Science Stories: Adventures in Bay-Delta Data

  • August 16, 2022

Some data just needs a little love

IEP collects a lot of data. Most people who work in the estuary have probably heard of FMWT’s Delta Smelt Index, or the Chipps Island salmon trawl, or the EMP zooplankton survey. But those “big name” surveys are only part of what we do at IEP! This is the first blog post in a series on “underappreciated” datasets where we highlight some of the data you might not be familiar with.

Yolo Bypass Fish Monitoring Program’s Drift Invertebrate survey

By Nicole Kwan, Brian Schreier, and Rosemary Hartman

In most of the estuary, we concentrate on invertebrates and other fish food that live under the water. However, in streams and rivers the contribution of terrestrial invertebrates falling into the water from surrounding vegetation and aquatic insects that ‘hatch’ on the surface of the water to metamorphose into their terrestrial adult form are also important food sources for fish, particularly Chinook Salmon and Sacramento Splittail. The Yolo Bypass, a large managed floodplain near Sacramento, is located on the boundary between the estuary and the river. As such, the Yolo Bypass Fish Monitoring Program (YBFMP) tracks both aquatic zooplankton and terrestrial drift invertebrates.

The YBFMP collects drift invertebrates year-round from two sites to compare the seasonal variations in densities and species trends of aquatic and terrestrial invertebrates between the Sacramento River and the Yolo Bypass. The crew piles into a boat and heads out, then tows a rectangular net that sits half-in, half-out of the water for ten minutes along the surface. Sometimes, when flows are really high, they can simply hold the net out on the side of their fish trap for ten minutes and let the water flow through it instead of towing it (Figure 1). The crew then rinses the sample into a bottle, preserves it with formalin, and sends it to a contracted lab for identification and enumeration (counting all the bugs under a microscope).

A woman in a life jacket stands on the deck of a screw trap with a rectangular net held in the flow at the surface of the water.
Figure 1. YBFMP scientist Anji Shakya sampling drift invertebrates in high flows next to the fish trap. Image credit - Naoaki Ikemiyagi Department of Water Resources.

There are a lot of interesting questions we can ask with these data, such as, what time of year do we catch the most chironomids (midges) (Figure 2)? Or, how does community composition and abundance differ between the Sacramento River and Yolo Bypass (Figure 3), and how does that relate to differences in hydrology and water quality?

A scatter plot of chironomid catch in the Sacramento River and Yolo Bypass with a trend line showing higher abundances in the spring in the Yolo Bypass and higher abundances in the summer in the Sacramento River. Sampling in the summer did not occur until more recent years (after 2010) - click to view image in new window
Figure 2. Log-transformed catch-per-unit-effort of chironomid midges caught in drift net samples in the Yolo Bypass Toe Drain and Sacramento River at Sherwood Harbor. Note the abundances of chironomids in the spring on the Yolo Bypass. The Bypass tends to have higher abundances than the Sacramento River in the spring, but lower abundances in the summer. Sampling in summer and fall only started in more recent years. Click on image to enlarge.

Stacked bar plot showing abundance and community composition of invertebrates collected in the drift net in the Sacramento River and Yolo Bypass by year. Insects are the most common group in all years and both sites. Gastropods are the second most common group in the Yolo Bypass, whereas oligocheates in the order clitellata are the second most common in the Sacramento RIver.  Abundances on the Sacramento River are usually about 25% of abundances on the Yolo Bypass - click to view image in new window
Figure 3. Catch per unit effort of organisms in the drift net categorized by taxonomic order and plotted over time. Insects dominate both the River and the Bypass samples, but the Bypass has consistently higher abundance of drift invertebrates. Click on image to enlarge.

One particularly unexpected thing we’ve seen in the data is high abundances of snails in the samples. Snails normally live on the bottom of the water or on vegetation, so seeing them floating on the surface was surprising. We see a lot of variation in snail abundances between years, and we’re not sure why (Figure 4). The wet years of 2017 and 2019 had particularly high snail catch, but other wet years weren’t similar. A fun mystery for someone to investigate!

Bar graph with large standard error bars showing snail catch by year and water year type (average, wet, or dry) - click to view image in new window
Figure 4. Mean (+/- one standard error) CPUE of snails (class Gastropoda) in drift net samples from the Yolo Bypass. Water year classes (Wet - W, Dry - D, or Average - A) is noted with letters under each bar. Notice how snail catch was very high during the wet years of 2017 and 2019, but also during the dry year of 2013 and the average year of 2003. Click on image to enlarge.

If you want to check out this data for yourself, it has been published on the EDI data repository and will be updated regularly. However, keep in mind that sample frequency, contracting labs, and methods have changed slightly over time. Be sure to read the metadata so you fully understand the data before using it. If you have any questions, just reach out! We’re nice people and we love talking about our data and helping others use it.

Further Reading

Categories: 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

diagram of organism giving presentation

Categories: BlogDataScience, General