California Hatchery Review Project Appendix VIII Coleman National

134 Pages·2012·2.67 MB·English

by  Robyn Redekopp

California Hatchery Review Project

Appendix VIII

Coleman National Fish Hatchery
Fall Chinook
Program Report

June 2012
Introductory Statement from the California HSRG

This program report was developed by contractor staff tasked with providing background information to
the California HSRG on hatchery programs, natural population status and fisheries goals in California.
The resulting report is one of many sources of information used by the California HSRG in their review
process.
Information provided in this program report was developed through interviews with hatchery staff,
regional, state and tribal biologists working in the basins and a review and summarization of the
pertinent scientific literature. The draft program report was then provided to interview participants for
review and comment on multiple occasions. Comments received were incorporated into the report and
the report finalized.
Because of the review process, it is believed the report represents an accurate snapshot in time of
hatchery operations, natural salmon population status and fisheries goals in California as of 2012. This
program report may or may not be consistent with the consensus positions of the California HSRG
expressed in the main report, as their primary involvement was in the preparation of Section 4.3,
“Programmatic Strategies”, which compares existing program practices to the statewide Standards and
Guidelines developed by the California HSRG.
Table of Contents

1  Description of Current Hatchery Program ...............................................................................1 
1.1  Programmatic Components ...............................................................................................1 
1.2  Operational Components ...................................................................................................1 
1.2.1  Facilities .....................................................................................................................1 
1.2.2  Broodstock .................................................................................................................2 
1.2.3  Spawning....................................................................................................................3 
1.2.4  Incubation ..................................................................................................................4 
1.2.5  Rearing .......................................................................................................................4 
1.2.6  Release .......................................................................................................................4 
1.2.7  Fish Health .................................................................................................................4 
2  Populations Affected by the Hatchery Program ......................................................................5 
2.1  Current Conditions of Affected Natural Populations ........................................................8 
2.1.1  Battle Creek (Spring, Fall, and Late-Fall Chinook) Populations .............................12 
2.2  Long–term Goals for Natural Populations ......................................................................15 
3  Fisheries Affected by the Hatchery Program .........................................................................16 
3.1  Current Status of Fisheries ..............................................................................................16 
3.2  Long-term Goals for Affected Fisheries .........................................................................17 
4  Programmatic and Operational Strategies to Address Issues Affecting Achievement of
Goals .....................................................................................................................................17 
4.1  Issues Affecting Achievement of Goals ..........................................................................17 
4.1.1  Natural Production Issues ........................................................................................18 
4.1.2  Ecological Interaction Issues ...................................................................................18 
4.2  Operational Issues ...........................................................................................................18 
4.3  Programmatic Strategies .................................................................................................19 
4.3.1  Broodstock ...............................................................................................................19 
4.3.2  Program Size and Release Strategies .......................................................................21 
4.3.3  Incubation, Rearing and Fish Health .......................................................................23 
4.3.4  Monitoring and Evaluation ......................................................................................28 
4.3.5  Direct Effects of Hatchery Operations on Local Habitats, Aquatic or Terrestrial
Organisms. ...............................................................................................................33 
5  Literature Cited ......................................................................................................................34 

List of Figures

Figure 1.  Percent of total survival to fisheries of Coleman fall Chinook fingerlings
(brood years 1998 – 2003). ......................................................................................17 

California Hatchery Review Project – Appendix VIII
Coleman National Fish Hatchery Fall Chinook Program / June 2012 i
List of Tables

Table 1.  Fall Chinook broodstock collected at Coleman NFH, 1990 – 2008. ........................3 
Table 2.  Populations in the Central Valley fall-run and late fall–run Chinook ESU,
ordered from north to south (unlisted ESU). ...........................................................11 
Table 3.  Populations in the Central Valley spring Chinook ESU, ordered from north to
south (ESA listed as threatened). ............................................................................11 
Table 4.  Fall Chinook salmon escapement in Battle Creek (2001-2010). .............................13 
Table 5.  Late-fall Chinook salmon escapement in Battle Creek (2001-2010). .....................13 
Table 6.  Spring Chinook salmon escapement in Upper Battle Creek (2001-2010). .............14 
Table 7.  Estimated ocean contribution for fall Chinook salmon from Coleman NFH, by
brood year, based on the number of salmon released. .............................................14 
Table 8.  Total percent survival (catch plus escapement) and exploitation rates for
Coleman Hatchery fall Chinook: 1998-2003 brood years. ......................................16 
Table 9.  Broodstock Source. .................................................................................................19 
Table 10.  Broodstock Collection. ............................................................................................19 
Table 11.  Broodstock Composition. ........................................................................................20 
Table 12.  Mating Protocols. ....................................................................................................21 
Table 13.  Program Size. ..........................................................................................................21 
Table 14.  Release Strategy. .....................................................................................................22 
Table 15.  Fish Health Policy. ..................................................................................................23 
Table 16.  Hatchery Monitoring by Fish Health Specialists. ...................................................23 
Table 17.  Facility Requirements. .............................................................................................25 
Table 18.  Fish Health Management Plans. ..............................................................................26 
Table 19.  Water Quality. .........................................................................................................26 
Table 20.  Best Management Practices. ....................................................................................27 
Table 21.  Hatchery and Genetic Management Plans. ..............................................................28 
Table 22.  Hatchery Evaluation Programs. ...............................................................................29 
Table 23.  Hatchery Coordination Teams. ................................................................................29 
Table 24.  In-Hatchery Monitoring and Record Keeping. ........................................................29 
Table 25.  Marking and Tagging Programs. .............................................................................31 
Table 26.  Post-Release Emigration Monitoring. .....................................................................31 
Table 27.  Adult Monitoring Programs. ...................................................................................32 
Table 28.  Evaluation Programs. ..............................................................................................32 
Table 29.  Direct Effects of Hatchery Operations. ...................................................................33 

Appendices

Appendix A-1 Hatchery Program Review Questions
Appendix A-2 Coleman Fall Chinook Program Data Tables
Appendix A-3 Hatchery Program Review Analysis Benefit-Risk Statements

Appendix B Natural Populations Potentially Affected by the Hatchery Program
California Hatchery Review Project – Appendix VIII
Page ii Coleman National Fish Hatchery Fall Chinook Program / June 2012
r
e
v
Ri
o
nt
me er
ra Riv
Sac Cloud Pit River
c
M
Livingston Stone Fish Hatchery
(USFWS) I - 5
k
e
e
r
C
r
ea ")XW
Cl
Keswick Dam
Shasta Dam
XW
XW #
Whiskeytown Dam Redding Cow Creek Coleman Fish Hatchery
(USFWS)
Cottonwood Creek ")Battle CXWreek Coleman Dam
B e e g u m C re e k
w ood Creek ReAdn tBelluo pffe C ree k
SF C otton Red Bluff#XW Creek
Mill D e e r C re e k
Red Bluff Diversion Dam
k
T h o m e s C re e k State Chico Cree
XW Hwy 9 Big
Black Butte Dam Stony Creek 9# Feather River Fish Hatchery
(CDFG)
Chico
r
Rive Creek
ento Butte ")XW XW Oroville Dam
m
Thermalito Annex Rearinga Facility ")
r
c
(CDFG) Sa Feather River Hatchery Dam
State Hwy 99 Honcut Creek Yuba River 80
I -
F
e
a
th
e
r
Coleman Hatchery Fall Chinook Program R Bear River
iv t
e
Lakes and Other Waterbodies ")I - 5Hatcheries r CoonA Cubreuerkn Ravine
Rivers Juvenile Release Sites
Roads Adult Collection Sites
# XW
Cities Dams
1 in = 18 miles
Miles
0 4 8 16 24 32
C:\04GISData\ProjectData\CaliHSRG\MapProjects\CentralValley2\ProgramByProgram\ColeFChinook.mxd Published Date : 12/8/2011

1 Description of Current Hatchery Program
Coleman National Fish Hatchery (NFH) was completed by US Bureau of Reclamation (USBR) in
1943 to partially mitigate for habitat and fish losses caused by construction of two Central Valley
Project features, Shasta and Keswick dams. The hatchery is funded by the USBR and operated
by the USFWS. Coleman NFH occupies 75 acres adjacent to Battle Creek, a tributary to the
Sacramento River, about 20 miles southeast of Redding.
Shasta Dam blocks 187 miles of salmonid spawning and rearing habitat. Fall and late-fall
Chinook are produced to mitigate for this habitat loss and to contribute to harvest in the ocean
and river. The Coleman program is also intended to provide adequate escapement to the hatchery
for broodstock. The fall Chinook program is integrated with the natural spawning population in
Battle Creek. The late-fall Chinook program is integrated with the natural spawning populations
in Battle Creek and the Sacramento River.
1.1 Programmatic Components
The fall Chinook program is operated as an integrated harvest program intended to contribute to
sport harvest in the Sacramento River and sport and commercial ocean fisheries. The program
annually releases 12 million fall Chinook in April at a size of 90 fish per pound (fpp), which are
expected to contribute a total of 120,000 fish to harvest and escapement over the life of the brood
(60-75% for harvest). The program is considered to be integrated because (1) founding
broodstock were endemic Battle Creek and upper Sacramento fall Chinook; (2) co-mingled
spawning has long occurred in the hatchery and river; and (3) the morphology, behavior, genetics
and life history of the hatchery- and natural-origin fish are similar. Based on the 25% Constant
Fractional Mark, the hatchery- and natural-origin composition can now be assessed in the
hatchery broodstock. It is anticipated that composition of the hatchery broodstock will be
measured in all future years. Eight percent of juveniles were marked from 1995 to 1998 followed
by initiation of the constant fractional marking program in 2006, which marks and tags 25% of all
hatchery juveniles. Using this better data beginning with brood year 2005 (2006 release), an
estimated 13% of fall Chinook collected at Coleman in 2009 were natural origin.
The barrier weir and fish ladders at Coleman allow managers to control the movement of fish
upstream of the hatchery. Precluding hatchery fall Chinook from upper Battle Creek is a priority
in order to protect ESA-listed spring Chinook that spawn upstream of the hatchery.
1.2 Operational Components
1.2.1 Facilities
Facilities at Coleman include the main hatchery building containing incubation stacks, trays and
early rearing tanks, administration building, feed storage building, warehouse and storage
buildings, spawning building, ozone treatment plant and three residences. Exterior features
include twenty-eight 150-foot-long concrete raceways, thirty 80-foot-long raceways, adult
holding ponds, fish ladder, pollution abatement pond and facilities for congregating, collecting,
holding and spawning broodstock.
A barrier weir spans Battle Creek approximately six miles upstream from its confluence with the
Sacramento River. All upstream migrants are directed into the Coleman ladder which bifurcates
and either guides fish into the hatchery or allows them to continue migrating up Battle Creek.
Adults entering the hatchery are routed into a holding pond. Two additional ponds located in the
California Hatchery Review Project – Appendix VIII
Coleman National Fish Hatchery Fall Chinook Program / June 2012 Page 1
spawning building allow extended holding of fish after they are initially sorted. During sorting,
fish can be routed to the spawning station, holding ponds, or released to Battle Creek upstream of
the weir.
Fish that do not enter the ladder either remain in lower Battle Creek and spawn naturally or move
downstream to the Sacramento. Management objectives are to prevent fall Chinook from
reaching upper Battle Creek. The barrier weir is designed to block upstream passage at flows up
to 800 cfs and allows selective passage up to 3,000 cfs, at which point the stream overflows its
banks. In 2009, the number of fall Chinook that escaped past the weir was less than 0.002% of
the estimated fall Chinook that spawned naturally in Battle Creek.
The hatchery building contains 178 vertical incubators and 67 fiberglass tanks. Outdoor rearing
facilities are twenty-eight 150-foot-long raceways and thirty 80-foot-long raceways, all of which
have predator protection.
Three water intake structures and associated conveyance facilities are used to deliver water from
Battle Creek to the hatchery. The water delivery system is highly complex and has numerous
piping interconnections between facilities. Water from all three intakes can be shunted to the
ozone water treatment facility or sent directly to various fish rearing areas.
From the hatchery’s inception until about the past ten years, disease and sediment problems
associated with the water supply confounded fish culture at Coleman NFH. High sediment loads,
generally associated with high flow events in Battle Creek, periodically caused mortality of
juvenile and adult salmonids at the hatchery. Likewise, recurrent disease outbreaks, possibly
associated with the hatchery water supply, resulted in increased mortality of juveniles (Foott and
Williamson 1997). More than 10 significant pathogens have been detected in salmonids at
Coleman NFH (Foott 1996).
To reduce sediment in the hatchery water supply and to alleviate recurrent disease problems, a
water treatment facility capable of filtering 45,000 gpm and ozonating 30,000 gpm was
constructed at Coleman and began operating in the late 1990s. Ozone production capability
reached full capacity in 2000, but construction and final build out did not conclude until 2002.
Operation of the ozone water treatment facility has substantially reduced the occurrence of
disease in hatchery production and the potential for disease transmission to naturally-produced
stocks. Since brood year 1999, juvenile salmonids propagated at the Coleman NFH have been
reared and released with no incidence of IHNV.
1.2.2 Broodstock
Since 1987, fall Chinook broodstock have been selected only from natural- and hatchery-origin
adults returning to Coleman NFH. The hatchery has a policy to not import eggs from other
hatcheries, and no such transfers have occurred since 1983. Current and projected broodstock
requirements are 2,500 pairs of mixed natural- and hatchery-origin fall Chinook. Fish are
randomly selected as broodstock from the total number of ripe adults having a fork length greater
than the jack cut-off length. Beginning in 2010, the length designation of adults was changed
from greater than 650 mm to greater than 700 mm for fall Chinook and greater than 600 mm for
late-fall Chinook based on review of CWT data. These cut-off values are now evaluated at the
beginning of each spawning season to check accuracy. Jacks are incorporated at a rate of up to
5% of the total number of fish spawned.
Adult holding ponds operate from October through February. The branch of the ladder to the
hatchery is opened intermittently during this period, depending on broodstock needs and salmon
California Hatchery Review Project – Appendix VIII
Page 2 Coleman National Fish Hatchery Fall Chinook Program / June 2012
abundance below the weir. Fall Chinook are collected from early October through mid- to late-
November, after which the branch of the ladder to the hatchery is generally closed until late
December, when it reopens to collect late-fall Chinook. This practice promotes separation of
spawn timing and reduces hybridization between fall and late-fall Chinook. Hatchery-origin
Chinook that enter the branch of the ladder to the hatchery when it is periodically opened between
late November and late December are culled. Since 2002, closures of the branch of the ladder to
upper Battle Creek have been extended to August 1 through February to exclude fall Chinook
from accessing spring Chinook critical habitat in upper Battle Creek.
Fall Chinook are phenotypically sorted into three categories: (1) ripe for spawning; (2) excess to
be culled; and (3) unripe to be held for possible spawning. Unripe fish may be placed in holding
ponds if the availability of broodstock is uncertain (typically late in the spawning season). Pre-
spawning mortality from 2001 through 2008 ranged from 0.7% to 24.8% (mean 7.3%). The
higher mortality number reflects additional handling that occurred when few fish returned and the
retention/handling of unripe fish.
Adults in excess of those needed to meet daily egg-take goals and in excess of the habitat
carrying capacity downstream of the weir are culled. From 2001 through 2007, 53,000 fall
Chinook were distributed to Native Americans, the California Emergency Food Link and/or the
Department of Justice.
1.2.3 Spawning
Males and females are paired 1:1 and males may be spawned with more than one female, if
required. Up to 5% of the total spawners are jacks. The number of broodstock collected and
spawned from 1990 through 2008 is shown in Table 1. Eggs are transferred to the incubation
building and placed in Heath trays for incubation.
Since 2003, more than 5,000 additional fall Chinook adults have been spawned each year to
maintain adaptive genetic variation over time. When eggs reach the eyed stage, culling is
performed to achieve the production target. Culling is done both to eliminate numeric buffers
that have been built into the spawning period and are no longer needed, as well as to achieve
specific egg take-by-day goals.
Table 1. Fall Chinook broodstock collected at Coleman NFH, 1990 – 2008.
Collected Spawned
Return Year
Females Males Jacks1 Total Females Males Total
1990 6,405 7,095 1,150 14,650 5,411 5,502 10,913
1991 5,834 4,242 613 10,689 4,692 3,709 8,401
1992 2,970 3,266 1,039 7,275 2,693 2,674 5,367
1993 3,753 3,269 565 7,587 3,487 2,770 6,257
1994 4,308 7,240 7,443 18,991 3,771 4,728 8,499
1995 11,138 13,656 1,883 26,677 3,882 4,277 8,159
1996 8,888 9,935 2,355 21,178 4,264 4,713 8,977
1997 24,467 20,171 6,032 50,670 4,104 4,840 8,944
1998 19,809 22,166 1,878 43,853 3,136 4,462 7,598
1999 10,670 12,377 3,921 26,968 2,297 3,101 5,398
2000 9,554 11,233 872 21,659 2,552 2,853 5,405
2001 6,965 11,804 5,919 24,688 3,863 4,210 8,073
2002 19,089 42,860 41,134 66,062 5,607 6,980 12,587
2003 41,446 41,290 5,352 88,088 4,054 4,425 8,479
California Hatchery Review Project – Appendix VIII
Coleman National Fish Hatchery Fall Chinook Program / June 2012 Page 3
Collected Spawned
Return Year
Females Males Jacks1 Total Females Males Total
2004 21,104 31,078 17,032 69,214 3,375 3,663 7,038
2005 77,425 62,553 2,694 142,672 3,805 3,434 7,239
2006 30,727 24,075 985 55,787 4,222 4,063 8,285
2007 6,399 4,950 198 11,547 4,295 3,311 7,606
2008 4,662 5,452 460 10,574 3,910 3,600 7,510
1Jacks are included with males for counts of spawned fish only.
1.2.4 Incubation
Typically the fertilized eggs of two females are placed in an incubator tray that holds 10-11,000
fall Chinook eggs. At the eyed egg stage, densities are reduced to about 7,800 eggs until
ponding. A standard disinfection protocol is followed using iodophor solution and periodic
formalin washes. Non-viable eggs are removed after eye-up.
1.2.5 Rearing
Fall Chinook are transferred to outdoor rearing ponds after they button-up and swim well. Flows
in the raceways range from 600 to 800 gpm and the rearing density is typically about 0.5
pounds/cfs. Fall Chinook are fed semi-moist pellets based on percent body weight per day. Food
conversion rates are from 1.03 to 1.06 pounds of food per pounds of fish. Rearing loadings (FI)
are 1.5 and densities (DI) are 0.3 at release (these are maximum values). Juvenile fish health
status is monitored routinely and appropriate treatments applied to alleviate disease-contributing
factors.
1.2.6 Release
The annual fall Chinook release target from Coleman Hatchery is 12 million smolts at 90 fish per
pound (fpp) and a total length of 75 mm. Of these, three million (25% of total release) receive a
coded-wire tag and adipose fin clip. Approximately 90% of the fall Chinook production is
released in April into Battle Creek downstream of the barrier weir. Smolts are released from the
hatchery in two large groups as a strategy to decrease predation during emigration and to decrease
concurrent residence time with natural-origin salmonids in the Sacramento River. Monitoring
shows rapid emigration patterns from Battle Creek and through the Sacramento at a rate of at
least nine miles per day (Snider and Titus 2000).
Approximately 10% of the fall Chinook smolts are transported and released in San Pablo Bay in
May. Smolts have been released into San Pablo Bay since 2008, a practice that is considered by
the USFWS to be experimental and temporary. It was prompted by the extremely low abundance
of fall Chinook returning to the Central Valley in 2007 and will continue until the ocean fishery is
reestablished. Smolts are placed in a net pen barge at either Mare Island or the Conoco Pier, then
towed to open water for release. The objective is to expedite smolt emigration and decrease
losses due to predation. This results in increased fish survival thereby providing more adults to
commercial and recreational ocean fisheries.
1.2.7 Fish Health
Pathogen outbreaks have been detected at the Coleman NFH in returning hatchery broodstock.
Infectious hematopoietic necrosis virus (IHNV) is commonly detected in 46-100% of the adult
fall and late-fall Chinook that return to Coleman NFH. Steelhead are resistant to this disease
strain. With the inception of ozone treatment in 2000, this pathogen has not been detected in
juveniles reared at Coleman. Chinook are separated from steelhead during the initial broodstock
sorting process.
California Hatchery Review Project – Appendix VIII
Page 4 Coleman National Fish Hatchery Fall Chinook Program / June 2012