Crime Scene San Francisco: Who Is Responsible for the Disappearance of Delta Smelt?

Delta smelt are becoming harder and harder to find in the San Francisco Estuary. Some of the suspects in their disappearance are invasive fish species that were introduced from other places into the Estuary. These invasive fish can impact their new habitat by eating the native species that were originally there. However, it is hard to understand what the invasive fish are eating. We found that we can use the DNA in the stomachs of invasive fish to figure out what they have eaten. We caught a common invasive fish in the Estuary, called the Mississippi silverside, and analyzed the DNA from their stomachs to see if it matched delta smelt DNA. We discovered that some Mississippi silversides had delta smelt DNA in their stomachs! We therefore believe that Mississippi silversides are one of the culprits causing the disappearance of delta smelt.

A Survey of X2 Isohaline Empirical Models for the San Francisco Estuary

This work surveys the performance of several empirical models, all recalibrated to a common data set, that were developed over the past 25 years to relate freshwater flow and salinity in the San Francisco Estuary (estuary). The estuary’s salinity regime—broadly regulated to meet urban, agricultural, and ecosystem beneficial uses—is managed in spring and certain fall months to meet ecosystem objectives by controlling the 2 parts per thousand bottom salinity isohaline position (referred to as X2). We tested five empirical models for accuracy, mean, and transient behavior. We included a sixth model, employing a machine learning framework and variables other than outflow, in this survey to compare fitting skill, but did not subject it to the full suite of tests applied to the other five empirical models. Model performance was observed to vary with hydrology, year, and season, and in some cases exhibited unique limitations as a result of mathematical formulation. However, no single model formulation was found to be consistently superior across a wide range of tests and applications. One test revealed that the models performed equally well when recalibrated to a uniformly perturbed input time-series. Thus, while the models may be used to identify anomalies or seasonal biases (the latter being the subject of a companion paper), their use as inverse models to infer freshwater outflow to the estuary from salinity observations is not expected to improve upon the absolute accuracy of existing outflow estimates. This survey suggests that, for analyses that span a long hydrologic record, an ensemble approach—rather than the use of any individual model on its own—may be preferable to exploit the strengths of individual models.

Apparent Seasonal Bias in Delta Outflow Estimates as Revealed in the Historical Salinity Record of the San Francisco Estuary: Implications for Delta Net Channel Depletion Estimates

Accurate estimates of freshwater flow to the San Francisco Estuary are important in successfully regulating this water body, in protecting its beneficial uses, and in accurately modeling its hydrodynamic and water-quality transport regime. For regulatory purposes, freshwater flow to the estuary is not directly measured; rather, it is estimated from a daily balance of upstream Delta inflows, exports, and in-Delta water use termed the net Delta outflow index (NDOI). Field research in the 1960s indicated that NDOI estimates are biased low in summer–fall and biased high in winter–spring as a result of conflating Delta island evapotranspiration estimates with the sum of ungauged hydrologic interactions between channels and islands referred to as net channel depletions. In this work, we employed a 50-year observed salinity record along with gauged tidal flows and an ensemble of five empirical flow-salinity (X2) models to test whether a seasonal bias in Delta outflow estimates could be inferred. We accomplished this objective by conducting statistical analyses and evaluating whether model skill could be improved through seasonal NDOI flow adjustments. Assuming that model residuals are associated with channel depletion uncertainty, our findings corroborate the 1960s research and suggest that channel depletions are biased low in winter months (i.e., NDOI is biased high) and biased high in late summer and early fall months (i.e., NDOI is biased low). The magnitude of seasonal bias, which can reach 1,000 cfs, is a small percentage of typical winter outflow but represents a significant percentage of typical summer outflow. Our findings were derived from five independently developed models, and are consistent with the physical understanding of water exchanges on the islands. This work provides motivation for improved characterization of these exchanges to improve Delta outflow estimates, particularly during drought periods when water supplies are scarce and must be carefully managed.

Aliens From an Underwater World

About 3.1 billion people around the world live within 100 km of the coastline. If you are one of those people, then you also live near an estuary. What you probably do not know is that many alien species live in this underwater world, and we are not talking about extraterrestrial species from outer space. Are you scared? Well, do not be! These alien species are from planet Earth. In this article, we will tell you what alien species are, why scientists study them, how any species may become an alien, and how a few alien species may become an invasive species. You will also learn how you can help scientists find and track alien species, and how to defeat them. Along the way, we will give examples of alien species living in the San Francisco Estuary in North America, a paradise for hundreds of alien species.

Small Shorebirds Feast On Green Slime To Fuel Their Long Migration

Shorebirds wade in shallow waters along shorelines searching for food. More than a million shorebirds visit the San Francisco Estuary each year during their migration to feast on the insects, worms, clams, and crabs that live on or under the surface of the sand or mud. The abundant food in the Estuary provides shorebirds with the energy they need to migrate thousands of kilometers, between their breeding areas in the Arctic and their wintering areas along the Pacific coast of North and South America. Scientists have discovered that, during migration, small species of shorebirds eat a green slime called biofilm that grows on the surface of the mud. Larger shorebirds do not eat biofilm. This article describes how the bills and tongues of small shorebirds help them eat biofilm, what biofilm is, and why biofilm is an important food for those birds during migration.

Diary of Wimpy Fish: How to Grow Up in a Conservation Hatchery and Survive in the Real World

Conservation hatcheries are like luxury fish hotels that raise threatened and endangered fish that are nearing extinction in the wild. Raising fish in the controlled environment of the conservation hatchery usually takes away the issues that caused the population to dwindle in the first place. However, there is one problem: the fish get used to the conservation hatchery and become wimpy, meaning they become domesticated and do not do as well as wild fish in if they are returned to the natural environment. Managing the genes of hatchery fish is one way to block domestication and raise fish that are as close as possible to wild fish. In the San Francisco Estuary watershed, there are conservation hatcheries for the endangered delta smelt and winter-run Chinook salmon. Read on to learn about how these conservation hatcheries help hatchery fish be as tough as possible and survive in the wild.

Can Plants Be Engineers?

When we think of engineers, we think of making a machine, like a car. Are there engineers for ecosystems? When an organism can make big changes to its environment, we call it an ecosystem engineer. In aquatic ecosystems like the San Francisco Estuary, underwater plants can be important ecosystem engineers because they can change water flow and water clarity. In the Estuary, a plant called Brazilian waterweed, which was introduced by humans, is one of the most important ecosystem engineers. With its leaves and stems, this plant traps tiny particles floating in the water, making the water clearer. Clearer water has made it easier for more plants to grow and these changes helped some non-native fish species to increase in number, while some native species declined. Introduction of Brazilian waterweed has led to an entirely different ecosystem, which has also affected how people use and take care of the Estuary.

Estuaries, A Happy Place For Fish

Anchovies, salmon, sardines, gobies, mullets, flounder, bass, barbels, eels, shad, and even sharks—what do they have in common? Well, at certain points in their lives you may find them in estuaries, the final sections of rivers before they meet the ocean. Some fish live in estuaries their entire lives. However, some fish species prefer living in the freshwater parts of estuaries, others only live close to the ocean, and a few others spread throughout the estuary. Some species prefer living close to the bottom, some in marshes, and some constantly swim around in the estuary. Some prefer eating other fish, while other species like worms, or insects, or microscopic animals. Unfortunately, many estuarine species are in danger, and all because of humans. In this article, we will tell you why estuaries are such special places for fish and describe some of the species that call the San Francisco Estuary their home.

Living Fossils: Sturgeon of the San Francisco Estuary

Sturgeon are fish that are considered living fossils. Their ancestors date back over 200 million years, to the same time as dinosaurs. These fish can grow taller than humans (over 2 m), weigh over 160 kg, and live as long as humans. Sturgeon species have special adaptations, such as a vacuum-like mouth and body armor called scutes. There are 27 species of sturgeon worldwide. Two species, green and white sturgeon, are native to California, USA, and are some of the largest animals in San Francisco Bay. Sturgeon populations have declined due to habitat loss, water management, overfishing, poaching, pollution, and climate change. Sturgeon cannot jump over barriers like salmon can, so structures like dams that block water also block sturgeon from reaching their natural spawning habitat farther upstream in the river. Scientists are using new technologies to monitor sturgeon populations and discover the unique behaviors of these dinosaur-era fish in California’s rivers and estuaries.