Delta smelt symposium, part 2: Causal links to population declines and data gaps

Hypomesus_transpacificus Delta smelt sliderbox

Hypomesus transpacificus (Delta smelt)

Could it be water exports, predation, food web, contaminants, drought … ?

Coverage of the Delta and longfin smelt symposium, Is Extinction Inevitable?, continues …

The first round of presenters at the Delta smelt symposium have shown us that although we’ve learned a lot about the Delta and longfin smelt, their populations are still declining; however, the population genetics do give us some hope for recovery.

(Click here for part 1: Symposium coverage, part 1: Delta and longfin smelt: Is extinction inevitable?)

Now the presenters turn to the question of why.

Presentations featured in today’s post

Click on the link to jump to presentation or simply scroll to read each in sequential order:

TOM CANNON:  Contributing Cause of Delta smelt decline: Water Exports

The federal and state water projects south Delta exports are a major factor in the decline of the Delta smelt, he says

Tom CannonBIO:  Tom Cannon studied entrainment of estuarine fishes in the Hudson River from 1972 to 1977 after graduating from the University of Michigan with degrees in Fisheries and Biostatistics.  He then moved on to the Bay-Delta where he has focused on the fish population effects of entrainment with shorts stints away studying hydropower effects in Alaska, Lower Columbia River, and Lower Missouri River.  In recent decades he has worked on the CVPIA and CALFED programs, and studied the populations, habitats, and life history requirements of Delta Smelt and Chinook Salmon in the Central Valley and Bay-Delta Estuary.  He continues contributing in retirement focusing on treatments that would help recover smelt, trout, and salmon in California.

In this presentation, I’m going to make the case that the major cause of the Delta smelt has been the entrainment of smelt at the south Delta export facilities,” began Mr. Cannon.  “Since the mid 1970s, there has not been sufficient protections during the winter spawning season and the spring-summer rearing period to maintain the smelt population.  From 1978 to 1994, we had the D-1485 standards, and they had very limited winter spring protections.  After 1995, we had D-1641 standards.  They improved the winter conditions but left out the summer conditions.

During the recent four years of drought, already limited protections were relaxed by the State Board, causing the Delta smelt to become virtually extinct, in my opinion,” he said.

Tom Cannon Smelt_Page_02Mr. Cannon said back in 1981, he was studying striped bass at the time and noticed the smelt were wiped out, too.  He pointed out the red circle, noting it was the largest one-year decline.  “This led to the poor production after 1981; it was followed by the recovery period, 1991-2002.  The recovery was spurred on by low exports from 1990-1992.  Those were drought years, but there wasn’t any water so they didn’t export, so the smelt started recovering because there were no exports, not because salinity was right or outflows were up high; it was just low exports.”

The decade of decline after 2001 was followed by a weak recovery in 2011; since 2012, the indices have all been record lows, he said.

Tom Cannon Smelt_Page_03He then presented a graph showing fall-winter salvage of Delta smelt from 1981 to 2002.  “These were mostly adults,” he said.  “People forget that we were getting 20,000 to 80,000 smelt in the salvage in 1980, 81, and 82.  1981 was the highest peak. During the recovery or right after the recovery, 2000-2002 were relatively high, too.”

Tom Cannon Smelt_Page_04He next presented a graph of the spring salvage for Delta smelt for the same time period, noting that in 1981, there was 400,000 salvaged Delta smelt, juvenile Delta smelt mostly in May.  “You can see it got high again in the recovery periods; this supports my idea that 1981 was the first collapse and things weren’t very good after that.

Tom Cannon Smelt_Page_05Mr. Cannon then presented a chart for January of 1981, noting that the outflows are shown in the blue line and exports are shown in the red line.  “You can see that we had high exports and low outflow,” he said.  “You can’t have that any more, the OMRs are protecting the smelt and salmon and everything else, but look at the numbers of Delta smelt that were salvaged every day, 2000.  In comparison, we had 8 all winter this year.  This again supports the idea that this was a major impact to the population.”

Tom Cannon Smelt_Page_06He then presented a similar graph for the spring-summer of 1981.  “You don’t get to see the larvae because they are entrained and nobody monitored them at that time,” he said.  “The outflow went from 35 down to 0 twice in April while there were maximum exports.  That’s probably indicative of tremendous loss of larvae at the south Delta export pumps.  As the larvae reached salvageable size, you can see we were getting 5 to 10,000 a day through May, while exports were only about 4 or 5,000.  It’s because about this time, they started shutting off the state pumps because they were taking half a million stripers a day at that time.  I don’t think anyone was worried about smelt then.”

The standards at the time were governed by the State Board’s D-1485 standards.  “In the winter, there were no export restrictions at all, so exports were maximized most of those years, pre-1994,” he said.  “The spring-summer standards, pre-1994, were again monthly standards with no export limits in April.  I can’t believe we even considered operating that way; we would never do that today.”

Tom Cannon Smelt_Page_08 Tom Cannon Smelt_Page_09

Tom Cannon Smelt_Page_10He then presented a graph showing exports from 1956 to 1986, pointing out noting that exports in 1981 were the second highest after the 1970s; the state project came online heavily during this period.

Tom Cannon Smelt_Page_11He then presented a graph showing exports for the month of April from 1970 to 1986.  “April exports are the highest they’ve ever been in the history that we’ve been recording; they were 8 to 10,000 in 1981 and 82.”

Tom Cannon Smelt_Page_12Mr. Cannon presented a graph showing Delta outflow and exports during the spring of 1991.  “In 1991, with a monthly average outflow index, we went from 16 to 0, because all they had to do is hit the average under the standards, and exports were flat out maximum just about,” he said.  “You can imagine the larval smelt in a year like that would have all gone down the tube.  They didn’t export much after that because it was end of the drought period and there wasn’t any reservoir water.”

Tom Cannon Smelt_Page_131996 was the first year after the standards changed to D 1641, and operations were completely changed.  “We had the VAMP, we had the shelf of the VAMP, and then we had no protections any longer in the summer,” he said.  “In May we got high salvage as they become of size to be salvaged at the state pumping plant.  It eventually tapers out in mid June because the water temperature gets too hot and you don’t get any more salvage at that time.  Maybe they go downstream, maybe they just die in place.”

Tom Cannon Smelt_Page_14Mr. Cannon then presented a chart for the winter 2003, noting that during this time, there were no limits on Old and Middle River (OMR) flows.  “We had maximum diversions all winter long, and we had these high salvage numbers of adult smelt.  Now this is a lot lower than they did in 1981, but still this was a recovery period and this is what happened to them during the recovery period, just pre-POD years.”

Tom Cannon Smelt_Page_15He next presented a graph for the Pelagic Organism Decline (POD) years, 2003-05.  “You can see these are all maximum exports for all the winters.  There’s no OMRs to protect the fish.  You get the adults, and you get the spring young …and a gradual decline until there’s hardly any left,” he said.  “So these years, these high exports wiped out the recovery.  There’s no doubt in my mind about that.”

Tom Cannon Smelt_Page_17Mr. Cannon then presented a slide showing the temperature at Rio Vista for 2011 through 2015.  “I just wanted to show that with the standards relaxed, the Delta in the middle of the summer, this is Rio Vista, gets too hot.  Because of the relaxations of the standards, and that’s really kept the population at record lows right now.  2011 you can see it didn’t even get over 71 degrees, but it’s 75 in the last two years when the relaxations occurred to the greatest extent.”

Tom Cannon Smelt_Page_18He then pulled up a graph of the stock-recruitment relationship for summer to fall, noting that it’s very strong.  “It’s the Summer Townet and then the subsequent Fall Midwater Trawl index, and you can see that it’s a nice stock recruitment curve.  These red ones are high summer exports, the green ones are low summer exports, that’s where 1990, 91, 92.”

Tom Cannon Smelt_Page_19He then presented a graph of the fall to summer stock-recruitment relationship, noting that is also again a strong relationship.  “In the dry years, high entrainment/high exports are in the red,” he said.  “In the wet years, the next year you can produce more if you have a wet year in the year of the summer townet index, and then 2010 and 11 which gave us false hopes because we proceeded to wipe them out in 12, 13, and 14 anyway.”

Tom Cannon Smelt_Page_20Mr. Cannon said that the two spawning populations are the San Joaquin and the North Delta.  “They can’t go up the Sacramento because there’s no flood tides to ride upstream, so this year a lot of them went into San Joaquin and they went up to Cache Slough and the ship channel, and it’s the years when the San Joaquin flows are low and this strong flood tide, a lot of the adults go up the San Joaquin and spawn like this year.  Whatever few there were.  So that’s the mechanism that starts where they go spawn.”

Tom Cannon Smelt_Page_21The mechanism for the entrainment is after they spawn, the larvae get caught up in the transports of the exports,” he said.  “The red lines are negative flows, average daily flows, and this happens to be the recent survey in January; these were longfin smelt larvae, so you can see the longfin smelt larvae can get into this region as well, and the Delta smelt are much more vulnerable because they are more further upstream.”

In conclusion, I think the exports are the major cause of the Delta smelt decline and the decline started in 1981 with high entrainment of all the life stages,” said Mr. Cannon.  “There’s no evidence of larval entrainment but obviously there was a tremendous amount of larval entrainment; then we had continued exports and low Delta outflow that has prevented recovery.  The things we’ve done, like OMRs, outflow requirements, D 1641, all of them have helped, but the population crashed in 1981, and the little recoveries we get, we knock them off in the next dry year after the recovery.  The protections are simply inadequate.”

Question: The actual numbers of smelt that are on the salvage, those numbers are the numbers they actually record … it doesn’t represent the total number of smelt.

I didn’t have time to explain that they don’t get the larvae, they don’t get any juveniles under 20 mm, and the efficiency’s bad all the way to 50 mm,” replied Mr. Cannon.  “And then at Clifton Court Forebay, they lose 90% of them to predation before they get to the salvage, so these numbers are like tip of the ice berg.  The numbers lost are tremendous.  All the salvage fish die.  They also die if they come out of the San Joaquin and start heading south, like in a warm summer.  They can’t get to Clifton Court so they die on the way.  It might be cool on the San Joaquin, but by the time they get to Clifton Court, it’s 27 degrees in June, so that’s an indirect effect of entrainment.”

Question: You brought back memories … it was really hell in the drought 87-94.  But 2011 … 2011 set a record for volume of water exported, but we had a nice bump that lasted for a year and a half anyway in smelt production.

They were all in Suisun Bay and it was 71 degrees maximum,” Mr. Cannon said.  “That’s the other thing I didn’t mention.  In the wet years, they are in Suisun Bay, and even colder water.  In dry years, they are in Rio Vista in the hot water, so …

Questioner … I’m raising the issue that there is some interaction between flow and exports that fitted what you’re saying, but there are conditions in which exports are horrendous and there other conditions like in 2011 where everybody’s happy, and I’m still trying to figure out what that relationship is.

Well I’d like to take issue with Dianne Feinstein,” said Mr. Cannon.  “Here, that’s this January.  She wants to export 10000.  Why not? it’s 60,000 outflow.  Because the Delta Channel Cross Channel is closed and the fish are in the San Joaquin, they can’t get out of there.  They aren’t in the flow of the Sacramento River, so this happens.  So she said, ‘we weren’t getting any smelt, why can’t we raise the exports’, her staff said that.  We wouldn’t get this pattern this year because there’s only 8 left, but if they did do this again in January this year or February, they would be proportionally massacring the smelt that are left.  There’s not a lot of them, but it would still be bad for this reason right here.  Right now we have an OMR of -5000 which is about 5000 export.  It’s pretty protective.  It’s not great, but it’s protective.  I don’t think anybody would want to go to 10,000 right now, I hope.  Unless you want the water to go to the San Luis Reservoir and fill it, then that would be a good thing to do.”

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BRIAN SCHREIER: What have we learned about predation on Delta smelt?

Predation is a major source of mortality for Delta smelt and probably the dominant source of mortality, he says

Brian SchreierBIO: Brian Schreier has a master’s degree from UC Davis, and he currently is a Senior Environmental Scientist with the California Department of Water Resources.  He is the principle investigator for the Yolo Bypass Fish Monitoring Program, and he has conducted numerous studies on predation of larval and adult Delta Smelt in the North Delta.

The focus of Brian Schreier’s presentation was what is known about predation on Delta smelt. He said he’d throw in some anecdotes about longfin smelt, but acknowledged that we don’t really know a whole lot about predation on longfin.

Shreier smelt_Page_02Looking back to the earliest studies, there were a number of studies in the mid previous century looking at striped bass diets in the estuary, but Delta smelt were never found to be abundant in striped bass diets.  “A study in 1967 looked at 4500 striped bass diets; pond smelt as they were called back then occurred in only .4% of those diets; over 8500 diets looked at in a 1966 study, similar percentage,” said Mr. Schreier.  “This is the best indication we have of the role that smelt played in the ecosystem when they were abundant.  Longfin smelt, back then called Sacramento smelt, only occurred in 0.9% of diets.”

So the indication that we have is when the smelt were abundant, they still did not comprise a major component of predator diets or striped bass diets,” he said.

Moving forward to the POD and post-POD years, there were visual diet analyses that didn’t find any smelt in the diets of striped bass and largemouth bass.  “With these predators, we don’t expect a high amount of overlap, especially with largemouth bass where they are more in-shore, but we haven’t seen any evidence that smelt comprise a large amount of these predator’s diets.”

About 6 years ago, genetic tools were developed to look at predation on smelt and other fishes, the benefit being that genetic techniques have a much greater sensitivity, he said.  “For example, from experimental feeding trials, we know we can detect chinook DNA in striped bass diets up to about 60 hours post ingestion reliably, and Delta smelt are similar.  So Sean Hayes has taken these methods in the south Delta and looked at over 1000 predators to date and only found 9 Delta smelt.  Interestingly, that was across five different species of predators, so no single species was dominating there.”

Shreier smelt_Page_05In the north Delta, they conducted a fairly substantial gill netting effort across several different corridors in the north Delta, mainly targeting striped bass predation on chinook in areas like the Deep Water Ship Channel, and Liberty Island, looking at predation on Delta smelt.  “We targeted striped bass and we saved any pretty much any piscivorous fish we found,” he said, presenting pie charts indicating the amount of proportion of the thirteen species they were looking for that were found genetically in the diets.  A large proportion of the stomach contents did not have the thirteen species they were looking for; those are labeled on the charts as ‘empty’, he noted.

Shreier smelt_Page_06In largemouth and smallmouth bass, we saw no detections of either smelt species,” he said.  “We looked at over 700 white and channel catfish, and only detected one incidence of predation on Delta smelt.  Our main focus for the study was striped bass, we only detected predation on 8 striped bass with Delta smelt DNA in their diets.”

Circling back to longfin, we did a sample of only 65 pikeminnow, and 13 of those had longfin smelt detected in their stomachs, and those were from pikeminnow sampled in Rio Vista in December, so right during the start of the upstream migration for spawning for longfin,” he said.

Shreier smelt_Page_07They next looked at predation on Delta smelt larvae, conducting a fairly extensive survey in 2011 primarily focused on Mississipi silversides but also collecting other potential predators of larval smelt using multiple different capture techniques.  “For silversides, we only found that about 12% of the silversides were positive for smelt DNA in their digestive tracks, and keep in mind that this was in a period where we had pretty wet conditions and fairly good habitat conditions for Delta smelt, so I think of it as when the smelt would have had the best odds of avoiding predation,” he said.  “With that data, we were able to model the incidence of predation by silversides on larval smelt with some concurrently collected habitat variables, and this highlighted that turbidity was a key predictor of predation with a negative coefficient indicating that as turbidity increased, the incidence of predation decreased.”

Shreier smelt_Page_09Positive detections for predation on larval smelt was detected across a wide variety of species, some you would expect, some you might not expect, Mr. Schreier said.  “Interestingly, I’ll draw your attention to the exopalaemon shrimp towards the bottom; we just happened to save four on a whim just because we were curious.  One of those was positive; that’s kind of interesting, but when you think about how extremely abundant exopalaemon shrimp can be in the estuary, particularly in areas and times when smelt spawning is occurring, the predation on eggs and larvae could be fairly substantial.

Shreier smelt_Page_10Knowing that predators eat Delta smelt, what can we do?  “Just because we know that smelts maybe aren’t an important part of predator diets, that doesn’t necessarily mean that predation isn’t important to the smelt themselves,” he said.  “We have two knobs that we can turn to look at what we can do about predation.  The first one that comes to mind is that you can try to control the number of predators.  The kind of conceptual model implicit in this is that with a decrease in the abundance of predators, you would see a compensatory increase in the abundance of Delta smelt.  Of course, Delta smelt are a forage fish; their ecological function is to be eaten and to transfer energy up the food chain, so you would expect that they would be eaten.  Our conceptual models are all based around the notion that predation is the main source of mortality for Delta smelt, but when you look at that more nuanced, predation is the main source of mortality in a proximal sense, but in an ultimate sense, you have other factors that are kind of making smelt more or less susceptible to predation.”

When we look at controlling the number of predators, if we expect that to work, we would have assumed that predation is limiting,” Mr. Schreier said.  “What we’ve seen from Matt Nobriga’s 2013 paper where he looked at striped bass and Delta smelt abundances is that he saw no correlation between striped bass abundance and Delta smelt survival, indicating that predation in fact is not limiting for Delta smelt.”

In terms of proposing predator control in the Delta, predator removal experiments in the lower Mokelumne have shown that predator removal have a short term benefit to survival, but it is very spatially and temporarily restricted.  “Even after subsequent predator removals, you often don’t see a similar benefit to survival and that’s because a lot of times what you get is an overcompensation by predators moving into refill this vacated niche, and often you can even find an reduction of survival even over what you had originally.”

Shreier smelt_Page_11The second knob we can turn is the habitat features knob.  “Turbidity is in a conceptual model in every single life stage for Delta smelt, and we found that turbidity is correlated with reduced incidents of predation.  Looking at these different habitat features, certainly turbidity as a way to mediate the risk of predation seems to be somewhere where we can have an impact.”

Shreier smelt_Page_12So in conclusion, Delta smelt were likely never a major food source for any of the piscivorous fish that we have currently in the estuary, at least as far as we know, but predation is a major source of mortality for Delta smelt and probably the dominant source of mortality,” said Mr. Schreier.  “Many species eat them, given that they are a forage fish, they are being opportunistically preyed upon by pretty much anything with a big enough mouth.  But we have some evidence that turbidity can help reduce this risk of predation.”

The big caveat with all of this is that everything I’ve showed you today is all pre-drought collapse predation data, and it’s kind of up in the air what kind of role predation plays now that Delta smelt are at an extremely low abundance where even our targeted trawling can detect them, let alone how predators can detect them.  And for longfin, we really don’t know very much, so that’s another area of research we need to look into.”

Question: I would have liked to seen some estimates of the abundance of predators at the time.

I only had 12 minutes,” replied Mr. Schreier.  “Striped bass, as one of the POD species, they aren’t doing all that well.  For certainly for silversides, silversides have seen a dramatic explosion in their population since the turn of the century, so for predation on larvae, it’s certainly possible that an increased abundance of silversides could be limiting recruitment.  But for predation on adults, we have seen increases in the centrarchidae, the warm water basses, but we have very little evidence to suggest they are preying on Delta smelt.”

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DR. WILLIAM BENNETT: Over Under Sideways Down: Inertia of a Transforming Food Web and Extinction Debt for Delta Smelt

Extinction debt:  Are the Delta smelt dead, but just don’t know it yet?

Bill BennettBIO:  Dr. William A. (Bill) Bennett is an Associate Research Ecologist in the UC Davis Center for Watershed Sciences, and Bodega Marine Laboratory. He received B.S. and Master’s degrees from the University of Massachusetts, Boston, and Ph.D. from UC Davis. Bill has worked for over 20 years on the fishes in the San Francisco Estuary and marine environments in northern California, and an authority on the endangered delta smelt and striped bass populations. Bill has worked extensively with the Delta Science Program, Interagency Ecological Program, and is a coauthor of “Comparing Futures for the Sacramento-San Joaquin Delta”. 

Bennett smelt_Page_04Dr. William Bennett then discussed food webs and extinction.  But rather than spend his time explaining the food web, he would instead discuss how basically one food web is sort of taking over another one – sort of competition between food webs but on a larger scale.  “The basic premise I’m talking about is essentially the alien food web with the largemouth basses and Egeria and things is basically taking over the native food web.  Then I’ll talk about habitat loss, a phenomena called hysteresis in a dynamic regime change, and how that relates to extinction debt, and then I’ll relate it to, is extinction inevitable, the title of conference.

Bennett smelt_Page_05Dr. Bennett said it’s thinking about it at another level, not necessarily the nuts and bolts of interannual year class success or feeding success or temperature tolerances and things, but at much more of a decadal scale – things that are hard to fight against.  “Here we have this alien food web taking over the native food web.  This map shows the distribution of Egeria.  It’s a few years old so I’m sure it’s changed now, but it seems to me, looking at some of the newer publications, that Egeria is kind of percolating.  It happens in some areas; comes back in some areas, doesn’t come back in others, and you can see the only place it isn’t is on the Sacramento side, or that’s where it least is.”

Bennett smelt_Page_06He presented a graph which is a reconstruction of the trajectory for Egeria of how it took over.  “It’s a pretty straightforward S curve going on there,” he said.  “You can see it kind of flattened out in the mid 2000s, and it’s kind of fluctuating around the level.  Whether in fact that’s a carrying capacity or not is uncertain, but it seems to be doing that.  Once Egeria made this wonderful lawn on these lily pads, we get all the critters that live in lily pads in Arkansas and stuff, and so we see that largemouth bass and pluvial sunfish and regular sunfish and a host of other characters that basically show exponential population growth.  It lags the Egeria by about five or ten years, thereabouts.  And if you look at this in terms of transforming the entire Delta at the Delta scale, that’s pretty quick.  And certainly a lot quicker than a fish like Delta smelt can adjust to.”

Bennett smelt_Page_08Dr. Bennett then reviewed the history of how Delta smelt have used habitat through time, presenting a map of historical habitat use.  “These are stations sampled before the projects were constructed, 1948-49, this paper is often cited but it never really talks about Delta smelt.  The only Delta smelt in there are ‘pond smelt’ in basically numbers in the tables in the back in the appendix. … Even back then, far and away, most of the fish were in the lower Sacramento River in the sampling.  This is the sum of basically all the Delta smelt they caught in the two years of study.  The other thing you see is that they actually caught quite a few in the San Joaquin River.  You can see that that was still really good habitat for them then.”

Bennett smelt_Page_09Sampling in 1963-64 was the first study that gave us a grounding of what was going on with the organisms of the estuary; it didn’t change, it’s pretty much the same thing,” said Dr. Bennett.  “He actually says that he caught practically all of his pond smelt in the lower Sacramento River.  You can see that changes in the winter, they used to go down the San Joaquin, it was pretty easy to envision those fish were looking for places to spawn.”

Bennett smelt_Page_10Then some things happened.  What I’m going to do is describe what happened next in the framework of Alec MacCall’s basin model which he put together for sardines and for pelagic fish.  The whole idea is this:  You have resources that are distributed unevenly throughout our landscape; some places are better than others, depending upon who you are, and so the depth of the basin, the deepest part reflects the best optimal habitat quality for whatever organism you’re dealing with.  So in a regular study, you can see all the habitat seem pretty good. Smelt were pretty much distributed a lot of places, even though they do like the lower Sacramento River.”

Bennett smelt_Page_11He then jumped to the Fall Midwater Trawl after 2002.  “Now what you see is habitat quality overall has dropped tremendously, dropped a lot.  On the fringes where you used to see Delta smelt, you don’t see them anymore.  So this would reflect like stations in the South Delta where you just don’t catch them anymore.”

Bennett smelt_Page_13He displayed the current population line on the graph, noting that it’s low so there’s little connection between habitats; the population may become fragmented or limited in the amount that they can go between different habitats.  Noting that it was highly conceptualized, he showed where on the figure, the Suisun Bay and marsh, the North Delta, and Cache Slough fit in.

So how does this relate to extinction and extinction debt?  “It’s well documented that habitat loss is the single most cause of extinctions, particularly for small bodied organisms, such as the Delta smelt, living right at the edge of their traditional historic ranges,” Dr. Bennett said.  “Then this thing called extinction debt comes in.  It’s a concept that stems from metapopulation theory where you have a lot of subpopulations in little patches across a landscape and they are maintained by birth and death rates within a patch and movement between them, and you can somehow optimize that, and it gives you an idea how well you’re population is doing.”

Where the debt comes in is when you’ve degraded the habitat to such an extent, it’s gone below the ability to maintain persistence for the metapopulation, but they are still hanging in – the fish haven’t caught up to that yet – in other words, you’re dead and you don’t know it,” he said.  “This is lag time from when you actually cross that threshold until you actually disappear.  It turns out if you’re actually close to that margin, and then it goes below, the tail of how long the species maintains is quite long.  Longer than you would think, especially for a fish that has a generation time of one year.”

Bennett smelt_Page_15Dr. Bennett said he’s been studying how the system has changed.  “For the Delta, exports definitely have a problem, but I think they work at different scales, two scales in particular.  I’m going to talk about the decadal scale, basically what has happened since 2000,” he said, presenting what he called a phase plot, with Delta smelt on the x axis and water exports on the y axis; the 2-digit numbers on the graph represent the year.  “There’s been an increasing trend of summer exports since about 2000 because they couldn’t pump any other time of the year …  The first thing you see is that in the cyan, the population of Delta smelt used to be really variable in time, reflecting the changes in the system.  After 2000, which I’ve called out in the red numbers here, reflecting year, you can see they obviously haven’t been highly variable at all, and we all know that.  Flat lined basically … where exports have been very high, smelt abundance has been very low.

Bennett smelt_Page_16Now how do I know that this is a dynamic regime shift?,” Dr. Bennett said.  “It’s because we have these recent years, 2008, 2014, 2015 especially in the summertime where they ramp down pumping effects; this is the time of year that you think you would see something reflect in that and you can see they are absolutely flat-lined.  That means even though we took away the pressure of the water exports, which basically maintained the eastern and southern Delta as a freshwater lake and now we have all those critters that live in a fresh water lake, that was going on, and now it has happened to such an extent such that even when we take away the driver, there is no response in the population at all.

This reflects a sort of bifurcation in a dynamic model,” he continued.  “You cross some threshold, it drops, then you relax the forcing variable and you don’t see any movement up at all … it has to be a dramatic change in the system in the configuration of the habitat, in order to move this fish away from the extinction debt, which seems inevitable.”

Bennett smelt_Page_18The system behavior indicates the regime shift; this shows more evidence for why this is a dynamic regime shift, he said.  “One these indicators of when you may have gone to or you’re about ready to switch to a different state is that is each year to the next becomes increasingly correlated with another, so things slow down.  There’s no change, and we definitely see that in Delta smelt numbers.

Is extinction inevitable and how this relates is that the system has fundamentally changed very rapidly since about 2000, and the fish haven’t caught up to that. “One thing that’s really interesting is that throughout history and even now, the only place you really catch Delta smelt is the same place we caught them in 1948.  So this basin model really has some positive aspects to use in trying to rejuvenate Delta smelt because it gives you an idea of how they basically use the habitat.  That hasn’t changed, which is surprising.  Densities are obviously way down, but where you find them, it’s the same.”

The hysteresis associated with regime change, the ability to not bounce back, reflects this extinction debt,” said Dr. Bennett.  “They are absolutely trapped, and the only way to avoid it is to do something major to change the habitat and get them back so the habitat is above a critical level that can sustain them.  That’s a horrible way to end a talk.  I don’t like it, but these are concepts that are really worthwhile to think about when we have to bring up this miserable word, extinction.”

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DR. RICHARD CONNON: Sublethal Effects of Contaminants Regularly Detected in the Delta: Risks to Smelt

Sublethal effects of contaminants can and do lead to mortality

Richard ConnonBIO: Dr. Richard Connon is an assistant adjunct professor at School of Veterinary Medicine, Department of Anatomy, Physiology and Cell Biology, University of California Davis.  Dr. Richard Connon’s research interest is in the mechanisms behind organisms’ tolerance and adaptations to changing environments. His research focus is on the assessment of mechanistic – cellular/tissue responses to chemical insult, and resulting effects at higher levels of biological organization, such as behavior and reproduction. His interest extends to water quality, both in terms of human consumption and environmental health, with an emphasis on agricultural and urban contaminants; primarily pesticides and pharmaceuticals in the aquatic environment.

Connon smelt_Page_3Dr. Richard Connon then discussed the sublethal effects of contaminants, focusing on the effects on a number of Delta species, as well as Delta smelt itself.  He began by presenting a map by the Department of Public Health that shows the agricultural pesticide applications in the Delta.  He pointed out that these are only the agricultural pesticides; it’s not showing any of the pesticides that are applied directly to the waterways, nor is it showing the urban pesticides.  Also not shown are the pharmaceuticals and personal care products, the industrial chemical waste, the heavy metals, organic compounds, and the legacy contaminants in the Delta.  More recently, there are things like nanoparticles that carry specific heavy metals or other contaminants and plastics.

So there are multiple contaminants to the Delta waters from multiple sources and multiple origins as well,” he said.

Connon smelt_Page_4He then presented a map from the Department of Boating and Waterways showing the herbicides applied directly to the waterways from July of 2015.  “The yellow green boxes are essentially the locations where herbicides have been applied to control water hyacinth,” he said.  “Herbicides affect plants, it can also affect phytoplankton, so you can have an indirect effect by the food chain to fish, but herbicides also have direct effects on fish populations as well.  With herbicides, you have a lot of solvent, you have a lot of carrier contaminants, and you have things that delay the toxicity – inert ingredients from a pesticide application that you would use on your own home, and some of those inert ingredients come with an active ingredient that make it more toxic.”

Connon smelt_Page_5Dr. Connon then presented a slide showing the 75+ citations of research published over the last ten years.  He explained that the left hand side lists some different classes of contaminants and pesticides, as well as samples of Delta water taken from areas in which species have been found; across the top are responses that were measured using biomarkers, morphological changes, reproductive and behavioral end points.  “You could think of the responses towards the right end of the row being the more ecologically relevant end point, and the responses to the left being the more physiologic or mechanistic end point; we actually need to understand the mechanisms that drive those high level responses to the organisms.”

These are the results from tests with multiple Delta species.  The colors in the chart indicate the different modes of action the chemical has on the organism.  “Pesticides and pharmaceuticals, such as contraceptives, anti-depressants, analgesics, anti-inflammatories have been designed to elicit a specific response,” said Dr. Connon.  “When they get into the environment, they affect an organism within that known pathway, that mode of action that they have.  However, there are also these side effects that are essentially undesired effects from having taking pharmaceuticals.

Exposures to contaminants are general stress responses; an organism will indicate that they have actually been exposed to a contaminant with specific detoxification mechanisms or sequestrations.  For example, if exposed to a heavy metal, a protein can actually bind with that heavy metal and make it nontoxic, storing in the protein until the organism can actually dispose of it, Dr. Connon explained.

We’re seeing impacts on the immune system,” said Dr. Connon.  “Exposure to a contaminant can make a fish more susceptible to disease, but the reverse is also true. A diseased fish will be much more susceptible to contaminant exposure as well.”

We’re seeing an effect on osmoregulation; when we expose a fish in freshwater to a particular contaminant, and then transfer that to saltwater, we’re seeing that they are dying, so it’s actually impacting their capacity for osmoregulation,” he said.  “We’re seeing impacts to the nervous system and the muscular system, we’re seeing tissue damage, necrosis, but more importantly we’re seeing effects on growth and development, we’re seeing deformities in fish as the result of contaminant exposures, endocrine disruption so hormonal changes, androgens, estrogens, altered sex ratio, and finally we’re seeing behavioral alterations in the fish.”

The chart shows the results for a number of different species of fish that have been evaluated, the asterisks indicate the studies that have been performed on contaminants and Delta smelt.  Dr. Connon said there were no studies conducted as yet that he knows of on longfin smelt.

Pyrethroid insecticides are one of the most commonly detected insecticides found in the Delta.  “These last few weeks during the storms that we’ve had, we’ve actually measured a consistent flow of about 2 nanograms per liter of bifenthrin,” he said.  “One nanogram per liter bifenthrin is equivalent of 1 drop of pesticide in an Olympic sized swimming pool.  We haven’t done an endocrine disruption study on Delta smelt, but recent studies on the inland silverside has shown a delay in reproduction, a change in sex ratios of the offspring, and one of my grad students has done a multiple generation study and shown that 0.5 nanograms per liter actually causes morphological changes in a third generation of unexposed organisms.”

There are studies on Delta smelt highlighting sublethal impacts; what we’re missing are actual studies that link up or associate the responses of the contaminants with population growth or population decline, so we need more reproductive population studies of the Delta smelt,” he said.  “The studies that have been conducted show that the lower the concentration of pesticides, the more likely they are to act as endocrine disruptors, and that is because it’s not killing the organism, the organism can actually metabolize those pesticides, and in the case something like bifenthrin, it’s the metabolite of the pesticide that actually combine to the estrogen or androgen receptors that actually produce the hormone required.”

So in other words, dilution is not the solution to pollution,” Dr. Connon said.

There have been studies conducted on salmon that have shown that copper affects their behavior by affecting the olfactory system; more studies are being done to investigate the behavior of salmon in response to predators present in the environment.  “We have not done those kinds of studies on Delta smelt; it is something that would be interesting to do to associate the behavior responses that we see.  That particular study is on copper and Delta smelt, and we have seen impacts of contaminants on behavior of Delta smelt itself.”

Connon smelt_Page_6Contaminants alone are not the whole story, said Dr. Connon.  “The toxicity of a chemical will actually vary depending on the habitat and the physiological condition of the organism that’s been affected,” he said.  “The diagram is my attempt to create a three dimensional graph where you have temperature, turbidity, and salinity as three variables.  This is part of the fundamental niche study that we did with Nann Fangue for the Delta smelt, where we established the more optimum environment and delineated the fundamental niche, the maximum tolerance for these three variables.”

If you expose an organism to something within their optimal niche, as is done usually in ecotoxicology – you have an organism, you keep it in the laboratory at the optimum temperature in optimum conditions, the sensitivity of that organism is going to be less than if it were at the perimeter of the niche itself,” said Dr. Connon.  “It’s the breadth of the niche itself that gives the organism the tolerance to those environmental parameters but also to the contaminants itself.”

Connon smelt_Page_7But it’s actually much more complex than that,” he continued.  “What we have going on in the Delta is an interaction of contaminants, environment, and the organism.  The three of them interact with each other; this is known as a disease triad where contaminants actually interact with the environment as well as with the organism, and obviously the organism interacts with the environment as well.”

Contaminants can affect the organism in a direct manner, but also in indirect manners such as through the food web, but the organism itself can actually affect the contaminant as well say, for example, by metabolizing the pesticide and having different effects,” he said.  “We have direct effects, indirect effects, the organism and an interaction, and contaminants themselves are actually affecting and impacting the habitat of the fish.”

Connon smelt_Page_8Dr. Connon then gave his conclusions.  “Essentially contaminants affect organisms of multiple levels of biological organization, from mechanistic to whole organism behavior.  Environmentally relevant concentrations can and do lead to developmental, behavioral, and reproductive effects.  It also depends on the type of contaminants; organisms are not only exposed to single compounds, they are exposed to contaminants as mixtures – that is more true in the Delta than it would be upstream in smaller tributaries.  Mitigation of chemicals and sediment runoff can be achieved.  The contaminants can be managed.”

One thing I want to point out is the sublethal effects can and do lead to mortality,” he continued.  “A lot of people see sublethal effects as ‘oh well, they are still alive, so why should we care,’ and the last thing I want to point out is that we can’t assume that contaminants play a minor role; they play a part of a much bigger role of interactions with the habitat that the organisms live in.”

So with that …

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FRED FEYRER: The role of ocean conditions on longfin smelt in the San Francisco estuary

To fully understand the longfin smelt, we must understand the entirety of the habitat that’s occupied by this fish

Fred FeyrerBIO: Fred Feyrer is a Research Fish Biologist with the U.S. Geological Survey, California Water Science Center. He has studied fishes in the San Francisco Bay-Delta system for over 20 years.  His research focuses on applied ecology, ranging from life history studies of threatened and endangered species to the role of climate on species and communities.  Fred received his B.S. from the University of California, Davis and his M.S. from Sacramento State University.  He is originally from southern California and enjoys fishing and spending time with his family.

Feyrer smelt_Page_04Fred Feyrer’s presentation focused on the role of ocean for longfin smelt.

The eastern Pacific ocean is a really big place,” he began.  “The San Francisco estuary represents the southernmost distribution of the reproducing populations of longfin smelt, so when you take the broader look at the relative size of the habitats that these fish occupy and where they inhabit, how could the ocean not play an important role for longfin smelt, just as it does for other anadromous species such as chinook salmon or steelhead.”

Feyrer smelt_Page_06We have a little bit of data and some knowledge about longfin smelt occupancy in the ocean,” he said.  “We do know that they occupy the ocean; they don’t just stay in the bay and the estuary.”  He presented a graphic of the life cycle of the longfin smelt, noting that they can potentially be spending one to two years or even more in the ocean and marine type habitats in bays.  “This particular life cycle diagram came from a paper written by Joe Merz and colleagues and it’s a pretty good representation of the life cycle and the habitats used by longfin smelt.  The one thing I actually don’t like about it too much is that is sort of makes the impression that all habitats are equal and that the fish is spending equal time in each one of these habitats.”

Feyrer smelt_Page_10Looking at it from the perspective of the amount of time spent in each particular habitat, it’s a substantial amount of time that these fish are spending out in the ocean relative to the estuarine and the freshwater habitats,” he said.  “If you’re talking about an age 3 longfin smelt, now we’re really talking about a substantial portion of the life cycle of this fish being spent in a habitat that we have virtually no knowledge about.  We know almost nothing about what goes on with longfin smelt out in the ocean.”

Feyrer smelt_Page_13Mr. Feyrer then presented a map of the general range of longfin smelt.  “The San Francisco estuary represents the southernmost reproducing population of this particular fish.  The fish range is all the way up to the inlet in Alaska, so that’s a pretty big, broad range, so where do you even start with trying to understand what’s going on with longfin smelt out in the ocean?  We have some pretty good precedents set by our colleagues who study salmon and we have a fairly good body of knowledge and literature about what salmon do in the ocean.  Generally speaking, they cover a pretty general range and distribution, so that’s a really good model to sort of frame our thinking of the roles of the ocean for longfin smelt.”

Feyrer smelt_Page_15If you look at the life history diversity and the timing of which salmonids spend in freshwater habitats, it’s pretty diverse, he said.  “You can put longfin smelt in that same category, being an anadromous or semi-anadromous fish and what you see is that generally speaking, longfin smelt show a pretty similar life history strategy and life history plasticity as say potentially steelhead, where they spend relatively similar amounts of time in inland type of habitats, and have a relatively diverse life history pattern in which they may or may not be moving back and forth between these two habitats, so it’s another good model for us to base some of our longfin smelt inquiries about.”

Feyrer smelt_Page_17So what specifically about the ocean might be important for longfin smelt?  “We know from a lot of work that originally started back with Nate Mantua when he was at the U of Washington about the role of ocean conditions and how important they are for driving salmon returns back into the freshwater habitats.  That is analogous to some work being done locally here, where we have been able to demonstrate the role of ocean conditions and climate variability in the eastern Pacific as drivers of fish abundance and diversity in the San Francisco estuary, so we have a pretty good foundational base that suggests a lot of what goes on in the ocean that is driven by habitat and climate conditions can really be an important player for fishes that utilize the estuary.”

But with longfin smelt, we really don’t know what’s going on with longfin smelt in the ocean because we don’t have a lot of information and a lot of sampling programs that collect longfin smelt and are able to generate useful information and data; however, there are a few examples where we can glean a few things off with longfin smelt occurrence in the ocean, he said.

Feyrer smelt_Page_19One example a study conducted up in the Northwest in the Columbia River plume.  Mr. Feyrer noted that the vertical axis represents abundance measures, and that they are all on the same scale ranging from 0 to 4.  The top row of the chart shows the abundance for longfin smelt, the rest are for a variety of salmonids, including steelhead and chinook salmon.  “Although longfin smelt weren’t found in the ocean every single year of the study, I think what’s really key here is that they were fairly persistent and common in the sampling,” he said.  “Even in some years, longfin smelt are were actually more abundant than the salmonid species including chinook salmon in this study.  So this is a really good example of longfin smelt utilizing the ocean and being potentially really highly locally abundant in some systems in some areas.

Feyrer smelt_Page_20Another example closer to home is the NOAA Fisheries salmon surveys, Mr. Feyrer said, noting that the map on the left shows some of the local stations that the survey samples at each time they do their surveys.  “You can see there’s a pretty broad range here,” he said.  “In addition to salmon, they examined all the other fish they’ve collected, and the map on the right represents the sample stations where they’ve actually observed longfin smelt in the ocean during their surveys.  They actually don’t get a lot of longfin smelt in their particular surveys, but when they do get them, they tend to be relatively close to shore and in relatively shallow habitats, relatively speaking, compared to what they hit more broadly.  Over the course from 1998 to 2015 where they’ve observed the fish has generally been right there in the Gulf of the Farallons.”

Feyrer smelt_Page_21He then presented two graphs derived from the California Department of Fish and Wildlife’s Bay Study survey’s Otter Trawl dataset from 1981 to about 2012, explaining that they are simply histograms of the occurrence of longfin smelt in samples under particular conditions.  “These represent the counts of samples in which longfin smelt were present across temperature and salinity gradients.  This is basically to demonstrate that longfin smelt do occupy environmental conditions in terms of salinity that exist out in the Pacific ocean, and then also temperature.

In terms of this range of temperature for longfin smelt, Mr. Feyrer noted that there is a substantial amount of both seasonal and interannual variability in sea surface temperatures off the coast. He presented a map of temperatures from two example years.  “Here are two example years to make the point of the importance and the role of ocean conditions, especially sea surface temperatures.  A relatively cool year in 2008 versus a relatively warm year in 2015.  Longfin smelt generally like the range of temperatures from approximately 8 to about 14 degrees … so what you see here is you have a pretty dramatically different coastal conditions here that most certainly drive the abundance and the distribution of not just longfin smelt but all critters in the ocean.”

We have pretty good data, generally speaking, in the scientific literature demonstrating shifts in oceanic sea surface temperatures and how that drives the distribution and abundance of fishes on broader scales, and undoubtedly, that’s an important factor here for longfin smelt,” he said.  “There’s potentially a huge swath of habitat for longfin smelt to occupy in conditions that resemble this particular year, but then for example, this last year, that habitat is really constricted and constrained.  You have these really small patches of suitable habitat that lie along the coast; that warm blob that we had really did a number on potential habitat.”

Feyrer smelt_Page_23We also have to consider the effects of the San Francisco Bay estuary plume, said Mr. Feyrer.  “That doesn’t really come to mind a lot of times, but it’s really an important factor because it really is important in driving the local habitat conditions,” he said.  “John Largier at UC Davis has done some really great work that has demonstrated the physical processes associated with the plume.  Generally what happens is that during periods of relaxed upwelling and low winds, the plume tends to kind of come over the sill outside the Golden Gate, and it tends to maintain position up on the surface and has the tendency to kind of move northward; the opposite condition of that is when we’ve got pretty strong winds and strong upwelling; then that plume tends to kind of move down offshore and to the south.  So the interaction between sea surface temperatures, the conditions driven by the San Francisco Bay estuary plume, and other factors have to be really important in driving the local habitat conditions for longfin smelt and other species as well.

Feyrer smelt_Page_24I would argue that if you want to understand this, you really have to understand the entirety of the habitat that’s occupied by this fish,” he said.  “When you take this graph, you have to actually decrease this x axis by four orders of magnitude to actually be able to visibly see how many longfin smelt we’re getting in the fall.  That’s not just a flow effect.  We haven’t lost four orders of magnitude of flow in the estuary.  Certainly flow is important and it’s an important driver of juvenile abundance and various ecological processes in the estuary, but it’s a big deal, so what some colleagues and I have been really pushing for is to set up a coastal research program for longfin smelt to really try to understand what’s going on with the fish in these marine habitats.”

There’s so much we need to do and so much to learn,” he said.  “We are eons behind our salmon colleagues in terms of our knowledge of what this particular anadromous fish does in the ocean.  We really need to answer some fundamental science questions.  Things as simple as where are the fish distributed and what type of habitat conditions do they like in the ocean.  We can look at stock composition up and down the coast and we’ll know whether or not we’re getting Columbia River down fish down here or vice versa.  Simple things such as feeding, growth, condition, and mortality.  We have no knowledge on that but we know from the work that our colleague that work on salmon have done that these are really important drivers that really fundamentally change the stock structure and the population ecology of salmonids returning back to inland environments.”

Feyrer smelt_Page_02Mr. Feyrer then gave his summary points.  “First, in terms of ocean occupancy, longfin smelt are very widely distributed along the eastern-northeastern coast of the Pacific ocean and oftentimes can be locally abundant to the point that where up in the Columbia River area, they’ve been more abundant than salmon in some years.  The role of ecological processes and what those do to drive the ecological processes and dynamics of longfin smelt in the ocean and how these conditions drive physical habitat and food webs that will be important for longfin smelt.  Then obviously we have a lot of research needs because all of this is pretty much just arm waving at this point until we actually get some sound fundamental scientific data.”

Thank you.”

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SWEE TEH: A 3-Year Study of Environmental Stress on Health of Endangered Delta Smelt

Using biomarkers to differentiate the regional differences within the health of the smelt

Swee TehBIO:  Swee Teh is the Director of the Aquatic Health Program in the School of Veterinary Medicine at UC-Davis. He has been researching aquatic health, including the effects and interactions of physiochemical and contaminant (toxicant, carcinogen, and endocrine disruptor) stressors on aquatic organisms and ecosystems for >20 years. He is also the director of the Aquatic Toxicology Laboratory; a State Certified Laboratory engaged in monitoring and assessing ambient water quality and aquatic ecosystem health.

Swee Teh noted that the methods for the three-year study are published in the aquatic toxicology journal; in this presentation, he would be just discussing the results.

A 3-Year Study Swee Teh_Page_05In 2005, Mr. Teh was funded by the Interagency Ecological Program in 2005 to do a histopathology study on spring Kodiak Trawl Delta smelt.  ”Based on that study, here is the region that we analyzed, and we found that the fish that at the Central Delta have less lesions and back then, I didn’t know what that meant.  I thought maybe that region is good for the Delta smelt,” he said.

Later in the summer, they published a paper on Summer Townet data for Delta smelt that looked at multiple biomarkers to try to answer more questions about what happened to Delta smelt, and what was causing the decrease in their health.

In 2005, we thought the Central Delta was the place where smelt are the healthiest, and in the Summer Townet Study, we showed that the Suisun Marsh has better conditions and more foraging success than any other region; Suisun Bay was not, mainly because of food limitation,” said Mr. Teh. “We also found three regions, in the Sacramento, Upper Delta, Deep Water Ship Channel, and the Cache Slough and the confluence, we found fish have a little bit higher lesion score.

We wanted to test the hypothesis that the summer health of juvenile fish helps for their persistence into the fall, so we designed a study of the Fall Midwater Trawl integrating biomarkers of Delta Smelt health at multiple levels of biological organization in the fall of 2011, 2012, and 2013, and assessed regional differences in summer and fall.

I looked at three indicators of general condition: the length-weight ratio, liver weight ratio, and gonad to body weight ratio,” said Mr. Teh.  “We also looked at the short-term growth, reserve energy in the fish, and looked for the fish consumption status.  Finally we tried to relate this to environment and contaminant stressors using histopathology.”

A 3-Year Study Swee Teh_Page_09He noted that the x axis is the lesion score and the y axis is the region and the number of fish analyzed.  “As you can see, the condition and hepatosomatic index indicated that Suisun Bay and confluence region were similar to our Summer Townet Study were decreasing.”

A 3-Year Study Swee Teh_Page_10We found that Suisun Marsh and the Sacramento River region at the confluence where Rio Vista is, the fish there have good conditions,” he said.  “In the Suisun Marsh region and the Sacramento River region, they had a better hepatosomatic index, and what is more important thing is fish in the Sacramento region here have better gonadosomatic index. What does that mean?

A 3-Year Study Swee Teh_Page_11Then we looked at the next biomarker indicator we had, the RNA/DNA ratio which show what are their feeding success,” he said.  “If there are days they are not feeding, what happens to their growth, so we look at the RNA/DNA ratio and liver glycogen depletion.  In this case, the higher the bar, the worse it is, as opposed to the rest of the biomarkers that I have where lower means worse.”

A 3-Year Study Swee Teh_Page_12So for example, in the Suisun Bay area, we are seeing low RNA/DNA ratio, lower reserve energy, but high glycogen depletion, which means the low liver glycogen in the body.  Similarly, we see the same thing in Suisun Bay on the Summer Townet juvenile fish, and this indicated that Suisun Bay had a lower growth rate and reserve energy and have higher glycogen depletion.”

A 3-Year Study Swee Teh_Page_13 Next, they looked at the RNA/DNA, the triglycerides, and glycogen depletion, and compared that to the hepatosomatic index and the gonadosomatic index.  “Earlier I showed that fish in the Sacramento River region have better gonadosomatic index, meaning they have higher sexual maturation,” said Mr. Teh.  “Because of the increased sexual maturity, they require a lot of energy, so reduced growth, reduced energy reserve, and high glycogen depletion are most likely related to sexual maturation.”

A 3-Year Study Swee Teh_Page_15Then they looked at the indicators of food consumption.  “In the Suisun Bay, they have low food foraging, and then when you compare this with the RNA/DNA and triglycerides, it indicates that when you have low feeding success, low reserve energy, and low growth rate.”

A 3-Year Study Swee Teh_Page_16Similarly when we compared this to the Summer Townet Study, Suisun Bay turned out again to be the place where food limitation is an issue.”

A 3-Year Study Swee Teh_Page_18Finally we looked at the histopathology which is the indicator of maybe an environmental or contaminant stressor,” he said.  “When I say environmental stressor, it can be temperature, salinity, or it can be a toxicant, so here we found that it’s more similar to the Summer Townet Study; increased lesions were seen in all the regions.  But here we also saw increased lesions in Suisun Marsh.  Keep in mind, this is fish growing in the Delta seeing the complex environment and I do not expect them to be more healthy all the time, so it’s not surprising to me that I saw some lesions in the fish from the Suisun Marsh region.”

A 3-Year Study Swee Teh_Page_19Mr. Teh said that every year when they sample fish, there is always some outlier – tome fish that is significantly bigger than the same fish caught in the same month.  “So we asked the question, is this fish that would be the second year spawner?  So we looked at the health condition of it,” he said.  “The fish on the left in the slide was collected on September 13 during 2011.  It was a good cold wet year.  The fish had good glycogen in the liver, which is more healthy, and indeed this fish, if we didn’t catch it, would likely have spawned in Honker Bay within a week or two.  In September, under good conditions, they may spawn.”

The fish in the middle of the slide was collected in June of 2014.  “This fish was about 82 millimeters – that’s giant fish,” he said.  “We see more severe lipidosous and sinusoidal congestion may indicate some contaminant exposure.  In addition, we looked at the gonads, the ovaries of the fish, you see they have severe Oocyte atresia, which indicates the conditions are not adequate for them to reproduce, which may be correct for fish that have go through the first of two spawnings during January to May.  Now they may be just trying to be able to survive to the next year … preserving energy may help them to survive to next year.

The fish on the right of the slide was caught in September of 2014.  It had aneurysms and thrombosis.“I have never seen this combination before, I have looked at thousands of smelt, I’m not kidding, thousands of smelt, and I did not see lesions like this before,” he said.  “Aneurysm is a sign of acute toxicity.  If fish see in the wild the contaminant, all stress, the first signs of an effect is aneurysm.  But thrombosis is the more chronic effect, indicating that this fish have seen and have been around for more than at least two months. … thrombosis is more severe in this fish, which may survive until next year if they can do it.”

I think that the condition in 2014 were really, really bad for the Delta smelt as compared to 2011,” he said.  “This maybe a small percentage of the fish that help to recruit the Delta smelt.  The second year spawner, which always have larger eggs, more quality and fecundity.

A 3-Year Study Swee Teh_Page_20So in summary, my hypothesis is that Suisun Bay has poor conditions and food limitation,” said Mr. Teh.  “The Suisun Marsh has good conditions for the fish and they have greater foraging success as opposed to Deep Water Ship Channel, where contaminants might be an issue causing the higher lesion score.

The Sacramento River has better conditions and more sexually mature fish,” he said.  “Earlier I said that the Central Delta has the more healthier fish.  It’s the same thing for the Sacramento River.  I think that when the Delta smelt is healthy enough and strong enough, they will start moving up, so they will start migrating up the corridor here.  The same fish are more healthy and more sexually mature answers the question I see in 2005 where smelt in the Central Delta have less lesion score, because they were more robust and were healthier.

So in conclusion, using biomarkers helps us to really differentiate the regional differences within the health of the smelt; it also showed that Fall Midwater Trawl result is persistent, it corresponded well with the Summer Townet Study, and biomarkers at multiple levels of biological organization are essential to resolve or at least have a closer insight into environmental problems.”

A 3-Year Study Swee Teh_Page_02Areas of future study include looking at the differences in the Spring Kodiak Trawl.  “We would like to see the persistence from fall to spring, how that eventually affected their fecundity and reproduction and spawning effect, and also try to evaluate biomarkers for 2014 through 2016.”

Mr. Teh said if he has the chance to do more studies with biomarkers, he would want to add one or two resident species that are collected with the Delta smelt.  “Adding one or two resident species during our monitoring will help to answer the question whether the smelt in the same location or region are seeing something that affected the resident fish in the region.”

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DR. LOUISE CONRAD: Drought: The final straw for Delta smelt?

A look at what the recent exceptional drought conditions in the Delta have been affecting the Delta smelt

BIO: Dr. Louise Conrad is a Program Manager for applied research and data synthesis for the Department of Water Resources. Louise received a Bachelor of Science in Environmental Biology and Management and a Ph.D in Animal Behavior from UC Davis. Her favorite jobs have been conducting fish and frog surveys in high alpine lakes, managing a Coho Salmon captive broodstock program in the Russian River watershed, and electrofishing for Largemouth Bass in the Delta.

Dr. Louise Conrad has been leading a large team effort within the Interagency Ecological Program to synthesize effects of drought on the ecosystem.  She said she would be going over the results of the synthesis effort, which really was to look at the whole ecosystem, and then drill it down to the how the drought is manifesting itself in Delta smelt.  She also noted that the studies have not addressed the longfin smelt at this time.

Conrad smelt slides_Page_02What we were really trying to do is get a synoptic few of what happens to the estuary in a drought, and we were really interested in what’s happening in the current estuary that we have,” she said.  “The estuary has changed over recent decades, so we really looked at 2003 through 2015, which is after the Pelagic Organism Decline and is a time series that includes a lot of hydrologic variability.  2011 and 2006 were wet years, 2007-09 were also considered drought years.”

The team studied many different data types, mainly water quality and food web data, such as chlorophyll, and copepods, cladocera, high level consumers like clams and invasive fish, as well as Delta smelt responses.  “This was our effort to put all this together in a single analysis to understand what the effect of drought was,” she said.

Their analysis was structured around the Delta smelt conceptual model, drawing on a seasonal approach and taking the list of variables largely from the model.  “These are factors that we know are important to Delta smelt, and they are going to be important responses from the ecosystem that are relevant to management and to ecology, so this was our starting piece,” Dr. Conrad said.

Conrad smelt slides_Page_04Essentially we did a multivariate analysis for each of the seasons,” she said.  “This is a visual of what the estuary looks like in the drought from a salinity perspective.  The green area that you see is all relatively high salinity or greater than 6 ppt and the shades of blue are your low salinity zone areas, so in the drought, you had the low salinity zone pretty far upstream in the Rio Vista and Big Break area.”

The major results from our synthesis work were that in drought, you have increased nitrogen concentrations,” she said.  “We looked at ammonia and nitrate/nitrite and those all had elevated concentrations in drought periods compared to wetter periods.  Microcystis especially recently was very prevalent.  Aquatic weeds are doing very, very well in these conditions.  There’s water hyacinth, but we’ve seen an uptick in submerged vegetation and even water primrose has as much coverage as water hyacinth now.  So they are doing quite well.”

Largemouth bass are marching on a steady incline through the time series that we looked at and particularly are doing very well now; they are at higher densities than we’ve ever seen and silversides also increasing as well,” she added.  “Zooplankton, the copepods and the cladocera that we looked at in winter, spring, and summer periods are at lower densities.  So that’s a picture of what the drought looks like for the estuary now.”

Conrad smelt slides_Page_05She then turned to the Delta smelt, presenting a slide showing their predictions for what the team thought would mean for the Delta smelt.  “These responses – the abundance, the distribution, the growth, and the fecundity are all specifically items that come from our conceptual model of this is what we want to know.  Through the seasons we’re predicting abundance is going to go down because of this poor conditions; distribution should go higher up into the estuary because we think they will follow the low salinity zone, lower growth with lower food supply, microcystis exposure, and toxin exposure, then we’ll have reduced growth and that will result in reduced fecundity.”

Conrad smelt slides_Page_06Dr. Conrad then turned to focus on specifically summer growth, distribution and fecundity.  She presented a time series of fish caught in the Summer Townet Survey from 2003 through 2015.  “This is the range of growth; our estimated growth rate from each of these years is based on water temperature at Rio Vista.  A subset of these fish had otoliths analyzed from them and the hatch dates corresponded real well to the temperature at Rio Vista where we think Delta smelt hatch, so it’s a range that you can see.”

The drought years are highlighted in orange.  “In this most recent drought, we have fairly poor growth rates, but when you look at the other drought periods too, it’s not really a consistent response that we have poor growth in drought – for example, 2009 was a dry year and that’s some of our better growth in this time series.”

It’s important to look at this in the context of water temperature so that top graph is showing you the average water temperature where these fish were caught,” she said. “It is true that this drought is exceptionally warm, dry conditions, but that hasn’t in this time series anyway always been the case.  2008-09 were relatively cool periods and you see a little bit higher growth rates.”

Dr. Conrad also pointed out that 2006 was a wet year.  “Even in the summer, there was higher outflow happening at that period, and yet we see some of our poorest growth rates,” she said.  “It turns out it was also fairly warm, so it’s not a clear cut picture.  It’s complicated.  We have this result that when we have drought and lower flow, we have reduced food supply, but if it’s warm, it doesn’t mean that the Delta smelt are going to be able to respond to increased food.  We see that in 2006.”

Conrad smelt slides_Page_07So if you’re a Delta smelt and you are in this estuary and the low salinity zone is pretty far upstream, where are you going to put yourself?  What do you do?  “This is your home, it’s the only home you’ve got, so you gotta be here,” she said.  “You could be in the low salinity zone, that’s one option; stay put, there’s reduced food supply, there’s a lot of weeds, there’s microcystis, and sometimes it’s really warm, so what are your other options? You could go down to the basement of your home where it’s a little bit cooler maybe, higher salinity, but I think Nann Fangue’s work has shown us that they are physiologically able to handle this.  At 6 ppts, that sounds like it might be tenable.  However if you’ve read Bruce Hammock’s paper, he showed that if you’re in Suisun Bay, those fish had trouble finding food.”

What else could you do?  You could go up to your attic and maybe find some refugia up there, but it’s going to be warm in your attic, so maybe there’s a little refugia that you could find where there’s cool water coming from somewhere.”

So what do the Delta smelt do? Dr. Conrad looked at the Summer Townet Data, acknowledging it is a really simplistic look.  “I just divided the data between these three salinity zones that we just talked about,” she said.  “The graph on your left is showing you the water temperature, and as we would expect, it is warmer up in the fresher more upstream parts of the estuary.  If you look at that and remember back to Nann’s talk this morning, above 24 to 25 degrees, it starts getting pretty stressful for fish, but that’s actually where the fish are.  Over 50% of our Summer Townet fish are up in that freshwater area, about 30% are in the low salinity zone, and less than 20% are being caught in the higher salinity but cooler areas.  The upper freshwater area is where apparently they want to be; there’s food up there.”

Conrad smelt slides_Page_09Dr. Conrad then presented data she received from Jim Hobbs recently.  “This is a map of Summer Townet stations and the graph that you see there is comparing growth rates that he’s been able to look at from otoliths from 2010 through 2014,” she said.  “2012 through 2014 were really drought years, and the red bars are showing you the juvenile growth rates from fish caught in the Yolo Bypass.  There’s a screw trap and there’s beach seining and they do catch some Delta smelt; they’ve been increasingly catching more Delta smelt there.  The blue bars are showing you the growth rate from the fish caught in the rest of the Summer Townet Survey.”

We’re seeing some evidence of a positive response in the northern part of the Delta where they are having a little bit better growth in the Yolo Bypass,” she said.  “What is it?  I’m not sure we know, but that’s something that we can look into more.  Are there more refugia somewhere up there that we’re not measuring because our monitoring results suggested it was hotter, but maybe where these smelt are really spending most of their time, they found something good.  We can hope.”

Conrad smelt slides_Page_10Bruce Hammock from Swee Teh’s lab also shared with me this figure of how fecundity and egg quality has changed over a three year period.  These are fish that were caught in the Spring Kodiak Trawl, so these are adult fish.  For all three of these metrics: the number of eggs, the weight of the eggs, and the size of the eggs, in 2013 and 2014, there was a significant step down, so it does look like there’s maybe some areas where there’s better growth but that isn’t always in drought translating to increased fecundity.  This is going to have a positive feedback loop to the abundance, for if you don’t have a lot of fecundity,  if you don’t have a lot of eggs, you’re not going to make a lot more fish.”

Conrad smelt slides_Page_11She then returned to their predictions.  “Previous talks have shown us that abundance is down in the drought; as for distribution in the summer roughly here, I shaded that check mark, yes it’s up, but we don’t have a lot of comparison data because those northernmost stations in the Summer Townet didn’t start until 2011.  So it may be that they always used that, but they are located pretty far upstream.  And fecundity is reduced.  For growth rate, it looks like it is down in this current drought, but I think there’s an important caveat here that temperature and location of where the fish are is really important.  So a lot of nuances that are still available for us to look at.”

Conrad smelt slides_Page_12Dr. Conrad then posited the question, is drought the final straw?  “I think everybody may be thinking this in the back of your mind, this is not the first drought for Delta smelt.  They’ve done this before, right?  Well, maybe they have, but not necessarily like this.  Our estuary is dramatically different.  We don’t have the wetland habitats that we used to have in the early 1800s;  there used to be a lot of habitat diversity.  So we’ve eliminated the options for Delta smelt for where can they really go, and on top of eliminating their different habitats, we’re adding some microcystis and we’re adding aquatic weeds and predators and contaminants, and all the other stuff.”

Conrad smelt slides_Page_13I’m not going to say it’s the final straw, but we are really throwing the gauntlet down for them.  We’re seeing some signs in this data that they are looking for a place where they can deal with this situation of drought.  There may be a few places, but they could use some more,” she concluded.

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