By Kim Luke & John Durand
Zooplankton and their history in the San Francisco Estuary
Zooplankton are tiny aquatic organisms unable to swim against currents; they include microscopic crustaceans, small jellyfish, and larval life stages of other organisms (Figure 1). Although zooplankton are small in size, they have a big impact on the food web because they connect primary producers (mostly phytoplankton) to bigger consumers (like fishes). Most fishes rely on tiny, crustaceous zooplankton during early life stages, and some, like the endangered delta smelt (Hypomesus transpacificus), consume zooplankton throughout their entire life.
Zooplankton were once abundant in the San Francisco Estuary but declined dramatically in the late 1980s after the introduction of the overbite clam (Potamocorbula amurensis), which both competes with zooplankton for food and consumes zooplankton as they filter feed in water. This decline of zooplankton was followed by a decline in pelagic fish species in the 2000s, including plankton-eating longfin smelt (Spirinchus thaleichthys), delta smelt, threadfin shad (Dorosoma petenense) and the valued sport fish striped bass (Morone saxatilis).
Current restoration, monitoring efforts, and gaps in knowledge
The goal of tidal wetland restoration in the San Francisco Estuary is to enhance food web production, and there is an active and robust zooplankton monitoring effort across several agency programs (e.g., CDFW summer townet and fall midwater trawl, DWR zooplankton monitoring, and others) that spans much of the region. However, backwater habitats (i.e., more isolated areas away from open water) have received less attention due to their relatively small size and inaccessibility. For example, the upstream reaches of the Cache and Lindsey slough network in the North Delta have been relatively unstudied (Figure 2). The North Delta Arc is a swath of habitat from the Yolo Bypass to Suisun Marsh that holds exceptional promise for native fishes and habitat restoration. In this blog, we highlight our study looking at zooplankton trends in the North Delta Arc that are creating beneficial habitat for sensitive fishes.
Our study
We sampled zooplankton from 2014-2023, a period that included a mix of dry, moderate, and wet water years, including an extended drought. We focused on zooplankton density from March through May, when juvenile fish rely on zooplankton for food. To make that happen, we sampled five upstream reaches across the Cache and Lindsey slough networks, two remarkably different habitats (Figure 3-4).
The Cache Network is surrounded by agriculture with high levees lining the sloughs. The area received water from nearby agriculture, urban runoff, and the Sacramento River. During the study, the Cache Network tended to have more turbid (murkier) water and less submerged aquatic vegetation than the Lindsey Network.
The Lindsey Network had little water input from agriculture or urban sources, and mostly got Sacramento River coming in with the tides. The surrounding landscape is a mix of agriculture and riparian habitat. The network is home to the North Bay Aqueduct, which exports water for urban use, as well as the Calhoun Cut Restoration, which was completed in 2014. Notably, the Lindsey Network had more invasive submerged aquatic vegetation than the Cache Network.
Interesting insights
Through this study, we discovered that the different dynamics we noticed in the sloughs, such as differences in vegetation or water inputs, translated to noticeable differences in zooplankton densities. In the Cache Network, upper Cache Slough and Hass Slough tended to have high zooplankton densities relative to other sites. We attribute this to a mix of hydrologic and landscape features that make the network unique. The physical morphology of Cache and Hass sloughs tends to “hold onto” water for longer than a tidal cycle, in part due to a sandbar at the confluence of Cache and Hass sloughs that minimizes exchange with downstream sites and Sacramento River water. Water in this upstream basin carries urban and agricultural inputs that are richer in phytoplankton and nutrients than the Sacramento River water. Because the sloughs hold onto this nutrient- and phytoplankton-rich water, the plankton can quickly grow and reproduce, producing high zooplankton densities (Figure 5).
These habitat features are not unlike historic conditions that existed in the Delta and Central Valley before processes that began in the 1800s forever changed the landscape: siltation from gold mining, levees to protect towns and farms from flooding, dams to manage flows, and rip-rapped canals to efficiently transport water to fertile desert landscapes. Before those existential transformations of landscape, the marshy Central Valley and Delta captured and held water, grew high densities of pelagic food, and exported it with flood pulses of rain and snow melt throughout the spring and summer. Today these processes are largely lost but can be seen in the Cache Network which has modern landscape uses (urban and agricultural) with high residence time.
Key takeaways
Based on the results of our study, we see that on small scales, Cache Network dynamics may be used in restoration efforts to recreate historic levels of pelagic production. However, maximizing these benefits will require new restoration approaches focused on creating heterogeneous landscapes with the functional features required to recreate these results, coupled with adaptive management to test the results.
In order for wetland restoration to successfully support pelagic plankton production, key functional features must be included in design:
- Adjacency to seasonal or perennial freshwater sources that introduce nutrients and silt;
- Long sloughs with complicated bottoms that help sloughs hold on to nutrient and plankton-rich waters;
- Deep main channels that discourage invasive vegetation; and
- Shallow water habitat on margins that enhance phytoplankton production.
The Cache Network offers a successful model for landscape designers to incorporate food web elements into habitat restoration in tidal systems. It also serves as a reminder that small backwater areas can provide big benefits for food webs and shouldn’t be overlooked in monitoring efforts. Management, restoration, and policy decisions should consider these lessons when developing restoration projects and making decisions related to water and natural resources.
Kim Luke is an assistant research specialist at the Center for Watershed Sciences. Dr. John Durand is a research scientist studying aquatic ecology at the Center for Watershed Sciences and an instructor at UC Davis.
Further Reading
Alpine, Andrea E., and James E. Cloern. 1992. “Trophic Interactions and Direct Physical Effects
Control Phytoplankton Biomass and Production in an Estuary.” Limnology and Oceanography 37 (5): 946–55. https://doi.org/10.4319/lo.1992.37.5.0946.
Bashevkin, Samuel M., Rosemary Hartman, Madison Thomas, Arthur Barros, Christina E. Burdi, April Hennessy, Trishelle Tempel, and Karen Kayfetz. 2022. “Five Decades (1972–2020) of Zooplankton Monitoring in the Upper San Francisco Estuary.” PLOS ONE 17 (3): e0265402. https://doi.org/10.1371/journal.pone.0265402.
Durand, John, Chris Jasper, Brian Williamshen, Avery Kruger, Teejay O’Rear, and Rusty Hollmen. 2019. “North Delta Arc Study 2019 Annual Report: Cache and Lindsey Slough Water Quality, Productivity, and Fisheries.” Center for Watershed Sciences: University of California, Davis.
Durand, John R., Fabian Bombardelli, William E. Fleenor, Yumiko Henneberry, Jon Herman, Carson Jeffres, Michelle Leinfelder–Miles, et al. 2020. “Drought and the Sacramento-San Joaquin Delta, 2012–2016: Environmental Review and Lessons.” San Francisco Estuary and Watershed Science 18 (2). https://doi.org/10.15447/sfews.2020v18iss2art2.
Gross, Edward, Stephen Andrews, Brian Bergamaschi, Bryan Downing, Rusty Holleman, Scott Burdick, and John Durand. 2019. “The Use of Stable Isotope-Based Water Age to Evaluate a Hydrodynamic Model.” Water 11 (11): 2207. https://doi.org/10.3390/w11112207.
Luke, Kimberly. 2023. “Zooplankton Trends in the Cache-Lindsey Slough Complex, 2014-2021”. M.S. Thesis. University of California, Davis. https://www.proquest.com/docview/2866340801?pq-origsite=gscholar&fromopenview=true&sourcetype=Dissertations%20&%20Theses
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