UH Hilo marine scientists conduct unprecedented research on reef ecosystems along Hawai‘i Island’s west coast

Among other objectives, the researchers are trying to understand and predict how human and natural stressors influence what species are present in a reef ecosystem.

A collage of several photos of researchers aboard a large ship, in inflatable boat, in the ship lab, and at sea with island in the distance.
Images from a recent two-week ocean expedition headed by the National Oceanic and Atmospheric Administration where researchers from UH Hilo conducted unprecedented research on reef ecosystems. (Courtesy images used with permission).

By Susan Enright.

Faculty and student researchers from the University of Hawai‘i at Hilo participated in a recent ocean expedition headed by the National Oceanic and Atmospheric Administration. The researchers, who in April launched the two-week trip from O‘ahu aboard the NOAA ship Oscar Elton Sette, studied coral reef biodiversity all along the west coast of Hawai‘i Island from ‘Upolu Point to South Point.

NOAA, the Hawai‘i Division of Aquatic Resources, Arizona State University, and UH Hilo have been developing this large-scale collaborative project to measure reef biodiversity using a suite of complementary methods including aerial spectrometry mapping, environmental DNA surveys, benthic 3-dimensional photomosaics, and visual fish counts. These combined approaches to surveying reefs provide a detailed and powerful dataset to help assess the status and trends in coral reef health in the region.

This integration of methods has never been done at this scale in Hawai‘i before. The application of aerial mapping provided researchers with the capacity to select sites across a gradient of environmental parameters. This site selection approach will help determine characteristics influencing habitat structure and reef health, which in turn influences biodiversity in these marine systems.

John Burns pictured
John Burns

The group from UH Hilo was led by John Burns, assistant professor of marine science and expert researcher on the health of coral reefs who participated in the expedition’s planning and surveys. Burns, an alumnus of UH Hilo who founded the university’s Multiscale Environmental Graphical Analysis laboratory, commonly called the MEGA Lab, conducts long-term monitoring of coral health and creates 3D models of habitat structure for areas such as the Papahānaumokuākea Marine National Monument.

Kailey Pascoe, a longtime research technician at the MEGA Lab who is working on her doctoral degree at Arizona State University, led the 3D habitat mapping component of the recent project.


3D reconstructions of the reef habitats. (Courtesy video)


UH Hilo marine science undergraduates Lily Gavagan and Ashlynn Overly participated as dive technicians and contributed to both 3D habitat surveys and visual fish surveys.

Two graduate students in the UH Hilo tropical conservation and environmental science program, Crispin Nakoa and John Graves, assisted with eDNA sample processing and analyses. Environmental DNA (or eDNA) is a new and rapidly emerging tool for surveying marine ecosystems.

“This was one of the best expeditions I have participated in,” says Burns. “I was thoroughly impressed by our students and their ability to work as professional scientists and make meaningful contributions to an active project that will enhance our understanding of biodiversity on Hawaiian coral reefs.”

He notes that the ability of marine science undergraduates and graduate students in the tropical conservation biology and environmental science program to directly contribute to the data collection and analyses speaks to the high level of training and experiential learning provided at UH Hilo.

“It is fantastic to have programs at UH Hilo that are capable of training the next generation of scientists and can directly integrate students into large-scale collaborative projects,” Burns says. “This project exemplifies how the marine science department, the UH Hilo analytical lab, and the graduate program are providing high-level training that enables students to become professional scientists and conservationists that can improve our understanding of Hawaiian natural resources.”

Burns says the “numbers of this project were very impressive.” At the end of the objective the group completed:

      • 113 fish and “Structure-from-Motion” (3D) Benthic Surveys.
      • 81 eDNA surveys.
      • 507 individual eDNA sample bottles filtered.
      • 1,980 liters or 523 gallons of seawater filtered.
      • At least 388 SCUBA dives.
      • Roughly 13,580 minutes or 226 hours of underwater survey time.

Researchers on the expedition measured reef biodiversity using the suite of complementary methods. In addition to the eDNA surveys, they also conducted benthic 3-dimensional photomosaics and visual fish counts among other data collection methods.

The experimental eDNA work is particularly innovative. Every living thing in the ocean sheds DNA. As explained on the expedition’s blog, the divers on the expedition used suction pumps to collect water around West Hawai‘i containing small traces of fishes, corals, seaweeds, and other critters that live in these habitats. Divers collected one-gallon samples of water to be filtered and then preserved back on the ship.


On coral reefs around West Hawai‘i, divers used suction pumps to collect water containing small traces of fishes, corals, seaweeds, and other critters. (Courtesy video)


Companion dive teams surveyed the fish and benthic communities on the same reefs using traditional survey methods.

“We conducted a number of CTD/ADCP transects running east-west from shore,” says Burns, referring to measurements of conductivity, temperature, and depth (CTD), and shipboard acoustic Doppler current profiler (ADCP). “These data provide important context for our historical trawls off the Sette and research focusing on the mesopelagic boundary community and food-web dynamics.”

Unprecedented research

Chief scientist Jamie Gove, the co-lead with NOAA’s Pacific Islands Fisheries Science Center who leads the West Hawai‘i Integrated Ecosystem Assessment effort, says “the suite of complementary scientific information collected on this trip is unprecedented for reef ecosystems.”

“The eDNA coupled with the fish and benthic imagery across such large environmental gradients will allow us to fully test the capabilities and applications of eDNA and better understand human and natural drivers of biodiversity,” says Gove.

Later at the lab, trace amounts of DNA caught on the filters during the expedition will be extracted and sequenced for analysis. Using a metabarcoding approach, those DNA sequences detected in each sample will be compared to public reference databases to identify hundreds of species present on each reef.

This research is key to monitoring the health and diversity of complex coral reef ecosystems. Coral reefs are some of the most diverse ecosystems on the planet. Yet, researchers are still learning about how many species occur on any given reef and how that changes over space and time. Effective biodiversity monitoring will help close this information gap.


Map of Hawaii Island with markers along the west coast showing where researchers conducted their research.
The research expedition sampled along sites with a diversity of habitat types including flat to steep bottom topography, high coral cover to low coral cover, shallow to deep habitat, and a variety of ocean conditions. They also sampled along a gradient of sites with lots of human impact to remote sites with less human impact. (Courtesy image)

The researchers are also trying to understand and predict how human and natural stressors influence what species are present in an ecosystem. The research expedition sampled along sites with a diversity of habitat types including flat to steep bottom topography, high coral cover to low coral cover, shallow to deep habitat, and a variety of ocean conditions (such as waves and productivity). They also sampled along a gradient of sites with lots of human impact to remote sites with less human impact (such as wastewater pollution and fishing pressure).

Some sites overlapped with existing fish monitoring locations and recently surveyed locations. By sampling across varying human and environmental conditions, the researchers can compare which sites have higher biodiversity than others.

A media release says this research, a collaboration with NOAA, the Hawai‘i Division of Aquatic Resources, Arizona State University, and UH Hilo strengthens partnerships among the research institutions and increases information sharing. Further, the combined expertise of the researchers expands the use and effectiveness of the data collected.

“Teaming up with UH Hilo, DAR, and ASU was not only critical for the success of the project, but will also allow for these data to directly support ecosystem-based fisheries management and support numerous graduate student research opportunities for years to come,” says Gove.


By Susan Enright, a public information specialist for the Office of the Chancellor and editor of UH Hilo Stories. 

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