This project uses GoPro camera footage to understand interactions between shellfish aquaculture gear and wild fish communities.
To determine:
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.
Understanding if and how oyster cages function like naturally occurring habitats may help with regulatory and permitting processes when siting new shellfish farms. Regulatory challenges have been identified as one of the major bottlenecks to shellfish aquaculture expansion in the United States. This project is a close partnership between the NOAA Northeast Fisheries Science Center and Greater Atlantic Regional Fisheries Office. This partnership ensures that the results from this study will inform the regulatory review process. Our findings may support a more comprehensive review process for shellfish aquaculture projects, which considers environmental benefits as well as impact. Next steps include:
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.
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.
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.
This research is being funded by the Northeast Fisheries Science Center and NOAA's Office of Aquaculture.
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:
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.
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.
We outfitted oyster cages with two cameras:
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.
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.
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.
To compare fish interactions with different styles of oyster cages, we placed cage pairs at three Connecticut shellfish farms. Two cages of each type were deployed 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.
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.
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, Milford, and Noank, 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.
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.
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.
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:
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.
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:
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:
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.
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.
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 single 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 the shellfish farm and the rock reef. 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.
Paul Clark, Bill DiFrancesco, Mark Dixon, Erick Estela, Zach Gordon, Tyler Houck, Peter Hudson, Kristen Jabanoski, Yuan Liu, Gillian Phillips, Matthew Poach, Jerry Prezioso, Dylan Redman, Ian Robbins, and Barry Smith.
We've created a citizen science guide to help growers capture high quality underwater footage of their aquaculture gear to monitor the ecosystem interactions:
Rutgers University received funding from the Northeastern Regional Aquaculture Center to investigate fish and invertebrate interactions with oyster aquaculture gear and natural habitats using GoPro cameras in New Jersey. Their project engaged oyster growers in Barnegat Bay that use floating oyster bags and oyster bottom cages. Natural habitats included a marsh edge and bare sandy bottom. Scientists have posted video clips from the project on the lab’s YouTube channel, and you can find more project information at the lab’s website.
The Nature Conservancy and Northeastern University have 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 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 produced 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.
Four oysters held by oyster grower Mike Gilman
Sustainably grown, organic Alaskan kelp is harvested at the Seagrove Kelp Co. farm in Doyle Bay. Credit: NOAA Fisheries/Jordan Hollarsmith
Fishermen lowers sea scallops into the water. Credit: NOAA Fisheries.
