Juvenile Chinook challenges in the Central Valley: baked, boiled or bass food?

The predator issue: Just how bad is it? Dr. Sean Hayes discusses the results of recent studies on the San Joaquin

Coverage of the California Salmon and Climate Variability Symposium continues with Dr. Sean Hayes, Salmon Ecology Team Leader for NOAA Fisheries, who talked about his latest research into juvenile outmigration survival, in particular, focusing on predation studies on the San Joaquin.

First, Dr. Sean Hayes began by reminding about the scale of the challenges that California faces. “California is the seventh or eighth largest economy in the world – I think we just passed Italy and Russia and may be heading for sixth,” he said. “All of that is supported by a water infrastructure is the underlying guts; it’s a machine that we have to keep running to support all of this where we literally move water from here to there.”

So the question is, how have salmon been impacted salmon as the state has changed and only 15% of the historically 65 million acres of anadromous fish habitat remains. “I realize that the work that I’ve been doing at the science center and the work of my colleagues is we’ve basically been tasked with proving the bloody obvious for the purposes of convincing stakeholders to invest in change or to mitigate,” he said.

There are dams, agriculture, temperature issues, invasive predators, and ocean conditions – all of these are challenges that these fish face at various parts of their lifecycle, he said. “The biggest habitat in this whole machine is the Delta in terms of what it once was and what it is now and where we headed are with it,” he said.

“Habitat is in many respects just as much in jeopardy for us as it is for salmon, because it has be managed artificially to maintain this X2 line where we can’t allow salinity to intrude into the Delta, so we have to release water all the time, whether we want to or not. Otherwise if we don’t, sea water will intrude and essentially block of flow to the water support system that sends water to Southern California. If we don’t do that or if we don’t make any large scale repairs to this, our risks of inaction are a $250M* salmon economy, flood and safety, and livelihood of 5 million people living in the Delta region, $40 billion worth of agriculture, and freshwater supply for 25 million people.”

*Note: The Golden Gate Salmon Association disputes this number; says the salmon industry is worth more than $1.4 billion.

“The stakeholders all want to blame the ocean rather than each other, and so that’s where the science has really come in to just really nail down some fundamental questions and principles,” he said. “So in order for NMFS to actually move forward on something, they need something that can stand up against a lawyer in a courtroom and these resources have really good lawyers, so we need more data.”

Dr. Hayes said that they have been designing a series of studies to provide some simple metrics on juvenile outmigration survival: are the fish dying in the river or in the ocean; if they are dying in the river, is it due to predation or are they getting sucked into a diversion. Once we have the data, this will be integrated into life cycle models, he said.

He presented a graphic of acoustic telemetry data showing outmigration survival of late fall run Chinook from 2007 to 2011. “In most years, we were lucky if 3% of these fish made it to the Golden Gate,” he said “We had one anomalous year in 2011, a wet year, and suddenly we had 16% of the fish make it to the Golden Gate. This is a one point study, but we did find that over the course of the studies, the take home message was that the most effective life history strategy for a hatchery fish was to swim fish and get the hell out of the river because it’s broken. There was no time invested in growth opportunity, it was literally leave the hatchery, move, run. In spite of that, 84-97% of the mortality happens in just a two week period for these hatchery fish.”

Some might think that wild fish might be smarter and fare better, but that is not the case, he said. “The wild fish have to spend their entire lives living in this river, not the protection of the hatcheries, so their mortalities, we’re finding are often just as high.”

Dr. Hayes said that they are working on a series of studies happening now where they are tagging representatives of all the hatchery runs, tagging wild fish in the Mill, Sutter, and Battle Creek complexes as well as transporting fish to the Delta.

He then presented a slide of preliminary survival data. “For the late fall, survival is 3% in most years, 16% in a wet year,” he said. “The data has been pretty dismal for the other sub year and life history stocks with literally 0 to 5% making out in the studies we’ve been doing since 2012. With an anomaly that the winter run that we released in 2015 on the storm event and they did get to ride a very high pulse out and had the highest survival we’ve seen, so even during a peak drought year, there are adaptive management solutions and tools, but the fish are still dying in the river.”

There are many possible causes of this, predation be one of them. “One of the questions we get a lot is on the predator issue is that bass have here for 130 years, why are they a problem now? We used to have good salmon runs,” he said. “The reality is that in addition to all of our human issues and land use practices, the San Francisco Bay and Delta are under constant invasion by new species; we have Asian clams come in in the 70s or 80s and then followed by that, we’ve had aquatic plants come in, and we don’t know what introduced last week that we’re going to be managing for in ten years. The system is in constant dynamic change and we have to be always just learning about it after the impact has already set in, so that is a huge challenge for us. But in either case, it’s those variables that have perturbed the food web in such a way that the predators have become a bigger problem for salmon in the last few years.”

There are several different models for predation, he said. “There’s a predator exposure time of how just how long does a fish spend in the system – the more time you spend in the system, the more likely you are to encounter a predator and get consumed,” he said. “The gauntlet model is how dense are the predators in the system; the higher density, the higher the mortality rate.”

Dr. Hayes said they have found that this can possibly be habitat mediated. “My graduate student Megan Sable did a project on the Mokelumne and she looked at striped bass diet in portions of the river that were below the Woodbridge Dam in the regular river habitat and these fish were consuming 80% crayfish and there was no salmon in their diet,” he said. “Conversely, throw in a habitat feature that gives the striped bass predatory advantage and suddenly their diet gets switch to being 80% salmon at the base of the Woodbridge Dam, so this allows you to identify key principle pinch points in the habitat. Maybe we don’t need to worry about all of the habitat; we just need to identify the specific pieces of the habitat that are the real critical problems from a predator’s perspective.”

With respect to predation, some say that since it’s rare to see salmon in the diets of the predators, they probably aren’t eating them, he said. “Eric Loboschefkey’s paper was a game changer in my perception of this issue of predation,” he said. “They came up with a rough estimate that the striped bass population alone in the Central Valley alone needs to eat something like 25 million kilograms of fish per year. I did a rough back of the envelope calculation of what is the entire biomass of all the salmon in the Central Valley … Coleman had released 12 million hatchery fish and we estimated 700,000 made it to the Golden Gate, so could the striped bass have been responsible for eating the other 11.3 million missing hatchery fish, just on a bioenergetic level? All California juvenile added up roughly is maybe 240,000 kilograms, which means that if striped bass ate every single one of them, they would still be less than 1% of their diet, which in terms of statistics means that salmon are irrelevant to striped bass, much less all of the other predators in the system as a prey item, probably when you think about it.”

“So how do we go about studying this predation event if stomach contents isn’t going to be a way of evaluating it? We are still dealing with the stakeholders that say there is no proof that predators are a problem.”

In order to investigate this further, NOAA worked together with DWR to set up a large scale project on the San Joaquin to evaluate predation through a series of reaches. The first step was to develop a real in-depth baseline understanding of the ecosystem by using high resolution acoustic bathymetric sonar and fish finders to map the habitat in high resolution and then overlay on that the density of the predators in the environment throughout the 20 miles of the San Joaquin.

The next question was getting at the predator density hypothesis. “Can we manipulate predator densities at a level that might actually influence survivorship of the fish,” he said. “So we released acoustically tagged fish through the reach and then had known predator densities in all the reaches. We moved a bunch of predators from one reach to another so that we had basically three experimental types: a control reach, a removal reach where there’s reduced predator density, and then an addition reach where we actually increased predator density.”

They set up a series of nine sites: three control sites, three removal sites, and three addition sites throughout the last 20 miles of San Joaquin before it hits the Deep Water Ship Channel. They then released salmon to go through and they measured the survival of the fish working with acoustically tagged Chinook salmon.

“Acoustic tagging is a great tool for certain things; it’s great at showing mortality over large spatial scales, but it’s really not the best tool for evaluating mortality in discrete pin point locations,” Dr. Hayes said. “So we came up with a new tool. We basically built drifters that we send down the river with a live salmon on it to evaluate relative predation rate as these drifters are moving through various parts of the habitat and the various experimental types.”

They built a drifting system with a GPS tracker on it along with sensors to track time of day and temperature, as well as a Go Pro camera to verify what happens to the tethered salmon and a hook timer that is synchronized with the GPS so they can identify exactly when and where in that habitat the predation actually happened.

He then presented a slide showing some of the results. Twenty drifters were released with each colored line the track of a different drifter that moved through the habitat; each red dot is a where a predation event occurred on one of the drifters. They then overlay the predator locations over that, and found a spot where there’s predator density in the habitat feature that’s allowing for much higher levels of predation than in other parts of the system. “What you see is we had a high level mortality but it was right around one habitat feature in one portion of the river, so only 10% of all of this habitat that’s a problem,” he said.

Dr. Hayes said they’ve done about 5000-6000 releases through the river and they are now putting them into a model selection process to identify key habitat features that are both bathymetric as well as water and flow rates. The velocity of the drifter can be measured, which is a function of flow and pumping and other dynamics. “We can evaluate that on top of everything else as a covariate in predation rate and to move forward with identifying which variables are contributing to increased or reduced predator rates through the habitat,” he said.

But what at if it’s not just predation? There are other factors that could be in play, he pointed out.

He also noted that genetic diet analysis has shown that 3 to 5% of the diets in striped bass and largemouth bass show juvenile salmon, but channelcats had a really high level of representation of salmon across the samples. “It made me ask the question, are channelcats a voracious predator or are they just swimming along eating dead salmon off the bottom of the river which is a water quality issue? So we’re moving into that.”

They are studying the impacts of temperature now on all these life histories, getting at proving the ‘bloody obvious’ – does hot water kill salmon at various life stages, he said. “We’re really trying to nail down where those thresholds are, get aerobic scope measures, and just working with a really simple physiology model underlying all of that as to what are the limitations for salmon at all these life stages.”

“We have challenges in this system,” he said. “We have to manage and balance the needs of fish and humans in California. We also have challenges in our management paradigm. This is the salmon life cycle, and right now our metric of success in terms of how we manage things is smolts out. It’s just raw numbers and that’s how the hatchery quotas are managed and that’s how we run our business, and we need to get away from that and start focusing on life history messages … what do we do to get adults back because there are ways to get better smolts and fewer smolts into the ocean and get more adults back.”

Dr. Hayes said there are successes. “It used to be we just blamed the ocean and there was no leverage as an agency to manage this, so we slapped some science on, we built massive infrastructures to prove that mortalities are in the river, and we’ve proved bass eat salmon. … We’re doing it really well with really sophisticated tools but we’re also finding out that maybe we don’t need to go on a bass jihad and maybe we can manage small pieces of habitat to solve this problem.”

“There are creative opportunities,” he said. “These are wild fish that were tagged … the upper fish is a wild smolt coming out of the Mill Creek basin, and the lower one is a wild smolt coming out of the Sutter Creek being caught in the Sutter Bypass and so this is a fish growing up in a rice ditch and this is a fish coming out of native pristine habitat. So the idea of using habitats like the Yolo Bypass – I think we need to be expanding our focus to be moving even farther into the north valley and considering the rearing potentials that we have there as well.”

“And with that … “

Coming up tomorrow …

Coverage concludes with Dr. Ted Sommer discussing how floodplain restoration can help salmon adapt to the changing climate, and Dr. Peter Moyle presents his plan for saving California salmon.