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GoPro Aquaculture Project


Understanding the Interactions of Shellfish Aquaculture Gear with the Environment

Project Goal

technicians retrieving oyster aquaculture cage
Research technicians Gillian Phillips and Dylan Redman retrieve one of a series of experimental oyster aquaculture cages. Photo credit: NOAA Fisheries/Heather Soulen

To determine if oyster cages used in shellfish aquaculture provide habitat similar to naturally occurring rock reef environments and if an oyster farm (large group of cages) attracts fish differently than when a solitary cage is the only source of structure in a local environment.

Project Description

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 the biology, ecology, and habitat of an ecosystem. Off-bottom oyster cages are growing in popularity as a method for culturing large numbers of oysters in a small footprint. These cages create complex 3-dimensional structure 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.

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. Because of this, oyster cages may be providing benefits similar to those of rock reef habitats. While there is limited scientific data available on aquaculture gear as habitat, extensive anecdotal evidence from commercial shellfish growers suggests that both fish and invertebrates may be using the gear as habitat.

We’re conducting a series of field experiments to better understand how fish interact with oyster cages used in shellfish aquaculture farming operations.

This research is being funded by the NEFSC and NOAA's Office of Aquaculture.

Study Site Locations

Study sites are located in Long Island Sound near the Charles Island Oyster Farm off Milford, Connecticut. Sites include an inshore commercial oyster farm containing 40+ oyster cages, an inshore naturally occurring rock reef, and an inshore mixed feature habitat of empty shell, live oyster, and featureless seafloor.

locations of gopro cameras for this study
Map of study site locations.

Study Questions

  • Is the abundance and behavior of fish around oyster cages similar to naturally occurring rock reef habitat?
  • Does oyster cage density (number of cages in a shellfish farm) have any effect on fish abundance and behavior?
man putting cameras on cage
This oyster cage is outfitted with two cameras. This photo shows the camera mounted to record activity along the horizontal surface across the top of the cage, like a periscope. Photo credit: NOAA Fisheries/Renee Mercaldo-Allen.

Study Methods

To understand if the abundance and behavior of fishes around oyster cages are similar to those in naturally occurring rock reef habitat, we’re using a series of GoPro cameras to record activity around the cages over a complete tidal cycle. Using cameras as opposed to diver observations helps reduce the amount of human interference in our study. For our oyster aquaculture gear treatment, four oyster cages were outfitted with two cameras: one mounted to record activity along the horizontal surface 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. Once cameras are deployed on cages video recording starts the following day, recording happens for 8 minutes every hour from 7 a.m to 7 p.m, then cameras are retrieved two days later. The oyster cages themselves stay in the water for the entire field season.

underwater shot of T-platform
"T-platforms" outfitted with two cameras similar to oyster cage camera set up. These cameras are recording activity around a natural reef rock site. Photo credit: NOAA Fisheries/Jerry Prezioso.

To calculate abundance and behavior at naturally occurring rock reef habitat, we constructed four "T-platforms" with dual camera mounts. We then placed the platforms near boulders within the rock reef site. A team of divers scouted and then selected four boulders that we returned to every other week. A buoy attached to cinder blocks was placed at the center of the boulders. Divers swam down the buoy line and followed a series of lines placed along the bottom to relocate the same four boulders during camera deployment and retrieval. Divers then put the cameras on the T-platforms and retrieved the cameras two days later. The T-platform itself stays in place for the entire field season. Each T-platform is outfitted with two cameras that record video for 8 minutes every hour from 7 a.m to 7 p.m over a complete tidal cycle. The two cameras provide a field of view similar to that provided by our oyster cage camera system: one looks across the boulder and one looks down the side of the rock where it meets the sea floor.

To understand if oyster cage density has an effect on fish abundance and behavior we placed four cages about 50 meters apart at the inshore site adjacent the oyster farm, and four cages about 90 meters apart at the inshore mixed-feature habitat. We calculate fish abundance and behavior using a similar approach as that used for the cage/reef comparison: all cages were mounted with two cameras that record 8 minute segments every hour from 7 a.m to 7 p.m over a complete tidal cycle.

Collecting Environmental Data

During camera deployments, we also collected environmental data. To collect water temperature and light intensity data, we used HOBO Pendant® Temperature/Light 64K Data Loggers. Light is important factor affecting visibility and video quality and it may influence fish behavior. Because changing tidal currents may also influence how fish interact with cages and boulders within rock reefs, we used Lowell TCM-1 tilt current meters to collect information on speed and direction of water currents. A current meter and temperature/light data logger was attached to one cage at both the farm and mixed-feature sites and to a spare T-platform at the rock reef. Using YSI probes, we collected additional environmental data (i.e., salinity, dissolved oxygen, water temperature) during deployment and retrieval trips to each site.

data on monitor
Example output of HOBO Pendant® temperature and light data. Photo credit: NOAA Fisheries/Renee Mercaldo-Allen.

Describing Fish Communities using Environmental DNA (eDNA)

When fish and other organisms move around in the water, they leave traces of their DNA behind. Although this DNA is diluted, it can be extracted and analyzed. Each time we retrieve our GoPro cameras, we collect water for environmental DNA (eDNA) analysis. The eDNA method we’re using combines DNA-based identification and high throughput next generation sequencing to characterize the fish communities associated with oyster cages and rock reefs. Using eDNA we may detect fish that are in the area surrounding the cages or rock boulders, but that are not seen in 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.

Collaborators:

To date, we’ve observed black sea bass, tautog, cunner, scup, summer flounder, conger eel, hake, goby, oyster toadfish, and rock gunnel associating and interacting with oyster cages. Identifying fish to species level and counting fish are only the first steps in our video analysis.

We’ve partnered with fish ecologist Dr. Pete Auster from the University of Connecticut and the Mystic Aquarium to identify and quantify the different ways that fish are using oyster cages. So far we’ve seen fish feeding on the epibenthic fouling organisms growing on the cages, little fish escaping from bigger fish by darting inside the cage itself, and even female fish retreating inside the cage to escape male fish of the same species.

GoPro footage documenting scup (Stenotomus chrysops) feeding on epibenthic fouling organisms that have settled on ropes connected to a shellfish aquaculture cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting tautog courtship with the male tautog (Tautoga onitis) chasing a female. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage captures a double-crested cormorant searching for fish prey around an aquaculture research cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage captures a double-crested cormorant searching for fish prey around an aquaculture research cage as a tautog looks on. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage captures a double-crested cormorant searching for fish prey around an aquaculture research cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage captures a double-crested cormorant searching for fish prey around an aquaculture research cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting a subadult male tautog (Tautoga onitis) courting a larger female in front of an oyster cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting black sea bass (Centropristis striata) interacting and congregating around a shellfish aquaculture cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting scup (Stenotomus chrysops) feeding on epibenthic fouling organisms that have settled on ropes connected to a shellfish aquaculture cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting tautog courtship with the male tautog (Tautoga onitis) chasing a female. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting cunner (Tautogolabrus adspersus) swimming near shellfish aquaculture cage. Video credit: NOAA Fisheries/Milford Laboratory
GoPro footage documenting black sea bass (Centropristis striata) of various sizes swimming above, through, and around shellfish aquaculture cage. Video credit: NOAA Fisheries/Milford Laboratory

Project/Principal Investigators:

Project Team:

Paul Clark, Erick Estela, Peter Hudson, Yuan Liu, Renee Mercaldo-Allen, Lisa Milke, Gillian Phillips, Matthew Poach, Dylan Redman, and Julie Rose. Dive team includes Barry Smith, Mark Dixon, and Jerry Prezioso.

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