Science Stories: Adventures in Bay-Delta Data

More underappreciated data!

This is the second blog in our series on underutilized datasets from IEP.

San Francisco Bay Study’s Crab Catch dataset

Curated by Kathy Hieb and Jillian Burns

The San Francisco Bay Study has been sampling with otter trawls and midwater trawls throughout the San Francisco Bay, Suisun Bay, and Delta since 1980. Their fish data have been used in a number of scientific studies, regulatory decisions, and journal articles. However, did you know they measure and count crabs in their nets too?

Bay Study’s stations are all categorized as “Shoal” (shallow areas) or “Channel” (deeper samples). Crabs are collected by otter trawl, which is towed along the bottom of the water, scraping up whatever demersal fishes and invertebrates it comes across. Truth be told, it’s not the best way to catch crabs, because most crabs like hiding under rocks where they are out of the way of the net, but it does give us a metric of status and trends of some of the most common species of crabs, including the Pacific rock crab (Cancer productus), the graceful rock crab (Cancer gracilis, also known as the slender rock crab), the red rock crab, and everyone’s favorite, the Dungeness crab (Metacarcinus magister).

After the net has been towed on the bottom for five minutes, it’s brought on board the boat and the biologists count, measure, and sex the crabs they’ve caught (Figure 1). This can be tricky, because crabs can be FAST! Especially the smaller Dungeness crabs (Figure 2). The biologists have to be careful and pick up the crabs by their back side to avoid getting pinched by their claws, which definitely takes practice.

Once all the crabs are counted and measured, they are entered into a database that goes back to 1980. Bay's Study's Dungeness crab data have been used to help manage the commercial crab fishery because fisheries-independent data is valuable. From 1975 to 1978, an estimated 38-82% of the Dungeness crabs in the central California region rear in the San Francisco Estuary each year (Wilde and Tasto 1983). This dataset was also very helpful in tracking the introduction, expansion, and decline of the Chinese mitten crab (Eriocheir sinensis), which briefly took over the brackish regions of the estuary but declined as rapidly as it arrived (Figure 3. Rudnick et al 2003). Bay Study's crab data has also been combined with other datasets to see how the estuarine community as a whole responds to climate patterns and human impacts (Cloern et al. 2010).

However, a lot of questions remain to be asked of this dataset. Why did we see such high catch of Dungeness crabs in 2013 and 2016? What are the drivers between the lesser-studied crabs, such as the graceful rock crab? How does the salinity preference of each species of crab differ (Figure 4)? If you want to investigate these questions yourself, data are available on the CDFW file library website. But be careful, the data have a few hiccups in them, such as changes to sampling sites over time, missing samples during period of boat break-downs, and other caveats. Be sure to read the metadata and make sure you understand the data before using them.

Further reading

• Baxter, R., K. Hieb, S. Deleon, K. Fleming, and J. Orsi. 1999. Report on the 1980-1995 fish, shrimp and crab sampling in the San Francisco Estuary (PDF), Interagency Ecological Program Technical Report 63. Stockton, California. 503 pages. 
• Cloern, J. E., K. A. Hieb, T. Jacobson, B. Sanso, E. Di Lorenzo, M. T. Stacey, J. L. Largier, W. Meiring, W. T. Peterson, T. M. Powell, M. Winder, and A. D. Jassby. 2010. Biological communities in San Francisco Bay track large-sale climate forcing over the North Pacific (PDF). Geophysical Research Letters 37(L21602):6 pages.
• Cloern, J. E., and A. D. Jassby. 2012. Drivers of change in estuarine-coastal ecosystems: Discoveries from four decades of study in San Francisco Bay. Reviews of Geophysics 50(4):RG4001. 
• Rudnick, D. A., K. Hieb, K. F. Grimmer, and V. H. Resh. 2003. Patterns and processes of biological invasion: The Chinese mitten crab in San Francisco Bay. Basic and Applied Ecology 4(3):249-262.
• Rudnick, D., T. Veldhuizen, R. Tullis, C. Culver, K. Hieb, and B. Tsukimura. 2005. A life history model for the San Francisco Estuary population of the Chinese mitten crab, Eriocheir sinensis (Decapoda: Grapsoidea). Biological Invasions 7(2):333. doi:
• Rudnick, D. A., K. M. Halat, and V. H. Resh. 2000. Distribution, Ecology and Potential Impacts of the Chinese Mitten Crab (Eriocheir sinensis) in San Francisco Bay. Technical Completion REPORT UCAL-WRC-W-881, University of California. 
• Wild, P. W, & Tasto, R. N. (1983). Fish Bulletin 172. Life History, Environment, and Mariculture Studies of the Dungeness Crab, Cancer Magister, With Emphasis on The Central California Fishery Resource. UC San Diego: Library – Scripps Digital Collection.

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).

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?

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.

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!

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

• Benigno, G. M., and T. R. Sommer. 2008. Just add water: sources of chironomid drift in a large river floodplain. Hydrobiologia 600(1): 297-305.
• Goertler, P. A. L., T. R. Sommer, W. H. Satterthwaite, and B. M. Schreier. 2018. Seasonal floodplain‐tidal slough complex supports size variation for juvenile Chinook salmon (Oncorhynchus tshawytscha). Ecology of Freshwater Fish 27(2):580-593.
• Goertler, P., K. Jones, J. Cordell, B. Schreier, and T. Sommer. 2018. Effects of Extreme Hydrologic Regimes on Juvenile Chinook Salmon Prey Resources and Diet Composition in a Large River Floodplain. Transactions of the American Fisheries Society 147(2):287-299.
• Sommer, T. R., W. C. Harrell, A. M. Solger, B. Tom, and W. Kimmerer. 2004. Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA. Aquatic Conservation 14(3):247-261.
• For more key findings from the Yolo Bypass, check out the YBFMP Story Map