This project uses GoPro camera footage to understand interactions between shellfish aquaculture gear and fish communities.
To determine:
Shellfish aquaculture can increase food production, create economic opportunities in coastal areas, and enhance 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 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 epibenthic organisms can colonize and grow. Complex habitats like these often have greater density and diversity of species than a less complex habitat like a flat seafloor. Oyster cages offer similar features, and may be providing benefits similar to those of rock reef habitats. While few studies have investigated aquaculture gear as habitat, extensive anecdotal evidence from commercial shellfish growers suggests that both fish and invertebrates may be using the gear as habitat.
Commercial oyster growers use a variety of cultivation methods, and differences in 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, community composition, and behavior. Shelf and bag oyster 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 action cameras in stereo configuration to measure the body lengths of fish. This will allow us to document the size structure of the fish community associated with cages and boulders.
This research is being funded by the Northeast Fisheries Science Center and NOAA's Office of Aquaculture.
Our study sites are all located in Long Island Sound. We studied oyster cages at a high density oyster cage farm, single cages at low density on sand and shell seafloor, and boulders on a rock reef, in partnership with the Charles Island Oyster Farm.
The comparison of cage styles was conducted on three oyster cage farms:
To collect video for fish size measurements, 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.
We used a series of GoPro cameras to record activity around the structures and document the abundance and behavior of fish around shelf and bag style oyster cages and naturally occurring rock reef habitat. Using cameras as opposed to diver observations reduced the amount of human interference with fish activity. During all camera deployments near cages or boulders, timers were used 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 abundance and activity through changing environmental conditions over the course of a single day.
We outfitted oyster cages with two cameras:
Cages were brought onboard a boat, cameras were mounted on them, and then the cages were redeployed. 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 activity at naturally occurring rock reef habitat, we constructed four stands with dual camera mounts. We then placed the platforms near boulders within the rock reef site where they remained for the entire field season. Divers then put the cameras on the stands and retrieved the cameras two days later. The two cameras provided a field of view similar to that provided by our oyster cage camera system: one looked across the top of the boulder and one looked down the side of the boulder to where it met the seafloor.
To understand if oyster cage density affects fish abundance and behavior, we placed four cages about 50 meters apart at the inshore site adjacent to the oyster farm, and four cages about 90 meters apart at the inshore mixed-sand/shell (“Shell Bottom” in the map) 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 using timers as previously described.
Generally we deploy cameras during the active oyster growing season in Long Island Sound, from June to September. During the fall and winter of 2019–2020, we also deployed cameras monthly from October until February in Milford, to capture seasonal differences in fish activity around the gear and natural habitat.
To compare the habitat quality provided by shellfish aquaculture gear to that of natural habitat, we collected video in 2022 using GoPro cameras in stereo configuration mounted on cages at shellfish farms and near boulders on natural rock reefs at sites in Clinton, Milford and Noank, CT. We will measure the body length of fish recorded in the videos to determine fish population size structure and to assess 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 will use fish traps to collect juvenile black sea bass near oyster cages and boulders to measure their body length and weight. Using these methods, we can estimate the physiological condition of fish and compare the relative quality of oyster cages and boulders as juvenile fish habitat.
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, we collected water for environmental DNA (eDNA) analysis. The eDNA 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. Using eDNA we detected fish in the area surrounding the cages and rock boulders, even when they were not captured on the video. This may help create a more complete picture of fish community composition than video alone. Compared to capture-based methods, eDNA analysis is a comprehensive, rapid, non-invasive, and cost-effective method.
Analysis of underwater video by human coders can be time-consuming. We are often asked if we can use artificial intelligence to automate video analysis. In our case, it is challenging because visibility is often limited in Long Island Sound. While using AI to automate documentation of fish behavior is still a way off, there have been strides in using AI to count fish and identify species in video.
To find out more, we have collaborators who are working on 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 documented the behavior of two temperate-reef species, cunner and scup, in video we collected in 2018 on oyster cages at a shellfish farm and on boulders at a rock reef in Milford, Connecticut.
We observed small-bodied cunner feeding, taking shelter, escaping from predators, and acting territorial on cages and boulders. Scup occurred as single individuals or in large groups or schools, and commonly 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 will be able to compare the habitat services provided by the shellfish farm and the rock reef. Our behavioral observations to date suggest that cages create habitat for fish similar to that provided by natural boulder reefs.
We have collected and analyzed more than 1,600 hours of underwater video for fish abundance 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, technicians 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:
Identifying fish to species level and counting fish are only the first steps in our video analysis. We are also analyzing fish behavior in the video we have collected.
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. 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.
Paul Clark, Bill DeFrancesco, 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.
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 engages 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 are working 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 include constructed oyster reef, rocky reef, and bare sediment. The Nature Conservancy produced a video about this local project and how it contributes to the organization’s global aquaculture program.
We have shared our video collected in Milford with partners at the University of New Haven, who are analyzing videos of black sea bass and quantifying 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.
