Tiny aquatic animals called zooplankton are a critical food resource for fish. (Christian et Noé Sardet / Plankton Chronicles)

Using DNA to map out the food that keep fish alive

San Francisco’s estuary has had more than 95 percent of its historic marshes leveed and filled.

By Michelle Jungbluth

In April, a visitor to our research center’s open house watched a child dunk a net into a swimming pool, mimicking the act of how we trawl for tiny critters in the nearby estuary. Then that person asked me a question: “How bad is the health of the estuary, really?” As a new mother who has had to be careful to avoid eating local striped bass because of mercury levels in the fish, this question is one that hits me close to home.

Let’s look at the facts. San Francisco’s estuary, which includes waters from the Golden Gate all the way up through connected rivers like the Sacramento River and all the wetlands in between, has had more than 95 percent of its historic marshes leveed and filled. Our estuary is also the most invaded in the world, hosting more than 200 non-native species. These changes have led to such a dramatic shift in the structure of local food webs that the estuary can never return to a pre-invaded state. Partly due to the declining food resources that resulted from invasive species, scientists have also observed major declines in native and other established fish populations over the past few decades. But that doesn’t spell doom for the estuary — it just means we have to work harder to support native species and to keep a close eye on the use of freshwater resources that the area’s fish rely on.

Scientists like me are working to understand the complexities of how the estuary became what it is today and how we can help it recover. Since the introduction of the invasive clam Corbula amurensis in 1987, there has been a three-fold decline in phytoplankton, which are the photosynthetic algae at the base of the food web. Among other effects, the introduction of this formidable filter feeder led to shrinking populations of tiny aquatic animals called zooplankton — critical food for fish — which has contributed to declines in the amount of fish swimming in local waters.

Yet despite a highly altered environment and reduced amounts of the algae they rely on for food, zooplankton are still managing to make a living in the estuary. Where I work as a researcher in the laboratory of Wim Kimmerer, an adjunct professor of biology at the Estuary & Ocean Science Center, we’re studying these tiny, but important creatures. Our main research subjects are copepods: microscopic shrimp-like crustaceans that are near the base of the aquatic food web. Through many years of research into the relationship between algae and copepod growth in species in the estuary, Dr. Kimmerer and the graduate students he has mentored over the years have deepened our understanding of the bottom of the estuary’s foodweb.

One surprising finding is that even though measures of phytoplankton abundance in other systems can be closely related to copepod growth — an indicator of food resources available for fish — in the estuary, this does not seem to be the case.

Michelle Jungbluth, an adjunct associate professor of biology at San Francisco State University, is working help the San Francisco estuary recover. (Courtesy photo)

By studying what copepods eat and how they grow both in the laboratory in the field, we hope to be able to definitively say what feeds copepods in the estuary and as a result, how that supports the fish here.

Tracking the dietary lives of these tiny creatures has always been difficult — scientists have had to primarily rely on taking before and after snapshots of experimental water to determine what was removed during the course of a feeding experiment. Different kinds of plankton make for different kinds of meals: Some are nutritious, others are toxic and others can be hard to catch or to digest. By using DNA, we can pinpoint these different species and figure out which ones make up the diet of our important copepods.

Samples of zooplankton collected from the San Francisco estuary ready to be analyzed. (Courtesy photo)

Using DNA comes with challenges, too. There are databases full of these signatures, from studies by scientists from around the world. In our latest study of the diet of copepods, we will measure the DNA in the guts of the copepods, and then compare that DNA to what is known by using one such database. Since DNA studies in the estuary are relatively rare , we also have a lot of work to do to successfully connect DNA signatures to known organisms.

The hope is that resource managers in the Bay Area can use the findings to restore specific wetland habitats that better support zooplankton and fish populations,or find new ways to grow them in controlled environments.

Even though the health of the estuary may be very different from what it was before settlers moved to the Bay Area, scientists like myself and managers are working together to understand and provide better support for the organisms that live there. It isn’t easy, but few things worth doing are.

Jungbluth is an adjunct associate professor of biology at San Francisco State University; this story is part of a series looking at the sea and bay around us through researchers at the Estuary & Ocean Science Center at San Francisco State.

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