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Milford Lab's GoPro Aquaculture Project

This project uses GoPro camera footage to understand interactions between shellfish aquaculture gear and wild fish communities.

New England/Mid-Atlantic

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Overview

Project Goals

To determine:

  • Do oyster aquaculture cages provide habitat similar to that of naturally occurring rock reef environments?
  • Do we see more fish per cage on large farms with many cages than on small farms with few cages?
  • What does fish behavior tell us about the ecosystem services provided to fish by oyster cages?
  • Does oyster aquaculture cage style affect the habitat services provided to the local fish community?
  • What sizes and life stages of fish use oyster cages and boulders as habitat?
  • When are fish most abundant on oyster cages? Do we see the same species of fish every year on shellfish farms?

Project Description

Shellfish aquaculture produces food, creates economic opportunities in coastal areas, and enhances natural harvests. To foster successful, responsible, and sustainable aquaculture for the future, we need to understand how aquaculture gear may interact with marine ecosystems. Off-bottom tiered oyster cages are growing in popularity as a method for culturing large numbers of oysters on a small footprint. These cages create complex structures that may attract fish and other animals seeking food sources, shelter, and refuge from water currents or protection from predators. Because of the cages' structure, they may function like naturally occurring rock reefs, providing beneficial habitat to ecologically and economically important fish and invertebrates.

Informing Decision Makers

Aquaculture permitting and management does not currently fully consider habitat provisioning services provided by aquaculture gear. The US Army Corps of Engineers public interest review process (33 CFR § 320) is one logical avenue to consider habitat services. This process requires considering both adverse and beneficial effects during the permit application review. It includes evaluating a project’s effects on fish and wildlife. Many US states require a similar consideration of benefits and adverse effects of proposed aquaculture projects to fish and wildlife. Despite the requirement, the review is currently generally limited to adverse effects.

We held discussions with state and federal aquaculture permitting authorities in the Northeast regarding the status of, and potential barriers to, greater incorporation of environmental benefits in shellfish aquaculture permitting. We received feedback from managers that the habitat value of aquaculture projects could be considered more consistently if location and farm specific values were available in a form that could easily be applied during the permit review process. In response, we are working to develop tools to aid regulators in considering the potential habitat value provided by new and expanding shellfish farms. 

(Left) An oyster cage containing mesh bags full of oysters on the back of a boat. Two scientists are affixing GoPro cameras to the corners of the cage. (Right) A metal oyster cage on a boat deck with three shelves holding six mesh bags. Two GoPro cameras are affixed to corners of the cage.
(Left) A stacked tray oyster cage. (Right) A shelf and bag oyster cage.

Comparing Aquaculture Gear to Natural Habitat

Naturally occurring rock reefs in Long Island Sound create habitat complexity in an often otherwise flat and featureless landscape. Rock reefs add vertical height in the water column, crevices and shading for hiding, and surfaces on which colonizing organisms can grow. Complex habitats like these often have greater density and diversity of species than less complex habitats like a flat seafloor. Oyster cages offer similar features, and may be providing benefits similar to those of rock reef habitats. Anecdotal evidence from commercial shellfish growers suggests that both fish and invertebrates may be using the aquaculture gear as habitat.

Comparing Oyster Cultivation Methods

Differences in aquaculture gear structure may influence how farms interact with the local fish community. We examined two commonly-used styles of oyster bottom cage, to see if structural differences affected fish abundance and community composition. Shelf and bag cages have three open shelves with bags of oysters, which creates a variety of spaces for fish to use. Stacked tray cages have three enclosed trays of oysters with smaller-sized openings, which may restrict the size of fish that are able to access the cage interior.

Size Structure of Fish Community around Cages and Boulders

We collected video with GoPro cameras in stereo configuration to measure the body lengths of fish. This will allow us to document sizes and life history stages of the fish community associated with cages and boulders. Life history stages help us determine whether the gear serves as a nursery habitat for wild fish.

Funding

This research is funded by the Northeast Fisheries Science Center and NOAA's Office of Aquaculture.

Study Methods

Study Locations

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A map of the Connecticut coastline and Long Island Sound, with white words and stars indicating the locations of Norwalk, Westport, Milford, Clinton, and Noank (from West to East).
Map of field locations used for the GoPro Aquaculture Project on the Connecticut coastline of Long Island Sound.

Our study sites are in Long Island Sound, Connecticut. During 2018, we compared oyster cages at a dense cage farm, single cages placed at low density on a "sparse" farm, and boulders on a rock reef, in partnership with the Charles Island Oyster Farm.

In 2019, we compared oyster cage styles on three farms in western Long Island Sound:

  • Charles Island Oyster Farm, Milford, Connecticut
  • Copps Island Oyster Farm, Norwalk, Connecticut
  • Hummock Island Oyster Farm, Westport, Connecticut

In 2022, we placed cameras in stereo configuration on cages at three shellfish farms and boulders at three rock reefs in central and eastern Long Island Sound to collect video for fish body size measurements.

  • Charles Island Oyster Farms, Milford, Connecticut
  • Indian River Shellfish in Clinton, Connecticut
  • Noank Cooperative, Noank, Connecticut

Collecting Video

We used video from GoPro cameras to quantify fish abundance, behavior, and community composition around oyster cages and natural rock reef habitat. We used timers to record video for 8 minute intervals every hour from 7 a.m. to 7 p.m, over a complete 12-hour tidal cycle. This enabled us to sample fish activity through changing environmental conditions over the course of a single day.

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Black GoPro camera in clear plastic housing on a tripod underwater with the lens directed at a boulder covered in encrusting organisms.
Placement of camera facing boulder
 

Cameras on Oyster Cages

We outfitted oyster cages with two cameras:

  • one mounted to record activity across the top of the cage, like a periscope, and
  • one mounted to hang down from the corner of the cage to record activity along two sides of the cage and the area where the cage rests on the seafloor.

We brought cages onboard a boat, mounted cameras on them, and then redeployed them on the farms. Video recording started the following day and we retrieved cameras two days later. The oyster cages themselves stayed in the water for the entire field season.

Cameras on Natural Habitat

To record fish activity on rock reef habitat, we constructed four stands with dual camera mounts. We placed the stands near boulders on the reef where they remained for the entire field season. Divers attached cameras to the stands and as on the farms, video recording stated the day after deployment. Divers retrieved the cameras two days later. One camera looked across the top of the boulder and one looked down the side of the boulder to where it met the seafloor, providing a field of view similar to the cage mounted cameras.

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A is a map of the Connecticut shoreline showing Milford and Charles Island. B is a map of western Connecticut, showing study farm sites in Norwalk and Milford, Connecticut.
A. Three study sites in Milford, Connecticut B. GoPro study sites in Norwalk and Westport, Connecticut.

Cage Placement at Milford Shellfish Farm (Map A)

To understand if oyster cage density affects fish abundance and community composition, we placed four cages about 50 meters apart adjacent to a "dense" oyster farm with 40+ cages, and four cages at a low density about 90 meters apart representing a "sparse" farm on mixed-sand/shell habitat. We used the same recording approach as used for the cage/reef comparison.

Cage Placement Across Multiple Oyster Farms (Map B)

To compare fish interactions with different styles of oyster cages, we placed cage pairs at three Connecticut shellfish farms. We deployed cages of each type at shellfish farms in Milford, Norwalk, and Westport, to compare fish interactions between cage styles at multiple farms across a broader geographic area. We collected video as previously described.

Seasonal and Interannual Variability

Generally we deploy cameras during the active oyster growing season in Long Island Sound, from June to September. During 2019–2020, 2021-2022, and 2022-2023, we also deployed cameras monthly from October until late winter or early spring in Milford, to capture seasonal differences in fish activity around the gear and natural habitat. To assess variation in fish communities across years, we collected video on the same farm in Milford, Connecticut, each year from 2017 to 2022, excluding 2020.

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The top left is a map of 3 field sites along the Connecticut shoreline from west to east labelled A, B and C. A (top right) is a map of the Connecticut shoreline showing a cage site and a boulder site in Milford, Connecticut. B (bottom left) is a map showing a cage site and a boulder site in Clinton, Connecticut. C (bottom right) is a map showing a cage site and a boulder site in Noank, Connecticut.
Map of 2022 field sites in Milford (A), Clinton (B), and Noank (C), Connecticut.

Measuring Habitat Quality and Potential for Enhanced Fish Production

To better understand how fish use shellfish aquaculture gear and natural habitat throughout their life cycles, we collected video in 2022 using GoPro cameras in stereo configuration mounted on cages at shellfish farms and near boulders on rock reefs in Clinton (Map A), Milford (Map B), and Noank (Map C), Connecticut. We are measuring the body lengths of fish recorded in the videos to determine the sizes and life history stages of fish associated with oyster cages and boulders. These data will promote a better understanding of the ecosystem services provided to fish by aquaculture gear and natural structure.

In 2023, we collected juvenile black sea bass near oyster cages and boulders using fish traps to measure their body length and weight, and conduct energy density analysis. Using these methods, we will estimate the physiological condition of fish and compare the relative quality of oyster cages and boulders as juvenile fish habitat.

(Left) Two scientists wearing blue hardhats and orange life vests prepare an oyster cage with a calibration cube and two cameras for deployment. (Right) Two scientists wearing blue hardhats and orange life vests deploy a metal oyster cage off the back of a boat with two GoPro cameras and a sheet of plastic with small black and white squares.
Gillian Phillips (left) and Dylan Redman (right) prepare (left image) and deploy (right image) an oyster cage with dual cameras and a calibration cube to measure fish body length in videos.

Collecting Environmental Data

During camera deployments, we also collected environmental data because temperature, light levels and current flow can influence fish activity. We used data loggers to record water temperature and light intensity and tilt current meters to measure speed and direction of water currents. We attached a current meter and temperature/light data logger to one cage at each field site and to a spare camera stand at the rock reef. Using handheld probes, we also measured salinity and dissolved oxygen at each site.

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NOAA Diver Mark Dixon adjusts a GoPro camera underwater.
NOAA Diver Mark Dixon adjusts a GoPro camera underwater.

Describing Fish Communities using Environmental DNA (eDNA)

When fish and other animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. Although this DNA is diluted, it can be extracted and analyzed. Each time we retrieved our GoPro cameras from 2017 to 2019, we collected water for environmental DNA (eDNA) analysis. The method we used combined DNA-based species identification with high throughput next generation sequencing, or sequencing millions of copies of DNA in the environment simultaneously, to characterize the fish communities associated with oyster cages and rock reefs. 

Artificial Intelligence

Analyzing underwater video can be time-consuming for scientists. We are often asked if we can use artificial intelligence to automate video analysis. Our use case is challenging because visibility is often limited in Long Island Sound, and many objects that move in our videos are not fish. However, efforts are underway toward using AI to count fish and identify species in video.

We are working with collaborators who develop AI programs. If we can use AI to automate the process of identifying and counting fish in video, we will be able to process large quantities of video more quickly and efficiently. Our AI collaborators are:

Two fish swimming on top of a metal oyster cage underwater, with boxes and labels "tautog: 0.89" and "black sea bass: 0.92".
National Research Council Canada is developing a preliminary machine-learning model to recognize fish in underwater video. To train the model to identify fish, GoPro project team members used visual observations of body shape and coloration to identify fish species in oyster farm videos. Here, the image shows how the trained AI model has correctly identified a tautog (left) and black sea bass (right) (inside yellow squares), based on tail and body shape outline.

Fish Behavior

Observing fish behavior around aquaculture gear and natural structures can help us better understand how they provide habitat. Our team is documenting the behavior of temperate-reef species, including: black sea bass, cunner, scup, and tautog, in video we collected in 2018 at a shellfish farm and a rock reef habitat in Milford, Connecticut. We've partnered with two fish ecologists, Peter Auster from the University of Connecticut and the Mystic Aquarium, and Christian Conroy from the University of New Haven, to identify and quantify the different ways that fish are using oyster cages.

Results

We have collected more than 1,600 hours of underwater video to assess fish abundance, behavior, and community composition from the 2017–2019 and 2021-2022 field seasons. Because of challenging visibility in the water column and the need for nuanced fish behavior analysis to understand habitat use, scientists perform all video analysis.

To date, we've observed 21 species of fish in our videos associating and interacting with oyster cages. The four most common species observed in video have been:

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A gray/black fish with a yellowish eye swims through the bars of a metal oyster cage.
A tautog, one of the most commonly observed species, swims through an oyster cage.

Less-commonly observed species in videos include:

We’ve also observed a few fish species that have fallen out of cages during camera deployment/retrieval, but were not yet observed on video, including:

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Two scientist at computer reviewing footage taken by GoPro cameras.
Paul Clark and Gillian Phillips at Milford Lab reviewing GoPro footage.
  • Northern lined seahorse
  • Northern pipefish
  • Oyster toadfish
  • Rock gunnel

Environmental DNA Analysis

Using eDNA in 2017, we detected 42 additional fish species in the area surrounding the cages and boulders not captured on video. Complementing the video methods, eDNA provided a more complete picture of fish community composition.

Fish Abundance

During 2018, abundance of black sea bass, scup and tautog was consistently higher on cage farms compared to the rock reef. Cunner abundance was similar on farms and rock reef habitat. There was no difference in fish abundance between the three farms in Milford, Norwalk and Westport in 2019. 

Fish abundance was correlated with seasonal changes in water temperature and was highest in summer when the water was warmest. We observed recently settled young-of-the year black sea bass and scup at all sites, which may indicate that cages provide nursery habitat for young fish. Our results suggest that oyster cages contribute structure to seafloor environments, providing similar habitat for temperate reef fish as natural rock reefs.

Fish Behavior

So far we've seen fish feeding on the colonizing organisms that grow on the cages, little fish escaping from bigger fish by darting inside the cage itself, female fish retreating inside the cage to escape male fish of the same species, territorial behavior, courtship, and fish spawning.

Underwater clip of a silver fish called a scup feeding on material growing on the top of a metal oyster cage. Several other scup are visible in the background, and the top of the oyster cage looks like a metal grid.
A scup feeding on encrusting algae and animals growing on an oyster cage.

We observed small-bodied cunner feeding, taking shelter, escaping from predators, and acting territorial on cages and boulders. We frequently observed black sea bass resting on top of cages and chasing other fish away. Tautog demonstrated courtship behavior in and around aquaculture gear. Scup occurred as individuals or in large groups or schools, and often fed on colonizing plants and animals living on the aquaculture gear and boulders. Our team was excited to see an adult scup spawning adjacent to an oyster cage, right in front of our camera!

By counting the behaviors of individual fish on cages and boulders in the video we collected in 2018, we are comparing the habitat services provided by shellfish farms and rock reefs. Our behavioral observations to date suggest that cages provide fish with food, shelter, and other habitat services in a similar way as natural boulder reefs.

Publications

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This illustration shows an underwater view of three oyster cages surrounded by a variety of fish, including black sea bass, scup, cunner, and tautog, that are using the oyster cages as habitat for feeding, shelter, nurseries, courtship, and spawning.
Oyster farms create habitat that fish use for courtship and spawning, shelter, finding food, and as a nursery.

Get Involved

Our Citizen Science Guide (2022 update) breaks down our methods step-by-step, so that any grower with a GoPro camera can capture high quality underwater footage on their farm. The East Coast Shellfish Growers Association hosts a website where growers can submit interesting videos of marine life associated with aquaculture gear. They are looking for more submissions from the shellfish aquaculture community. To have your video considered for posting on their page, please contact Ann Rheault.

Related Projects

Rutgers University is investigating fish and invertebrate interactions with oyster aquaculture gear and natural habitats using GoPro cameras in New Jersey. Funded by the Northeastern Regional Aquaculture Center, their project engaged oyster growers in Barnegat Bay using floating oyster bags and oyster bottom cages. Natural habitats included a marsh edge and bare sandy bottom. Scientists posted video clips from the project on the lab’s YouTube channel, and you can find more information on the lab’s website.

The Nature Conservancy and Northeastern University partnered to investigate how oyster farming gear provides habitat for other marine species using GoPro cameras in Massachusetts. They worked with commercial growers in Duxbury and Cotuit, Massachusetts, who use shelf-and-bag bottom cages, bottom trays, and OysterGro gear on both intertidal and subtidal farms. Natural habitat and control sites included constructed oyster reef, rocky reef, and bare sediment. The Nature Conservancy made a video about this local project and how it contributed to the organization’s global aquaculture program.

We shared our underwater video with partners at the University of New Haven, who analyzed videos of black sea bass and quantified their territorial and station-keeping behaviors around oyster cages and rock reefs.

Contact Information

Project/Principal Investigators:

  • Renee Mercaldo-Allen - Northeast Fisheries Science Center
  • Julie Rose - Northeast Fisheries Science Center
  • Chris Schillaci - NOAA National Centers for Coastal Ocean Science
  • Lisa Milke - Northeast Fisheries Science Center
  • Kevin Madley - Greater Atlantic Regional Fisheries Office (past)
  • Tammy Murphy - Northeast Fisheries Science Center (past)

Project Advisors:

  • Sabrina Pereira - Greater Atlantic Regional Fisheries Office
  • Kaitlyn Shaw - Greater Atlantic Regional Fisheries Office
  • Alison Verkade - Greater Atlantic Regional Fisheries Office (past)

NOAA Fisheries Project Team:

Paul Clark, Bill DiFrancesco, Mark Dixon, Erick Estela (past), Zach Gordon, Tyler Houck, Peter Hudson (past), Kristen Jabanoski, Yuan Liu, Gillian Phillips, Matthew Poach, Jerry Prezioso (past), Dylan Redman, Ian Robbins (past), and Barry Smith (past)

Collaborators and Partners

From left to right, a male scientist wearing a hat, sunglasses, a red jacket and orange life jacket, a female shellfish grower wearing a gray shirt and overalls, a male shellfish grower wearing a hat and t-shirt, a female scientist wearing sunglasses, a black shirt and orange life jacket, and a male boat captain wearing a blue shirt with a black vest, sunglasses, and an red life jacket. The group of five people stand on a small boat with blue water and the green tree-lined coast behind them.
Milford Lab team members Dylan Redman (far left), Renee Mercaldo-Allen (second from right) and Bill DiFrancesco (far right) meet with oyster growers Beth and Kris Simonds (second and third from left) of Stonington Farms Shellfish.

Academic Partners

NOAA

  • NOAA Corps - Calandria DeCastro, Keith Golden
  • NOAA Northwest Fisheries Science Center - Beth Sanderson, Peter Kiffney
  • NOAA Alaska Fisheries Science Center - Bridget Ferriss (past)

Nonprofit Partners

  • The Nature Conservancy - Steve Kirk

Students and Interns

  • Eileen Bates (Bowdoin College)
  • Bobbi Bevacqua (Western Washington University)
  • Grace Cajski (Yale University)
  • Jack Jerrild (Mitchell College)
  • Deaven Maull (Washington College)
  • Max Mauro (University of Maine)
  • Sam Pletcher (Yale University)
  • Brandon Rose (Eckerd College)
  • Ryan Rubino (Texas A & M University)

State of Connecticut Aquaculture Division

  • David Carey
  • Shannon Kelly
  • Kristin DeRosia-Banick (past)

Shellfish Growers

U.S. Coast Guard

  • Office of Search and Rescue (Arthur Allen)

Learn More

Resources for Kids and Teachers:

Last updated by Northeast Fisheries Science Center on 03/20/2025