag diversion system leading to our collection raceway (to prevent previously PIT-tagged fish from entering our collection raceway) and diverts all the fish arriving in the JFF to our raceway.  When the requested number of fish are collected, the COE returns to sending the fish in the direction they were going prior to our collection.  If necessary, fish for the next day's tagging can be collected in one raceway, while we are tagging out of another raceway (which was collected the previous day).

2.  Filling/initiating the anesthetic systems - Because there is insufficient electricity to operate our entire tagging facility, we have a 45KW diesel generator to supply power to the lower story of the facility.  Before anything can happen in the mechanical room, the generator must be started and the power supply turned on.

Each morning the macro filter is reassembled and the 100 micron and 25 micron replaceable filters are set into their housings and sealed.  The overflow standpipes are inserted into the appropriate stations in the upper story of the facility.  After closing the drain valve, water is added to the collection box of each re-circulating anesthetic system.  When sufficient water has been added to cover the pump inlets, the pump is turned on to send water into the stations it serves.  Air is vented from the micron filter housings using relief valves.  Once water is flowing through the UV-light system, it is turned on and checked to ensure the lamps are lit.  The chiller is then turned on, and the upper and lower temperature limits are adjusted for the water temperature that day.  Water continues to be added to the collection box until all stations served by that system are full and the pump inlet is covered by sufficient water to prevent air from being sucked into the pump.  The water is allowed to circulate through the system for a period of time to ensure all the parts are functioning correctly.  Shortly before fish are to enter the tagging facility, sufficient anesthetic is added to the system to cause the fish to lose equilibrium.  The system is monitored during the tagging session to watch for water loss and to make sure the equipment is functioning properly.  Depending on the number of fish handled, the water in each system is changed every 2-3 hours during the tagging day.

3.  Preparing to move fish from the raceway to the pre-anesthetic tower - The raceway's fish crowder is moved to the downstream end of the raceway containing that day's fish.  After fish are scared away from the end of the raceway, the crowder screen is lowered to the bottom of the raceway, preventing fish from getting downstream of the screen.  A cable hoist on the crowder is connected to the lifting ring on the Aqualife fish-transfer device and the device and crowder are moved upstream 6-10 feet.  The fish-transfer device has a screen attached to the front which is vertically and horizontally tapered to encourage fish to move to the opening of the transfer device.  The device and screen are lowered to the bottom of the raceway and secured in place by tightening a pressure bar against the sidewalls of the raceway.  The cable hoist is disconnected, and a flex hose from the pre-anesthetic tower is attached to the outlet of the transfer-device using a camlock.  All edges within the camlock have been tapered to prevent fish striking them.  When it is time to process fish, an electric hydraulic pump, which is used to power the Aqualife fish-transfer device, is turned on.  The pre-anesthetic tower operator can control the speed of the hydraulic pump, which in turn controls the flow of water and fish from the transfer-device.

4.  Setting fish disposition pipes - All non-targeted fish are returned to a general raceway via a 15.2 cm pipe.  A section of this pipe is removed after tagging to allow the COE to safely walk around the raceways when we aren't operating.  Each morning this pipe is reconnected and positioned to return the rejected fish to the appropriate raceway.

If necessary, pipes leading from the tagging stations are moved into position to route the tagged fish to the appropriate holding space (a raceway, holding tank, truck, etc.).  If a holding tank or truck is to used, it must be filled with water prior to the beginning of tagging.  Each tagging station can be routed to a different location, although generally one group of stations go one way and another group go a different way.

5.  Final preparations - Each morning, the banks of cylinder counters at each sorting station are checked to make sure they are set to zero.  The counters are used to count every non-target fish, by species, run, and rear type.  These counts are recorded and reported daily and annually to the appropriate agencies.

The PIT tag readers, located at each sorting line, are turned on and tested.  Prior to sending fish to the tagging stations, they are scanned to ensure they aren't PIT-tagged already.  If a fish is already tagged, it is counted and returned to a general raceway with the non-target fish.

Each tagging station is checked to ensure the appropriate PIT tags are at the station.  Each tagging station is setup, which involves turning on the data collection computer and other data collecting equipment (balance, dizitizer (a CAD board), PIT tag reader, etc.) and making sure they are all functioning together.  The tagging data collection software is started and setup for that day's tagging.

The pump suppling fresh, flow-through water to the upper story is turned on (the upper story is too high for gravity flow from the JFF).  This water is used in the pipes taking fish out of the tagging facility.

Finally, the staff is instructed in what they need to do that day.  Sorters are told which fish to keep and the appropriate tagging station to send each type.  Taggers are told what they will be tagging at their station and what data to collect.

Processing fish

1.  Moving fish from the raceway to the tower - When tagging begins, the crowder screen is raised, allowing the fish in the raceway to approach the fish-transfer device.  The crowder is then taken to the upstream end of the raceway and the screen is lowered to the bottom of the raceway.  For the rest of the tagging session, the crowder is incrementally driven forward each time the number of fish entering the fish-transfer device decreases.  This action continues until all the fish in the raceway have been sent to the tower.  Depending on the number of fish in the raceway and how quickly the fish are processed, this can take a couple hours or a full day.

2.  Pre-anesthesia - When the column of water and fish from the transfer-device reachs the pre-anesthetic tower, it passes over a declining dewatering screen which removes most of the water, leaving the fish to slide down into one of two anesthetic boxes.  When a sufficient number of fish are in the box, a flip gate is closed, diverting fish into the other box.  Anesthetic is added to the full box.  After the fish lose equilibrium, a gate is opened and the fish and water flow through a pipe into the tagging facility, passing over a dewatering screen that removes all the water.  The fish are deposited into a distribution box, which is supplied with flowing water from the re-circulating anesthetic system, and routed to one of the two sorting stations.

3.  Sorting - Each sorting station is divided with a perforated plate into a main processing area and a final processing area.  In the main processing area, fish not of the needed species, run, and rear type are enumerated and placed in a half-pipe supplied with fresh flowing water.  The half-pipe joins with a full pipe connected to the 15.2 cm return line, and the fish are sent to a general transport raceway.  Because we often encounter steelhead kelts in the sorting stations, a 15.2 cm Y-junction allows the kelts to be placed in the return line as well.

Fish of the correct species, run, and rear type (target fish) are placed in a half-pipe running down the center of the sorting station to the final processing area.  There, fish are checked again to make sure they are target fish, then scanned for a PIT tag.  If a PIT tag is detected, the fish is counted by its species, run, and rear type and placed in the half-pipe leading out to the raceway.  If the fish does not have a PIT tag, it is placed in one of the 10 half-pipes leading to the appropriate tagging station.  The half-pipes join full pipes at the end of the second sorting station and run along one wall to the tagging stations.

4.  Tagging - Tagging follows the guidelines outlined in the "PIT Tag Marking Procedures Manual" (PIT Tag Steering Committee, 2014).  The fish trough at each tagging station is divided into a tagging and a processing section.  Two people, a tagger and a data collector, work at each station.  When a fish enters the tagging section, a PIT tag is injected into the fish using a pre-loaded 12-gauge needle.  The fish is then placed into the processing section.  The data collector scans the fish for the tag code, then weighs the fish.  The fish is then laid on a digitizer board, and it's forklength is recorded.  The data collector then records all the necessary fish condition data (descaling, fin erosion, parasites, injuries, etc.).  After the data collector confirms the data is in the computer, the fish is released into a pipe containing fresh flowing water through a hole in the station table.  The pipe exits the facility and leads to the appropriate destination.

Finish and clean-up

1.  Outside the facility - When tagging is finished, the hydraulic pump is turned off, and the fish-transfer device is removed in the reverse order it was placed in the raceway - the pressure bar is loosened, the flex hose removed, the cable winch clipped to the lifting ring, and the device is lifted out of the raceway and deposited at the end of the raceway.  After detaching the cable winch, the device is tipped to ensure no fish were left in the device.

2.  In the upper story of the facility - The overflow standpipes in the sorting and tagging stations are removed (after the drain valves for the collection boxes in the mechanical room are opened to prevent flooding).  The counts from the sorting stations are recorded.  The tagging files at each station are exported and the program closed.  The "nibs" in the digitizer pens are removed to allow the pens to dry overnight, and the digitizer, balance, and PIT tag reader are shut off.  The tagging facility has a network that allows one computer to download the tagging files from all the other computers.  After the files are downloaded, the computers are shutdown.  The files can then be taken to a internet connection and uploaded to the regional database (called PTAGIS) in Portland, OR.

3.  Mechanical room - The pumps, chillers, and UV-sterilization lamps are turned off, and the drain valves for the collection boxes are opened, allowing the water to exit the building via pvc pipes.  The macro filter is drained and cleaned, if needed.  The micron filters are removed and, if they aren't too dirty, pressure washed and allowed to dry overnight so they can be re-used the next day.  When the filters become too dirty, or if they are used for more than 4-5 days, they are replaced with new filters.  The collection boxes are rinsed to prevent a buildup of anesthetic and dirt.

4.  Final details - After a sufficient amount of time has passed since the last fish was sent down the exit pipes, generally after everything else has been taken care of, the pump suppling fresh river water to the upper story of the tagging facility is shut off.  When the water stops draining from the 15.2 cm return line, a section is removed and placed out of the way so the COE can safely walk around the raceways.

Because the distance from the top of the water to the top of the raceway walls is short and salmonids are strong jumpers, fish can jump from one raceway to another.  Also, fish tend to jump most in a location where water is falling into the raceway, i.e., at the upstream end of the raceway.  To prevent this, we installed aluminum barriers long the top of the raceway walls, blocking the first 20 feet of the upstream end of the raceway.  These barriers rise to within a couple inches of the bottom of the crowder, allowing it to safely pass over the barriers when being used to move fish out of the raceways.  To further reduce jumping between the raceways, we park the crowder over the upstream end of the raceways for the night.

Outside the facility - Aqualife fish transfer device; 480v electric hydaulic pump; COE fish crowder; pre-anesthetic tower with dewaterer and anesthetic boxes; 45KW diesel generator; two large holding tanks

Upper story - A dewatering box; two aluminum sorting troughs; 10 wall-mounted aluminum tagging stations; tagging equipment (computer, digitizer board, balance, PIT tag reader) for each station; shelving (to hold electronics); electrical and network outlets

Lower story, mechanical room - Three each of collection boxes, chillers, UV-sterilization systems, macro filters, and 100 micron and 25 micron filter housings; four 1/2 hp pumps (we use two pumps on one system as it generally services 8 tagging stations); work bench; balance (for weighing out anesthetic); fans (the chillers put out a lot of heat)

The facility itself is constructed of four 2.7m (h) x 2.4m (w) x 27.4m (l) conexes on a reinforced concrete pad.