Estuary News

June 2019

Super-Shore: A Multi-Habitat Experiment at Giant Marsh

Interview anyone of any stripe about the Giant Marsh living shorelines project and the same two words will be in every other sentence: high tide.

Each construction step of this California Coastal Conservancy-led effort to build new native oyster reefs interspersed with eelgrass off the Contra Costa County shore must consider the timing of tides. High enough to float a barge or Boston whaler into the shallows, do a day’s work, and get back out again on the next cycle. Three feet at least of draft – the amount of boat below the surface which varies depending on its weight — and preferably not in the middle of the night.

On April 18, as the contractor Triton Marine placed 180 1000-pound reef balls topped with clean Pacific oyster shell in the shallows off Point Pinole Regional Shoreline, the day time high tide occurred at 12:44 pm,  and lasted longer than in other seasons. That’s up to five feet above mean lower low water (MLLW), a mouthful of metric related to the high- low tidal cycle caused by the pull of the moon on the ocean and familiar to most people designing, building, or permitting projects within San Francisco Bay.

“What we didn’t expect was for Triton to want to rest the barge on the mudflat at low tide,” says Renee Spenst of Ducks Unlimited, which managed construction. Despite initial worries about damage to the bayfloor, regulators concluded the footprint was small and the local organisms in the oozes would rebound – a decision that helped optimize work periods for Triton, avoided night work which would bug the birds, and eliminated the need to explore alternatives such as heavy-lifting by helicopter.

“Subtidal work is not for the weary,” says the Conservancy’s Marilyn Latta, who led the three-year, 19-partner effort to birth this new living shoreline. The $3 million project is designed to test the ecological and shoreline protection benefits of nature-based infrastructure in San Francisco Bay, and was partially paid for with Cosco Busan oil spill settlement funds.

Scaling up from the Marin Test Run

When Latta and a team of scientists from the SFSU’s Estuary & Ocean Science Center (EOS), the Smithsonian Environmental Research Center, UC Davis and others built a pilot oyster reef on the San Rafael shore in 2012, four million native Olympia oysters settled on the new structures. The Marin pilot tested a variety of reef structure types and planting methods for associated eelgrass, and measured the response of wildlife. The results of these tests are informing the scale up at Giant Marsh project on the East Bay shore.

The impetus for all this experimentation is to beef up biodiversity. “Oysters and eelgrass are what we call foundation species,” says Katharyn Boyer, lead scientist for the San Rafael and Giant Marsh Living Shoreline projects, and a ecologist with the EOS Center. “This means they provide habitat and functions that benefit other species.”

Buffleheads find lots of food around eelgrass beds. Photos: Rick Lewis

There’s much more to the Giant Marsh project than expanding habitats for a mollusk and a seagrass, however. A map of the design shows a mosaic of plantings, oyster reef structures, and experiments extending from Bay shallows all the way to the edge of the uplands, and encompassing the tidal marshes in between. Seven habitat treatments with a footprint of about two acres are scattered across this shore zone habitat gradient over an area totaling 350 acres. In one spot, biologists are reintroducing the locally extinct California sea-blite — a salt tolerant succulent. In another spot, they will collect cobbles to which Pacific rockweed has attached itself and place them around some of the new reefs to add shelter and shade for the oysters. In still another, they will remove invasive Atlantic cordgrass and hybrids, and replant with the native species, then monitor the site to make sure the invader doesn’t make a comeback.

map of treatments

“We’re integrating eelgrass and native oyster restoration with wetland and upland transition zone restoration treatments at one location in the Bay for the first time,” says Latta.

“It’s easy to focus on a single species but to step back and consider the ecology of whole system – and how your target species might benefit as well – is an exciting way to think about doing restoration,” says Chela Zabin, a biologist with the Smithsonian Environmental Research Center also on the Giant Marsh team. “It makes sense, it’s more holistic.”

The team hopes to recreate or enhance the historic function of each kind of plant, habitat, and species in the shore zone. It also hopes to confront sea level rise head on in the habitats of thousands of people and the last few California Ridgway’s rails and salt marsh harvest mice. Nature-based infrastructure may be able o help us all adapt in ways seawalls cannot.

“The project is a great opportunity to understand what’s possible,” says Matt Graul of the East Bay Regional Park District, which shares ownership of the property dedicated to this big experiment with the State Lands Commission.

Chela Zabin
The World is Your Oyster

To help chose the best place to grow a new oyster reef, one of Chela Zabin’s jobs was to strap ceramic tiles, like those around your average kitchen sink, to three PVC poles and push them into the Bay mud. She installed the tiles at two different tide heights at seven sites in the waters off four Bay Area counties in 2015-16. 

Zabin is an artist turned Smithsonian center biologist. She wanted to see if there were enough native Olympia oyster larvae in each of the test sites to settle on the tiles and grow, among other experiments being performed by the living shorelines team at these test plots. Of the seven sites tested, Giant Marsh attracted the biggest crowd.

The ceramic tile tests were part of a comprehensive body of research on how to restore subtidal habitats and organisms in the Bay that has been underway for more than a decade. “Fourteen years ago we were doing small scale trials, everything from Save the Bay hanging oyster shell necklaces off piers to see if they attracted more oysters to our teams experimenting with planting methods for eelgrass,” says scientist Katharyn Boyer. “While we learned quite a bit about how to restore these species for their own sake, the big evolution in our thinking is to do restoration for all the possible ecosystem services provided by their habitats.” 

Test tile covered with oysters
Test tile covered with oysters and other life. Photo: Chela Zabin

“All the hard substrate we surveyed there, everything from our tiles to a [deflated] football, had oysters on it,” says Zabin. The Richmond shore surveys also failed to detect any of the Atlantic snails that drill into oyster shells. This invader arrived in the Bay over a hundred years ago with eastern oysters grown for food but now preys on the natives. “The snails don’t move much, and there are no new ones coming in, a combo that’s easy to work around [when you’re looking for a good spot to build a new oyster reef],” she says.

The Giant Marsh project has a much bigger footprint than the San Rafael pilot. Every piece of the new eastshore project is based on lessons learned and research questions raised by its predecessor on the Marin shore.  On the west side, for example, they learned that some reef designs held up better than others, and that eelgrass did better on the shoreside rather than the bayside of reefs.

A number of patterns also emerged that caught Zabin’s eye. “We saw more oysters lower down, more oysters on north sides, more oysters on horizontal than vertical surfaces. Taken all together, we’re thinking this is a signal that heat stress affects oysters.”

Which is one reason why this will be the first living shorelines project to try to incorporate rockweed, one of the brown macro-alga, or seaweeds, that naturally drape over rocky intertidal zones around San Francisco Bay.

EOS Center team plants eelgrass
EOS Center team plants eelgrass for Giant Marsh project.

“Rockweed doesn’t mind getting dried out to a crisp, so it could help oysters with heat,” says Zabin. Canopy forming seaweeds provide shade, structure, and moisture retention during low tides. In places where there’s rockweed, oysters can live higher into the intertidal zone, according to Zabin, an observation she wants to test at Giant Marsh.

“If rockweed really helps oysters survive better when the tide’s out, it could be really important with climate change, as oysters are exposed to higher and higher temperatures and risk of desiccation,” says Zabin. 

Michelle Orr
More than a Mere Meadow or Reef  

Asked about which way the wind blows off the Point Pinole shore, Michelle Orr takes a moment to consider. As an engineer for ESA (Environmental Science Associates) she’s designed dozens of marshes, floodplains, and habitat restoration projects along the West Coast and on inland waterways, but working in a subtidal environment is a new experience.

“We were looking for a site in terms of testing natural infrastructure that had some wind causing natural shoreline erosion, but not such strong winds or big waves that reef elements wouldn’t help. We wanted our structures to be effective,” says Orr, adding, like any engineer worth their salt, the answer to the original technical question. Apparently, the predominant winds at Point Pinole are from the southwest, with occasional strong winds from the northwest. These are the winds that generate the largest waves.

Initial data from the San Rafael pilot site had shown that the reefs reduced wave energy up to 30 percent.  Historic research at Point Pinole had also documented the erosion and retreat of the shore by up to 500 feet between 1855 and 1993.

In addition to wave energy, Orr and the living shorelines design team also had to think about shape and softness of the Bay floor, the swirl of sediment around any new structures, and the design, arrangement and size of the oyster reef elements. The team designed the reefs at different angles, densities, and distances from the shore to make the most of this living experiment (see map). 

“The longer the reef, the less waves can bend around it,” says Orr. “It can’t just be solid, you have to have ecological connectivity on both sides of the wall. That’s why we designed it in a checkerboard pattern.”

Giant Marsh Configuration and Element Geometry

Orr and the Giant Marsh team settled on three reefs situated 500-1,500 feet from the shore. The reef treatment farthest offshore is designed to achieve maximum ecological benefits for deeper water organisms, fish and fowl. The treatment nearest to shore offers a combination of ecological, wave attenuation, and shoreline erosion prevention benefits that amount to the kind of ‘natural infrastructure’ we may need in the future as the Bay rises. The treatment in the middle is a hybrid.

“From an engineering perspective, we spent the most time on the nearshore treatment,” says Orr. While Zabin’s tile surveys suggested the highest oyster densities occurred at MLLW, Orr knew she couldn’t create the reef at that level because it would be too far from shore to slow waves: “We tested the design closer and closer to shore, and higher and higher in the tidal range, and found there was a sweet spot at 1.5 feet above mean lower low water. It was a bit of trade off, fewer oysters but better wave attenuation. As sea levels rise, however, the nearshore reefs will get deeper and be covered by tides more often, so they will support more oysters into the future, which gave us some comfort.”

Marilyn Latta
Mining the Best Materials

Marilyn Latta has started to stockpile clean oyster half shell. Since the most accessible local source of supply – the Drakes Bay Oyster Company – recently closed, she’s keeping a few tons from the company stored in Nicasio near to the old oyster farm for future living shorelines projects.

“It was the only local entity with a shucking facility that separated the meats for sale separately, giving us half shell we could use,” says Latta. “If we place shell in the Bay it has to be free of disease and invasives, and the Drakes Bay company by-product was cured for two years in the sun to confirm it was clean.”

Shell is just one natural ingredient in the recipe developed for what Latta calls “baycrete,” the material from which the team creates reef balls and blocks. Baycrete is a mixture of sand and fossilized oyster shell mined from the Bay and Portland cement.

Photo: Beth Huning

“When layered up, shell has lots of nooks and crannies that provide plenty of attachment space, shade and moisture,” says scientist Chela Zabin.

At the San Rafael site, Latta and the living shorelines team tested a variety of building block shapes and materials mixtures for the reefs. “We had a layer cake and reef ball stack that didn’t hold up well physically, and the shell bags [eventually] accumulated so much sediment around the bottom it smothered the oysters,” she says. “At Giant Marsh we’re trying a combined design – a truncated reefball with shellbags on top so we use the shells where they are most valuable for oysters.”

“One of the big challenges for scaling up was making large volume of building blocks,” says Orr.  In the end, local labor from CiviCorps and the North Bay Conservation Corps built the blocks over three months in the summer of 2018, guided by a Florida oyster reef expert and with the help of a local contractor.

Conservation Corps building reef elements.
Conservation Corps building reef elements.

Latta is already thinking ahead about where to get more shells for living shorelines projects, and hopes to launch a shell recycling program with Bay Area restaurants (see upcoming article by ESTUARY reporter Nate Seltenrich in Bay Nature magazine).

Myla Ablog
Fill with Frills

It’s no surprise to anyone familiar with the Bay regulatory environment that this project – in all its multi-species, multi-habitat complexity — took time to get approved. Three years passed between inception and implementation, and two of those years involved permits.

“There have been oyster reef ball projects permitted and installed before, but never on this scale in California or the West Coast,” says US Army Corps of Engineers project manager Myla Ablog. “The process took longer. In addition, 2017-2018 was the year we had so much rainfall and so many fires we had more emergency permits to approve than in all years prior. It was also the year of the federal shutdown. So the oyster reefs came in two seasons behind on the installation.”

Initially, project leaders hoped Giant Marsh might be approved under the forward thinking nationwide permit for living shorelines the Corps released in 2017. If you can fit a project under a nationwide – which usually covers projects in the public interest — authorizations typically come faster. But for the subtidal work, permit conditions geared towards the East Coast and the Gulf Coast didn’t fit Bay conditions. 

Another setback came when the construction company hired to do the job – Triton Marine –finally worked out the details of how they would do it, which didn’t quite match up with original permit conditions. Instead of working only during high tides, which limits the work window, they asked if they could rest their barges on the bayfloor at low tide. “It sounds daunting to an applicant when you say we may need to ‘reinitiate,’” says Ablog, referring to having to go back to fish and wildlife agencies for another review.

“We have these beautiful wide mudflats that feed all the shorebirds around the Bay but create difficulties in terms of constructing new habitats in subtidal or tidal areas,” says the Bay Conservation and Development Commission’s Brenda Goeden. For the Hamilton tidal restoration project near Novato, she remembers, they had to run five miles of pipeline over the mudflats to move marsh-building material in the form of mud to the site – an expensive early experiment. “It’s really challenging to get barges into such shallow water. When Triton asked if they could just sit on the mudflat, we had to ask for how long, and what the square footage of the footprint would be?”

Another unexpected twist in the approvals process was the discovery of a number of seasonal hunting blinds right where the project was planned.

“We ended up relocating everything further north, which was a little hard because the bathymetry changed,” says Orr. “But we didn’t want boats running into our reefs or hunters shooting near our restoration sites.”

Of course the project had one big factor going for it – it aimed to make habitats for fish and wildlife better not worse.According to Ablog, “Projects that benefit the environment, or get done under the nationwides, rarely get a lot of press. [Everyone thinks] the federal government is slow and rejects everything, so applicants come in with knees knocking, afraid they’re not going to get a permit. But 95 percent of all applications do get permitted across the US. In California, our division permits billions of dollars worth of public, private and NGO projects every year.”

Katharyn Boyer
Giant Step into the Future 

Ecologist Katharyn Boyer, wading into the Bay in a wetsuit, has been on the cover of this magazine and the book Natural History of San Francisco Bay, among many other action shots. Her work – restoring eelgrass and studying other Bay habitats – regularly takes her into the shallows – sometimes upright on foot, sometimes belly-down on a surfboard pushing her way across the wet mud by hand, sometimes half slogging and half swimming. These are not easy places to get to.

Her labors mirror the kind of tenacity, grit and ingenuity required to undo some of the damage we’ve done to our shoreline ecosystems and estuarine environment in the process of growing the metropolitan Bay Area. They also reflect the opportunity smart people like Boyer, Latta, Zabin, and Orr –not to mention the 19 project partners — see in working with nature, not against it, to achieve mutual benefits. And finally their Giant Marsh project embraces the kind of big picture, silo-busting thinking we now need in spades to play bridge with climate change.

“We’re doing projects like this throughout the park district, we’re really committed to restoring these habitats,” says East Bay Park’s Matt Graul, which recently completed restoration of the nearby Dotson Family Marsh, for example. “The science says we don’t have much time, things are changing fast, so we need to act quickly.”

EOS Center scientists are training California sea-blite to grow over eucalyptus limbs culled from nearby trees to create taller arbors, places mice and birds can escape from high water. Photo: Kelly Santos. Concept & Diagram: Peter Baye

Giant and Dotson marshes sit on a county shore that’s getting lots of attention in terms of innovative, forward thinking improvements. At nearby Point Molate, the Coastal Conservancy recently removed derelict creosote-coated piers and the Red Rocks warehouse (hauling away 445 tons of debris). At Point San Pablo, an earlier 2016-2018 Conservancy project has already placed 200 oyster reef elements and planted four acres of eelgrass in the area. At another site, Chevron has worked with Baykeeper and the City of Pinole to open Point Molate Beach Park. All these projects also dovetail with the North Richmond Shoreline Community Vision that not only recommends implementation of the Giant Marsh project but also addresses local concerns about affordable housing and environmental justice.

The Giant Marsh project also nests nicely within recommendations of a new Adaptation Atlas co-published by the San Francisco Estuary Institute and SPUR. The atlas aims to help planners better understand existing habitats and science based goals for restoration in their watersheds that might help them adapt to climate change. It also describes in more detail 30 specific “operational landscape units” or OLUs, as a basis for adaptive decision-making including the Wildcat OLU where Giant Marsh is located (see map).

“This is the only OLU in the Bay where all the adaptation measures that we mapped are suitable,” says one of the atlas authors, SFEI’s Julie Beagle. “Its a great example of a project that is piloting and monitoring many living shoreline approaches, which have great potential to be used elsewhere.”

This potential was first recognized in the 2010 Subtidal Habitat Goals report, which in turn built on the potential realized in hundreds of acres of restored wetlands by the 1999 Baylands Goals report. Giant Marsh is the fifth and largest pilot living shorelines project to be built since 2010. “It’s good to see they are helping to meet subtidal goals set ten years ago,” says BCDC’s Brenda Goeden, one of a variety of agencies involved in the goal setting (SCC, BCDC, OPC, SFEP, and NOAA).

In the meantime, the team and the construction crew hopes to complete the oyster, eelgrass, and rockweed elements of the Giant Marsh project by July 2019.  But even that won’t be the end of it. The project includes additional cordgrass and transitions zone plantings, and a comprehensive monitoring plan that will measure everything from plant survival rates to wave energy deflection to biological response.

“We’re even trying to measure the degree to which these restoration projects sequester carbon and reduce acidification,” says Boyer, referring to planned tests of carbon levels in live and dead plant material above and below the soil. Low pH (high acid) waters hamper the ability of oysters to make shells. But eelgrass, through photosynthesis, can draw carbon from the water and raise pH. “The question we hope to answer is ‘Can we use restoration of eelgrass to promote that process? Can we actually measure a lasting effect locally?” says Boyer.

‘We’re encouraged to see experimentation with alternative methods moving forward,” say Goeden.

“We are going to see sea level rise effects magnify. We need to know what tools are in our toolbox sooner rather than later,” says Boyer.

Living Shorelines, Coastal Conservancy

Subtleties of the Subtidal, Bay Nature, Oct-Dec 2010

Two Urban Estuaries Soften Shores, Estuary News, March 2018

Human Centered Conservation in North Richmond, Estuary News, March 2018

Building Equity in the Urban Fabric and Forest, Estuary News June 2018

Hauling out to Higher Ground, Estuary News December 2018

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About the author

Ariel Rubissow Okamoto is both today’s editor-in-chief and the founding editor of ESTUARY magazine (1992-2001). She enjoys writing in-depth, silo-crossing stories about water, restoration, and science. She’s a co-author of a Natural History of San Francisco Bay (UC Press 2011), frequent contributor of climate change stories to Bay Nature magazine, and occasional essayist for publications like the San Francisco Chronicle. In other lives, she has been a vintner, soccer mom, and waitress. She lives in San Francisco close to the Bay with her architect husband Paul Okamoto.