Four researchers at Scripps Institution of Oceanography have earned state grants to study how climate change is shifting conditions on the Pacific Coast, including cliffs and tide pools.

Together they were awarded $1 million from the California Ocean Protection Council to create maps, models and other data sources that will help chart the changes to California’s coastline, and guide strategies to deal with them.

The council was created in 2004 as part of the California Ocean Protection Act, and works to maintain “healthy, resilient and productive ocean and coastal ecosystems.” The grants of $250,000 to each scientist are part of a larger project to fund research on topics such as sea-level rise and coastal resilience, marine pollution and renewable energy.

Marine biology professor Ronald Burton will use “DNA metabarcoding,” a method of high volume genetic analysis, to identify fish eggs and determine which species are spawning from La Jolla to Santa Cruz. Jennifer Smith, an associate professor of marine biology, is building 3-D images of rocky intertidal zones to study how sea-level rise will affect the wealth of marine life in tide pools.


Scientist Adam Young will map the stability of coastal cliffs and detect “erosion hot spots.” And associate professor Brice Semmens will develop a time series of bass species abundance dating back to the late 1940s in order to guide management of the popular recreational fishery.

With her grant, Smith will create vast 3-D models of the intertidal zones off the California coast, with images that include soaring flyovers of the topography, as well as granular snapshots of each tide pool. It’s important, she said, because the intertidal zone is one of the most diverse marine habitats on the coast.

“In San Diego, we have a lot of different intertidal organisms, everything from bright green surf grass, seaweed, all kinds of muscles, barnacles, limpets, sea hares, octopus, small rockfish, nudibranchs and sea slugs,” Smith said.

Her work will also serve as a gateway to the ocean for tourists and other beachgoers, offering a glimpse of sea life that would otherwise only be visible to divers.


“It functions as a window into the ocean for people who may not be comfortable going into the ocean,” she said. “It tends to be one of the more important environments for engaging people in marine ecosystems.”

But it’s an elusive space that’s fully accessible for only a few hours, a few times a year, at extremely low tides. So Smith’s team is working to capture those moments with models built from millions of ordinary, individual pictures.

“We use a fairly low-tech approach, where we have a camera that we pull on a pulley, from the highest area to lowest area,” she said. “We end up with thousands of images. It’s like mowing the lawn of the intertidal.”

Researchers enter those images into a software program that stitches them together to create a 3-D model of the underwater landscape.


“We have a snapshot of everything that was there at that moment, and then spend the next few months exploring that habitat from our desks,” she said.

They plan to share the images with schools, scientific organizations and coastal tribal nations in California. And they will use them to project how sea-level rise could affect those ecosystems.

“This is especially important under the current climate scenarios, where we’re dealing with future sea-level rise, which will affect these intertidal habitats the most,” she said.

Burton’s project builds upon previous genetic analysis methods to identify and track fish spawning en masse.


“DNA metabarcoding is an advance from what we call barcoding,” Burton said. “It means we can identify an organism based on a small sequence of DNA.”

The technique allows scientists who are studying fish spawning to tell which species the tiny, gelatinous eggs belong to.

“Identifying a big fish isn’t hard, any expert can do it,” he said. “But identifying a fish egg is difficult, because most fish eggs look alike. They’re all small balls, they’re all about 1 mm across.”

Barton and his team have pulled fish eggs from Scripps Pier with a plankton net every week for six years, doing DNA barcoding, egg by egg, to find out which fish are breeding.


Over that time, they have sequenced over 20,000 eggs, at a cost of about $2.50 per egg. Although it’s a bargain compared to a 23andMe test, it gets pricey to test that many fish eggs.

Under the new “metabarcoding” system, however, scientists will grind up hundreds of eggs from each sample and sequence them together. By looking at the percentage of DNA snippets from each species, they can calculate how many of each fish species are spawning.

“So you have this mix of their DNA, presumably in the same proportion as eggs,” he said. “Then, at the end, we get back these sequences, and we look at how many of them are anchovy, versus mackerel or sand dab.”

Semmens will also use genetic identification techniques to create a 70-year timeline for bass populations off California.


“Down here in Southern California, recreational fisheries are really an engine of the economy,” he said.

State fisheries regulators are trying to assess sportfishing stocks, he said. But until the 1980s, all bass were lumped in one category instead of separated by species, such as kelp bass or spotted bay bass. However, California Cooperative Oceanic Fisheries Investigations, or CalCOFI, a partnership of Scripps Oceanography with marine regulators, maintains samples dating back to the 1940s.

“It was started by sardine fisheries after the sardine crash up in Cannery Row,” Semmens said. “That program has collected data, and also ichthyoplankton and trawls that we do in stations all over California. We could use that data to re-create the last 70 years of bass species.”

The trawl samples are preserved in formalin, and difficult to identify by eye, he said. But newer genetic technology can take those pickled fish eggs and match them to species, creating a history of which types of bass flourished during which different oceanic conditions, such as El Niño and La Niña periods.


“The end goal is to assess bass populations so that we can manage fisheries so recreational fishermen will have ample fish to catch into the future,” Semmens said.

Young will use laser data captured from overflights of the California coastline to create high-resolution maps of the state’s sea cliffs. The maps will show how coastal bluffs have shifted over the last two decades, and help predict what they may look like decades from now. Researchers will also test rock strength at different locations to see which areas can best resist erosion, and identify “hot spots” where cliffs are receding rapidly.

“Those areas that are retreating faster, we may be able to focus on those,” he said. “It’s important that we measure accurate historical erosion rates, so we can make better projections for the future.”

deborah.brennan@sduniontribune.com


Brennan writes for the San Diego Union-Tribune.