Author Archives: Tom Cannon

Delta science – so much talk!

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As we enter the second year of Temporary Urgency Changes for Delta operations, the State Water Board is leaving Delta fish with no protection from our waste and the summer heat while allowing the storage and diversion of millions of acre-feet of water for cities and farms. Little or no water left the Delta for the Bay this spring, and even less will leave this summer. The Smelt Working Group charged with protecting two species of endangered smelt is about to take its summer hiatus as South Delta water temperature hits 25°C. The State Board has recently been forced to reduce Shasta Reservoir agricultural releases for fear of running out of cool water for winter run salmon again this summer.

The State Board’s “drought relief” orders keep little water reaching the Bay and allow salt water to encroach into the Delta. The False River Barrier has been installed to keep salt out of south Delta water diversions at the expense of north Delta habitat. Interior, USFWS, NMFS, EPA, and CDFW, our resource protection agencies, have “concurred” with the Temporary Urgent Change Petitions from Reclamation and CDWR, and the State Water Board has complied. 1

Meanwhile, the remnants of the Delta Smelt population have become isolated in the Sacramento Deep Water Ship Channel. Reclamation scientists assure us that the smelt will be fine and will descend into the cooler water at the bottom of the channel. The lack of smelt in their traditional designated critical habitat of Suisun Bay and the western Delta low-salinity-zone is apparently not a concern.

In the midst of all this “devastation”, the Delta Science Program held a Delta Challenges Workshop this past March.

“On March 16, 2015 the Delta Stewardship Council’s Delta Science Program hosted a workshop to summarize the risks and challenges facing the Bay-Delta system. These challenges include a multitude of stressors that threaten our ability to achieve the Delta Plan’s coequal goals. Numerous reviews, reports and articles describe the stressors and risks facing the contemporary Delta, but this information is spread across diverse publications, journal articles, and lengthy technical reports. The information has not yet been presented in a highly concise, readable way by an independent set of distinguished science experts.” 2

 

The Workshop

Dr. Moyle suggested that we prepare for the worst: “We have to prepare for the extinction of Delta smelt: “It seems very likely to happen in the next year or two,” Dr. Moyle said. “The Fall Midwater Trawl index has never been lower, we’re basically not getting any in any of our samples, and then most recently, the Kodiak Trawl sampling has found very few, even in places they normally aggregate.” He noted that the results of the most recent Kodiak Trawl, a survey aimed at catching smelt in the places where they’re supposed to be, and where they have been in the past, were pretty dismal. “They got 6 smelt, 4 females and 2 males. So the smelt are pretty much gone from this system. We don’t know yet but they could easily have reached a threshold that they can’t get back over, that they can’t survive. We need to be thinking now of answers to questions like: how will we know when the smelt is extinct in the wild? Who declares that? How can the captive populations present in Byron, how can these captive populations be used for re-introduction when better conditions return, at least temporarily, or even should they? And how does management of the Delta change if the Delta smelt are gone? What do we do, essentially, in the absence of Delta smelt?”

Others spoke on adaptive management: “Dr. Goodwin asked Maria Rea about doing large landscape-scale experiments. “To really do an experiment on the scale that needs to be done, and it’s an experiment so you don’t necessarily know what the outcome is, that puts people making decisions in a very difficult position, and I just wonder, how, as a science/policy/management community, what needs to be done to allow these landscape-scale experiments to go on?”

“We do need to get better at experimentation,” Maria Rea answered, noting that with salmon, they’ve done a bunch of tagged fish studies, some with active adaptive management. “The Vernalis Adaptive Management Program had an active component to it, but the number of fish tagged was insufficient to allow any real conclusions to be drawn from that, and so I think we’ve got quite a bit of work to do to. If we’re going to do a large-scale experiment and actually manipulate the system, then let’s make sure we’re growing enough fish and getting enough tags to put in the system that will actually be able to deduce something from the data that we get.”

The need for more money for more science came up: Dr. Luoma noted that since between 1997 and 2010, there was a large injection of science into the system, tens of millions of dollars. “That was a sign of what we need to keep things moving rapidly,” he said. “That money has dried up … If we’re going to really continue on this journey of trying to make progress, it’s obvious we need a big injection of science somewhere managed by the science program. We need an injection of science that allows us all to work together. That’s desperately needed now or else we’re just going to start flailing.”

“We need to explore performance measures, of having something that we can track that helps the policy makers understand the question, what has to happen next. “I think it was Bill Dennison who ran that workshop several years ago, showed us what you can do with a really organized system of performance measures that gets the public involved, gets the policy makers involved. We can do that, we just haven’t done it. I think this is something we really have to focus on doing right.”

Of course, there is always the concept that the Delta continues to evolve and remains hard to understand: Dr. Mike Healey began by noting that one of Jim Cloern’s comments especially resonated with him. “His comment that the Delta is a continually evolving system and we’re never going to be able to fully pin it down. Several people have been talking about wicked problems. Wicked problems have a formal definition in planning and management, and one of the characteristics of wicked problems is that they can’t be solved, they can only be managed. I think that’s probably what we’re looking at is coming up with a system of management that will be hopefully be relatively effective, rather than imagining that we can clearly define this problem and ultimately provide a solution.”

Then there is always the “reality check” and a “happy place somewhere down the road”:
“Once you’ve answered that question, you need to then concern yourself with what’s actually feasible but most of us want something that we’re really not going to be able to get, so we’re going to need to be able to make a reality check and decide what among the things we’d like to have we can actually accomplish, and then the final question is, how do we get to where we want to go from where we are now? And I think we still have a lot of work to do on those latter three questions,” he said. “We’re not anywhere near coming up with the final management plan for this problem as yet, I don’t think,” he said. “But I hope that whatever we can come up with can make some kind of a contribution to making progress, down the road towards that happy place.”

A potential for “boldness” from “outsiders” who can provide a “fresh look” at the problems:
“I really think there is an opportunity here for some boldness, and I hope that we as a foursome will be a bit bold,” he said. “I really do hope that we basically embrace ideas that we can agree upon and present them to you as things that would be the next steps moving forward, or at least our ideas of what that might be, because we need to move beyond just simply continuing to monitor this system. We really need to begin to actually implement some projects, some experiments, and really move that next step down the road to actually beginning to deal with some of the changes that are being imposed on the system and seeing if we can come up with a better and more beneficial ending with some of our attempts. I know it’s fraught with lots of difficulty, and we’re going to make lost of mistakes, but I think we need to be bold and move forward. And hopefully we can give you some ideas on how we think that might be best done.”

And finally, “something learned”, “fun”, and a “ridiculous challenge”:
After public comment, Letty Belin with the Department of the Interior then gave some final thoughts. “I think it’s been an extraordinary day,” she said. “I bet you there’s not a single person in this room that hasn’t learned something significant. I’m still amazed that we got this incredibly talented and experienced panel to accept what I acknowledge is a ridiculous charge. If I had this assignment, I would first turn it back to the teacher and say this is impossible, you cannot summarize this stuff in 15 to 20 pages, and then I’d ask what size can the font be, can it be like .333 but anyway I know it’s particularly fun to hear your reactions and use words like fun.

“I can’t tell you how important I think this effort is,” she continued. “I think it’s going to be incredibly helpful, because policy making in such a complex scientific environment, we need guideposts and people, you all who have both the scientific expertise and the wisdom gained through that, we really are fortunate to be able to get your expertise, so thank you so much.”

Not a word on the drought or changes to Delta water quality standards, or the effects of having no freshwater flow into the Bay.

  1. At a State Board drought workshop earlier this year, the Board chairperson asked the NMFS representative what “concurrence” meant. The NMFS rep responded by stating he had looked up the definition in a dictionary, but they really did not understand its meaning in this case. ↩
  2. http://mavensnotebook.com/2015/04/24/delta-challenges-workshop-part-4-fish-birds-and-habitat/ ↩

Hatchery Reform – Part 3

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Previously… Part 1: Central Valley Salmon and Steelhead Hatchery Program Reform & Part 2: Hatchery Reform

Contingency Release Strategies for Coleman National Fish Hatchery Juvenile Fall Chinook Salmon due to Severe Drought Conditions in 20141

“Substantial data are available to show that transporting Coleman NFH fall Chinook salmon to the west Delta would likely produce substantial increases in ocean harvest opportunity but will also result in a significant increased rate of straying as they mature and return to freshwater. The levels of straying anticipated are likely to compromise some of the hatchery objectives, including contributions to harvest in the upper Sacramento River and the ability to collect adequate broodstock at the Coleman NFH in future years, particularly 2016. Although the levels of straying anticipated from releasing fish into the West Delta are unfavorable, this release strategy may in fact represent the best possible option when faced with the possibility of losing the entire 2013 production year. In future years, under less extreme conditions, the standard protocol for releasing Chinook from the Coleman NFH will continue to be on-site releases into Battle Creek.”

There are two measures the Coleman Hatchery could adopt that would help to alleviate the straying problem associated with out-planting hatchery production. (1) Barging smolts to the Bay from Knights Landing area (above the mouth of the Feather River) would help imprint smolts on the Sacramento River. During barging, water is continually circulated through the fish tanks unlike during trucking. (2) Fry out-planting to the Yolo Bypass (Sacramento River source-water) would produce more natural smolts that would be less inclined to stray.

“The 1988-1992 period represents the most recent extended severe drought in the Central Valley. At that time the Service released nearly the entire production of fall Chinook to off-site locations to circumvent poor conditions in the lower Sacramento River and Delta. Conditions in the river and Delta were poorest during the spring of 1992 emigration season. Releases from the Coleman NFH into the West Delta in 1992 survived at a rate nearly 18 times higher than releases into Battle Creek, with a commensurate increase in ocean harvest. Owing to their markedly improved survival, West Delta releases from that same year also outperformed on-site releases in regards to returns to the hatchery. More than twice as many adult returns to the Coleman NFH in 1994 resulted from West Delta releases as compared to releases conducted into Battle Creek. If the Coleman NFH had released all production on-site in 1992 the hatchery would not have had sufficient returns of adults to meet production targets in 1994.”

Similar results are likely for the 2012-2015 drought. Despite these facts, there are many people who believe straying is unacceptable. These individuals hold out hope that “wild” Fall Chinook may someday recover in the Valley. To keep up such hopes we should adopt the two recommendations above, as well as continue to improve spawning and rearing habitats in the rivers. Our best hope for wild native genetic fish recovery is to incorporate natural habitats above the dams in trap-and-haul projects. At present, Fall Run Chinook and Steelhead are generally not being actively considered for these new programs.

“Implementation and Contingencies: The Service and California Department of Fish and Wildlife (CDFW) have coordinated a schedule for the delivery (trucking) of hatchery production from the five state and federal hatcheries to acclimation net pens in the west Delta. However, if a precipitation event occurs in March or April, environmental conditions/criteria may be re-assessed and if none of the criteria above are forecast to occur, then groups of Coleman NFH fall Chinook salmon juveniles meeting appropriate size criteria for an on-site release (i.e., at or about 90/lb) may be released into Battle Creek per usual procedures. Further, criteria are expected to be assessed during the three following periods: mid-March, first of April, and mid-April. If criteria above are not met or expected to be met within a three week window, then on-site releases of appropriately sized fish will also occur shortly thereafter. Criteria may also be re-assessed one to two weeks prior to scheduled trucking dates and, again, if criteria above are not met or not predicted to be met within a three week window, then on-site releases of those groups of fish will be considered to instead occur on-site shortly thereafter. If during any of these assessments, existing/predicted conditions are expected to meet the criteria triggering consideration of the alternative release strategy, then preparations will begin, continue, or be implemented to truck appropriate groups of fish to the acclimation net pens in the west Delta as scheduled.”

These drought-year plans focus on early river releases and trucking to the west Delta. Both of these options will lead to poor survival. Instead, fry-fingerling out-planting to the Yolo Bypass, Sutter Bypass, and Bay-Delta should be considered for Jan-Feb. Barging to the Bay should be considered for Mar-Apr smolt releases. If trucking is retained, it should be further to the west (e.g., Collinsville or Pittsburg), not Rio Vista which is in the zone of influence of the South Delta Export pumps.

Hatchery Selection. Oregon Department of Fish and Wildlife. 2011.2

“Our results support the finding outlined by others that even contemporary hatchery practices (e.g. using wild brood stock, pairwise matings) can produce fish that have lowered reproductive success in the wild. This evidence suggests that hatcheries may need to consider how to replicate the intricacies of natural breeding behaviors if they are to produce fish for supplementation programs that truly help recover endangered populations.”

In-hatchery replication of natural breeding behavior is another complicated subject worth further consideration in Central Valley hatchery programs. For more on the subject see: http://www.hatcheryandwild.com .

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

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. ↩