The flowering plants – not to be confused with seaweed – are considered “coastal canaries.”

These sensitive indicators of ocean health will die when water runoff carries high loads of nutrients or sediment, or when boating activity disrupts their root systems.

Changing water conditions, ocean warming, and acidification may also predispose these plants to the wasting disease that once wiped out most of the seagrass along the U.S. Atlantic coast.

You need a boogie board and a wetsuit to garden with Katharyn Boyer, a biology professor at San Francisco State University in California.

They come in handy along the shorelines of the San Francisco Bay where Boyer and her colleagues are replanting eelgrass. For more than a decade, she’s experimented with methods to replenish these underwater plants that create key habitats and buffer zones for coastal ecosystems. Figuring out reliable ways to grow more eelgrass could revitalize these critical areas and help other scientists reverse seagrass losses around the world.

Seagrasses are disappearing at rates that rival those of coral reefs and tropical rainforests, losing as much as seven percent of their area each year, according to the IUCN. While only eelgrass grows along the muddy shorelines of San Francisco Bay, more than 70 species of seagrass worldwide cover a global area estimated at up to 600,000 kilometers squared (about 373,000 square miles) — an area roughly the size of Madagascar.

The flowering plants — not to be confused with seaweed — are considered “coastal canaries.” These sensitive indicators of ocean health will die when water runoff carries high loads of nutrients or sediment, or when boating activity disrupts their root systems. Changing water conditions, ocean warming, and acidification may also predispose these plants to the wasting disease that once wiped out most of the seagrass along the U.S. Atlantic coast.

In the Bay Area, the long strands of eelgrass provide shelter for fish nurseries, prime substrate for the sticky eggs of herring, and food for the small “grazers” that eat the algae coating on the grass. The plant beds also forestall erosion by trapping sediments and slowing down waves or currents. Although researchers estimate around 9,490 hectares (more than 23,000 acres) of the San Francisco coastline could support eelgrass beds, these plants grow on less than one percent of that shoreline.

“There are so many different environs in San Francisco Bay, we’d like to come up with a template that helps us determine what methods would work best for each site,” says Boyer, who keeps her office at the Romberg Tiburon Center for Environmental Studies stocked with wetsuits.

Surveys of the San Francisco Bay Area showed that eelgrass beds were on the upswing between 2003 and 2009. Since then, replanting success rates have been unpredictable. Restoration efforts got a boost from damage mitigation funds set aside after the 2007 Cosco Busan oil spill, when a tanker dumped more than 50,000 gallons of crude bunker into Bay waters. The herring industry was hit especially hard, estimated to have lost about one-quarter of the next year’s spawning among the oil-contaminated eelgrass fronds.

Now, a third of the way into a nine-year restoration program, Boyer is part of an effort to add four acres of eelgrass to the coastline each year. Ideally, adding this acreage will enable the new eelgrass beds to continue self-propagating after the project is over.

Replanting the eelgrass is painstaking work. Boyer brings out the boogie boards to haul gear or plants around shallow water sites where she anchors the new transplants with bamboo stakes. Each eelgrass shoot is twist-tied to the upper end of a stake. Then, cupping a hand over the plant, the end of the stake is buried. In about two weeks, the roots take hold. Another method, developed by her colleagues, uses “sucker sticks” to attach eelgrass with string and then groups the sticks on lengths of PVC piping, to more easily maneuver the plants in deeper waters — where the “gardeners” wear thicker wetsuits.

Many variables can affect planting success, notes Boyer. Genotyping may help identify if there’s a “universal donor,” one type of eelgrass that can grow anywhere. Or, plants may thrive on diversity and grow best when grouped with eelgrass from different areas. This year, scientists sequenced the eelgrass genome for the first time, and that information may offer more clues to maximize planting success.

Transplanting microbes from the sediment of the donor site, along with the plant, may augment growth, too. Boyer is also investigating how plant vitality might be affected by grazers that eat the epiphytes — the single-celled and larger forms of algae that grow on seagrasses. Some of these mesograzers, such as the invasive Ampithoe valida, which resemble tiny shrimp, may cause more harm than good by eating the eelgrass along with the algae.

“We try to do our restoration in an experimental way, to learn from each area and do better next time,” says Boyer.

One failure, still unexplained, occurred in Corte Madera Bay, where healthy grass beds died suddenly after years of apparently healthy persistence. Although Boyer wants to keep looking for an answer, she says there isn’t time for that — not if scientists plan to meet the goal of getting 36 more acres of seagrass planted before the nine-year project ends.

If there have been surprising failures, there have also been unexpected successes. Eelgrass is thriving in Elkhorn Slough, an estuary about 100 miles south of San Francisco. Bordered by agricultural fields, the runoff is rich with fertilizer, making the water prone to algal blooms that usually kill seagrass. When algae coats the eelgrass, it diminishes the light available for photosynthesis and plant survival. Despite these conditions, the eelgrass in the Slough is abundant. That anomaly made Brent Hughes, a marine biologist from the University of California at Santa Cruz, wonder: Why?

“One day, I received a rare dataset of sea otter abundance in Elkhorn Slough from a citizen science program; 15 years of data. I was floored when I overlaid trends in eelgrass with trends in sea otters, they fit like a glove,” says Hughes.

The rise in the slough’s sea otter population correlated with the increase in eelgrass beds. Hughes theorized that the otters’ big appetites — they eat at least 25 percent of their body weight in prey every day — impacted eelgrass growth. He thought the otters’ food choices might improve conditions for the plant, similar to the way otter consumption of sea urchins promotes the growth of kelp beds.

However, the ecosystem dynamics in the slough were complex. To sort them out, Hughes conducted field experiments, placing cages — or not — over crabs in the eelgrass, and lab trials that recreated the food web in buckets, called mesocosms. His results showed that when large crabs were abundant, they ate the invertebrates that usually removed algae from the eelgrass. Yet when sea otters were present, they ate most of those crabs, allowing the invertebrates to flourish and keep the eelgrass free from harmful algal epiphytes.

“Now that we have determined that sea otters can promote healthy eelgrass, what other indirect effects could they have? For example, can they enhance the restoration success of eelgrass?” asks Hughes.

This wouldn’t be the first place where top predators influenced the growth of seagrass. In other areas, scientists have shown that sea turtles graze down the grass, creating a healthier growing environment.

Hughes is also collaborating with Boyer to identify and count the tiny herbivores that live off the slough’s eelgrass. Although Boyer is surprised they haven’t yet found invasive invertebrates that are common in San Francisco Bay, so far, they’ve only noted native grazers, such as Taylor’s sea hare, a cryptic invertebrate that blends in perfectly with the eelgrass.

Taking inventory under a microscope is time-consuming, but new funds will go toward training camera-linked software to complete the identifications, a process that could eventually allow for citizen scientists to join the effort.

Getting eelgrass to grow in more abundance will help maintain better water quality and boost the entire ecosystem. Many people hope that the underwater meadows will contribute to keeping carbon out of the atmosphere, too.

“First we need to figure out how to grow eelgrass on a larger scale,” says Boyer. “If we can really do that, then we’ll need a huge team of people who can help garden the Bay.”