Getting to the Bottom of It: An Overview of the Environmental Monitoring Program’s Benthic Monitoring in the Delta

Wells slides_Page_33DWR’s Dr. Betsy Wells takes a look at the creatures that live on the bottom of the Delta

Creating a better understanding of bottom-dwelling, or benthic, invertebrate communities enhances our knowledge of the Sacramento-San Joaquin Delta ecosystem. These communities are a crucial link in the Delta’s food web and are a classic bio-indicator of aquatic ecosystem health.

In this seminar, Dr. Betsy Wells, Environmental Scientist with the Department of Water Resources, offers her perspective of the benthic monitoring program and discusses the bottom-dwelling communities’ geographic, seasonal, and historical patterns, explaining how the creatures at the bottom of the Delta, everything from clams to worms to amphipods, make up an amazingly diverse community that tells an ecological history of the Delta.


Wells slides_Page_03What is benthic ecology?  “Essentially it’s whatever lives at the bottom of a water body,” began Dr. Wells.  “It is what lives at the bottom at the interface of the water and the sediment, whether in the sediment, on the sediment, or associated with the sediment.”

She presented an illustration on the flier for the National Benthic Ecology Conference that depicts the variety of species that are normally found in the benthos, from sea grasses and sea weeds to oysters and mussels and sea stars and cod and lobsters and scallops.  “You get this massive diversity and variety of life forms in the benthos – more than a lot of other ecosystems, which is one of the things I find so exciting about it,” she said.  “However, I just want to point out though that this is a great picture of some of the stuff we could be looking at if we were in Maine.

Wells slides_Page_04Since the benthos is at the bottom of the water body and 70% of the earth roughly is covered in water, that means that 70% of the earth is covered in benthic habitat, pointed out Dr. Wells.  “So before you think of the benthos as such a niche thing to study, by surface area, benthic ecology is one of the bigger things out there.  Its everything from very shallow, such as a Chinook salmon redd up in Washington State, all the way to the very deep, like James Cameron’s immersal that went down to the bottom of the Mariana Trench – all of those are benthic habitats.  They have nothing else in common but they are benthic.”


Dr. Wells then gave the reasons why benthic ecology is studied.  The first reason is because benthic communities are a classic bioindicator or a proxy for how the health of the water body is doing.  “A lot of people who have worked in streams, and this is primarily how they know them,” she said.  “They look at the benthic community as a sense of how the ecosystem and the community as a whole are doing.”

Wells slides_Page_05There are a number of reasons for this.  “First, they are the animals that are associated with and are in the sediment, so they are geographically stable,” she said.  “If you study fish, you know pretty well, fish move.  If you study zooplankton or phytoplankton, they move as well, either with the currents or passively drifting.  If you’re buried in the sediment, you’re more geographically stable, that means as I go out to a spot with GPS, and I can go out again the next month, and I can sample that same community and know that that has a relationship to the community from the month before, which is really convenient as a researcher.”

Secondly, the benthic organisms are on a really convenient time frame for research – not too short and not too long.  “If you’ve got a response to some sort of input or disturbance, whether it’s a chemical change, a pollution flume, a change in salinity, a deoxygenation event, or a biological change like a new invader or a predator that’s come through, you usually get a response in the benthic community of a few months to several years,” she said.  “Of course, there are outliers … but in a few months to several years, you can go out and document changes that happen as well as the response from changes that happen.  Things that respond really quickly like phytoplankton, blink and you will miss them.  Things that respond really slowly like redwoods, you could be waiting for decades to see the response and the recovery back from say a forest fire, so a few months to a few years is really convenient for human and funding time frames, so for that reason, they are really a great thing to look at as a community indicator.

Finally, benthic communities tend to be fairly highly diverse, both in numbers of species and in ways of life, she said.  “You get everything … you get worms, you get clams, you get snails, you get fish associated with the bottom, you get crabs, you get pretty much any way of life, whether predator, scavenger, you get filter feeders living in the sediment, living on the sediment, being parasitic.  You find it all in the benthos. … You get a very nuanced, fine grained look at how communities are responding, because all these different ways of life and all these different species will have different responses to the different inputs.  So as opposed to say a guild of fish that all do the same thing, you can get a very finely nuanced set of data from the benthos, which is really useful to us.”

Dr. Wells then explained how the benthic community can be used as bioindicators.  Basically a bioindicator measures some element of the community, such as species richness, the biomass, or the functional diversity (all predators or all grazers or both).  “If you have a whole bunch of pollution tolerant species that may indicate you had some pollution in the past, or if you have pollution sensitive species, that sort of indicates the place hasn’t been all that polluted,” she said.  “You measure a whole bunch of different metrics and come up with a combined index of all of these things for sort of a final grade for the place we’re looking at.

Wells slides_Page_06She presented a map of a benthic index for the Chesapeake Bay, noting that the green areas are a healthier benthic community, and the red areas are less healthy.  “It’s a real good visual way of saying what is the overall health of a water body,” she said.

A number of benthic indices have been developed; some of them are designed for streams, others for rapid assessment, and some are adaptable to the marine environment or lakes, so there are a number of different to choose from, depending on the monitoring situation.

However, benthic indicators do have their limitations.  “They don’t work that well in the upper estuary, and I wish I had a definitive answer why,” she said.  “The best answer that I can come up with is that the Delta as a whole tends to be largely changed.  It’s a very altered ecosystem; there aren’t a lot of pristine places left to serve as reference sites.  The other thing is that it’s a very alluvial system where you don’t have a lot of points of disturbance like an outfall in the Bay … the impacts tend to be really widespread, so when you try to say this place is impacted, what would it look like if it were pristine, it’s really hard to say why, and it’s very hard to come up with a good reference site.”

The other thing is that the Delta and the estuary are so variable, mostly because of the saline gradient,” she continued.  “Trying to compare Suisun Bay to Clifton Court Forebay where the pumps are, they don’t have anything in common, so it’s not even comparing apples and oranges, it’s like apples and arthropods.  … We could probably come up with some other indices but for right now, benthic indicators are not high on our list of let’s do.”

Wells slides_Page_10So even though they don’t serve as useful bioindicators for the Delta, the benthos is still monitored because it is a central and critical part of the larger food web.  She presented a diagram of a food web from New York’s Long Island ecosystem, noting that it’s a clear diagram of a tidal river and a lot of the species shown in the diagram are representative of species that are in the Delta.  “Some of the species are actually the same ones, because they came from here the crab, the striped bass – we got it,” she said.

When we look at some of the conceptual models of Delta food webs, again benthics are central and are often a major pass through point from primary productivity to secondary productivity and up to the things that a lot of people care about – like fish and birds,” she said.  “You either have to go through the planktonic route or you go through the benthos.”

The benthos contributes a lot to the food web.  “A lot of fish and invertebrates eat the worms that they find on the bottom,” she said.  “Anthropods are also a major part of different fish diets, and clams – birds, fish, other invertebrates seem to like clams, so they contribute a lot to the food web.”

Dr. Wells noted that a lot of research has been devoted to the place of the benthos in the food web, whether it interacts with phytoplankton and bacteria, how they interact with fish diets, how the fish diets have changed in relationship to benthos.

Wells slides_Page_14I’m going to tell a simple story about a very complex phenomenon to illustrate some of the places of benthos in the food web,” she said.  “The Pelagic Organism Decline (POD) was a phenomenon starting about 2002 where multiple fish species at once started to go into nose dives in terms of their populations, and people had a lot of interest in why this was happening.  These four fish were especially the focus of a lot of the POD research; they have different ways of life, different life histories, what could be causing this?  This is a very complex phenomenon.  The benthic food web portion is only a small part, not necessarily the biggest part, but it is a part of it.

Dr. Wells noted that there are a lot of other factors involved, such as habitat, chemical influx, top down pressures like salvage and predation that also contributed to the POD, but the benthic part is of interest to her, so she will be focusing on just that portion.

Wells slides_Page_15Here’s a really simplified Delta food web,” she said.  “Fish on top eating invertebrates like these are mysid shrimp, who in turn eat things like phytoplankton and zooplankton.  You get more phytoplankton and zooplankton, you get more mysid shrimp, you get more fish.  The Delta is happy.  Then the Asian overbite clam invaded San Pablo and Suisun Bay in 1986, and this an extremely efficient filter feeder; it really hoovers out a lot of the phytoplankton from the water column, and it grows in incredible densities.  We regularly get tens of thousands per square meter on the bottom.  I think our record so far is north of 150,000 per square meter; granted most of those were really little, but the densities are pretty amazing, and they eat a lot of the phytoplankton and take the food web kind of down at the knees.”

Wells slides_Page_16Dr. Wells presented some graphs from research that has followed the invasion of the clams in 1986, pointing out the portions marked with red arrows.  “This is chlorophyll A levels in Suisun Bay and in the Delta at large, and after 1986, a lot of them were down pretty dramatically, especially in Suisun Bay to where they are today, which is pretty low levels.  The msyids plunged, and this has been tied pretty firmly to the loss of phytoplankton brought on by the clams.”

This is only part of what may have contributed to the decline of the fish,” Dr. Wells continued.  “It’s not exactly a smoking gun, but it is probably part of the overall picture, so the benthos is a big part of the food web and it can have these effects that ripple up through the food web.”

Finally, another reason for monitoring benthos is that D-1641 mandated comprehensive environmental monitoring.  “This is performed by the Environmental Monitoring Program under the IEP umbrella, and benthic monitoring is part of that, so we perform this in tandem with zooplankton, phytoplankton, and water quality monitoring; it’s part of this integrated program.”


Wells slides_Page_18Dr. Wells said the way the benthic monitoring is done is that they go out monthly to each of ten different stations from San Pablo Bay in the west, all the way into Stockton and Clifton Court Forebay.  Currently, ten stations are being monitored, but in the past, a total of 53 stations were monitored, so there are a lot of historical data that snapshots in the past.  “The current stations we’ve been monitoring for a solid 20 years, so 20 years by itself is a pretty nice solid dataset, and you can extend it back further with these historical stations.”

Sampling is done on a boat, using a PONAR, which is basically a big double barreled dredge with two scoops, that is lowered down from a boat until it hits the bottom; it takes double scoops of sediment.  The taxonomist goes through them, sorts them, counts and identifies every single organism down to a half millimeter large.

In the end, there are a lot of small vials filled with very small to large organisms.  The samples are bright pink because a coloring agent is added that turns the organisms bright pink which aids in helping to pick them out against a background of sand and mud.

Dr. Wells noted that for the entire 40 year history of this project, there has been only one taxonomist, Wayne Fields.  “I don’t know many datasets that have this kind of continuity of information input and this high level of information input,” she said.  “It’s a pretty amazing dataset and Wayne has been a massive part of this effort through the 40 years.”


The samples contain most of the invertebrate tree of life; she said they get a least a few samples form every branch.  “Right now, regularly we get specimens from eleven different phyla which is an amazing variety of functional group, body form, and way of life.”

However, the distribution is dominated by the arthropods, by the analids (segmented worms), and the mollusks; then there is a slice of everything else, she said.  “So with many biological distributions, you get a few things that dominate numerically, and then a bunch of rare things.”

Some of the species found in a recent sampling of the Delta’s benthos.

Some of the species found in a recent sampling of the Delta’s benthos.

“The main product that we’re sampling is the data: the where, the when, the what, the how many,” Dr. Wells said.  “Just the basic data of what we found when we were out there.  All of our data for the last four years is publicly available right now online.

Future plans for data include a new web portal that will give more context to the benthic invertebrates and tell data stories about them, as well as be an interactive data portal; she said they are hoping to have that up in the next year or so.


Over the 40 years of sampling, they have found a total of 463 species and over 140,000 individual taxonomic samples; they’ve collected nearly 6 million individual organisms over 40 years.  “It’s a lot of data, so I’m going to try and give you some patterns to think about,” she said.

Wells slides_Page_30 The first thing is that there are really strong seasonal patterns.  “As you might expect, with some short-lived things, you’re going to find some strong seasonal patterns,” she said, presenting two charts from a sampling site by just upstream of the Benicia bridge.  “The charts are from 2014, which is a nice representative year.  What you see is a massive peak in potamocorbula recruitment that peaks in late summer or early fall.  In some years, it’s an order of magnitude larger in the peak recruitment times than in the rest of the time.  That’s just a huge change, and the reason is they that reproduce in the summer, and then ones that weeded out or eaten, and then it falls again in the winter.  So that’s a big numeric pattern.”

Dr. Wells noted that the two graphs are actually the same graph, just at different scales.  She also pointed out that the potamocorbula is really numerically dominant to everything else, but there are some other dominant species out there.    “You get a couple of different anthropods, you get a sea squirt, you get a barnacle, and all of those have their own distinct patterns, so you can go out one month and go out six months later and see almost nothing the same in those two different months.  That’s one of the reasons we sample every month because some of these have really sharp peaks.  If we didn’t go out every month, we might miss things.  So there’s a really strong seasonal pattern at a lot of these sites.  Some of them are there year round.”

She emphasized that the main driver at all the sites is salinity.  “Salinity is a master variable,” she said, presenting a picture of a model of the low salinity zone that was done for DWR.  “This just to show that yes, salinity in fact does get lower as you go upstream on a roughly west to east gradient, which is convenient for us.”

She then presented a graph of aggregated data from the last decade, noting that the bottom axis of the graph is the sampling sites organized from the highest salinity on the left hand side to the lowest salinity on the right hand side, which is roughly from west to east.

If you look at the sites in San Pablo Bay, you get a very distinct marine or at least polyhaline clade that as you move up to Suisun and Grizzly bays, a lot of those just drop out, you just don’t see them there,” she said.  “Instead you get potamocorbula taking over and being the numerically dominant bivalve out there.  As you move further up the confluence and up into the Sacramento and San Joaquin Rivers, all of a sudden what you’re getting really is a couple of really truly freshwater clams, corbicula and pisidium, so you get this complete changeover in species identity because of salinity.  There is 0% overlap at the upper and lower sites.”

Wells slides_Page_33When you look at some of the arthropods, it’s the same pattern,” she said.  “You get these marine clades down at D41 and D41A in San Pablo Bay, it shifts up into the organisms you find more in Suisun Bay, and then you really shift into freshwater assemblages as you go upstream.  It’s rare that you find a single variable that explains so much of the variability, and I just want to point out, this is a massively overwhelmingly important driver for the benthic community here.   In wet and dry years, as you can imagine, that changes.  You get that months-to- years response to an input.”

Dr. Wells noted that another pattern she has noticed is that there are more non-native species found downstream, and much fewer upstream.  She hypothesized that it could be due to a lack of vectors upstream, or possibly it’s because the upstream areas are not a hospitable site to new arrivals.  “It’s kind of an interesting puzzle,” she said.

It’s even more pronounced when you count every individual in the population.  “D7 is one of the test spots where you see a lot of potamocorbula, the invasive clam, and most of it is dominated from 1986 onward,” she said.  “You don’t see this as much upstream.”

Another really strong pattern that’s been seen these last few years of the drought is that water has a big effect, but more on downstream than upstream, she said.  “It’s kind of a reverse way about thinking about the Delta, because people think about wanting to keep the freshwater areas fresh, but if you’re benthic, as long as it’s fresh enough, you don’t change that much, but downstream it really matters.”

Wells slides_Page_36Dr. Wells then presented a slide with two plots, the plot on the left is for a site in San Pablo Bay and the right is a site at Clifton Court.  She explained that each point on the plot represents a month of data for the sites over the course of a decade; the points that are closer together are more similar in the number and identity of species that we found, and the points that are further apart are more divergent; they have different species in different numbers.

Referring to the plot on the left for San Pablo Bay, she said, “There’s a really strong wet year to dry year pattern; the spots over in sort of the lower left hand corner are 2014 and 2013, and they are really dry years.  When you compare them to 2016 and 2011, the wet years, they are much further apart.  In fact, I looked at the percentage of dissimilarity, and you get 98-99% dissimilar.  It’s as though it’s an entirely other site between wet and dry years; it completely flips over.”

Further upstream, the water year type seems to make much less of difference.  Referring to the plot on the right for the site at Clifton Court Forebay, she said, “You do see quite a spread in terms of some years and other years, but it’s not according to water year, and I don’t know exactly why.  Is it pumping patterns, or temperature, or nutrients? I’m not sure what explains this pattern.  There is quite a spread but it’s not water year.

Wells slides_Page_37Dr. Wells noted that when you look at the range of ten stations that they are currently sampling, they fall into groups according to salinity.  “San Pablo Bay sites really group together, Suisun and Grizzly Bay are their own clade.  Confluence is really its own thing, and then you get the rivers which are all kind of like each other, and again it’s by salinity,” she said.  “It really is the major driver.”

The benthic monitoring program publishes status and trends on the benthic monitoring year in the IEP newsletter, most recently in the November 2015 IEP publication.


Wells slides_Page_40 Other researchers have been using the data that the benthic monitoring program hasb been providing.  In a 2010 paper, ‘Benthic assemblage variability in the upper San Francisco Estuary: A 27-year retrospective, Peterson and Vayssieres studied 27 years of data, asking not just how do the sites group together, but is salinity explicitly the driver, she said.  “The answer is yes.  Yes, you do get these same groups.  San Pablo Bay, Grizzly Bay, Sacramento River, Old River, they all sort of group together according to salinity and geographic location, and 97% of that variability is explained by mean annual salinity, which is kind of a blunt tool but it explains a lot of variability.”

Wells slides_Page_41In 2013, Bruce Thompson took DWR’s monitoring data with seven other datasets of benthic data, asking if the pattern holds for the rest of the greater San Francisco Bay estuary.  “Yes it does.  He actually found some really cool groupings,” she said.  “If you look at his key, aligohaline, mesohaline, polyhaline, it really is salinity that is organizing the benthic community throughout the greater San Francisco estuary.  I think it’s a really neat extension of the monitoring that we’re doing and I’m so glad that our data contributes to papers like this.”

Another extension of the benthic monitoring work is a collaboration with USGS on the grazing rates for invasive clams.  “The folks at USGS are kind of curious about new modeling water and hydrodynamics and phytoplankton flows and they were asking, we have the counts of all the clams we’ve ever collected in the past, there are two invasive clams, ptamocorbula and corbicula, can we estimate how much they were grazing in the past?  So they went through our historical samples, pulled out every clam and measured it.  Almost 6 million organisms were those clams so that’s a lot of measuring.  They converted those measurements into biomass and then grazing rates, and they actually came up with estimates that can be used for big modeling projects.  So if you’re trying to model phytoplankton supply in the Delta and you want to know, what’s the minus term of stuff that got eaten and lost to the benthos, this work is going to help supply that, so that’s really neat that some of our historical data got used for that.

She then presented one of the graphs from the paper showing data from 1987, the year after the potamocorbula invasion.  “There’s already quite a big amount of grazing pressure in the Carquinez Straits and in the lower Suisun Bay, much bigger than corbicula .. which had been there for many years,” she said.  “I like seeing our data being expanded into this more effect of the benthos on the food web.”

Wells slides_Page_44Another effort using benthic data was the State of the Estuary report which was spearheaded by the San Francisco Estuary Partnership.  The report developed indicators to measure the health of particular attributes, everything from water fowl to water quality and flows.  “In my case, it was benthic invertebrates.  A lot of the benthic bioindicators don’t work for the upper estuary, but we came up with some indicators such as diversity, native/non-native balance, and came up with sort of a historical trend to say how are we doing.  The answer’s complicated, the answer’s always complicated.”

Wells slides_Page_47One of the more interesting efforts going on is the Drought Monitoring, Analysis, Synthesis Team (MAST) which is a multi-agency group that has gotten together to basically to say what does the drought look like out in the Delta.  “What we’ve been doing is getting together a lot of different biotic and abiotic data, including some of the clam grazing numbers and saying how does drought stack up differently.  If you’ve living in the Delta, how does it look different if it’s a non-drought year.  This is in-process right now, we’re hoping to get a manuscript out sometime by the middle of the year … this is a very exciting effort, and little sneak preview of how it looks different.  The really dry years do look really different than the wet years, so check in for more details.”

And that’s it …


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