Wetland restoration has been identified as a key management tool for increasing food availability for at-risk fishes in the San Francisco Bay-Delta Estuary. To characterize the benefits of restoration sites, it is critical to quantify the abundance and composition of food resources for fish in and near the wetlands.
One of the important food sources is zooplankton, which are small, floating animals that drift in the water. Zooplankton eat the bacteria and algae that form the base of the food web and, in turn, are heavily preyed upon by fish, insects and other zooplankton.
Characterization of zooplankton communities in and near wetlands is considered particularly important, but accurate analysis of zooplankton samples is time-consuming and expensive. So the recently established Fish Restoration Program Monitoring Team conducted a study that leveraged data from existing IEP surveys along with additional monitoring to characterize shallow-water zooplankton communities before restoration.
At the 2021 Bay-Delta Science Conference, Rosemary Hartman, Environmental Program Manager with the Department of Water Resources, discussed the study.
The Fish Restoration Program is an agreement between the Department of Fish and Wildlife and the Department of Water Resources to address specific habitat restoration requirements of the Biological Opinions for the State Water Project and Central Valley Project and the Incidental Take Permit for State Water Project operations. The program’s primary objective is to restore 8,000 acres of habitat for the Delta smelt and Chinook salmon, including 800 acres of habitat for the longfin smelt. The Fish Restoration Program is also tasked with monitoring tidal wetland restoration sites.
Tidal wetland restoration is designed to increase shallow, productive habitat for at-risk fish species. The basic idea is that the incoming tide floods the shallow, productive vegetated habitat, allowing fish access to it. And when the tide goes out, some of the food production in the wetland will move into the channel where the fish are as well.
“But we really don’t know much about how tidal wetlands work because we have so few of them in the Delta and Suisun Marsh,” said Dr. Hartman. “So we aren’t quite sure how zooplankton abundance is similar or different in the channels and the deepwater habitats. And that’s important to know if we are going to inform the effectiveness of our restoration.”
She noted that it’s a lot of work to turn a zooplankton sample into data. Since several existing surveys already sample the deep water channels, they wanted to leverage those surveys. So they started a project where the Fish Restoration Program conducted sampling just inside wetlands or outside future restoration sites while the IEP conducted its surveys in the deep water.
The study questions were:
- Are zooplankton communities similar in tidal wetlands and deep channels?
- Is there higher abundance in the wetlands versus the channels that would show that there’s higher production and more food resources for fish and wetlands?
- Can we use the long-term monitoring programs to compare wetland zooplankton and open water zooplankton?
The study was conducted for the years 2017 to 2019. Throughout the spring, as the 20-millimeter survey sampled zooplankton and the Fish Environmental Monitoring Program sampled zooplankton and water quality, the Fish Restoration Program also sampled using a townet in the shallow water nearby.
The three surveys have very similar setups; they all use 150- 160 micron mesh nets with flow meters in them of the same diameter; however, they are on slightly different kinds of frames.
The monitoring was conducted at several sampling sites in the Delta and Suisun Marsh that were all near existing or future wetland restoration sites, as well as some reference sites.
“Once we collected all of his data, we had to get it to talk to each other,” said Dr. Hartman. “There were some differences in the final datasets. Some of the programs use different levels of taxonomic resolution, which makes it hard to compare the different datasets. Some things were as simple as column names being slightly different or the data format being slightly different. We had to figure out how we could put it all together in a way that we could compare the three datasets.”
With the help of the IEP’s Zooplankton Synthesis Team and the leadership of Sam Beshevkin from the Delta Science Program, a web application was developed that downloads the data from different places, puts it all together, deals with differences in taxonomic resolution, and integrates it into one dataset that can then be compared.
Zooplankton community composition
Below is a graph of relative community composition, or in other words, the percentage of each taxa in a given sample. The taxa are represented by different colors and show the average per survey month and site. The months are shown across the top. The sampling sites are on the right-hand side. Within each box from left to right, there is the 20-millimeter survey, the Environmental Monitoring Program survey, and the Fish Restoration Program survey.
“What we want to do with this graph is just kind of squint and look at patterns in color,” said Dr. Hartman. “So if we look within a box, for example, June at Stacy’s Island, we can look across these three surveys and see, are the colors similar and about the same abundance? There are some differences … but they’re still pretty similar. Whereas in any of these boxes, there are some differences in between the three surveys, but it was in the same ballpark.”
Looking across the boxes, there is a lot more variation over the month or between locations. “This is telling us that the shallow water versus deep water within a given location is a lot less than the differences over the course of the month or between locations,” she said.
Dr. Hartman pointed out some of the differences: From March to June, there are more grays and pinks, which are the cyclopoid copepods, and in June, more yellow and purple, which are the calanoid copepods. The restoration sites are ordered from brackish to freshwater; she noted there are more calanoid copepods in brackish water and more rotifers and cladocerans in freshwater, shown in blue and green.
Dr. Hartman then applied some statistical methods to the data.
The first method was a non-metric multidimensional scaling analysis to determine how similar the communities were. On the graph below, each point represents a sample; points that are close together are more similar, while points farther apart are more different. The color of the points indicates which survey the data came from; the circles are around the center of each survey.
“The surveys, the circles, almost completely overlap,” she said. “There’s a little bit of difference, but they’re all kind of overlapping. So this is telling us that there aren’t many differences between these three surveys when we look at them overall. I also did a permutation multivariate analysis of variance, which gives us a P-value telling us whether or not they’re different, and we did get a significant P-value. However, it only explained 3% of the variance, so very little variance is explained by the surveys.”
The graph below shows the same data, with the colors indicating the month.
“We see a lot more differences,” said Dr. Hartman. “Not much between March and April, which is red and blue. But as we move from May and June, we do start seeing a lot more differences as those cyclopoids start decreasing and the calenoids really take off.”
The line on the graph below shows the distance from the Golden Gate to the point, which is a proxy for wherein the salinity field the point lies.
“As we go from fresh to brackish water, we see a shift in the points as we go from communities dominated by cladocerans to ones with more copepods to ones that even contain bamacle nauplii,” she said.
A joint species distribution model, shown below, was used to analyze the data for each of the species. In this figure, the covariates are listed across the bottom the species are listed on the y axis. All the red boxes are species that increase with a particular covariant; blue boxes are species that decrease, and white means no significant difference.
The first three columns are the three surveys; 20-millimeter is on the left and is the baseline. The Environmental Monitoring Program shows the changes from that baseline. She noted that most of the boxes are white, meaning there aren’t many differences; there are more differences between the Fish Restoration Program and the baseline. Still, about half of them are white, so not significantly different.
“When you look over the course of months, or distance from the Golden Gate, you have more colored boxes than white boxes, so a lot of differences,” she said. “In particular, notice a lot of red up here; these are all of the cladocerans, and they increase the further you get from the Golden Gate, the more freshwater you’re into.”
Dr. Hartman pointed out that while her main analysis took care of differences in taxonomic resolution, some surveys have a higher taxonomic resolution level than others.
“For example, the 20-millimeter survey just lumps all of a lot of their cladocerans together, whereas the Fish Restoration program actually goes through and gets them to family, genus, or even species, and that gives a lot more information about some of the rare species. We might have more differences in the rare species that aren’t incorporated into this analysis just because we don’t have the taxonomic resolution.”
Total catch
“Now the fun or the surprising part,” said Dr. Hartman.
Looking at the differences in total catch, some things were not surprising, she said. At the lower left is a box plot of each survey over a month, and on the right is catch per unit effort (CPUE) versus distance from the Golden Gate.
“We see a significant increase over time,” she said. “It’s not surprising; more critters in the summer, a slight increase in freshwater versus brackish water.”
“What really blew me away was that when you look at these surveys, blue is the Fish Restoration Program, and they tended to be significantly lower in abundance than the other two surveys. This was exactly the opposite of what we were expecting. We thought the shallow water and the wetlands would have higher abundance.”
Why is that? Dr. Hartman went over the possibilities. Is it really due to the shallow water, or could there be anything else going on, something to do with sampling effort?
“The surveys are similar, but there are a lot of differences,” she said. “Their boats are very different sized. Their net placement is different. Oblique versus surface tows. One of the biggest differences was the difference in volume.”
Out of all the spring surveys, the Fish Restoration Program tended to have lower CPUE, but also had the lowest volume and lowest bottom depth. “There were very big differences in volume across all the surveys. Could that be part of what’s going on?
Below is a plot of total CPUE for 20mm and EMP for 2000-2017. It shows that over 20 years, the 20-millimeter had a consistently higher catch, which Dr. Hartman noted was surprising because the surveys are in the same habitat.
Looking at the volume, they found a slight decrease in CPUE at higher volumes for most of the surveys, but it wasn’t very explanatory, she said.
The Fish Restoration Program does sometimes take channel samples, so when the data for channel samples, diked wetland samples, and tidal wetland samples were analyzed, they found the channel samples were slightly higher than muted tidal or tidal samples, but it wasn’t a statistically significant difference.
“Maybe we just need more samples, and that’ll come out,” she said. “Or maybe the gear isn’t as efficient when in shallow vegetated water or mucky tidal wetlands as in channels.”
Summary and conclusions
“To summarize, we didn’t find many differences in community composition between shallow and deep water,” said Dr. Hartman. “We did find higher abundance in deep water, but I just don’t believe it. But it could be there. So it just definitely refuted our hypothesis.”
“The real conclusion we want to take from this is we need to look beyond zooplankton when we’re in tidal wetlands,” she said. “Previous analysis shows a much higher abundance of amphipods, insects, and epibenthic critters in wetlands versus channel samples. We also want to look across the surveys; don’t just take one survey’s word for it because we’re finding big differences between surveys. I want to do some paired gear evaluations where everyone is towing their gear, and the exact same stretch of channel, exact same habitat so we can really figure out whether these differences are consistent.”
QUESTIONS & ANSWERS
QUESTION: Do you have a good sense of how important rare zooplankton taxa are ecologically?
“Short answer is, I don’t,” said Dr. Hartman. “In general, though, rare taxa are not as important ecologically as some of the more common taxa. The exception is usually when you have predators. So if some of the rarer taxa are predatory taxa, that can really have a big impact on the other zooplankton, and you would probably see it. But, for the most part, the ones that don’t get identified regularly are probably ones that aren’t as ecologically important. But there might be some interactions that we’re not aware of. Honestly, at the species level, we just don’t have a lot of information about a lot of these critters.”
QUESTION: Could this possibly be the consumption of zooplankton in wetlands by fish?
“Definitely, that’s my favorite theory of why we might see less zooplankton and wetlands is they are all getting eaten there because there’s so many fish and other critters,” said Dr. Hartman. “Because the tides move things in and out so fast, it would be a little surprising, but, you know, definitely a good theory.”
QUESTION: Are there any efforts to sample macroinvertebrates at these sites?
“Definitely,” said Dr. Hartman. “I made just a brief mention in my conclusion slide when I said we should consider other critters besides plankton. In some previous analyses, we found that wetlands always have way more macroinvertebrates, especially ones associated with vegetation, because there’s so much vegetation in wetlands. Amphipods, isopods, and the freshwater insect larva are common in these wetlands. And because they’re larger, they’re an even better source of fish food.”
QUESTION: Could we just be sampling or not sampling the right wetland habitats?
“Potentially,” acknowledged Dr. Hartman. “The comparisons I made here are trawls that were at the outlet of the wetland or even just alongside future wetland sites that aren’t even breached yet. We also have a lot of data from interior wetland sites, and some of those comparisons might yield different results.”
- Zooplankton: Not just for [fish] breakfast anymore!, blog post from Dr. Rosemary Hartman at the IEP website
- Food for Thought: Connecting Zooplankton Science to Management in the San Francisco Estuary, essay at the San Francisco Estuary & Watershed Science journal
