Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Hatchery Reform – Part 2

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Previously… Part 1: Central Valley Salmon and Steelhead Hatchery Program Reform

Environmental Factors Affecting Smoltification and Early Marine Survival of Anadromous Salmonids. 1980. GARY A. WEDEMEYER, RICHARD L. SAUNDERS, and W. CRAIG CLARKE1.

“There is reason to suspect that in many cases apparently healthy hatchery fish, though large and silvery, are not actually functional smolts and their limited contribution to the fishery, even when stocked into the same rivers from which their parents were taken, results from their being unprepared to go to sea. This failure to produce good quality smolts probably arises from an incomplete understanding of exactly what constitutes a smolt, as well as from a lack of understanding of the environmental influences that affect the parr-smolt transformation and which may lead, as a long term consequence, to reduced ocean survival.”

This paper is over thirty years old (1980), yet it still rings true. It is most certainly a complicated subject that is an on-going concern in hatchery science and management. There remains room for improvement if funding is available for hatchery program upgrades.

“In the absence of complicating factors such as altered river and estuarine ecology, smolt releases should be timed to coincide as nearly as possible with the historical seaward migration of naturally produced fish in the recipient stream, if genetic strains are similar. At headwater production sites, much earlier release may be called for… The desired result is that hatchery reared smolts which are genetically similar to wild smolts enter the sea at or near the same time.”

It has been apparent for many decades that Central Valley Fall Run and Spring Run Chinook have a classic “ocean-type” life-history pattern, wherein young spawned in the fall head to the ocean early in their first year rather than as yearlings. Even within the ocean-type, Central Valley Fall Run have two types: one has fry rearing in the estuary (Bay-Delta) and the other in rivers. Of these two types, Valley hatcheries have chosen to manage for the latter. Hatcheries pump out smolts by the millions in April and May, on top of a smaller number of “wild” river-smolts. I believe the “river-smolt” type has been the minority contributor at least since all the dams were built. There simply is not enough river habitat, and what there is has been severely degraded by dams, water management, and physical habitat damage (e.g., levees and land use). The majority contributor is the Bay-Delta or “estuary-smolt” type. Fry that move to the estuary in December-January grow quickly and enter the ocean as smolts in March, a month or more before the river-type. This is a huge advantage for the estuary-type. The hatchery programs could focus more effort on this type by out-planting fry to the estuary or lower river floodplains immediately above the estuary (e.g., Yolo Bypass). Experimental out-planting of hatchery fry to rice fields in the Yolo Bypass has proven promising2. There are also many natural habitats in the lower river floodplains and Bay-Delta that could accommodate out-planting.

This post is part of a 4 part series on hatchery reform, check back into the California Fisheries Blog over the next week for Parts 3 and 4.

Drought Effect on the Bay

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During the past four years of drought little has been said about the specific effect of the drought on the Bay, especially the upper Bay. Suisun Bay is a very important part of the San Francisco Bay Estuary as it receives freshwater flow from the Delta and is the low salinity mixing zone of the Bay-Delta ecosystem. Suisun Bay is also critical habitat of many listed estuarine and anadromous fishes. The drought has brought something new: unprecedented high salinities to Suisun Bay from relaxed Bay-Delta Plan Delta outflow and salinity standards. In the chart below (Figure 1) salinity levels as measured by micro-mhos of electrical conductivity (EC) were high (>15,000 EC) at Port Chicago in west Suisun Bay in April and May 2014 and 2015. Normal dry year levels are shown by 2012, when the Delta Outflow standard is 7100 cfs and the Collinsville salinity standard is 2780 EC. In 2014 and 2015, the standards were relaxed to save reservoir storage. The Outflow standard was reduced to 4000 cfs. The salinity standard location was moved upstream into the Delta. Although unregulated flow dominated most of the Apr-May period in 2012 (Figure 2), the regular standards applied in the latter half of May.

Figure 1. Salinity (EC) in Suisun Bay in April-May 2012, 2014, and 2015.

Figure 1. Salinity (EC) in Suisun Bay in April-May 2012, 2014, and 2015.

The potential ramifications of these unprecedented low outflows and high salinities are wide ranging and substantial.

  1. Invasive species will increase their presence in the Bay-Delta. Clams, zooplankton, and fish communities will change. Invasive Potamocorbula clams abundance has likely increased and moved further upstream1. More clams mean less plankton and higher selenium concentrations in clams.

    “The biomass of the larger copepods is less than it was before the introduction of the clam Corbula amurensis, because of competition for food and grazing by clams on the early life stages of copepods. The resulting low abundance of copepods of suitable size, and the long food chain supporting them, may be contributing factors to the decline in abundance of several estuarine fish species.”2

    “Many scientists in the U.S. geological survey, who have been studying the Bay for decades, also concur with Strong, that the clam is likely the culprit”.3

  2. Young Longfin and Delta Smelt have been forced to rear in the Delta rather than the Suisun Bay. Mysid and Bay shrimp production will be lower.
  3. Concentration of contaminants will be higher in Suisun Bay, possibly leading to toxicity to plankton, benthic invertebrates, and fish.
  4. Unbalanced levels of ammonia, nitrogen, and phosphorous nutrients will lead to trophic changes in the plankton community (e.g. more blue green algae and lower diatom production).
  5. Less inflow to Suisun Bay means less organic carbon and other nutrients necessary to stimulate the estuary’s food chain. Turbidity from river sediment will be lower.

Less inflow to the Delta and less outflow to the Bay also mean more nutrients, plankton, and fish are drawn to the South Delta export pumps. Even with restricted pumping at 1500 cfs limit, the effect is proportional and significant. In reality, Delta outflows are lower than the NDOI estimates provided by DWR and Reclamation. A 14-day running average relaxed standard of 4000 cfs often leads to “real” outflows closer to zero4.

More on the effects of outflow on Suisun Bay can be found at:
http://www.sfestuary.org/wp-content/uploads/2015/03/Estuary-MAR2015-v8a-finalWEB.pdf .

Figure 2. Delta outflow (NDOI) in April-May 2012, 2014, and 2015.

Figure 2. Delta outflow (NDOI) in April-May 2012, 2014, and 2015.

Record Heat in the Delta: A Challenge to Reclamation

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Despite a relatively cool May, the Delta is very warm under conditions of low river and Delta flows and low outflow to the Bay that the State Water Board has allowed by weakening flow standards. As in 2014, water temperatures in early June approach the lethal level for Delta Smelt of 73°F1 (Figure 1). The water temperatures now (and in 2014) are several degrees higher than in 2012, the last year in which the normal dry year flow standards were followed.

The first heat wave of summer, with air temperatures forecasted from 95-100°F, is predicted to begin early next week. Water temperatures in the entire Delta are expected to reach the lethal level of 73°F or higher. The water temperature may be further degraded in the north and central Delta by the opening of the Delta Cross Channel in combination with the new False River Barrier (FAL location on map).

Delta Smelt are presently confined primarily to the Sacramento Deep Water Ship Channel, where water temperatures are already near lethal levels (Figures 2 and 3). Reclamation scientists theorize that smelt can survive in deeper, cooler waters. I challenge Reclamation to prove this theory by monitoring water temperature and taking dissolved oxygen profiles throughout the Sacramento Deep Water Ship Channel all summer.

Figure 1. Water temperature in the Delta in first week of June 2015. Based on water temperatures recorded at CDEC stations (blue dots).

Figure 1. Water temperature in the Delta in first week of June 2015.
Based on water temperatures recorded at CDEC stations (blue dots).

Figure 2. Water temperature in the Sacramento Deep Water Ship Channel, May 28 - June 6, 2015.

Figure 2. Water temperature in the Sacramento Deep Water Ship Channel,
May 28 – June 6, 2015.

Figure 3. Distribution of Delta Smelt catch in 20-mm Smelt Survey May 2015. All but three young smelt were captured in the Sacramento Deep Water Ship Channel . Water temperature at the time of the net deployment in the Channel was 65°F (at surface).

Figure 3. Distribution of Delta Smelt catch in 20-mm Smelt Survey May 2015.
All but three young smelt were captured in the Sacramento Deep Water Ship
Channel . Water temperature at the time of the net deployment in the
Channel was 65°F (at surface).

 

  1. Incipient lethal temperatures for Delta Smelt in laboratory conditions are 75-77°F. In the wild, Delta Smelt are virtually never found in water whose temperature is greater than 73°F. ↩

Central Valley Salmon and Steelhead Hatchery Program Reform

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Dr. Peter Moyle of the University of California, Davis commented last year commented on California salmon and steelhead hatchery reform at the California Fish and Game Commission’s Workshop on Strategic Improvement in California’s Anadromous Hatcheries, held in Sacramento on February 4, 20141.

Dr. Moyle remarked that hatcheries fail to meet their primary dual purposes of sustaining commercial and sport fisheries and assisting in recovery of wild (naturally spawning) salmon and steelhead. Hatchery strategies have led to the complete dominance (90%) of hatchery salmon and steelhead in most rivers, which will ultimately lead to “periodic shut-downs of the fisheries and extinction of most runs, even those supported by hatcheries.” He concluded that a much more radical reshaping of hatchery policy is needed.

He recommends two types of hatcheries: conservation hatcheries that focus on recovery of wild populations, and production hatcheries that focus on sustaining commercial and sport fisheries. He suggests abandoning wild salmon and steelhead management in favor of production hatcheries for some runs (e.g., Fall Run Chinook salmon).

Only the federal Sacramento River hatcheries near Redding operate in the recommended manner. The federal Livingston Stone Hatchery is a model conservation hatchery for endangered Winter Run Chinook Salmon. The Coleman National Fish Hatchery on Battle Creek is a production hatchery for Fall Run, Late Fall Run, and Spring Run Chinook, as well as steelhead. Only wild Late Fall Run, Spring Run, and Winter Run Chinook and steelhead are allowed to pass Coleman’s diversion dam to spawn in upper Battle Creek. Upper Battle Creek thus serves as a wild fish conservation hatchery.

The state hatcheries on the Feather, American, Mokelumne, and Merced rivers operate as production hatcheries, mitigating for the blockage of these major Central Valley salmon tributaries by dams. These hatcheries focus on Fall Run Chinook and steelhead, although the Feather River Fish Hatchery also supports Spring Run Chinook.

Only undammed Sacramento Valley tributaries Deer, Mill, Big Chico, Antelope, and Butte creeks support reliable native runs of wild Spring Run Chinook. Native-wild Spring Run are sustainable in these streams because habitats are accessible at higher elevations where over-summering habitat with deep, cool-water holding pools exists.

One way to improve production of wild fish is to develop conservation hatcheries that combine trap-and-haul programs with over-summering habitats above the dams, as recommended in the Central Valley Salmon Recovery Plan2. This would require a capture-sorting effort, as is presently done at Coleman Hatchery on Battle Creek. Wild fish would be trucked above the dams. Juvenile fish produced above the dams would be trapped and trucked downstream for release below the dams. Conservation hatchery components could be established initially at the four state hatcheries to get the program started with appropriate “wild” genetic stocks.

Wild populations of Winter Run and Spring Run could be established above Shasta Reservoir on the Sacramento River. Spring Run could be established on some combination of the upper Feather, Yuba, American, Mokelumne, Tuolumne and Merced rivers. Wild steelhead could be established above the dams in any of these rivers.

Meanwhile, production hatcheries of salmon and steelhead could continue below the dams. Marking production fish would allow separation of wild and hatchery fish, as well as mark-selective fishery harvest to preserve wild fish until such time wild stocks are sustainable. Trucking/barging of production smolts to Bay would reduce predation and competition with wild fish while increasing populations of production fish for harvest.

Dr. Moyle also recommended establishing wild salmon sanctuaries, as is currently being established on upper Battle Creek. The areas above the dams are good candidates for such sanctuaries. Undammed Valley Spring Run rivers are also good candidates. Isolated tailwaters on the lower Yuba, Mokelumne, and San Joaquin rivers may also be candidates.

More on hatchery reform options can be found at: http://cahatcheryreview.com/summary-conclusions/.

Bay-Delta Fisheries Devastated by Weakened Protections

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Water quality standards under the jurisdiction of the State Water Resources Control Board provide bare minimal protections to the State’s major ecosystems in Critically Dry years. But with the extended drought in seven of the past nine years, protections have been weakened to the point where ecosystems and fisheries dependent on them have been devastated. Yes, rice acreage is down 25%1, but fish production is down 95%, with some species lost forever. Salmon numbers have been maintained by hatcheries and trucking hatchery production to the Bay, but not without a huge mortgage on future wild populations. Hatchery salmon already make up over 90% of ocean and river fisheries. Delta Smelt, Longfin Smelt, Steelhead, Green and White sturgeon, Striped Bass, and wild Chinook Salmon populations have declined another 90% in the past four years, after losing 90% in each in the past several decades. Farm production will return, but some fish will not. The ecosystem will return, but with a much different makeup of new food web plankton species from Asia, greater proportions of non-native sport and pan fish, and a greater assortment of the invasive aquatic plants that already fill waterways. The Delta will be featured more often on the Bass Masters Classic.

And what about the Bay? Only a few hundred thousand acre-feet of water of the millions released from reservoirs this summer will reach the Bay. Water quality and marine fish and shellfish will soon show signs of decline. The Bay-Delta is a major nursery for anchovies, herring, and Dungeness crab. Anchovy stocks are already collapsing2. Sea lions are starving and dying.

How hard would it be to at least maintain the antiquated minimum protections adopted in 1995 Bay-Delta Standards? The Bay is “allocated” a base of about 5 million acre-feet of water each year in the form of a base Delta outflow of 7,100 cfs. This standard for critically dry years is the first to suffer from State Board drought orders. The Board has reduced outflows requirements to 3000-4000 cfs (Figure 1). Such low outflows are in reality closer to zero (see earlier blog3). The amount of water “short” from the critical year base in the important February – June period is approximately 300,000 acre-feet. This amounts to less than 5% of the total 10 million acre-feet of reservoir releases into the Central Valley in 2014 and expected in 2015. The amount is less than 10% of the 5 million acre-feet presently in storage in Central Valley reservoirs. The water could be restored to the Bay by reducing water contractor allocations and/or reservoir storage.

The Delta had one plankton bloom that came and went this spring4. Plankton blooms are needed to drive the Bay-Delta food chain. Without freshwater flow to the Bay there will be no blooms and little food through the summer for Bay-Delta fishes. Water quality will suffer as well. The prognosis for the Bay-Delta and other California ecosystems is grim. California fisheries will suffer for decades to come.

Figure 1. Delta outflow as calculated by the California Department of Water Resources for Feb-May, 2015. Top red line represents 7100 cfs minimum standard. Lower red line represents typical weakened level of protection.