Science Stories: Adventures in Bay-Delta Data

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  • January 24, 2025

What lives in the mud?

(spoiler alert, not just clams)

By Rosemary Hartman, with advice from Betsy Wells.

Benthic samples (things that live in mud)

The Environmental Monitoring Program has been collecting data on water quality, nutrients, zooplankton, phytoplankton, and benthic invertebrates for almost 50 years. Data from the benthic invertebrate sampling program has been key to documenting the invasion of the clam Potamocorbula amurensis and corresponding decrease in phytoplankton (Carlton et al. 1990; Kimmerer and Thompson 2014). However, the program catches a lot more than just clams. They bring up crustaceans, worms, amphipods, isopods, and lot of other critters you have probably never heard of. All of their data are published regularly on the Environmental Data Initiative website (Wells 2024), and there is a lot to be learned by looking through it.

What does sampling look like?

It’s not easy to look at what lives in mud that is 20 feet under water. EMP’s intrepid crew uses a ponar grab – a pair of metal “jaws” that can be held open until it hits a solid surface (like the river bottom). Then the weighted jaws snap shut, picking up a healthy helping of mud and associated critters (Figure 1). The survey crew then dumps the mud out into a mesh tray and slowly washes the mud away, leaving the critters.

Animated diagram showing how a ponar drops to the bottom of the ocean and clamps shut in the mud.
Figure 1. A gif demonstrating how a ponar grab works. A pair of metal "jaws" is lowered to the bottom of the water where it springs shut, scooping up a sample of mud and associated invertebrates.

What do they catch?

Well, when we look over the entire time period (1975-2023), 85% of the catch is made up of about 15 taxa (Figure 2, Figure 3). The most common is the invasive overbite clam, Potamocorbula amurensis. Second most common is a tube-dwelling amphipod, Americorophium stimpsoni. Next up is another amphipod, Amplesca abdita, followed by the polychaete worm Manayunkia speciosa. The rest of the “usual suspects” include some more polychaetes, several oligochaete worms, a few more amphipods, the Asian clam Corbicula flumninea, ostracods (also known as “seed shrimp”), and cumaceans (also called “comma shrimp).

Interestingly, there are also 41 species that have only ever been recorded once in the history of the program (Figure 4, Figure 5)! These include several crabs which are probably too fast to show up more frequently (Yellow rock crab – Metacarcinus anthonyi, blue-handed hermit crab – Pagurus samuelis, knobknee crestleg crab- Lophopanopeus leucomanus, and pea crab – Pinnixa scamit), the sea spider – Ammothea hilgendorfi, eleven different species of midge larvae (family Chironomidae), a dragonfly nymph (the blue dasher – Pachydiplax longipennis), and a few more worms and amphipods.

Pie chart showing the top 15 taxa caught by EMP's benthic survey.
Figure 2. Percent of total catch over the entire history of the EMP program (1975-2023) made up by the 15 most common taxa. (Click to enlarge)

The head of M. speciosa with lots of tentacles, Limnodrillus hofmeiseri, that looks like an earthworm, Potamocorbula amurensis, a small, white clam. N. hinumensis that looks like a shrimp with a fat head, C. fluminea, a dark, round clam, and A. spinicorne, that looks a bit like a shrimp.
Figure 3. Some of the most common taxa collected by EMP's benthic survey. Clockwise from top life: Manayunkia speciosa (a polychaete worm), Limnodrillus hoffmeisteri (an oligochaete worm), Potamorbula amurensis (overbite clam), Nippoleucon hinumensis (a cumacean – comma shrimp), Corbicula fluminea (Asian Clam), and Americorophium spinicorne (Amphipod). All images from DWR's Environmental Monitoring program, used with permission.

Timeline showing occurrences of rare taxa that were only found once in the history of the program, all of which occurred between 1996 and 2024. Insects were most common, followed by worms.
Figure 4. A timeline of instances when a species was found once in the EMP program, and never again. (Click to enlarge)

Photographs of a large yellow crab, a crustacean that looks like a spider, and two worm-like midge larvae.
Figure 5. A few taxa from the Delta that have only been seen once! The yellow rock crab, Metacarcinus anthonyi, the sea spider (Ammothea hilgendorfi) and midge larvae (family Chironomidae, several species). Yellow rock crab picture from Harmonic at English Wikipedia, (used under license CC BY-SA 3.0). Sea Spider picture from The Trustees of the Natural History Museum, London (used under license CC BY). Midge larvae image from CDFW's Stockton lab.

Who is Manayunkia speciosa anyway?

One of the top players in our benthic team is the polychaete worm, Manayunkia speciosa (first picture in Figure 3). If you’re not familiar with polychaetes, they are in the same phylum as earthworms (the annelids) but a different class (Polychaeta, not Oligochaeta). You can tell the difference because the oligochaetes are very “worm shaped” without a clear head and with only a few hairs. Polychaetes, on the other hand, have a lot of spines and hairs all over them. They sometimes have leg-like fins that ungulate along their sides, and they always have a distinct head. In the case of M. speciosa, he is a tube-dwelling worm, which means he sticks a bunch of sand and mud into a little house in the bottom of the river and lets his long, wavey feelers stick out, catching bits of food as they wave by. Most types of polychaetes are salt-water critters, but M. speciosa prefers freshwater, so he is found primarily in the freshwater stations sampled by EMP (Figure 6). M. speciosa is particularly important to the broader ecology of the Delta because they can carry the nasty salmon disease Ceratonova shasta, a myxozoan parasite (Foott 2017; Stocking et al. 2006).

Map of EMP's sampling stations with sizes based on average catch of M. speciosa. Catch is much higher in the eastern, freshwater regions.
Figure 6. Average catch per meter squared (log-transformed) of M. speciosa at all of EMP’s freshwater stations since 2000. (Click to enlarge)

One of the curious things about M. speciosa is that he can be very common, but not in every year. Looking at the average catch per m2 from all the freshwater stations, it can vary from a low of 7 individuals in 1978, to a high of 4,387 individuals per square meter in 1991 (Figure 7)! But why do we see these big swings? A lot of critters in the Delta have population swings based on how much rain we get, so we see patterns based on water year type (broad categories of precipitation from critically dry to wet, indicated by colored point shapes on Figure 7). We see that a lot of the really high population spikes in M. speciosa are during critically dry years. Other researchers have found that M. speciosa seems to do better in slow-moving water (Alexander et al. 2014), so maybe they get flushed out during high-flow years? But other high population years are categorized as “wet” or “above normal”, so that can’t be the only factor. An experiment by Malakauskas et al. (2013) found that while they can get dislodged at high flows, they have high survivorship after being dislodged, so high flow events might just spread them around.

The highest abundance of M. speciosa occurs in the late winter and spring (Figure 8) – the periods of highest flow in the Delta. This is a little different than the pattern of abundance in the Great Lakes – one of the few other places they’ve been studied – where the peak abundance was in May-August (Schloesser et al. 2016). A study of lab-reared M. speciosa found they have an annual life cycle and can reproduce throughout the year, but had highest egg production in the spring and summer, with babies staying in their mother’s tube for 4-6 weeks before emerging (Willson et al. 2010).

Line graph showing mean annual M. speciosa abundance over time. Abundanced peaked in 1976-76, 1991-1995, and 2005.
Figure 7. Average CPUE of M. speciosa in all the freshwater stations sampled by EMP from 1975-2023. (Click to enlarge)

Line graph showing average M. speciosa CPUE by month. There is much higher abundance in spring than summer.
Figure 8. Mean CPUE of M. speciosa by month for all the freshwater stations sampled by EMP, 2000-2023. (Click to enlarge)

M. speciosa seems to prefer fresh water, and California has a lot of fresh water outside of the Delta. Where else is it found? The Surface Water Ambient Monitoring Program (SWAMP) conducts benthic invertebrate surveys all over the state – sponsored by the State Water Board and implemented by CDFW. It turns out that in over 34,000 samples collected by SWAMP since the year 2000, M. speciosa has only been found 118 times, and most of those detections were in the Delta (Figure 7). However, research conducted on the Klamath River in northern California has found a lot of M. speciosa on that river, particularly in the slower reaches downstream of a major dam (Alexander et al. 2014; Stocking and Bartholomew 2007), so the lack of detections may be more “not knowing what to look for” than not being there. M. speciosa is also quite small, and may be too small to be caught in SWAMP’s sampling gear on a regular basis.

Map of all SWAMP Sampling sites distributed across California. Sites where M. speciosa has been found are highlighted. Most are near the Delta with only a few in other places.
Figure 9. Samples collected by the Surface Water Ambient Monitoring Program from 2000-2023 showing catch of polychaetes (including M. speciosa). Grey points indicated samples without polychaetes, colored circles indicating samples with polychaetes, with larger circles having more individuals. (Click to enlarge)

I wish I could end this blog post with a clear graph of something that is driving abundance of M. speciosa, but after two days of playing with the data, I haven’t found anything useful. So I will leave you with links to the data and so you can figure it out for yourself! Let me know if you have any ideas.

Check out EMP's website for more annual reports and more background information!

References and further reading:

Categories: BlogDataScience, Underappreciated data
  • December 30, 2021

Lots of Interagency Ecological Program (IEP) scientists research fish. Of the 22 surveys in IEP's Research Fleet, 17 are primarily focused on fish. But fish in the San Francisco Estuary are hard to catch these days. Over the past thirty years, Delta Smelt, Longfin Smelt, and even the notoriously hardy Striped Bass have declined precipitously (CDFW FMWT data). To figure out how to reverse these declines, we need an understanding of the “bottom-up” processes that exert control on these populations—we need to study fish food. Therefore, we need to increase our understanding of what pelagic fish eat: zooplankton.

Magnifying glass with cartoon images of several zooplankters

If you’ve spent any time around fish people, you’ve probably heard the word “zooplankton”, but you might not really know what it means. Zooplankton are small animals that live in open water and cannot actively swim against the current (“plankton” means “floating” in Greek). They include crustaceans (copepods, water fleas, larval crabs, etc.), jellyfish, rotifers, and larval fish. Most of them are hard to see without a microscope, so they are easy to overlook – but you’d miss them if they weren’t there because most of your favorite fish rely on zooplankton for food.

Fortunately, the IEP Zooplankton Project Work Team has been tackling the problem head-on. The group got started when Louise Conrad and Rosemary Hartman were both collecting zooplankton samples near the same restoration site. They thought “We’d be able to say a lot more about the restoration site if we combined our data sets!” But with samples collected using different gear and identified by different taxonomists, it proved more difficult than they originally thought. They needed a team of experts to help them figure out how to deal with the differences in their data. So the Zooplankton Synthesis Team was born! The original team included Karen Kayfetz, Madison Thomas, April Hennessy, Christina Burdi, Sam Bashevkin, Trishelle Tempel, and Arthur Barros, but soon grew as more people heard about the discussions they were having.

The team started by identifying the major zooplankton datasets that IEP collects and dealing with tricky data integration questions:

  • Can you integrate data sets when the critters were collected with different mesh sizes?
  • What do you do when one data set identifies the organisms to genus and another one identifies down to species?
  • What if these levels of identification change over time?
  • Does preservation method impact the dataset?

diagram of three data sets being put into a machine and turning into one data set

To integrate data sets, the team standardized variable names, standardized taxon names, and summarized taxa based on their lowest common level of resolution.

While working through these sticky questions, they compiled what they learned about the individual zooplankton surveys into a technical report (PDF) describing each survey and how they are similar and different. They published a data package integrating five different surveys into a single dataset and Sam put together a fantastic web application that allows users to filter and download the data with a click of a button.

The team had put together the data, but there was more work to do. They realized they needed to do more if they wanted people to use their data. Lots of data on zooplankton get collected, but few research articles are published about zooplankton, and zooplankton data are rarely used to inform management decisions. To get the broader scientific community excited about zooplankton in the estuary, the ZoopSynth team worked with the Delta Science Program to host a Zooplankton Ecology Symposium with zooplankton researchers from across the estuary and across the country (you can watch the Symposium recording on YouTube.). From this symposium they learned a few important lessons to help increase communication and visibility of zooplankton data and research:

  • Managers and scientists should work together to develop clear goals and objectives for management actions. Is there a threshold of zooplankton biomass or abundance to achieve? Or is the goal simply higher biomass of certain taxa? This will make it easier to design a study that provides management-relevant results.
  • Scientists should understand the management goals and keep the end goal in mind. If the end goal is fish food, study taxa that are most common in fish diets. If the primary interest is contaminant effects, focus on sensitive species.
  • We need to start using new tools like automated imagery and DNA along with traditional microscopy to collect better data faster.
  • We need to maximize the accessibility of zooplankton data to scientists and managers. Scientists should share data in publicly available places in easy-to-read formats. Similarly, managers should share lessons learned from management actions widely, and use them for adaptive management. Both scientists and managers should be encouraged to ask questions of each other to ensure both understand the best uses for zooplankton data.

These lessons, (and more!) are summarized in a recent essay published in San Francisco Estuary and Watershed Sciences. If that’s too much reading, the team also produced some fact sheets summarizing the major take-home messages of the essay and the symposium:

The team has expanded into an official IEP Project Work Team that meets monthly to discuss new zooplankton research ideas, share analyses, look at cool pictures of bugs, and talk about trends. If you’re interested in joining, contact Sam at Sam.Bashevkin@Deltacouncil.ca.gov

diagram of organism giving presentation

Categories: BlogDataScience, General