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Featured Survey

  • Smelt Larva Survey:
    • When the weather turns cold and stormy it can mean it’s spawning season for many of our native Estuary fishes. The Smelt Larva Survey is out on the water during the wet winter keeping tabs on the reproductive activities of our endangered and threatened species of smelts. The Smelt Larva Survey began in 2009 and provides near real-time distribution data for Longfin Smelt larvae in the Delta, Suisun Bay, and Suisun Marsh. These data are used by agency managers to assess vulnerability of Longfin Smelt larvae to entrainment in south Delta export pumps. The gear is highly efficient at retaining small larvae, and the project also collects data on other larval fish species.

Featured Publications

  • In what may be one of the most comprehensive and important reports ever published on the subject in our Estuary, a crack team of researchers from the USGS has published an important treatise titled: “Physics to Fish: Understanding the Factors that Create and Sustain Native Fish Habitat in the San Francisco Estuary.” The report is available at the USGS Publications Warehouse, and is most assuredly worth a read.
  • In an attempt to describe the many factors affecting relative sea level rise (RSLR) in the Sacramento-San Joaquin Delta, Baranes and colleagues published a Nature scientific reports entitled “Sea level rise and the drivers of daily water levels in the Sacramento-San Joaquin Delta.” Their deconstructive technique is an interesting one and may be useful when applied to many of our longer-term datasets comprised of data traces resulting from several to many long-term processes.
  • An article on a related theme has been published in Environmental Biology of Fishes authored by Clause and three co-authors. “Wetland geomorphology and tidal hydrodynamics drive fine-scale fish community composition and abundance” discusses the combination of factors that contribute to the fish community structure we see and are an important part of our restoration conversations and objectives.
  • Environmental DNA has published a method article “CRISPR-based environmental DNA detection for a rare endangered estuarine species.” In the piece Nagarajan and colleagues discuss “the development of an eDNA detection assay for delta smelt (Hypomesus transpacificus), an endangered fish in the San Francisco Estuary, using SHERLOCK (Specific High-Sensitivity Enzymatic Reporter Unlocking).” This technique holds promise for new ways to detect and track rare and endangered species in our Estuary.
  • Challenges associated with environmental DNA surveying techniques is the subject of an article presented by Holmes and co-authors in PeerJ. In “Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches,” the researchers discuss how turbid field conditions can complicate the search for and detection of the endangered Delta Smelt.
  • San Francisco Estuary and Watershed Science has included a research article from Hutton and co-authors describing “A simplified approach for estimating ionic concentrations from specific conductance data in the San Francisco Estuary.”
  • A well-known team of Kimmerer, Slaughter, and Ignoffo have added “Copepod egg production estimates are biased by female mortality” to our literature on local zooplankton in Limnology and Oceanography. This article articulates a bias in reported production rates of Pseudodiaptomus forbesi, and important food source for San Francisco Estuary fishes of management interest and concern.
  • In an important contribution to our understanding of predation on fish in our watersheds Peterson and colleagues presented a research article in San Francisco Estuary and Watershed Science under the title: “Diets of native and non-native piscivores in the Stanislaus River, California, under contrasting hydrologic conditions.” The authors state: “The frequency of native fishes in predator diets was similar across years, despite contrasting hydrologic conditions; 2019 (wet year), 2020 (dry year), and 2021 (critically dry year). Our results show that Pacific Lamprey were frequently consumed by native and non-native piscivores, and that juvenile Chinook Salmon experience substantial predation early in their migration, regardless of hydrologic conditions.
  • “Managing a cyanobacteria harmful algae bloom “hotspot” in the Sacramento-San Joaquin Delta, California” is sure to receive attention from our local decisionmakers and water managers, and is available from the Journal of Environmental Management. From the article abstract: “Cyanobacterial harmful algal blooms (CHABs) have become a persistent seasonal problem in the upper San Francisco Estuary, California also known as the Sacramento-San Joaquin Delta (Delta). The Delta is comprised of a complex network of open water bodies, channels, and sloughs. The terminus of the Stockton Channel is an area identified as a CHAB “hotspot.” As CHABs increase in severity, there is an urgent need to better understand CHAB drivers to identify and implement mitigation measures that can be used in an estuarine complex like the Delta.”
  • For readers interested in making estimates of light penetration into our Estuary’s turbid waters, an article from Richardson and USGS colleagues will be of interest. Titled “A simple approach to modeling light attenuation in the Sacramento-San Joaquin Delta using commonly available data,” their method can be found in the San Francisco Estuary and Watershed Science Journal.
  • William H. Satterthwaite and colleagues have again provided a valuable contribution to our evolving understanding of Chinook Salmon in our Estuary through a research article published in San Francisco Estuary and Watershed Science. The article is: “Comparing fishery impacts and maturation schedules of hatchery-origin vs. natural-origin fish from a threatened Chinook Salmon stock.” This considered piece examines effects of ocean fisheries on stocks of Central Valley Spring-run Chinook, and they consider the effect of enhanced maturation rates on hatchery and wild salmon within the system. They also state “Tagging data from the years available indicate that ocean fisheries may reduce spawning run sizes (all ages combined) by 40% to 60% during periods of high fishing effort.”
  • “Accurate species identification is critical to monitoring programs because misidentifications can lead to incorrect assessments of population status and trends.” So say Stagg and co-authors in yet another article published recently in the San Francisco Estuary and Watershed Science Journal. They describe efforts to hone their techniques in “Proofing Field and Laboratory Species Identification Procedures Developed for the Non-Native Osmerid Species Wakasagi (Hypomesus nipponensis) Using SHERLOCK-Based Genetic Verification.”
  • Would you like to keep migrating juvenile salmon from entering the interior Sacramento-San Joaquin Delta? Then you’ll want to read a recent report made available by the USGS as an Open-File Report by Swyers and colleagues. The report is: “A Machine Learning Tool for Design of Behavioral Fish Barriers in the Sacramento-San Joaquin River Delta.”
  • In a Science and Policy for the Delta essay, Dettinger, Wilson, and McGurk write: “As California water agencies and institutions prepare their strategies and plans to secure the state's future water supplies and minimize flood risk, they would do well to consider how to keep water in the headwaters longer to mitigate inherent challenges posed by climate change.” From “Keeping Water in Climate-Changed Headwaters Longer,” the authors explore ways to adapt to climate changes we see coming across our Estuary and watershed. A strategy that uses our headwaters to manage the way we think about and store water for later use is the core of this probing piece, and should cause us all to reconsider how and why we manage our limited water resources in California. 

Featured Dataset Publications

Check out the IEP Calendar for upcoming Project Work Team, Stakeholder Group meetings and other IEP related events!

  • February 8, Data Science PWT Meeting 1:00 p.m. to 4:00 p.m. CANCELED
  • February 14, IEP PWT Chair & Stakeholder Group Meeting 1:30 p.m. to 3:30 p.m.
  • February 28, Zooplankton PWT Meeting 1:30 p.m. to 3:30 p.m.

Other Events or News

Frontiers for Young Minds: Where the river meets the ocean - Stories from San Francisco Estuary

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