STATE OF ESTUARY: Standing too close to the elephant: addressing scales in restoration and fisheries conservation

Dr. Rachel Johnson discusses the interconnectedness of the San Francisco’s freshwater, estuarine, and marine systems

The San Francisco Estuary is an important habitat for native fishes at different life stages. In order to understand the important role it provides for growth, survival, and reproductive success of native species, it is critical to explore the science and policies of the estuary at broad and finer spatial and temporal scales. The issue of scale is fundamental to the ecology and management investments for resident and migratory species, and discrepancies in scientific understanding can often be attributed to differences in these scales.

Dr. Rachel Johnson is a research biologist with the NOAA’s National Marine Fisheries Service and UC Davis with over 15 years’ experience working on various aspects of conservation and fisheries biology and its application to resource management in California. In this presentation from the 2019 State of the Estuary conference, Dr. Johnson discussed the importance of developing a holistic framework among aquatic ecosystems and management authorities.

What I am going to be talking about is what it means to stand to close to an elephant, and the consequences of not considering the big picture when we think about the San Francisco Estuary,” she said.  “I’m going to be sharing two stories from my own research that I think really highlight the interconnectedness of our biological systems between the freshwater, estuarine, and marine systems, and how management actions that we can take in any one of those aquatic ecosystems influences one another.

She began with the parable of the eight blind monks and the elephant, who having never encountered an elephant, each began to feel different parts of the animal.  The monk closest to the trunk was convinced it was a snake; the monk feeling the tusk was certain it was a spear, and so on.  And rather then recognizing that each one of them was touching one part of a larger hole, they began to discount each other.  And so the parable reads, ‘These men of Indistan disputed long and loud, each in his own opinion exceeding stiff and strong, though each was partly in the right and all were in the wrong.’

I share this because we scientists are not immune to standing too close to the elephant, and in some cases, it could be due to the fact that we have more and more refined tools to look at more and more detail, and so it becomes increasingly hard to step back,” Dr. Johnson said, noting that the monks in the picture on the slide obtained from a Google search all have lab coats on.  “Apparently we are often thought of as standing too close to the elephant.”

She recalled how in a conversation with Felicia Marcus (former Chair of the State Water Board), she asked how they can produce science that decision makers like her could really use, and Felicia answered, ‘You scientists, you get so passionate and in love with trying to understand what you’re trying to understand, that sometimes it’s really hard for you to step back and see what we decision makers need to know.’

I take that to heart,” said Dr. Johnson.  “I think it’s because we are passionate people and at the same time, I think that we as scientists have tools to really step back and work with decision makers, stakeholders, and really try to put the pieces together of the San Francisco Estuary.

In 2010, William Schlesinger wrote of the need for translational ecology in an op-ed for the Journal Science noting that ecologists could be a bit myopic: ”Today’s environmental scientists have a powerful array of tools and techniques to measure and monitor the environment, and to interpret vast and diverse data.  Yet, unless the discoveries of ecological science are rapidly translated into meaningful actions, they will remain quietly archived while the biosphere degrades.

Since then, a definition of translational ecology has evolved:  ‘The intentional approach in which ecologists, stakeholders, and decision makers work collaboratively to develop and deliver ecological research that ideally results in improved environmental decision making.’

She presented a slide with a conceptual model developed by Carolyn Enquist which has the information generators on the left, information users on the right, and in the middle, those who have the important role of being able to take the research and information and to align the science that needs to be done so smarter and smarter decisions collectively are made as we move forward.

To highlight the connection between the biology and the decision making that we have in our systems and their interdependency, Dr. Johnson had two science stories.


The first story was about contaminants and a number of deformed Sacramento splittail.  One of the tools used in the lab to look for answers are the ear bones (called otoliths) which are like tree rings which record the diet of the fish and information about the waters they are swimming through which includes the contaminants they were exposed to.

The slide on the upper right is a dose response curve.  At the lower end of the curve, contaminants can influence individuals and have meaningful impacts at the molecular levels.  At the top end of the curve, there are the environmental disasters and the contaminants in the environment that have big ecosystem effects and cause large die offs.

The area in the middle is really here is really the hardest part for us to understand in aquatic ecosystems,” said Dr. Johnson.  “It’s because a lot of contaminants are fluctuating at low levels in the environment and they might be having direct or indirect mortality in organisms, but it’s very difficult to monitor and to visualize and see if it’s occurring.”

The story of the Sacramento splittail is about selenium, which is the ‘Goldilocks’ of elements because we need it nutritionally but at low levels, but it’s toxic at high levels.

Selenium is a naturally-occurring element found in soils and in crude oil.  However, the problem is that human activities can increase the level of selenium in the environment; agriculture, mining, oil refineries, and coal-fired electricity all of are all important human activities that can concentrate selenium in the environment.

It’s possible to be deficient; cows may need to have selenium added to their diet in some areas with selenium-deficient soils.  On the other end, if selenium is elevated in the environment, there can be deformities in fish and wildlife.

There are two point sources for selenium coming into the San Francisco Bay: one pathway is through the oil refineries around the Bay, and the other from irrigated lands in the San Joaquin have elevated levels of selenium in the soils that, due to the way that the water circulates, it increases and accumulates the selenium that then flows into the Bay.

There are a number of fish that live in the San Francisco Estuary: the Delta smelt, multiple runs of salmon, and many others.  One of those is the Sacramento splittail which is only found in the estuary.  In 1999, the USFWS listed Sacramento splittail as threatened; that decision was vacated in 2003.  The splittail are a minnow that live for about seven years.  The splittail use floodplains for spawning and rearing; in the spring when the hydrograph recedes, the juveniles come into the estuary.

Some colleagues at UC Davis were doing a physiology study on splittail, and they had collected a number of them.  They were using a new underwater camera and noticed there were a lot of splittail that had spinal deformities (marked by red dots on the slide on the lower left).

It’s actually rare to actually see deformed animals in nature because usually something eats them, and so we wanted to take this opportunity to try and diagnose why it is that we had so many of these fish that had these deformities,” said Dr. Johnson.

The fish were then x-rayed and three different kinds of spinal deformities were found that are consistent with selenium toxicity.  They also examined the otoliths (earbones), each of which has a band laid down daily (similar to tree rings) that is a record of the age and what they have been exposed to in their diets.

The slide on the left shows the conceptual model.   Selenium is bioaccumulated in the invasive clams, and splittail like to eat these clams; females can sequester the selenium in their ovaries which then gets transferred into the yolk of the larvae.  So the juveniles could be getting selenium through the maternal transfer, which would be evidenced in the otoliths in the very center.  The alternative pathway is that when the juveniles were born in the San Joaquin, they were feeding on this elevated selenium in the food web, and then they would get these spinal deformities and that would be seen in the otoliths as outside of the maternal influence.

They took the otoliths to Cornell University which had equipment capable of measuring selenium concentrations, and the results are shown at the left.  The red areas show elevated selenium and for all of the fish analyzed, they all showed a haloing effect outside of the core which is suggestive of the juveniles feeding on the elevated food web in the San Joaquin.  However, some of the individuals had elevated levels in the core.

Dr. Johnson then presented a chart of population means with the age on the x-axis and the selenium concentration on the y axis.  “These are the population means for that group, and it’s higher than these treatment groups which are these fish that were reared in captivity their entire lives or fish collected in the Bay that didn’t have spinal deformities,” she said.  “What we found was that yes, that food likely had an impact from the juveniles directly eating it, but they are all elevated from their moms.

What we think is going on is that there is an interaction between these two,” Dr. Johnson continued.  “We think that these individuals that have these spinal deformities got some contribution from mom that brought their body burdens up high enough so that when they were feeding on this elevated food web in the San Joaquin, they got the double-whammy.”

Implications for management

What that means is when we think about coming up with our protective thresholds in our aquatic ecosystems, we need to take into consideration protected levels, because organisms might be moving among water bodies that have different levels, but it might be the interaction and the accumulation that they might be getting in these different water bodies that we also need to be protective of,” Dr. Johnson said.

The fact that we have these deformed fish in nature, that they were just caught and observed in nature suggests that our water bodies still remain impaired, even though a lot of hard work is being done to reduce those levels in the environment,” she continued.  “Lastly, those earbones are really a powerful tool to be able to track the diaries of fish that are being exposed to contaminants on a sublethal level.”


The second story is one about the interconnectedness of the habitats and management actions.  With respect to restoration projects to benefit salmon in the estuary, the success of the restoration effort could potentially be influenced by the number of fish are harvested for food and how many are allowed to return to spawn, as well as the flows that are provided for the salmon in the rivers, Dr. Johnson said.

She began by recounting how she attended a Collaborative Adaptive Management Team workshop where the key question being discussed was what the role of the Delta was for juvenile salmon.

This is a topic I am deeply passionate about,” she said.  “They had brought the fish biologists together and they asked, what part of the Bay and Delta and estuary do the baby salmon use?  And I have no idea what part of the Delta they use.  I know the Delta’s important, but I felt a little bit as an agency scientists with a sharpie marker, like sharpie gate, I was literally circling this map, but I had no idea where these baby salmon might find to be important habitat, but other smarter people do.”

We know these baby salmon leave their natal rivers when they are very small, too small to tag and too small to get to the ocean on their own, so they need to rear somewhere else when they are leaving their tributaries.  A recent study of otoliths (or earbones) suggested that in the San Joaquin, up to 25% of the adults that returned used the Delta as rearing habitats.  The graph on the lower right of the slide shows adults that returned to the lower American river; the light blue portion is the time spent rearing in the Delta.

Everywhere we looked, we see that the Delta is an important place, not just for transiting for salmon, but for rearing for salmon,” said Dr. Johnson.  “And work out of our labs suggests that even endangered winter run chinook salmon that enter the Delta pretty large, spend a considerable amount of time rearing in the Delta before they are sea ready.”

Dr. Johnson knew that the Delta was important, but she didn’t know what part of the geography or which local projects are needed for rearing habitat.  What science is needed to know which habitats might be important for them?

Dr. Stuart Munsch, a colleague, was analyzing monitoring data collected through the beach seining effort on the Sacramento, the Delta, and the Bay, looking at small-sized fish from December through May.  He was trying to understand the distribution and abundance of salmon as they are using these different habitats.  In order to understand which of the fish might be using restored sites in the Delta, they needed to know how many fish were entering the Delta in a given year.

The graph is a stock recruit curve; the number of spawners is on the x axis and the number of babies produced is on the y index.

What it shows is if you have about 200,000 adults, it produces about this many babies, but if you have a lot more adults spawning, you’re not going to get a lot more babies,” Dr. Johnson explained.  “If you have lower flows for the same number of adults, you have a fewer number of babies that are produced that enter the Delta.  When you have high flows, we can actually produce a lot more babies as a function of flow for the same number of adults, and this difference is the potential that we have in our salmon populations to make more babies that we can eat in the ocean and that our habitats can provide.”

She presented a slide (lower, left) showing the data underlying the graph.  “A lot of these are skewed here to the smaller number of spawners over here on the left side of the graph, and that’s not by accident,” she said.

From a harvest management perspective, this is what we’re targeting in terms of the number of fish that we want to return to our rivers; there’s about 122,000 individuals returning,” Dr. Johnson said.  “We’re targeting this number of adults to come back and spawn which produces this number of babies, and yet if we allowed more fish to return to our rivers to spawn and we provided them with actual flow support, we could actually have so much potential in what our salmon could produce.”

Researchers then took that information and, looking at the Eco Restore sites, they considered the probability that juvenile salmon will use these sites.  The white line on the graphs is the 50% probability that fish will use that restoration site.  She explained that there is a number of spawning adults and flow, and there is a flow threshold and a spawning adults threshold, so you need to be able to have a certain number of adults and your flow needs to be above this threshold to get 50% of those fish to be occupying individual sites in the Delta.

Dr. Johnson then gave the implications.  “In restored sites that are closer to the Sacramento River, you need fewer adults and lower flow to get more juveniles using that restored site; if you have sites that are really far away from the Sacramento River or very far to the ocean, fewer juvenile salmon are predicted to use those habitats,” she said.  “So what this means is if you’re a practitioner working in these systems, this gives you a framework to try to figure out if you build it, will they come, and it turns out that if you build it, they will come if these other conditions and these other management tools are in place.”

Implications for management …

It turns out that our current escapement goals appear to limit natural production, and that flows are really important to be able to provide a threshold where juvenile salmon will actually use restored habitats that we’re actively managing for salmon,” she said.  “We need to be cautious about trading in flow for restoration for the very interconnected nature that I just shared with you.


In order to have one estuary and one science, we need to look for the connections across processes and across disciplines and geography,” Dr. Johnson said.  “I ask you, what piece of the estuary puzzle are you holding?  And who do you need to work with to plug it in to the jigsaw puzzle and figure out the story that the estuary has to tell?  I encourage you all to work across boundaries, work with scientists, include end users and decision makers on your teams to help try to put all the pieces of the San Francisco estuary together.

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