Ann E. Holmes | Geology Reports

USGS2022

Environmental DNA methods for ecological monitoring and biodiversity assessment in estuaries

Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for aquatic eDNA detection and interpretation were developed primarily in freshwater environments and have not been well established for estuaries and marine environments that are by nature dynamic, turbid, and hydrologically complex. Environmental context and species life history are critical for successful application of eDNA methods, and the challenges associated with eDNA detection in estuaries were the subject of a symposium held at the University of California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed in the symposium to evaluate eDNA methods in the context of monitoring and biodiversity studies in estuaries. We first provide a concise overview of eDNA science and methods, and then examine the San Francisco Estuary (SFE) as a case study to illustrate how eDNA detection can complement traditional monitoring programs and provide regional guidance on future potential eDNA applications. Additionally, we offer recommendations for enhancing communication between eDNA scientists and natural resource managers, which is essential for integrating eDNA methods into existing monitoring programs. Our intent is to create a resource that is accessible to those outside the field of eDNA, especially managers, without oversimplifying the challenges or advantages of these methods.

Estuaries and Coasts↗

USGS2018

Zooplankton dynamics in the Cache Slough complex of the upper San Francisco Estuary

We studied abundance and dynamics of zooplankton in the tidal freshwater Cache Slough Complex (CSC) in the northern Delta of the San Francisco Estuary during June, July, and October 2015. We asked whether the CSC was an area of high zooplankton production that could act as a source region for open waters of the estuary. Abundance of the copepod Pseudodiaptomus forbesi was similar to that in freshwater reaches of the central and eastern Delta and higher than that in the adjacent Sacramento River. Growth rate of P. forbesi was higher than previously measured in large estuarine channels because of higher temperature and phytoplankton biomass in the CSC. Samples of P. forbesi examined with molecular techniques contained an unexpectedly high proportion of DNA from cyanobacteria and little DNA from more nutritious phytoplankton. We also examined tidal exchanges of phytoplankton biomass and copepods between Liberty Island, a shallow tidal lake within the CSC, and the adjacent southern Cache Slough, which links the CSC to the Sacramento River. We calculated zero net flux of phytoplankton over 127 days between June and October. The tidal flux of copepods, calculated using tidal flow from an in situ flow station and half-hourly sampling over three 24.8-hr tidal cycles, varied a great deal because of temporal patchiness and day/night variation in abundance. Overall, the tidal flux was indistinguishable from zero, while the tidally-averaged water flow (and therefore the net copepod flux) was always into the wetland. Our results show some promise for the CSC as a productive habitat for planktivorous fishes and as a laboratory for learning how to design future wetland restoration. However, we remain cautious about whether wetlands such as the CSC may export large quantities of food organisms that can support fishes in other regions of the estuary.

San Francisco Estuary and Watershed Science↗