Transect Magazine: Seeing the Forest for the Trees

This story originally appeared in the Winter 2026 edition of Transect.

Imagine a dense, dark forest clear-cut until a vast grassland grows in its place.

That’s what ecologists call a state shift — a dramatic, persistent, and large-scale transition of an ecosystem into something new, with devastating consequences for the broader ecosystem and the humans that depend on it.

Bigelow Laboratory Senior Research Scientist Doug Rasher has dedicated his career to understanding the causes and consequences of state shifts on reefs.

“These dramatic state shifts erode the functions and services that natural ecosystems provide,” Rasher explained. “My research aims to reveal what’s driving these state shifts on reefs, how they reverberate across the broader ecosystem, and how we might prevent or reverse them.”

Rasher studies tropical coral reefs, as well as rocky reefs found in the ocean’s colder, temperate regions. Instead of coral, the foundational species there are kelps, which thrive in nutrient-rich, cold water and create dense forests that provide habitat, food, and clean water.

Like coral reefs, kelp forests face a multitude of threats, from overfishing and pollution to species invasions, heat waves, and intensifying storms. It was actually in kelp forests where ecologists provided one of the first examples of a trophic cascade, observing how the loss of a key predator, like sea otters, led to the proliferation of herbivorous sea urchins that overgrazed kelp until the reefs were barren.

In many parts of the world, the most acute pressure these days, though, comes from ocean warming, as many kelp forests find themselves in temperatures at the limit of what they can tolerate.

“Since kelps are a foundational species that create this important ecosystem, understanding how they are responding to climate change can aid in understanding a plethora of downstream effects,” said Rene Francolini, a recently graduated University of Maine PhD student in Rasher’s lab.

The Gulf of Maine’s relatively simple food web and rapidly warming conditions make it particularly vulnerable. Yet, when Rasher arrived in Maine over a decade ago, he was surprised to find there was relatively little research happening within its kelp forests.

“The Gulf spans over 1,000 kilometers and is one of the fastest-warming ocean regions in the world, making it both an ideal natural laboratory and a bellwether for kelp forests globally,” said Shane Farrell, another University of Maine PhD student in Rasher’s lab who is now a postdoctoral scientist at the University of Galway. “Our discoveries about the causes and consequences of change here may help conserve kelp forests worldwide.”

In 2018, Rasher was funded by Maine Sea Grant to census Maine’s kelp forests for the first time in more than a decade. The team, which included partners at the Maine Department of Marine Resources, published their findings last year.

Their work revealed the widespread collapse of kelp forests along Maine’s southern coast, driven largely by warming. In their place, small, carpet-like turf algae, which don’t provide the same ecosystem benefits, has taken over. But the work also showcased how kelp forests are still thriving in northern Maine, where temperatures are rising more slowly. That motivated Rasher to dig deeper into these regional differences and the consequences of the state shift.

MOVING FROM CAUSE TO CONSEQUENCE

In 2019, Bigelow Laboratory and partner institutions across the state were awarded a significant, five-year grant from the National Science Foundation to advance understanding of Maine’s coastal ecosystems using environmental DNA. The DNA that organisms shed into their surrounding environment, eDNA can be used as a powerful tool for tracking species that are hard to see, new to an ecosystem, or just passing through.

Through the Maine-eDNA program, Postdoctoral Scientist Yasmina Shah Esmaeili joined Rasher’s lab to compare eDNA and traditional methods, like diver-based visual surveys, for assessing ecosystem biodiversity. Shah Esmaeili, now a visiting assistant professor at Texas A&M University at Galveston, was instrumental in developing the reference libraries that enable scientists to match the DNA they find in the ocean with known, identified species.

The program also enabled Farrell, Francolini, and fellow University of Maine PhD student Dara Yiu, to start their doctoral studies, co-advised by Rasher and University of Maine scientists as part of a cohort of eDNA graduate students around the state.

“My vision was to help each student develop a thesis project that leveraged our shared data, but also expanded in a unique direction to explore a particular consequence of the state shift,” Rasher said. “Collectively, the students’ projects paint a picture of recent and dramatic change in Maine’s kelp forests, both with respect to how they look and how they function.”

For three years, the supersized Rasher lab studied sites along the entire coast of Maine, in spring and summer, collecting water and kelp samples for genetic sequencing, conducting visual censuses of fish and kelp coverage, and more.

Each student then took the large dataset to examine kelp forests from a different perspective.

“There is no one right way to study a problem, which is abundantly clear when you see how we used so many different tools and approached questions from multiple points of view,” Francolini explained.

“Different tools serve different purposes,” Yiu added. “We needed a variety of approaches to look at all these facets of the ecosystem.”

Yiu, now a postdoctoral scientist at the University of Nevada, Reno, focused on reef fishes. In addition to applying fish-centric eDNA tools to track the arrival of new species, she also learned stable isotope methods to examine how the loss of kelps is changing the flow of energy through the food web. Her work showed how predator-prey dynamics are fundamentally different on turf-dominated reefs compared to kelp forests and confirmed for the first time that kelp forests provide critical energy to the food web in this region.

Farrell focused on the turf algae itself, trying to understand how this state shift was impacting the chemistry and microbiology of the reef. He developed eDNA tools to understand the makeup of the turf, which can contain a variety of species that are hard to differentiate underwater. He also discovered how turf algae release chemicals that kill young kelp, contributing to a feedback loop where turf algae inhibit forest recovery and lock the system in a degraded state.

Francolini meanwhile worked to identify whether there were distinct genetic populations of kelp along the coast. But like the others, she also focused on new arrivals into the system, using eDNA to track invasive lacy bryozoans. This small organism grows in colonies on kelp fronds, leaving kelps prone to breakage and impeding their ability to reproduce and photosynthesize. Francolini aimed to model how this invasive species might proliferate as the Gulf of Maine continues to warm.

For these students, being part of Rasher’s lab and the Maine-eDNA cohort provided technical skills in bioinformatics, molecular biology, science communication, and scientific diving. More than that, though, it allowed them each to grow into curious and capable scientists.

“This experience was life changing. I entered my PhD without a clear direction and left knowing my passion lies in integrating interdisciplinary techniques to study kelp forests,” Farrell said. “I started at Bigelow as a 20-year-old intern, and seven years later, I left as a doctor. Along the way, I gained lifelong collaborators, mentors, and friends.”

Their varied projects also highlight the value of early-career researchers, such as PhD students, in advancing Bigelow Laboratory’s mission.

“Having a large group of PhD students, undergraduate interns, technicians, and postdocs working together on a common project was amazing because it led to multi-disciplinary perspectives and approaches,” Rasher said. “I learned so much from them as well, and what we were able to achieve by working together was greater than the sum of its parts.”

Photo Captions:

Photo 1: Senior Research Scientist Doug Rasher dives to collect samples from a kelp forest (Credit: Brian Skerry).

Photo 2: A cunner fish swims through a kelp forest around Cashes Ledge, an offshore seamount with a thriving marine ecosystem where Rasher is gaining insight that could help build the resilience of kelp forests on the coast (Credit: Brian Skerry).

Photo 3: Maine eDNA student Shane Farrell examines algae samples in the lab (Credit: Leah Campbell).

Photos 4-5: Members of the lab, including Farrell and fellow Maine-eDNA student Dara Yiu, dive to collect ecological data, water samples, and pieces of kelp and turf algae (below) for further study (Credit: Rene Francolini, Leah Campbell).

Photo 6: Yiu and Rasher catalog samples after a dive survey (Credit: Shane Farrell).

Photo 7: Vials contain the internal chemistry the team extracted from different seaweed tissue (Credit: Shane Farrell).