BROWN BAG SEMINAR: From Measurements, Models and Maps to Management

The USGS and the Delta Stewardship Council are recruiting the next Delta Lead Scientist who is appointed by the Council based on a recommendation from the Delta Independent Science Board. As part of the process, each candidate was invited to give a brown bag seminar presentation of their research and experience, as well as their vision for the Delta Science Program. Ultimately another candidate was chosen,but here is Dr. Lisamarie Windham-Myers presentation on mercury and carbon sequestration in the Delta.


In the Delta, flows are pretty much the driving issues for decisions, but Dr. Windham-Myers noted that the way water flows through landscapes has a functional aspect to it.  “The way water flows through landscapes affects all the biogeochemistry happening on them and one of the big ones is water quality,” she said.

The graphic on the slide shows the terrestrial-aquatic interface landscapes across the Delta.  “We have choices about where to emphasize putting some of these or encouraging certain conditions and or not, and the implications of all those decisions,” she said.  “It’s thinking about how water interacts with landscapes so it affects not just flow but water quality and also things like the carbon budget of the land that the water is on.”

A main focus of Dr. Windham-Myers’ work in the Delta has been water quality, as it is a major issue and one that affects a lot of decisions.  This includes things like the need to make habitats that create the turbid conditions that endangered species like, having lower dissolved organic carbon and salinity to maintain water quality for drinking water, and toxicity issues such as nutrients, microcystis, and selenium.

We have a highly regulated system in the bay with all of these factors, but our water quality here is fragile in these particular scenarios, and there’s also year to year variability, so management plays a big role in water quality and our decisions on landscape management should play a role,” she said.

All water bodies in the US have some sort of mercury fishing advisory, but the Delta has a TMDL for methylmercury.  She said it’s a hard wall to climb, and for that reason, there’s been a lot of work on it.

One of the cool things about the Delta is the spatial structure of the distributions of methylmercury in water which has often been referred to as the Delta donut,” said Dr. Windham-Myers.  “The idea is that the center of the Delta is lower in methylmercury concentrations in fish and it’s true in the waters as well.  So higher on the periphery, lower in the center.”

The graphics on the slide show the mercury concentrations in fish, and the Central Delta is low and really the only place in the Delta where sportfish are below the EPA guideline of .3 PPM in the tissue.  The big question is why.

When we revisited the Delta mercury strategy in 2016, we tried to look at why that is, and everybody had an explanation,” she said.

Prior to that meeting, they had asked the CASCADE modelers to do a run using methylmercury as a tracer to see if transport alone that would explain the distribution.  Using Frank’s Tract as a marker, the model run showed that the water is coming into it from the south and in the beginning from the north as well, and when the pumps turn on, the water starts moving down to the south.

The strength of this model was not that any particular site was correct at any one time; it was that we could then assess the relative role of transport in the concentrations that we saw,” Dr. Windham-Myers said.  “At the end, you end up with kind of a clean Franks Tract and probably a lot of the methylmercury was heading south.  We ended up with a reasonable distribution, but it really wasn’t perfect.”

She presented a slide (lower, left) showing the results which show the timing and source of the tracer, which is basically a numerical tracer that is put in the model.  The bottom shows when the Delta Cross Channel is closed vs. open.  “At the beginning of the water year in October, the Delta cross channel is open, and at that point, Franks Tract gets flushed out pretty quickly and gets replaced by Sacramento River water,” she explained.  “And then the channel gets closed, and at that point, it starts to become San Joaquin water, Mokelumne water, and Cosumnes water that gets in there.  It gets higher through the summer, and then when we open up the cross channel again, it starts to get quickly filled in again with Sacramento River water.  And so this is basically what the water sources look like through time at this site.”

The bright red curve on the graph (upper, right) shows methylmercury in the Central Delta.  “There was a diminished peak through summer and then declined, but they were much higher than what the basin estimated values were for the TMDL which should have been about .06 nanograms per liter,” said Dr. Windham-Myers.  “So this implies that there were probably some methylmercury losses in that system, so demethylation, particle settling, or other things, but the idea is that the transport alone gave us this pattern, now we know where to look to see where these processes might be occurring.”

The blue is the peripheral sites, so north and eastern sites, they are higher for sure, but they are also much lower than the estimates that we had for the northern basins that were more like .3 nanograms per liter,” she continued.  “This is where the TMDLs are going to be active, and what we can see is that, they didn’t quite reach that, so probably there’s some methylmercury production going on in those landscapes.  There are a lot of seasonal wetlands in there, there are a lot of agricultural wetlands, and what we know from other work is that those wetlands do export methylmercury.”

Seasonal agricultural wetlands are the dominant wetland in California when rice fields are counted as wetlands.  “We know that these systems do export methylmercury, particularly in the winter when there’s flows going through, but the summer is a concern, too, for the species that are on the landscapes as that’s when they get more exposed.”

Dr. Windham-Myers has been involved with a lot of multi-disciplinary groups looking at questions on rice fields and other seasonal wetlands to see if there are any knobs that can be turned to reduce methylmercury production or increase methylmercury loss on these lands.

We have had marginal success,” she said.  “It sometimes worked, but they are often not scalable of they’re not predictable between year to year variability. … So the overall story is that these landscapes do produce methylmercury and we can probably improve our modeling of them using some of these functional relationships.”

Those results came from several field sites which are really just points on the landscape.  An emerging technology is seeing if it would be possible to monitor water quality from satellites, including methylmercury.

There was a project that I was involved with in 2016 that basically found a relationship between the ‘brown stuff’ in the water, something you could see from a satellite,” she said.  “We were able to find a relationship with methylmercury and therefore we could create maps like the map of Suisun, and you can see that up near Rush Ranch, up here near the top, there’s higher concentrations that implies that the marsh is a source of methylmercury to the system.  These kinds of maps may be possible.”

This is called the Mercury from Space project.  “The idea is we’re timing some really in-depth field sampling to those overflights of LANDSAT to see if we can make maps of where methylmercury is in the water but tying it to optical properties that we actually can see like brown water and sediment in the water,” she said.

With a NASA Eco Forecasting grant, they were studying the ability to model the accretion of Rush Ranch, so they were out in the marsh, measuring things like suspended sediment concentration in the water to see they could be remotely sensed with LANDSAT, and then populate these models that needed biomass, suspended sediment concentration, and the Digital Elevation Model.  They found that they could use these to run the accretion models as their results were similar to the Marsh Equilibrium Model results.

Because our results were so similar, we argued that yes, we should be able to use remote sensing to run these at other sites as well,” she said.  “You don’t have to stick with the one site where you have all of your field data.”


Dr. Windham-Myers then discussed some of the findings from the marsh accretion study and sea level rise.  If there is only have about a half a meter of sea level rise by the end of the century and the ongoing levels of suspended sediment concentration, Rush Ranch will be fine.  She said it will look exactly the same: it has the upland fringe, it has basically a mid to high marsh platform, and it’s rather flat with only about 20 centimeters of elevation change across the entire 8 hectare area.

If there is a meter of sea level rise by the end of the century, then there will be marsh subsidence.  It’s going to move into a low marsh setting that has its own stability constant; we can model what we think is going to happen, but we won’t know for sure, she said.  If there is about 2 meters of sea level rise, there would be some unvegetated mud flat expansion in some of those channels, and it will be a much more denser situation.  As for other sites in Suisun, they are already diked and subsided, and if nothing is done,  we expect that it will become medium to deep subtidal at about four feet deep and will become a shallow lake, much like Franks Tract.

This really points to the idea that the time is now to really get moving while those elevations are still in the range of being retrievable as marsh, if we decide that that is a habitat feature that we want to emphasize,” she said.

The Delta used to be a huge marsh complex.  The map on the slide is from the San Francisco Estuary Institute who did an historical ecological study that found that the Delta used to be mostly freshwater emergent marshes; now it’s mostly agricultural, shown in the rose colors.  This corresponds to the soil cores, which are showing very deep carbon-rich soils across the entire Delta.

Judy Drexler at USGS has collected cores all over the Delta and has great stories about the rates of decomposition and their accretion histories, said Dr. Windham-Myers; she worked on a project with Ms. Drexler looking at paleosalinity to see if the Central Delta sites have ever seen salinity.  For two of them, they had some salinity experience, but basically been fresh their whole lives.

So the salinization of the Delta, if this comes or how this occurs could actually have pretty big impacts on the soils because this is just not their formation history,” she said.

Regarding wetlands today, Dr. Windham-Myers said the amount of data availability on carbon cycling in wetlands in San Francisco Bay Delta is an embarrassment of riches.  There’s huge eddy covariance network that’s been set up across the Delta from the freshwater sites all the way to the saline sites.  We know from these at eddy covariance towers that wetland plants create a lot of biomass and they suck up a lot of CO2 from the atmosphere.  We also know that drained peat soils release a lot of CO2 in the atmosphere.  There’s just no question about that, but the data here is extremely rich to make those arguments, she said.

Dr. Windham-Myers has also studied are the sensitivities to drought conditions or salinity and carbon sequestration.  The chart on the left of the slide shows carbon exchange at the Rush Ranch site in 2014.

For example, 2014 was a really dry year and there was uptake of carbon, so negative emissions and take up of carbon, but then it’s pretty much gets expired by the end of the year, and we end up with no real net carbon uptake,” she said.  “But in a nice wet year like 2017, there was very rapid uptake of CO2 into those plants and not so much respiration and there was a really large carbon drawdown at that site, probably a reaction to salinity.  It’s an important point that year to year variability is real for CO2 uptake.”

We know that carbon dioxide is being emitted from soils and if the soil is flooded, it could prevent some of that carbon dioxide release, but we also know they make methane.  The chart on the left of the slide shows the significant methane emissions from flooded corn fields collected in 2012-13.

They are actually basically at the same range of scales of data that we find in the natural wetlands, so if we’re going to continue to decide to flood up about 80% of our cornfields in the winter, this is something that’s part of the equation that’s has maybe been underestimated,” said Dr. Windham-Myers.

There are a lot of tradeoffs in doing carbon monitoring and carbon accounting, but the tail that wags the dog for most carbon markets for wetlands is methane – are you making it or are you not, because it plays such an outsized role in the greenhouse gas budget,” she continued.  “For example, if you’re emitting one gram of methane, if you use the sustained global warming potential which is really how the science has gone, you need to be sucking up 42 grams of carbon dioxide at the same time, and that is a very hard bar to jump over.”

Dr. Windham-Myers noted that the chart on the left shows that some of the sites do uptake a lot of greenhouse gases, but the majority of the sites are making more methane than the CO2 that they are taking up.  Rush Ranch, which is brackish tidal marsh, is staying below the line because it’s not making methane and the same is true for the Puget Sound site, which is a USGS reference and restoration.

When you have salinity in the system and particularly when you have sulfate in the system, it inhibits the production of methane, and this is one of the reasons that tidally connected systems are really good carbon sequestration systems,” she said.

With tidal connections, a question is what about lateral flux?  How much carbon is actually leaving the system as opposed to just staying put? Delta Science Fellow Matt Bogard using data from the California Water Science Center was able to close the carbon budget and estimated that 40-50% of the carbon is leaving the system laterally.

This is not a bad thing,” she said.  “This is probably supporting food web development.  There was a really nice Delta paper about copepods liking to eat macrophyte bits, so there’s actually real potential benefits to this kind of lateral flux.  I think of tidal systems as having basically dual functions; they are good carbon sequesters as well as feeders to the food web.”

Dr. Windham noted that there are a few other sites where this amount of data is being collected, so it’s about looking for general principles out of the datasets and coming up with general patterns that can be applied elsewhere.


Scientists tend to know their one site really well, but if you’re going to try and make decisions, particularly on the large scale, you need to start looking across those systems, Dr. Windham-Myers said.  In 2014, she worked on a study with 18 co-PIs to pull the datasets and models together from all over the country to try to help the EPA get coastal wetlands into the National Greenhouse Gas Inventory, which had only been proposed at that point.  It was a productive project, generating 12 publications and 6 data releases on the Oakridge National Labs DAC.

One of them by the way was a tidal boundary for the US because no agency wanted to make a tidal boundary for the US, but we needed it to do this kind of work so I encourage you to go use it,” she said.  “Not only that, but it’s probabilistic, so you can choose your confidence level when you use it.

The first paper showed the really tight relationship between bulk density and loss on ignition, which is a test that measures the organic content of the sediment; if there is no organic matter, it’s like pure sand, totally mineral; if it’s 100% organic matter, it’s just pure peat.  As you move from a mineral soil to a peat soil, the bulk density goes down, precipitously at first and then a shallow end of the curve.

Referring to the plot on the left, she said, “because there is such a tight relationship of these datasets from all over the country, when you start to look at them along this curve you see a very tight clustering around the mean, and the mean is about .03 grams of carbon per cubic centimeter.  So, what this meant was that it was actually not hard to justify at a national scale and estimate of 27 kg of carbon per meter squared.  That makes accounting pretty easy.  It doesn’t mean that there is no variability, it just means that the variability is not mappable; it’s not related to whether you’re fresh or saline, it doesn’t matter what kind of vegetation you have on top, and it didn’t matter what climate you were in.  Everywhere from Maine to Florida to Puget Sound had the same pattern.”

Biomass also had the same general pattern.  “This was surprising as well,” she said.  “You would think because we had these six sentinel sites all over the country, they had very different biomass relationships but instead they had the same distributions.  Every one of these six sites had some flux that were 0 and some flux that were 3000 grams of carbons per meter squared.  And so the fact there was the same distribution as you moved around the country meant that they all congealed on a pattern.  We could map much, much finer detail of the actual biomass at a given 30 meter pixel, but the overall distribution was similar so it wasn’t hard to apply a single value.  I also want to emphasize that there’s much more carbon in the soils then there is in the biomass and the biomass is turning over every year while the soils are continuing to grow.”

While they were confident about findings on carbon and on biomass, there was still a lot of uncertainty around methane, and they didn’t have enough datasets and not enough spatially representative data on habitat types to answer the questions.  Another uncertainty was what happens to the carbon when wetlands become open water; did it drown or erode?

The Coastal Carbon Research Coordination Network, run out of the Smithsonian, is a consortium of biogeochemists, ecologists, pedologists, and coastal land managers with the goal of accelerating the pace of discovery in coastal wetland carbon science by providing our community with access to data, analysis tools, and synthesis opportunities.  The Coastal Carbon Research Coordination Network works to accelerate the pace of discovery in coastal wetland carbon science by providing the community with access to data, analysis tools, and synthesis opportunities.  The Coastal Carbon Atlas is an application that allows users to view the locations and details of data associated with wetland soil carbon profiles.

It’s changed the game for people doing coastal wetland projects for carbon credits because you can go in and actually show what preserving your site would do to reducing emissions,” said Dr. Windham-Myers.  “It also helps the scientists ask where are the gaps and what do we need to explain these patterns, because we’re not seeing the answers in some of our current maps, so things like getting better elevation maps around the world … things like coastal salinity maps that doesn’t yet exist, but it’s something we know would be very helpful for predicting methane emissions in particular.”

She also noted that the website allows access to the raw data and makes the sharing of it possible so users can see how the numbers were derived.

I’m going to end this discussion of data synthesis by obviously the old African proverb, if you want to walk fast, you go alone; if you want to walk far, you go with others, and definitely I had to go with others category,” she said.  “If you bring others in and let everybody look at the data, you’ll see it through different lenses and you’ll learn a lot about your dataset that you didn’t know when you went in.”

Some of the consortium groups and projects she has worked on:

Wetland fluxnet synthesis for methane: understanding and predicting methane fluxes at daily to interannual timescales: It’s global effort to take all the eddy covariance flux data from around the world and look at methane, and it’s changing the game on what we understand about methane globally,” she said.

A Blue Carbon Primer: “It’s the state of science, policy, and management … and it covers everything you would need to know to understand how to do to carbon accounting in this world, everything from the policies that are available to how do you operationalize to what do we know now versus what did we know then.  There’s a whole chapter on the Sacramento Delta by Judy Drexler that’s really excellent.”

The Global Carbon Project: The Global Carbon Project integrates knowledge of greenhouse gases for human activities and the Earth system.  Projects include global budgets for carbon dioxide, methane, and nitrous oxide and complementary efforts in urban, regional, cumulative, and negative emissions.

It’s important to talk to people who have different approaches and datasets, she said.  “One of the things you learn when you start to look at the state of that carbon that goes in is that about half of the carbon that gets taken up on land is actually headed out the aquatic continuum – it goes into lakes, it goes into reservoirs, it goes out to the coast – it doesn’t stay on land.  That has been proposed many times by people, but we now have the impetus in the science community to document that and show where it’s going.  A lot of it makes it to the ocean, then it gets buried.  And so one of these questions about what’s happening to the ocean and how much of that carbon gets buried is a really open science question now but at least we’re finally looking at that bigger picture.”


Dr. Windham-Myers said that all the projects and ideas that people are putting out there are inspiring to her.  When she moved back to California after working on the East Coast for 15 years, she was inspired by the PPIC publication, Envisioning Futures for the Sacramento-San Joaquin Delta.

I loved the idea that all of the ideas were on the table,” she said.  “Put them all out there and let’s review them all so that we can at least all come together, so whether we were keep the Delta fresh or whether it was going to be fluctuating in terms of salinity, whether we were going to reduce exports and potentially have a more saline system.  The fact that we looked at all of those brought the community along to then accept some of the future recommendations of the Council and other agencies.”

When she was in the Netherlands, one of the words she learned was ‘polderen’ which is a verb that means consensus-based decision making.  “The reason it’s useful to me is that it’s basically the idea that everyone who lives on the polder needs to have their idea heard in order for everybody to agree to move forward on a plan, and this is true for extreme events as well as not so extreme events,” she said.  “You might think it makes you go slow, but it gets everybody on board and I think it could be made a lot faster if we actually shared data, so I’m very much into stakeholder data driven visualization.  Let everybody see the data.  Let everybody enjoy the exploration process.”

One of the new visualization tools is Tableau which really brings the data to life, she said.  It allows you to look at many different metrics across the landscape.  It can be used with any data source and it makes it easy for stakeholders to peruse the data.  Users can look at the uncertainty and drill down to the raw data.

The tools are out there, and the rest of the world is moving forward with these really good ways of sharing data and analyzing it in a stakeholder framework and that’s the way I think all of our science enterprises should be moving in that direction,” she said.

At the USGS, one of the projects she is working on is developing a coastal watershed hazard plan and ecosystem assessment.  One of the goals is to start working with salinity because it is a good tracer and you can consider some more simple metrics of how it’s changing a little more conservatively than others, she said.  One of the best things the team did was organize a meeting where they brought in a social scientist who had the framework for them to be thinking of, which was how do you ask the important science questions and then make it useful for the people at the end.

There was no public stakeholder; there were 28 different kinds of stakeholders, and everybody wanted something different, so you have to think about bringing them into the process because if they are involved, they will help ask the right questions,” Dr. Windham-Myers said.  “He also basically would ask the really tough questions, like ‘who cares?’  He got it down to the point where we could think about the implications in terms of dollars and lives, and then from that, look at what kind of adaptations are on the table, what could we possibly do, and then create data dashboards that were at the scale that would help a decision maker actually look at not just current data, but also projected out into the future as well as into the past.”

I do believe in the one Delta, one estuary, one science,” she said.  “I think we should be working together.  I think we should be bringing the data to stakeholders to conduct their own exploration, see the observations we’ve made through different eyes, and one of those things that’s bringing people together are these brown bags, so thank you.”


QUESTION: We have a lot of legitimate scientific controversies here in the Delta.  We don’t agree, and based on your history working here and elsewhere, what do you think the role of the science program is in handling those controversies and trying to bring them to resolution?

DR. WINDHAM-MYERS: “I’m guessing that the controversies have more to do with the implications of science or what you would do with the science, rather than the science itself, or the interpretation of data … Solving controversies to me is really getting everybody looking at the same thing and talking about the same question. My experience has been that if you focus on a particular aspect of the model results, and let everybody ask the questions, what if we try this and what about this … what’s the disconnect, which really gets to the answer of where the controversy is coming from. So I think the role of the Delta Science Program is to bring people along.  It’s the impetus to getting people to agree.  I think science can be the broker of that, so I’m optimistic that the role of science is appreciated by the larger world and community.  Scientists are generally ranked high as somebody people trust, so I think it can help solve controversies more than encourage them.  I think bringing people along is the smart answer in the long run.”

QUESTION: The finding that you can sort of generalize for soil carbon globally and you can generally for biomass carbon globally, it was great to see that, and that should be really useful obviously for trying to figure out carbon budgets.  I’m curious though, there is a lot of heterogeneity… is there a lot of pushback of individuals saying, that’s a nice generalization, but we’re special, you can’t put us in that category.  What’s the level of pushback there and does it effect the utility of that generalization?

DR. WINDHAM-MYERS:Absolutely, healthy pushback on that kind of global statement. The cool thing about it is that it then necessitates getting the data to support your point, so if you think that there is something special, why is that?  Explain why that is.  It’s actually pushed us to start looking at things like hydrology.  Frankly, one of my big things lately is Darcy’s Law.  I think Darcy’s Law is behind almost all of this carbon sequestration, and we have forgotten about Darcy’s Law in wetland science for so long … the cool thing about people finding outliers is then you can then ask the question why and really get at, get to the raw data … Some of the papers that came out in Nature were those papers, one that I’ll highlight was from Australia about sea level rise was … the higher the sea level rise, the more carbon sequestration you get.  That would never have been accepted if people weren’t looking at a large data set.”


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