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Eyes Underwater: Complementary Tools Can Determine How Fish Use Oyster Aquaculture Gear

September 27, 2021

Scientists document the underwater world of shellfish farms using video and environmental DNA.

A group of small fish are visible through somewhat turbid water above the top of a metal oyster cage.

Researchers at NOAA Fisheries’ Milford Laboratory have been using commercially available underwater video cameras to watch fish around oyster cages at shellfish farms. But what about species that are difficult to capture on camera? They combined the video approach with eDNA sampling techniques to detect more species. With colleagues at Rutgers University, they have started to build a more robust picture of how oyster cages can provide important habitat for a remarkable number of species. The methods and results are documented in two new scientific papers.

How to Catch Fish on Video?

During the 2017 oyster growing season, the NOAA Fisheries Milford Lab began evaluating the habitat value of shellfish aquaculture gear. They used underwater video to see what was happening around the cages, and environmental DNA (eDNA) sampling and analysis to detect animals they couldn’t see. The study was recently published in Aquaculture Environment Interactions.

“We’re grateful to be at the point where we can share our methods with researchers and growers,” said project co-lead Renee Mercaldo-Allen.

Two people wearing orange life jackets and hard hats stand on the stern of a boat on either side of a rectangular metal oyster cage with a visible camera and blue marine hose attached to the corner. Long Island Sound and the Milford, Connecticut, coastline is visible in the background.
Dylan Redman (left) and Gillian Phillips (right) examine an oyster cage equipped with GoPro cameras on board the Milford Lab’s R/V Loosanoff in Long Island Sound. Credit NOAA Fisheries

During the summer, the team mounted GoPro cameras to three oyster cages on a commercial oyster farm in Long Island Sound. They also placed three near boulders representing natural habitat. An oyster cage is a metal structure in which oysters are grown in mesh bags or trays. Cages are increasingly popular with growers because more oysters can be grown on a smaller footprint while being protected from predators. Cages introduce structure to otherwise flat seafloor, and structure tends to attract fish.

Two people wearing orange life jackets stand on the stern of a boat deploying a metal t-shaped platform with two cameras attached into the water.  Long Island Sound and Charles Island are visible in the background.
Dylan Redman (left) and Gillian Phillips (right) deploy a “t-platform” equipped with GoPro cameras, which is designed to collect video of fish on natural boulder/rock reef habitat while introducing minimal structure into the environment. Credit NOAA Fisheries

Project co-lead Julie Rose said, “We saw a lot of fish in and around the cages. This substantiates what growers have been telling us for a long time. Our data will be useful to coastal communities, regulators, and resource managers who make decisions about aquaculture.”

Capturing Fish on Camera

The team saw seven fish species on video. Of the four most abundant species, black sea bass, scup, and tautog were consistently associated with oyster cages, while cunner were more abundant around boulders. On rare occasions, they observed banded rudderfish, butterfish, and yellow jack. Black sea bass, scup, and butterfish are federally managed commercial species, and tautog is popular recreationally. Watch video clips of fish swimming around the cages.

“I was surprised by how abundant small fish were close to shore in Long Island Sound. There was a distinct possibility that we might not see anything,” commented biological technician Dylan Redman. Though the initial study was too limited in scope to draw conclusions about fish behavior, behaviors such as foraging and courtship were categorized and are currently being analyzed.

Working Out the Camera Methods

Dylan Redman says that trial and error was required to work out methods for successful video collection. The team wove together a wide range of skills, including field methods, fish taxonomy, and software expertise, all put to good use because of the complexity of this project.

Creativity and attention to detail were critical as they evaluated different camera lenses and mounting systems. They looked for placement locations that allowed viewing as much of the cage as possible. They also tested interval and continuous video recording, ultimately using hourly intervals to capture fish activity throughout a whole day.

“We tried to create a minimalistic camera mount system that wouldn’t add structure that might attract fish. It had to be durable for the marine environment, and rigid enough to stabilize the camera. We used marine hoses with wire wrapped inside, making it rigid but flexible,” Redman explained.

The team found that a combination of top- and side-mounted camera placements provided the best view of the cage. The top mounted camera is like a periscope, and the side-mounted camera views two cage sides and where the cage meets the seafloor.

Two divers at the surface of the water between an orange buoy. They are wearing masks and Scuba equipment, and the diver on the right has a yellow snorkel.
NOAA research divers Jerry Prezioso (left) and Mark Dixon (right) prepare to retrieve GoPro cameras from Long Island Sound. Credit NOAA Fisheries

“If you set up the camera mount on land, then put it in the water, the view changes. You lose a percentage of what you’re going to see because of the refraction of seawater,” Redman noted.

Input from research divers Mark Dixon and Barry Smith also shaped the methods. They explained what was feasible to deploy underwater, and the team designed the camera mounts accordingly. The divers located boulders on the rock reef to represent natural structured habitat and designed “t-platform” camera mounts to record video on each boulder, again minimizing structure. Redman explained, “We couldn’t do this work without our research divers.”

Tracking Fish By What They Leave Behind: Environmental DNA

 A person wearing an orange life jacket takes a water sample in a plastic bottle from a gray, rounded piece of oceanography equipment held by a person wearing an orange life jacket and hard hat on the stern of a boat, with Long Island Sound and the coastline visible in the background.
Yuan Liu takes a water sample for eDNA analysis from a Niskin bottle held by Gillian Phillips. Credit NOAA Fisheries

Similar to underwater cameras, eDNA sampling is a non-invasive tool to study fish populations without catching them. This is particularly useful in areas where the shape of the seafloor makes sampling with nets difficult. The method looks for traces of DNA that fish leave behind when they shed scales, waste, and other cells. Molecular scientists like Milford Lab’s Yuan Liu take a water sample and copy a specific region of the DNA. Then they match it to known sequences for fish species in a reference library.

In 2017, Liu took water samples while the GoPro cameras were deployed. She detected 47 species of fish, including six that were also captured on camera.

“A strength of eDNA is that it represents the whole water column, but in this case it gave us a more complete picture of who was interacting with the cages,” said Liu. “The cage and reef sites were two kilometers apart, but we saw some separation between them in the fish detected using eDNA.”

By using eDNA methods, researchers can help detect fish less likely to be captured by video. Pairing eDNA with camera deployments provided a more comprehensive look at the species using oyster farm and reef habitats. In subsequent years, the Milford team expanded their study to include multiple oyster farms in Long Island Sound.

Who’s Visiting a Barnegat Bay Oyster Farm?

A long, narrow fish in the water is just below and parallel with a line. Above the line is a mesh bag filled with oysters.
An Atlantic needlefish captured on video underneath a floating bag of cultivated oysters in Barnegat Bay, New Jersey. Credit NOAA Fisheries

The Milford project sparked a collaboration between Daphne Munroe, an associate professor at Rutgers University, and Milford’s Julie Rose. Munroe received a mini-grant from the Northeastern Regional Aquaculture Center to deploy cameras on an oyster farm in Barnegat Bay, New Jersey in 2018. Project coordinator Jenny Shinn learned to identify fish with help from Milford’s Paul Clark and Gillian Phillips. Four interns also helped with field work and video analysis.

The Rutgers team compared two common types of oyster aquaculture gear, floating bags and bottom cages, with nearby natural marsh habitat. Their study was also recently published in Aquaculture Environment Interactions. They deployed a set of six cameras repeatedly to compensate for challenging water visibility caused by sediment and plankton.

During the 2018 season, 250 hours of video captured all tidal conditions and 8,937 individual observations of fish and invertebrates. Those observations included 21 species, including several commercially and recreationally important species such as summer flounder, blue crabs, and striped bass. Watch clips on the Munroe Lab's YouTube channel

Several species were seen only on aquaculture habitats, including some that primarily live on oyster reefs and many juveniles. This suggests that aquaculture gear may provide comparable habitat to oyster reefs, which have declined from their historic range because of human impacts.

Though they weren’t able to quantify behaviors, the team observed many fish behaviors at the farm such as foraging, shelter-seeking, and predation. They saw needlefish hunting silversides under floating bags of oysters. A terrapin was seen cruising by the gear. Toward summer’s end, the gear was visited by some southern species, including juvenile permit and gray snapper.

“We actually saw greater diversity on the farm versus the marsh edge. This was surprising, considering that boats and people were working on the farm during recording,” Munroe said, “We have since collected data to compare species diversity when people are present and absent.”

Underwater Video as an Outreach Tool

Two people wearing orange life jackets and hard hats affix a GoPro camera to the side of a metal oyster cage on the stern of a boat with Long Island Sound visible in the background.
Dylan Redman (left) and Gillian Phillips (right) affix GoPro cameras to an oyster cage, preparing it for deployment. Credit NOAA Fisheries

As the pandemic changed the landscape for public outreach, Munroe and Shinn worked with the Organization of Biological Field Stations. They created a virtual field trip with lesson plans for middle and high school students based on their videos.

Munroe has always been interested in interactions among shellfish aquaculture and coastal ecosystems. She presented the study results at the Shellfish Growers Forum in Cape May, New Jersey, in 2019. Many shellfish growers were excited about the findings. She shared Milford Lab’s Citizen Science Guide with growers who were interested in collecting video on their own farms.

The Rutgers and Milford Lab research teams are pooling their experiments to assess habitat value of shellfish aquaculture gear on a regional scale. Munroe and Shinn hope that data on the ecological role of oyster farms in coastal habitats will help inform regulators and coastal residents about the benefits.

Reflecting on the data they collected, Shinn said, “There’s an active community of animals using oyster farms—more than meets the eye. Much more than you can see from your house or the shore.”

Implications for Managing Ecosystems

 fish with black stripes swims underwater above a metal oyster cage.
A tautog swimming above a shelf and bag style oyster cage. Credit NOAA Fisheries

In addition to being an engaging public outreach tool, the videos of fish interacting with oyster cages are also invaluable for managing ecosystems.

Alison Verkade is a Marine Habitat Resource Specialist at NOAA’s Greater Atlantic Regional Fisheries Office. She provides technical assistance to the GoPro Aquaculture Project and guidance on research questions important for management. Her job includes reviewing coastal activities for impacts to fish habitat, including aquaculture.

Verkade said, "Being involved and providing advice on the study design from the beginning helps ensure an understanding of the strengths and limitations of the data for managers, and that the science will be useful for making management recommendations and decisions. Our team is bridging the gap that sometimes exists between science and natural resource management.”

Last updated by Northeast Fisheries Science Center on June 30, 2023

Environmental DNA