Category Archives: Hatcheries

A “Winter-Run Critical Habitat Conundrum”

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Figure 1. Lower American River floodplain referenced in recent science paper as non-natal rearing habitat of endangered winter-run Chinook salmon. Note the many borrow pits from Paradise Beach downstream to Discovery Park, remnants of a historical levee-building era.

Conundrum: A confusing and difficult problem.

The consulting firm FishBio reported in a February 12, 2018 blog post: “Just when you think you’ve got a species figured out, sometimes they show up where they’re “not supposed to be” and make you reconsider. This recently happened in the fish world, when adult winter-run Chinook salmon, an endangered fish previously thought to only inhabit the mainstem Sacramento River downstream of Keswick Dam, were found to have actually reared in multiple Sacramento River tributaries as juveniles.” The study referenced by FishBio found that roughly half of the returning adult winter-run had reared as juveniles for a several weeks or more in habitats other than the mainstem Sacramento River. It has long been known that winter-run had used these habitats1, but the proportion of the population that had done so was not known. The recent study has helped answer that question. Such a life-history pattern is obviously important, as proven by this study.

Juvenile winter-run salmon have frequently been detected in winter in habitats along the Sacramento River from Redding to Rio Vista in habitats where they are not commonly expected to be. In wet years, winter-run are carried into the Butte-Sutter and Yolo bypasses (and other Sacramento River floodplain areas like the lower American River) where they rear as noted in the recent study. I personally have collected large numbers of winter-run juveniles in the 1990’s in Butte Basin, the Bypasses, and the lower American River floodplain (Figure 1). In many cases, floods had carried or backed-up water along with winter-run juveniles into these areas. I have also collected winter-run juveniles (and other juvenile fall/spring salmon) in Suisun Bay, downstream of the Delta. A 2013 report by biologist Michael Healey of the California Department of Fish and Wildlife found that winter-run migrate up Auburn Ravine in Sutter County to rear.2

“These newly identified areas, called “non-natal habitats” because they differ from where the fish was born, can be divided into four distinct groups, including the Mount Lassen tributaries (Mill, Deer, and Battle creeks), the Sacramento-San Joaquin Delta and Feather River, the American River, and a final group rearing in an uncertain location that is not in the Sacramento River.” Again, these are not “newly” identified. Non-natal refers to rearing in adjacent river systems where fish were not born. These habitats are part of the lower Sacramento River floodplain and other accessible habitat of winter-run.

“So even though we might think winter-run are “not supposed to be” using these tributaries, the fish are actually spreading the risk of extinction across multiple habitats to safeguard their future.” These are the natural floodplain and tributary rearing habitats of winter-run. The problem is that there is not enough of these habitats left, and those that are left are often too ephemeral or are in poor condition. In many cases, the young salmon are gain access to floodplains but are later blocked from exiting, only to eventually die and not contribute to the population. Juveniles that enter the lower reaches of tributaries of the Sacramento River are sometimes cut off by seasonal dams or stranded in fields by unscreened irrigation diversions. Often, non-natal habitats (e.g., dredger ponds and borrow pits) are also winter refuges and permanent habitat for predatory warm water fish.

Yes, these non-natal rearing habitats should be recognized, protected, restored, fixed, enhanced, and created where possible to help save the winter-run salmon population. In the meantime, such habitats will continue to support winter-run as they have in the past. There is no “conundrum”.

  1. P.E. Maslin, W.R. McKinney, T.L. Moore. 1996. Intermittent streams as rearing habitat for Sacramento river Chinook salmon. Anadromous Fish Restoration Program, Stockton, CA, United States Fish and Wildlife Service (1996), pp. 1-29 ↩
  2. https://plummerj.files.wordpress.com/2015/01/healey-cdfw-2013-auburn-ravine-rotary-screw-trap-monitoring-report-rs.pdf ↩

Feeding Stripers Again

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Oroville hatchery steelhead smolts being released into the lower Feather River near Boyd’s Pump in early February. CDFW photo.

State and federal agencies have begun stocking over a million steelhead smolts from Central Valley hatcheries into the Sacramento River and its tributaries.1 Fishing reports in the SacBee and other sources note that the annual stocking provokes a strong striper bite in the river, one of the more popular fisheries in the Central Valley.  The yearling smolts are the perfect food for stripers.

Shasta, Oroville, and Folsom reservoir releases are each at about 3000 cfs, low for mid-winter.  As a result, along with the record warm weather, river and Delta water temperatures (Figures 1-4) have been in the preferred range for striped bass feeding (55-65°F).

The federal Coleman hatchery near Redding released its steelhead smolts in January during high flows, before the warm weather arrived and stripers began feeding in earnest.  But at Thermalito Afterbay on the Feather River, the state is stocking a quarter of a million steelhead and feeding bass. And the feds are will be stocking a half-million endangered winter-run salmon hatchery smolts near Redding in February and March.

The striped bass will soon decimate the Feather River steelhead and will be well positioned for the annual April hatchery salmon smolt stocking season in April.  In the meantime, the stripers attracted by massive chumming will be knocking off the wild juvenile salmon and steelhead heading for the ocean.

Why do hatcheries continue to waste so many of the over 20 million salmonid smolts raised each year to mitigate for all the dams on Central Valley rivers?  Smolts cost more than $1 each to raise.

Hatchery managers and their partners need to barge hatchery steelhead and fall-run salmon smolts to the Bay.  Barging smolts would likely increase adult returns sharply in coming years.  Both steelhead and salmon populations are relatively homogeneous genetically, which reduces concerns about the effects of straying.  Coleman smolts should be barged from near Hamilton City.  Oroville smolts should be barged from Verona.  Nimbus smolts should be barged from Discovery Park.

If releases of hatchery smolts into the rivers are to continue, water managers need to at least provide pulsed flows from Shasta Reservoir to help the fish succeed in reaching the Bay and ocean.  Shasta storage is 106% of average.  A 5% allocation to pulsed flows would amount to approximately 140,000 acre-feet, enough for seven days of an 10,000 cfs extra flow to the Sacramento River.  Pulsed flows would also reduce water temperatures.  Hatchery managers should also not  release smolts into the rivers during warm spells that stimulate striper feeding.

State hatcheries plan some trucking of salmon smolts to the Bay-Delta this year, as they have done in past years.  Trucked fish should also be barged or at least taken to the Golden Gate, not just to Rio Vista.

In addition to barging and trucking, and pulsed flows, hatchery managers need to accelerate a pilot program to stock hatchery salmon fry into lower river and Delta floodplain habitats for rearing closer to the Bay.  In these habitats, fry would grow faster than their hatchery counterparts and get to the ocean quicker.

Anglers should take advantage of the great striper fishery.  But let‘s at minimum give the salmonid smolts some chance of reaching the ocean, so we can also once again have great salmon and steelhead fisheries.

 

Figure 1.  Water temperature in early February 2018 in the Sacramento River at the mouth of the Feather River

Figure 2.  Water temperature in early February 2018 in the Sacramento River below the mouth of the American River near Sacramento.

Figure 3.  Water temperature in the lower Sacramento River upstream of the mouth of the Feather River at Wilkins Slough

Figure 4.  Water temperature in the lower Sacramento River in the Delta near Rio Vista.

Hatchery Salmon Are Trained to Be Dysfunctional

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Research has often shown that hatchery salmon perform less well than their wild counterparts.  The reason for this has often been attributed to genetic factors such as parent selection or to the lack of opportunity for Mother Nature to cull misfits.

Recent research indicates that poor performance of hatchery fish may stem more from the their environmental experiences than from their genetics.  Some older theories that suggested that hatchery fish were just raised dumb now have gained a new following.  New research from Canada suggests that atypical food and feeding combined with overcrowding in hatcheries weakens inherent genetic abilities to cope with the natural environment.

In California’s Central Valley, we have added the burden of releasing hatchery smolts late in the natural emigration season outside of peak flow periods, into warmer waters that are full of other fish that want to eat them.  When the salmon from the hatcheries get hungry,  there is no flood of fresh food pellets.  Their new environment results in starvation, thermal stress, and much higher vulnerability to predation.  Still, hatchery fish make up 70-90% of California’s salmon runs, because Valley habitats no longer support historic levels of wild salmon production.

In recent posts, I have advocated raising hatchery fry in Valley floodplain habitats.  UC Davis studies have shown high rates of growth of hatchery fry raised in flooded rice fields during the winter.  New planning efforts call for more flooded Valley habitats, including rice fields, but these efforts focus primarily on wild juvenile salmon.  There has been no testing to date of the performance of hatchery fry that rear under controlled floodplain conditions.  In light of the recent Canadian research, the ability of floodplain-reared hatchery fish to survive, and the degree to which they stray, warrant evaluation.

How do we increase salmon runs in 2018 and beyond?

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Over the past few months, I wrote posts on the status of specific runs of salmon in rivers throughout the Central Valley. In this post, I describe the overall status of salmon runs and the general actions to take to increase both escapement and fish available for commercial and sport harvest.

It was just over a decade ago that there were nearly one million adult salmon ascending the rivers of the Central Valley (Figure 1). At the same time, there were a millions more Central Valley salmon being harvested each year in sport and commercial fisheries along the coast and rivers of the Central Valley. Improvements in salmon management in the decade of the 1990s by the Central Valley Project Improvement Act, CALFED, and other programs had paid off handsomely with strong runs from 1999 to 2005. New and upgraded hatcheries, along with trucking hatchery smolts to the Bay, significantly increased harvest and escapement to spawning rivers.

Figure 1. Central Valley salmon runs from 1975 to 2016 including fall, late fall, winter, and spring runs. Source of data: CDFW GrandTab.

By 2008-2009, escapement had fallen by over 90% to a mere 70,000 spawners of the four races of salmon.  Fishery harvests were greatly restricted by 2008.  The winter run, the most threatened of the four runs fell from 17,296 to 827 spawners in just five years.  Drier years from 2001-2005, poor ocean conditions in 2004-2005, record-high Delta water diversions, and the 2007-2009 drought were contributing factors in the declines.  Impacts to coastal communities and the fishing industries were severe.

Extraordinary recovery measures included closing fisheries and trucking most of the hatchery smolt production to the Bay or Delta.  Federal salmon biological opinions (2009, 2011) limited winter-spring water-project exports from the Delta.  Hundreds of millions of new dollars were spent on habitat and fish passage improvements in the Valley to increase salmon survival and turn around the declines in runs.  A look at Figure 1 indicates that these efforts proved effective in limiting run declines from the 2012-2015 drought compared to the 1987-1992 and 2007-2009 droughts.

However, the prognosis for the future is again bleak, especially for wild, naturally produced salmon.  The consequences of the 2012-2015 drought  have not fully played out.  Once again, projected runs are low, and harvests are likely to be restricted.  Actions are needed to minimize long-term effects and to help bring about recovery of wild salmon productivity and fisheries in general.

Actions for 2018:

  1. Reduce harvest: Sadly but necessarily, the Pacific Fisheries Management Council and states are likely to take this first step of– restricting the 2018 harvest in the ocean and rivers to protect wild runs.
  2. Improve spawning, rearing, and migrating conditions: Sadly, this past year’s rearing and migrating conditions in the Sacramento River were unnecessarily compromised.   Water temperature at Red Bluff reached above the 56oF prescribed in the biological opinion and Basin Plan.  The higher temperatures resulted from low Shasta Reservoir releases (less than 5000 cfs – Figure 2) despite a virtually full Shasta Reservoir.  The low flow and higher water temperatures likely affected salmon egg incubation, rearing, and emigration-immigration success.  Reservoir releases will be necessary to meet flow and temperature targets in all Central Valley rivers and the Delta.
  3. Limit Delta exports: Delta exports this past spring reached unprecedented highs not seen in recent decades, resulting in high salmon salvage rates at the Delta fish facilities (Figure 3).1 With high water supplies from this past wet water year 2017, there will be high exports again unless there are some constraints.  If anything, winter-spring exports should be reduced to allow salmon to recover.  April-May exports should be reduced, like they were in the 1990’s and 2000’s, to 1500 cfs.

Near term actions over the coming year:

  1. Transport hatchery smolts to Bay: The transport of millions of fall-run smolts from state hatcheries on the Feather, American, and Mokelumne rivers to the Bay provides higher rates of escapement and contributions to the fishery and low rates of straying.  Barge transport to the Bay offers potentially lower rates of predation and straying for federal hatcheries near Redding.
  2. Raise hatchery fry in natural habitats: Recent research indicates that rearing hatchery fry in more natural habitat conditions increases growth rates, survival, and contributions to escapement and fisheries.  Raising hatchery fry in rice fields is one potential approach.
  3. Restore habitats damaged by recent record high flows in salmon spawning and rearing reaches of the Central Valley rivers and floodplains: In nearly every river, habitats were damaged by the winter 2017 floods, requiring extraordinary repairs and maintenance to ready them again to produce salmon.
  4. Take further actions to enhance flows and water temperatures to enhance salmon survival throughout the Central Valley: Actions may include higher base flows, flow pulses, or simply meeting existing target flow and temperature goals.

In conclusion, managers should take immediate actions to minimize the damage to salmon runs from the recent drought and floods, using this past year’s abundant water supply.  They should avoid efforts to exploit the abundant water in storage for small benefits to water supply at the expense of salmon recovery, and should make every effort to use the water in storage for salmon recovery.

Figure 2. Upper Sacramento River flows and water temperatures in May 2017. The target water temperature for Red Bluff is 56oF. Source of data: USBR.

Figure 3. Export rate and young salmon salvage at South Delta federal and state export facilities in May 2017. The target export rate limit for May should be 1500 cfs. Source of data: USBR.

Mokelumne River Salmon Run

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Reports1 indicate strong runs of fall Chinook salmon on the Mokelumne, American, and Feather rivers this fall. The success is generally attributed to better management of hatcheries, project operation (flows), and habitat restoration. The most logical explanation is that hatcheries transported their salmon smolts to the west Delta and Bay for release in recent years. During the 2012-2015 drought, most Valley hatcheries trucked their smolts to the Bay or Delta. Trucking in 2014-2015 likely led to the high numbers returning this fall, including the large number of strays from the Battle Creek hatchery near Redding. The straying among the hatcheries is problematic but manageable (the American and Mokelumne hatcheries shipped eggs to the Battle Creek hatchery this year). The runs also have benefitted from spawning and rearing habitat restoration over the past two decades. The Mokelumne success story is somewhat unique in that restoration efforts have been more intensive and diversified, and the hatchery program has been more progressive in a number of aspects (e.g., transporting smolts via barge).2

The Mokelumne Hatchery program has so many new elements it is hard to say which has been most effective. The run has steadily increased. However, most of the adult escapement, including in-river spawners, is of hatchery origin. Besides all the straying, many fish scientists and managers remain concerned about the dominance of the hatcheries and lack of wild fish recovery throughout the Central Valley. Can the dam-free rivers without hatcheries retain wild salmon populations with all the hatchery strays “polluting” their gene pools? Do hatcheries bring complacency and lead to lack of protections for wild fish and their habitats? These are tough questions. However, one thing is for sure: given the dominance of hatchery salmon, it is safe to say there would be far less salmon and few salmon fisheries in California without the hatcheries. Some “wild” salmon rivers may not even have significant salmon runs without hatcheries hatchery strays (e.g., Yuba, Putah, Cache, Cosumnes, Calaveras, San Joaquin, Stanislaus, etc.).

The importance and dominance of the hatchery program to the Mokelumne salmon run can be seen in the long term escapement estimates 1975-2016 (Figure 1). Note that the near record low run in 2008 led to the record high run in 2011. This reflects the fact it does not take a lot of salmon reaching the hatchery to produce enough smolts to produce a record run under high survival conditions for the smolts. In addition, with good survival and strong runs throughout the Valley in wet year 2011, there were high numbers of strays from other rivers that added to the Mokelumne run.

Analysis of historic coded-wire-tag return data for the Mokelumne hatchery smolt releases by release year indicates some reasonably good returns (>1%) for the recent 2009 to 2013 release years (Figure 2). Release years 2009 and 2010 were exceptional, with 2 to 6 % returns. This likely reflected the normal and wet water years of 2010-2012. Release years 2011-2013 generally had poor river and ocean rearing conditions as well as poor adult return and spawning conditions upon their return. Good survival for release years 2009 and 2010 likely contributed to the record run of adults and grilse (jacks – early return adults) in 2011.

While little tag return data for release years 2014-2016 are yet available, it is likely that the 2015 release had high survival on the order of the 2009 and 2010 releases to bring about the near record run in 2017. High 2017 returns may have occurred from a number of factors, including barging smolts and spring flow pulse in 2015, good river conditions in late summer and fall 2017, and good ocean conditions in 2016-2017.

Regardless of specific causal factor, it would seem that there are lessons to be learned from the Mokelumne River salmon management program. Further questions may be needed to get to the specific root factors in the Mokelumne success story (EBMUD and CDFW may already have the answers to these questions):

  • What is the proportion of hatchery fish in the run? Since 25 % of the hatchery smolts are marked it should be possible to estimate the proportion of hatchery and wild river-born salmon in the adult run. With genetic sampling, the contribution of wild genes may also be determined.
  • Which release groups were barged? (Not indicated in the RMIS database.)
  • What were conditions in the Delta during and after releases?
  • What were straying rates and conditions during adult runs? Were strays to other rivers including Putah Creek taken into account? What were contributions from other hatcheries? (Some answers can be gleaned from RMIS database.)

In summary, near record fall run salmon hatchery runs in 2017 indicates potentially increased hatchery contributions that could be built upon to improve salmon fisheries dependent on the Central Valley hatcheries.

Figure 1. Mokelumne River salmon run estimates for 1975-2016. (Source: Grandtab)

Figure 2. Percent survival to adult of Mokelumne hatchery smolt releases near Sherman Island in the west Delta in spring of years 2009 to 2013. Source of data: http://www.rmis.org/