The findings, published in the Journal of Phycology, come at a pivotal moment. Sugar kelp is one of the dominant species in Maine’s kelp forests, providing food, habitat, and clean water that support a rich marine ecosystem. It is also the biological bedrock of the state’s burgeoning kelp aquaculture industry, the largest of its kind in the United States, which relies on the annual harvest of reproductive tissue from wild kelp populations. As ocean warming continues to drive the steady decline of these forests, understanding the genetic architecture of what remains has become an urgent scientific and economic priority.

Senior Research Scientist Doug Rasher, the study’s senior author, and his team have published several previous studies documenting how rising water temperatures are eroding Maine’s kelp forests. That loss has cascading impacts on coastal ecosystems and threatens the wild resource upon which the aquaculture industry depends. Responding effectively, the researchers argue, requires a detailed map of the structure and potential genetic barriers among the remaining forests.

“We wanted to explore questions of genetic diversity within the state of Maine because that’s the spatial scale that’s relevant to managing wild kelp forests, developing effective restoration programs, and establishing best practices in aquaculture,” Rasher said. “We brought it down to the scale that really matters from a management perspective.”

To build that map, the team collected genetic material from sugar kelp at 11 sites spanning Maine’s “outer coast.” These locations were chosen deliberately: they are far enough offshore to be subject to the oceanographic forces that influence the entire coastline, yet close enough to shore to be plausible future sources of reproductive tissue for the aquaculture industry. The analysis revealed moderate levels of genetic diversity within each study site and identified at least four distinct populations distributed along the coast.

The evidence suggests that genetic mixing occurs readily between sites within each population, presumably driven by currents dispersing kelp spores during their early life stage. But kelp are mobile for only a very brief window of time before settling on the seafloor for the remainder of their life cycle. Even with the strong currents that characterize the Gulf of Maine, spores seemingly do not travel far, and there appears to be little gene transfer between the four populations.

“Having distinct populations means there are different genetic signatures along our coast, and some populations could have individuals that are more or less suited to thrive in varied environments,” said lead author Rene Francolini, a former University of Maine PhD student in Rasher’s lab. “That’s important for restoration work or when we think about farmers who might collect reproductive tissue in one location and outplant seed in another.”

That distinction carries real-world consequences. Previous research has shown that genetic diversity can bolster resilience to marine heat waves, providing populations with the raw material to adapt as conditions shift. It also supplies critical variation for selective breeding in aquaculture, where traits such as growth rate, thermal tolerance, and morphology can determine the success of a farm. If farmers harvest reproductive tissue from one genetically distinct population and deploy the resulting seed string in waters dominated by another, they could inadvertently disrupt local adaptation—or, conversely, miss an opportunity to match the best-suited genotypes to the right environments.

Earlier studies had examined kelp population genetics at both a much larger scale, across all of New England, and at a very fine scale between adjacent bays. This study is the first to treat the Maine coast as a holistic unit, filling a critical gap between those extremes. “There’s clearly a wealth of genetic variation along the coast that needs to be considered in management and restoration and that holds great potential for innovation in aquaculture,” Rasher said.

A technological breakthrough made the study possible. Last year, another research team published the first complete sugar kelp genome—a reference resource that enabled Rasher’s group to map genetically distinct populations with far greater precision than previous marker-based approaches. The genome also opens the door to identifying specific genes unique to each population, genes that might help wild kelp forests adapt to warming waters or prove valuable in an industry setting.

“With a complete genome available, we can actually identify genes of interest and examine whether any of these genes are uniquely expressed in a given population,” Francolini said. “We have yet to be able to connect these genes to a specific function, but when we do, we will be able to pinpoint kelp variants that are uniquely strong candidates for improving kelp conservation, restoration, and aquaculture outcomes.”

The implications extend well beyond Maine. Kelp forests worldwide are retreating in the face of marine heat waves, and restoration practitioners are increasingly turning to genetics to guide their efforts—selecting donor populations that harbor heat-tolerant variants, avoiding outplanting genotypes poorly matched to local conditions, and preserving the evolutionary potential of fragmented populations. Maine’s sugar kelp, with its newly resolved population structure and a complete genome to work from, offers a template for how such efforts might proceed elsewhere.

For the aquaculture industry, the study arrives as the sector matures. Maine’s kelp farmers have built a regenerative ocean farming economy on the annual wild harvest of sorus tissue—the reproductive material from which farm seed is propagated. The new findings suggest that sourcing decisions, long made largely on geography and convenience, could be refined with genetic information: matching seed sources to outplanting sites within the same population, or deliberately drawing on genotypes from populations whose unique gene variants confer advantages in particular environments.

The research was supported by the NSF Established Program to Stimulate Competitive Research (Grant #OIA-1849227), the Louise H. & David S. Ingalls Foundation, Maine Sea Grant, and the Nature Conservancy. Co-authors include Research Scientist Robin Sleith of Bigelow Laboratory, as well as Kristina Cammen and Damian Brady of the University of Maine.

As warming continues to reshape the Gulf of Maine, the genetic diversity cataloged in this study represents both a warning and an opportunity—a reservoir of variation that, if managed wisely at the regional scale the researchers advocate, could help kelp forests endure and even thrive in the decades ahead.

Seagrasses in coastal ecosystems like Chesapeake Bay serve as the backbone for biodiversity, offering essential habitat, food resources, and nursery grounds for a plethora of marine organisms. While both eelgrass and widgeon grass provide vital habitat services, this research delineates a crucial distinction between their ecological roles. The results indicate that as eelgrass meadows succumb to environmental stressors and give way to widgeon grass, there will be a noticeable decline in the total invertebrate biomass these habitats support. The team projects a staggering 63% reduction in invertebrate biomass by 2060 should current trends persist without intervention.

Eelgrass, renowned for its broad leaves and structured canopies, creates a complex physical habitat that accommodates larger invertebrates such as pipefish, blue crabs, and isopods. These broader leaves facilitate a dense canopy that not only provides shelter but also influences sediment stability and nutrient cycling. Conversely, widgeon grass, characterized by its narrower, more delicate leaves, offers a higher surface area-to-biomass ratio. This trait permits a greater abundance of smaller invertebrates to attach and flourish. However, despite this numerical abundance, the ecological value and biomass contribution of these smaller organisms do not equate to the ecosystem functions delivered by eelgrass-associated fauna.

The research spearheaded by Lauren Alvaro, a recent master’s graduate from William & Mary’s Batten School, encompassed meticulous fieldwork in Mobjack Bay. Her team performed comprehensive surveys on distinct seagrass beds—pure eelgrass, pure widgeon grass, and mixed species meadows—to quantify both plant biomass and the assemblage of invertebrate communities within these habitats. Their findings underscore that while widgeon grass supports more individual invertebrates per gram of plant mass, the total biomass of animal life supported by eelgrass beds remains significantly higher. This discrepancy underlines the critical role of seagrass structural traits in shaping faunal communities.

Central to this shift are the multifaceted environmental pressures reshaping the Bay’s underwater landscapes. Increasing water temperatures, nutrient loading from agricultural and urban runoff, and habitat fragmentation from coastal development have heightened stress on eelgrass populations. Unlike eelgrass, widgeon grass exhibits a robust tolerance for warmer temperatures and fluctuating salinities, enabling it to thrive where eelgrass declines. However, this resilience comes with ecological trade-offs, especially in terms of habitat quality and food resource availability for higher trophic levels, which rely on the size and biomass of the invertebrates within these meadows.

Projected ecological consequences extend well beyond invertebrate communities. The term “secondary production”—a measure of biomass available to predators such as commercially valuable fish and blue crabs—could be drastically diminished. Current estimates attribute approximately 66,139 tons of invertebrate biomass living within Chesapeake Bay’s seagrass beds, with 35,274 tons of new animal biomass generated each growth season. A decline in meadow quality as eelgrass is overtaken by widgeon grass threatens this crucial energy source for the food web, potentially cascading up to affect fisheries, ecosystem stability, and even coastal economies dependent on these resources.

The intricate relationship between seagrass structure and faunal assemblages also influences predator-prey dynamics. The larger, more structurally complex eelgrass beds foster higher abundances of larger prey species, which are inherently more valuable to predators than the smaller invertebrates supported by widgeon grass. This shift in prey community size distribution may render food webs more fragmented and less efficient, with potential reductions in fishery yields and biodiversity. Although quantifying exact impacts at the fishery scale remains challenging, the researchers warn of likely declines in both commercial and recreational species across the Bay.

This seagrass succession illuminates broader themes in marine ecology regarding the influence of climate change and anthropogenic stressors on foundational species worldwide. The replacement of sensitive, slow-growing species by more tolerant, opportunistic ones is mirrored in other ecosystems, such as the shift from Florida’s mangroves to salt marshes or the global transition from coral-dominated reefs to algae-covered seascapes. Understanding the ecological ramifications of these shifts is imperative, as foundation species underpin the resilience and productivity of entire habitats.

From a management perspective, these insights underscore an urgent need to prioritize the preservation and restoration of eelgrass meadows within Chesapeake Bay. Strategies to improve water quality through nutrient reduction, combined with protection against habitat degradation, could help maintain eelgrass populations and their invaluable ecosystem services. Simultaneously, research into the ecological nuances of widgeon grass may reveal opportunities to mitigate the negative impacts of this transition, potentially through habitat enhancement or species-specific fisheries management.

The study’s lead and senior authors emphasize that this seagrass dynamic is not an isolated event but a symptom of broader environmental changes challenging coastal ecosystems. They advocate for integrated approaches combining ecological monitoring, modeling, and targeted restoration to safeguard the Bay’s biological integrity. Moreover, the work illuminates the necessity of maintaining diverse habitat structures that support a range of species sizes and functional roles within marine communities.

This research also advances our conceptual understanding of how foundational species govern ecosystem processes and biological communities. By unveiling how slight morphological differences between seagrass species propagate substantial changes in food web architecture, the findings invite further exploration into seagrass ecosystem functioning under future climate scenarios. The study serves as a clarion call for scientists and coastal managers alike to anticipate and address the ecological consequences of species shifts driven by a warming planet.

As stewardship of the Chesapeake Bay continues amid increasing environmental pressures, the integration of scientific insights such as those from this seagrass study will be pivotal. By illuminating hidden connections between plant structure and animal communities, and their implications for ecosystem productivity, this research charts a path towards sustainable management of one of the United States’ most important estuarine habitats.

The full study can be accessed through the Marine Ecology Progress Series and offers an indispensable resource for ecologists, marine biologists, and conservationists committed to understanding and preserving seagrass ecosystems in the face of unprecedented environmental change.

Subject of Research: Impact of shifting foundation seagrass species on faunal communities and ecosystem functions in Chesapeake Bay

Article Title: Changing foundation species in Chesapeake Bay (USA): implications for faunal communities of two dominant seagrass species

News Publication Date: 4-Sep-2025

Web References:

• SAV Monitoring and Restoration Program: https://www.vims.edu/research/units/programs/sav/
• DOI: http://dx.doi.org/10.3354/meps14901

Image Credits: Frederick Corey Holbert

Keywords: Marine ecosystems, Marine food webs, Marine conservation, Fisheries