Predation by non-native fish in the Sacramento-San Joaquin Delta

For more information contact Melinda Baerwald: mrbaerwald(at)

Background and Significance of Study


The Sacramento-San Joaquin delta is host to one endangered fish species, the Central Valley winter-run Chinook, and four threatened fish species, the Delta smelt, green sturgeon, Central Valley spring-run Chinook, and steelhead, as well as several that are not listed but have drastically reduced population sizes when compared to historical averages. The common cause of the decline of these fish is habitat loss, however, predation by non-native fish is believed to contribute to their decline and has not been thoroughly studied(Baxter et al., 2010).

Traditionally, fish diets are assessed using visual identification of gut contents. However, these types of studies are limited by the length of time the prey are visually identifiable, making the method biased towards prey composed of hard tissue and prey recently ingested (Sheppard & Harwood, 2005). DNA-based methods for diet analysis offer two notable advantages over visual identification methods: (1)They can detect prey for a much longer time period than visual analyses, and (2) they can detect prey composed of soft tissue, such as eggs and larvae (Symondson, 2002).

We collect predators throughout the North delta and use genetic assays (qPCR) to detect incidence of predation on our species of interest. When sampling the predators, we characterize habitat conditions at every location. Predation may vary spatially and temporally, but also with respect to biotic or abiotic habitat conditions. There are numerous factors that may affect predation between species, such as uneven predator and prey abundances, distributions, and feeding preferences, as well as habitat conditions such as water temperature, turbidity, pH and density of submerged aquatic vegetation, to name a few. By surveying predator diets and discovering correlations between predation and environmental factors, we hope to glean information about particular conditions associated with increased predation of at-risk species.

Predators collected: Striped bass, largemouth bass, smallmouth bass, Sacramento pikeminnow, channel catfish and white catfish.

Prey detected: Delta smelt, Chinook salmon, rainbow trout/steelhead, Sacramento splittail, green sturgeon, white sturgeon, wakasagi, longfin smelt, threadfin shad, and Mississippi silverside .

Future Work

Our future goals for the project include using next-generation DNA sequencing (NGS) to identify all prey species present in a predators gut simultaneously. By creating ‘barcodes’ for all potential prey, we will be able to identify fish, crustacean, mollusks and other prey taxa using a technique call ‘metabarcoding.’




Brandl, Scott, et al. “Ten real‐time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta.” Molecular ecology resources 15.2 (2015): 278-284.