Seagrass Study Points to Promising Pathway for Ocean Restoration

Story by:

• Brittany Hook- [email protected]

Topics covered:

• Seagrass
• Marine Biology
• Coastal Restoration

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A new study led by UC San Diego's Scripps Institution of Oceanography and the Salk Institute for Biological Studies reveals the potential of a new hybrid seagrass to advance ocean restoration efforts in California and beyond.

Seagrasses help preserve the ocean by offering food and shelter for sea life, calming rough waters, reducing erosion and storing excess carbon dioxide. Dozens of seagrass species protect coastlines around the globe, including the common North American eelgrass, Zostera marina.

But these beneficial underwater meadows are under threat from boating, dredging, disease and extreme weather.Restoration efforts that simply replant more eelgrasses fail around half the time, leading researchers to explore new approaches.

In a recent studypublished in Nature Plants, scientists at Scripps Oceanography and the Salk Institute point to genomically-informed restoration as a solution.

Scripps Oceanography researchers discovered the new hybrid seagrass by chance in the waters of San Diego's Mission Bay. The hybrid is a cross between the shallow-water Zostera marina and its deeper-water cousin, Zostera pacifica, whose tolerance for low-light conditions is a favorable trait as coastal waters become increasingly murky.

Using advanced genomic technologies and methods, the research team investigated the Zosterahybrid, finding that the genes that control the internal timing mechanism - called the circadian clock and inherited from Z. pacifica - may help the hybrid tolerate low light.

"Our study reveals how a newly discovered hybrid seagrass is a candidate for future coastal restoration efforts, thanks to its unique genomic profile, or plant DNA," said lead author Malia Moore, a recent Scripps Oceanography PhD graduate. "What's especially exciting is that this is the first functional study of an eelgrass hybrid species that was previously unidentified, and it's found right here in our own 'back yard' off San Diego."

The study was supported by federal research funding from the National Science Foundation and private philanthropy focused on developing plants to capture and store more carbon.

"If this hybrid inherits Z. pacifica's low-light toolkit, it could become a new avenue for restoration, guiding where and how we plant new seagrasses and which genes or lineages are most likely to survive in murky waters," said senior author Todd Michael, a research professor at Salk and adjunct professor at Scripps Oceanography. "Further field tests will be needed, but the genetics suggest a promising path to more resilient seagrass meadows."

What we know about eelgrasses, and why restoration efforts have failed

Eelgrasses cycle nutrients, improve water quality and prevent coastal erosion, among many other functions. These abundant benefits have made them a prime target for coastal restoration efforts. As a result, scientists have investigated their genetics and attempted to replant them in areas where they once thrived.

These efforts produced a fully sequenced Z. marina genome in 2016, as well as decades of restoration efforts for researchers to examine for successes and failures.

One major source of failure was made clear in a 30-year retrospective: Z. marina cannot survive low-light conditions. The species has developed mechanisms to endure the predictable, seasonal low light that occurs every winter by using up emergency sugar stores to survive until spring or entering a period of dormancy. But coastal runoff and dredging in the bays that eelgrasses inhabit have reduced light availability year-round, pushing the seagrass to its stress limits.

"We were searching for the genetic underpinnings of how seagrasses cope with low-light conditions," said Moore, who was co-advised by Michael at Salk during her graduate studies. "If there are some genetic individuals that are more resilient, and that's encoded in their genomes, could we find that? And could we then use those insights to inform restoration efforts that tackle this intolerance to low light?"

Discovery of the unique hybrid and how it functions

In the fall of 2022, one of Moore's colleagues at Scripps Oceanography, chemist Alex Bogdanov, spotted a unique-looking seagrass while snorkeling in Mission Bay. Remembering Moore's interest in seagrasses from a peer-to-peer presentation on campus, he thought it was worth bringing to her attention.

The tip proved rewarding. Soon after, Moore visited the site and later confirmed in the lab that it was indeed a previously unrecorded hybrid species.

"It was really exciting when I swam out to the site and saw the eelgrasses. I could immediately spot the hybrid because its leaves underwater were thicker than the surrounding grasses," said Moore. "This discovery was made possible due to the collaborative nature of the Scripps community. It was a chance find, but it also highlights the power of sharing our work."

So how did the hybrid come to be? Like many developed coastal bays, Mission Bay is a human-managed ecosystem shaped by routine dredging that maintains its network of coves and channels. Its seagrass beds are managed through mitigation practices, where disturbed areas are replanted and monitored, resulting in a population that is regularly disrupted, restored and genotypically mixed.

Researchers point to a previous restoration effort in the bay that brought Z. pacifica and Z. marina into close proximity on the seafloor, setting the stage for hybridization and emergence of the new eelgrass. Hybrids tend to outperform their parent species in extreme environments, such as in the low-light conditions that stress Z. marina. They can also serve as critical intermediates, bridging gaps between shallow-water and deeper-water species.

In the lab at Salk, genomic analysis confirmed that the hybrid was a first-generation cross between Z. marina and Z. pacifica.While the genome is a straightforward catalog of the many genes in an organism, the transcriptome represents the genes that are actively being used - in this case, those being used in low-light conditions. The researchers sequenced the hybrid's genome and compared its transcriptome with Z. marinato test whether it had inherited Z. pacifica's low-light tolerance.

At Scripps Oceanography, the team grew the hybrid and Z. marinaside by side in a low-light tank, comparing their transcriptomes to pinpoint differences in light response. The researchers dubbed the tank setup as "extreme gardening," as growing these finicky sea plants is challenging - the eelgrasses support each other through complex underground networks of rhizomes and are very particular about their soil.

Further analysis revealed key differences between the hybrid and Z. marina in light regulation, sugar use and stress responses. Even under reduced light, the hybrid expressed genes involved in photosynthesis - an effect not observed in Z. marina. Some of the most prominent divergences were in genes controlling their circadian clocks, including the central time-keeping gene called Late Elongated Hypocotyl.

Where the eelgrass hybrid fits in the future of coastal restoration

Bringing this hybrid eelgrass into coastal restoration efforts will require follow-up research and collaborations with ecologists, who are experts at mapping out the many ways that introducing a new organism might impact its environment.

"How reproductively viable is the hybrid? Is it attracting different fish and invertebrates? Is it creating as much biomass? There are a ton of questions we still need to answer about how the hybrid might affect the ecosystems that it's planted in," said Moore. "Now, we have a hybrid and natural population to study how restoration may work."

But the future is bright for restoration efforts, according to the authors. Modern technologies yield insights into how plants are specifically adapted to different environments. By learning the biological mechanism that explains why one plant survives in a specific location while its neighbor perishes, scientists can embark on genomically informed restoration by developing plants tuned to specific environments so that they can protect coastlines, shelter sea life, clean murky waters and more.

"With the genomic resources uncovered in this study, we can replace trial-and-error plantings - which fail in up to 60% of Zostera projects - with genomically informed restoration," said Michael. "This would allow for the selection of genome-environment-matched plants to markedly improve establishment and long-term success."

Other authors include Nicholas Allsing, Nolan Hartwick and Allen Mamerto of Salk, Emily Murray of Scripps Oceanography and Salk, and Rilee Sanders of Scripps Oceanography and Paua Marine Research Group.

The work was supported by the Salk Harnessing Plants Initiative through TED Audacious, Bezos Earth Fund, and Hess Corporation; Bill and Melinda Gates Foundation; National Science Foundation; and Tang Genomics Fund.

- Adapted from the Salk Institute