Hybrid “Super Seagrass” Might Save Coastal Ecosystems

Seagrasses protect our oceans, providing secure harbor for sea life, calming tough waters, and storing extra carbon dioxide. Dozens of seagrass species defend coastlines across the globe, together with the widespread North American eelgrass, Zostera marina. But these useful underwater meadows are beneath menace from boating, dredging, illness, and excessive climate. Restoration efforts that merely replant extra eelgrasses fail round half the time—so, what now?

Scientists from the Salk Institute and Scripps Institution of Oceanography at UC San Diego say one answer is genomically knowledgeable restoration. In the waters of San Diego’s Mission Bay, a brand new hybrid seagrass has begun to develop. The hybrid is a cross between the shallow-water Zostera marina and its deeper-water cousin, Zostera pacifica, whose tolerance for low-light situations is a good trait as coastal waters change into more and more murky. The researchers used superior genomic and transcriptomic applied sciences to research the hybrid, discovering that the genes that management the interior timing mechanism—referred to as the circadian clock and inherited from Zostera pacifica—could assist the hybrid tolerate low mild.

The scientists say this genomic profile might make the brand new hybrid seagrass a candidate for future coastal restoration efforts in California and past.

The research was printed in Nature Plants on October 29, 2025, and was funded by each federal analysis funding from the National Science Foundation and personal philanthropy centered on creating crops to seize and retailer extra carbon.

“If this hybrid inherits Zostera 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,” says senior creator Todd Michael, PhD, a analysis professor at Salk. “Further field tests will be needed, but the genetics suggest a promising path to more resilient seagrass meadows.”

What we find out about eelgrasses, and why restoration efforts have failed

Eelgrasses cycle vitamins, enhance water high quality, and forestall coastal erosion, amongst many different features. These plentiful advantages have made them a primary goal for coastal restoration efforts. As such, scientists have spent a while finding out their genetics and making an attempt to replant them on once-covered seafloors. These efforts produced a totally sequenced Zostera marina genome in 2016, in addition to many years of restoration efforts for researchers to scour for successes and failures.

One main supply of failure was made clear in a 50-year retrospective: Zostera marina can not survive low-light situations. Zostera marina has developed mechanisms to endure the predictable, seasonal low mild that happens each winter by consuming up emergency sugar shops to outlive till spring or coming into a interval of dormancy. But coastal runoff and dredging within the bays that eelgrasses inhabit have decreased mild availability year-round, pushing the seagrass to its stress limits for longer than it’s biologically ready.

“We had been trying to find the genetic underpinnings of how seagrasses deal with low-light situations,” says first creator Malia Moore, PhD, a former graduate scholar researcher at Scripps Institution of Oceanography at UC San Diego, the place she was co-advised by Michael at Salk. “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?”

Launching a brand new period of genome-informed plant restoration

When Zostera pacifica and Zostera marina grew to become seafloor neighbors, they hybridized to create a daughter eelgrass. Luckily for the Salk and UC San Diego staff, a strong mattress of this hybrid grows regionally in San Diego’s Mission Bay. Hybrids are likely to outperform their dad and mom in excessive environments, comparable to within the low-light situations that stress Zostera marina. Hybrids may function important intermediates that bridge gaps between species, just like the shallow-water Zostera marina and deeper-water Zostera pacifica.

The researchers sequenced the hybrid’s genome and in contrast its transcriptome with Zostera marina to check whether or not it had inherited Zostera pacifica’s low-light tolerance. While the genome is an easy catalog of the various genes in an organism, the transcriptome represents the genes which are actively getting used—on this case, these being utilized in low-light situations.

The genome helped the researchers affirm that the hybrid was a first-generation cross between Zostera marina and Zostera pacifica. After confirming the cross, the staff grew the hybrid and Zostera marina facet by facet in low-light tanks and in contrast their transcriptomes to pinpoint variations in mild response. This tank setup was dubbed “extreme gardening” by the researchers, as rising these finicky sea crops is a feat of its personal, since eelgrasses help one another via complicated underground networks of stems and are very specific about their soil.

After profitable excessive gardening, transcriptomic evaluation revealed that Zostera marina and the hybrid had differing gene expression throughout mild regulation, sugar use, and stress responses. Despite receiving decreased mild, the hybrid expressed genes concerned in photosynthesis—an impact not noticed in Zostera marina. Some of probably the most outstanding divergences had been in genes controlling their circadian clocks, such because the central time-keeping gene referred to as LATE ELONGATED HYPOCOTYL (LHY).

The circadian clock in crops does far more than inform the plant when daybreak and nightfall happen; it additionally integrates the quantity of sunshine the plant has skilled, and controls progress accordingly. The scientists hypothesize that these circadian genes allow Zostera pacifica and the hybrid to gather mild for an extended interval over the day. In distinction, Zostera marina stops within the morning, which could possibly be the important thing to extra resilient eelgrass beds that endure seasonal storms and algal blooms.

Where the eelgrass hybrid matches in the way forward for coastal restoration

Bringing this hybrid eelgrass into coastal restoration efforts would require follow-up analysis and collaborations with ecologists, who’re specialists at mapping out the various ways in which introducing a brand new organism would possibly impression its setting.

“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,” explains Moore. “Now, we have a hybrid and natural population to study how restoration may work.”

But the long run is shiny for restoration efforts. Modern genomic and transcriptomic know-how yield insights into how crops are particularly tailored to totally different ecologies. And, by studying the organic mechanism that explains why one plant survives in a selected location whereas its neighbor perishes, scientists can embark on genomically knowledgeable restoration by creating crops tuned to particular environments in order that they’ll defend coastlines, shelter sea life, clear murky waters, and far more.

“Most studies collapse genomes into a single consensus, but our assembly of the hybrid separates the Zostera marina and Zostera pacifica subgenomes, allowing us to unambiguously track gene expression from the Zostera pacifica subgenome through to the hybrid,” says Michael. “With these genomic resources, we can replace trial-and-error plantings—which fail in up to 60 percent of Zostera projects—with genomically informed restoration, selecting genome-environment-matched plants to markedly improve establishment and long-term success.”

Reference: Moore ML, Allsing N, Hartwick NT, et al. Hybridization and low-light adaptability in California eelgrass (Zostera spp.). Nat Plants. 2025. doi: 10.1038/s41477-025-02142-2

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