Brian M. Schreier

Ten real‐time PCR assays for detection of fish predation at the community level in the San Francisco Estuary–Delta

The effect of predation on native fish by introduced species in the San Francisco Estuary–Delta (SFE) has not been thoroughly studied despite its potential to impact species abundances. Species‐specific quantitative PCR (qPCR) is an accurate method for identifying species from exogenous DNA samples. Quantitative PCR assays can be used for detecting prey in gut contents or faeces, discriminating between cryptic species, or detecting rare aquatic species. We designed ten TaqMan qPCR assays for fish species from the SFE watershed most likely to be affected by non‐native piscivores. The assays designed are highly specific, producing no signal from co‐occurring or related species, and sensitive, with a limit of detection between 3.2 and 0.013 pg/μL of target DNA. These assays will be used in conjunction with a high‐throughput qPCR platform to compare predation rates between native and non‐native piscivores and assess the impacts of predation in the system.

TaqMan assays for the genetic identification of delta smelt (Hypomesus transpacificus) and wakasagi smelt (Hypomesus nipponensis)

We have developed species‐specific TaqMan assays for two California fish species, the threatened delta smelt (Hypomesus transpacificus) and the introduced wakasagi smelt (Hypomesus nipponensis). The assays are capable of correctly identifying each species with 100% accuracy, with no cross‐species amplification. We anticipate these assays will prove useful for future scientific studies requiring genetic species identification (e.g. predation of smelt) or monitoring (e.g. detection of delta smelt near water diversions).

Examination of Predation on Early Life Stage Delta Smelt in the San Francisco Estuary Using DNA Diet Analysis

AbstractWe examined predation by nonnative Mississippi Silversides Menidia audens, other small fishes, and invertebrates on the early life stages of the endangered Delta Smelt Hypomesus transpacificus, which is endemic to the Sacramento–San Joaquin Delta in California. Mississippi Silversides and other putative predators were collected primarily via boat electrofishing in the northern reaches of the upper San Francisco Estuary, an area targeted for substantial tidal wetland restoration to enhance habitat for Delta Smelt and other endangered fishes. Predators’ digestive tracts were removed and analyzed for the presence of Delta Smelt DNA by using quantitative PCR TaqMan assays. Across all sites, 69 of 550 Mississippi Silversides tested positive for Delta Smelt DNA. The number of sampled Mississippi Silversides that were positive for Delta Smelt DNA was significantly greater in offshore habitats than in nearshore habitats. Delta Smelt DNA detection data indicated that a wide variety of other species were al...

Generation of Quantitative Polymerase Chain Reaction Detectability Half-Lives and Comparison of Sampling Protocols for Genetic Diet Studies of San Francisco Estuary Fishes

AbstractSeveral factors affect the probability of genetic analyses to detect prey in predator gut contents, including biological differences in the prey and predator species as well as differences in sampling and laboratory methodologies. Understanding these biases allows researchers to more appropriately put genetic prey detections in an ecological context. In this study, we determined the detectability half-lives of DNA from two prey species in the guts of two predators. The half-life detectability of juvenile Chinook Salmon Oncorhynchus tshawytscha in Striped Bass Morone saxatilis was 66.2 h, and that of larval Delta Smelt Hypomesus transpacificus in Mississippi Silverside Menidia audens was 26.4 h. Additionally, we performed a series of laboratory trials to examine the effects of variables in sample collection and preservation methodologies on the detectability of prey. Differences between methodologies were minimal, providing confidence that laboratory analyses will not be greatly affected by inconsi...

Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta

Many estuarine and freshwater ecosystems worldwide have undergone substantial changes due to multiple anthropogenic stressors. Over the past two decades, the Sacramento-San Joaquin Delta (Delta) in California, USA, saw a severe decline in pelagic fishes, a shift in zooplankton community composition, and a rapid expansion of invasive aquatic vegetation. To evaluate whether major changes have also occurred in the littoral fish community, we analyzed a beach seine survey dataset collected from 1995 to 2015 from 26 sites within the Delta. We examined changes in the Delta fish community at three different ecological scales (species, community, and biomass), using clustering analyses, trend tests, and change-point analyses. We found that the annual catch per effort for many introduced species and some native species have increased since 1995, while few experienced a decline. We also observed a steady pattern of change over time in annual fish community composition, driven primarily by a steady increase in non-native Centrarchid species. Lastly, we found that littoral fish biomass has essentially doubled over the 21-year study period, with Mississippi Silverside Menidia audens and fishes in the Centrarchidae family driving most of this increase. The changes in the catch per effort, fish community composition, and biomass per volume indicate that a shift has occurred in the Delta littoral fish community and that the same factors affecting the Delta’s pelagic food web may have been a key driver of change.