Flipping the cages on sustainable aquaculture: a study on oyster aquaculture technique and policy to reduce pathogens

Progress report for LS23-379

Project Type: Research and Education
Funds awarded in 2023: $358,557.00
Projected End Date: 03/31/2026
Grant Recipients: South Carolina Sea Grant Consortium; South Carolina Department of Natural Resources Marine Resources Research Institute; College of Charleston ; Minorities in Aquaculture
Region: Southern
State: South Carolina
Principal Investigator:
Sarah Pedigo
South Carolina Sea Grant Consortium
Matthew Gorstein
South Carolina Sea Grant Consortium
Dr. Peter Kingsley-Smith
South Carolina Department of Natural Resources Marine Resources
Mike Marshall
South Carolina Department of Health and Environmental Control
Dr. Matthew Nowlin
College of Charleston
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Project Information


Sustainable aquaculture industries, such as oyster aquaculture, are critically important to support protein production for the global human population (FAO, 2020), and are an increasingly important economic driver for coastal states of the U.S. (USDA, 2019). The oyster aquaculture industry provides socio-economic and environmental benefits that include viable agriculture jobs, local and affordable protein options, and beneficial ecosystem services such as water quality enhancement, habitat provision, and eco-tourism opportunities. Advancements in gear technology and the ability to generate year-round revenue through triploid summer harvest have enabled the expansion of the oyster aquaculture industry in South Carolina. A key factor influencing the economic viability of oyster farming is pest and pathogen management for both human health and aesthetic quality of product. One best management practice is to periodically air dry oyster cages to reduce biofouling (i.e., the unwanted settlement of epibenthic organisms, such as barnacles on oyster shells). This routine is strictly controlled by South Carolina Department of Health and Environmental Control (SC-DHEC) since aquaculture oysters are destined for the (typically) raw consumption, half shell market. Exposing oysters to the air (and elevated temperatures) can increase human health risks associated with consuming live, raw seafood due to increases in naturally occurring pathogenic Vibrio bacteria, Vibrio vulnificus and Vibrio parahaemolyticus (Su & Liu, 2007). SC-DHEC requires a minimum of a 14-day resubmergence period after air drying to allow oysters to depurate their tissues and return to ambient Vibrio spp. levels. In highly productive environments, oysters and cages can become re-fouled during this period, causing the farmer to incur additional labor expenses to clean the oysters before harvest. Farmers must strike a balance between maximizing production efficiency while providing a safe, sustainable product, and have requested an in-depth study on best management practices for air-drying and resubmergence. Providing the best available science to inform local regulations is needed to effectively and responsibly manage the oyster farming industry. The collection of Vibrio spp. data at the local (e.g., state-specific) level may enable an optimization of resubmergence requirements; though to do so, cooperation across multiple state and federal agencies is necessary.

This study will undertake a whole-systems approach to collect field data, understand inter-agency communications, and develop policy recommendations to maximize agricultural sustainability and efficiency for the coastal shellfish aquaculture industry. The project team will experimentally measure Vibrio spp. dynamics following aquaculture industry handling practices, and create an advisory committee to facilitate transparent communication across stakeholder groups. Oyster tissue samples will be collected at three different farms for analysis of Vibrio spp. at different pre-handling, post handling, and post-resubmergence time points (i.e., 5, 7, and 14 days after resubmergence), with trials repeated on two occasions during Vibrio control months (i.e., May-September). In addition to field data collection, an analysis of current policies and decision-making practices will be conducted to evaluate how the data may inform regulations in an efficient manner to foster a sustainable oyster farming industry that works in harmony with environmental, economic, and sociopolitical parameters.

Project Objectives:

The objectives of this project are as follows:

  1. Engage with off-bottom oyster aquaculture partners to plan for and prepare aquaculture lease study sites for project implementation.
  2. Conduct resubmergence trials (e., handling and desiccation of oysters and gear at farm sites) and collect oyster tissue samples for analysis of Vibrio spp. at specific time intervals at multiple sites, as described in the methods below.
  3. Continually engage with a PAC of public health, environmental and fisheries managers, and industry experts at state and federal levels throughout the development, implementation, and dissemination of the proposed work to maximize the use of the data in guiding public health requirements for off-bottom aquaculture.
  4. Conduct an analysis of the policy process to translate results into policy recommendations, following the completion of data collection.
  5. Conduct education and outreach efforts to disseminate project results and best management practices to the South Carolina aquaculture industry.


Click linked name(s) to expand/collapse or show everyone's info
  • Thomas Auld - Producer
  • Julie Davis - Producer
  • Josh Eboch - Producer
  • Trey McMillan - Producer
  • Gary Sundin - Technical Advisor
  • Lauren Faulk
  • Andy Hollis
  • Henry Davega


Materials and methods:
  1. Engage with off-bottom oyster aquaculture partners to plan for and prepare aquaculture lease study sites for project implementation:
    1. Active aquaculture leases, located in tidal creeks of South Carolina, will serve as experimental sites for completing resubmergence trials. To plan for implementing research activities into active operations, farmers will be engaged in year 1 to discuss best practices for carrying out trials, while also minimizing conflict with ongoing business operations. Facilitated meetings will be organized by Consortium specialists for farm partners, SCDNR research entities, and SC-DHEC regulators to disseminate unified messaging on project objectives; make sure concerns of all parties are addressed; foster collaboration between industry, regulators, and researchers; and set realistic expectations. The project team will continually receive guidance from the farmers on their routines for following resubmergence protocols so that the study provides accurate and useful information.
    2. Farmers serve a key role in this project. Their technical expertise will be leveraged to prepare the study sites, which includes cage deployment and providing technical assistance for general aquaculture practices. Farmers also have the crucial role of providing animals for completion of the research phase. They will be responsible for growing oysters from seed to market size. Oyster grow-out takes approximately 1 year. To ensure farmers have market size oysters available for the trials, the PI will coordinate with farmers in years 1 and 2 to align on numbers of oysters and trial timelines.
    3. We also understand that requesting to use portions of active lease sites has potential to disrupt farm practices, and that operating a farm at any capacity requires the ability to pivot and respond to needs abruptly. Given the potential an industry member needs to resign their participation, the project team is prepared to engage other farmers through the proper SARE process, if one or more identified farms is unable to participate.
  2. Conduct resubmergence trials (e., handling and desiccation of oysters and gear at farm sites), and collect oyster tissue samples for analysis of Vibrio spp. at specific time intervals at multiple sites:
    1. Trials will be conducted in years 2 and 3 of the study. A total of two trials at three separate farm locations will take place each year and will align with the peak of (August) and end of (September) Vibrio control months (May-September). Farmers will deploy, stock, and prepare gear for trials, and aid in completing handling practices.
    2. SCDNR shellfish researchers will lead procedures to collect samples. Consortium specialists and the graduate student will assist with sample collection and shipping, and the US FDA Gulf Coast Seafood Laboratory (GCSL) will analyze all oyster tissue samples for vulnificus, total V. parahaemolyticus, and pathogenic V. parahaemolyticus (tdh+/trh+).
    3. Floating cage, 6-bag systems will be used in trials. Bags will be stocked at appropriate densities (150-200) with market size oysters (approximately 76mm in shell height), placed into floating gear, and will be deployed two weeks before the start of each trial. Treatments will include a control (cage with six replicate bags, to remain submerged throughout the experiment) and a treatment (cage with six replicate bags, to undergo handling and air drying). A third cage will be used for restocking cages as sampling occurs to maintain appropriate densities.
    4. For each trial, bags of oysters from the treatment cage will be removed from the cage at the beginning of the trial and subjected to standard oyster aquaculture handling measures (g., tumbling and desiccation). This includes transporting bags of oysters to land-based industry facilities to tumble the oysters using tumbler/grader equipment. Oysters will be restocked into bags and desiccated on land, exposed to ambient environmental conditions for a total of approximately 24 hours. While tumbling and desiccating practices are not typically carried out in unison by oyster farmers, this method creates a worst case scenario for evaluating Vibrio spp. recovery levels in oysters, which is important to understand when considering public health. After 24 ± 2 hours, handled oysters will be placed back into the treatment cage and resubmerged at the lease site. A sample of oysters will be collected before handling procedures to act as a baseline for Vibrio spp. levels. Following the desiccation period and before being resubmerged, another sample of oysters will be collected. Additional oyster samples will be collected at 5, 7, and 14 days following resubmergence in order to quantify the trends of Vibrio spp. levels.
    5. At each oyster sampling event, an aggregate sample of 15 oysters will be collected from each of three bags within the treatment cage, and from three bags within the control cage. Following removal of oysters from the bags, oysters from the third non-experimental cage will be used to restock the bags to maintain a consistent oyster density within each bag. These restocked oysters will be marked to ensure they are not collected during subsequent oyster sampling events. Continuous temperature and salinity data loggers will be deployed in each cage to collect ambient environmental data for the duration of each trial.
    6. All oyster samples will be immediately put on ice to bring down the internal temperature prior to shipping. Once oysters have reached a temperature of 50°F, they will be packed in a cooler with ice packs and a continuous temperature logger to ensure appropriate temperatures are maintained during shipping. Coolers will be shipped overnight to the GCSL to ensure the samples can be processed within 36 hours of collection.
    7. In total for each trial, Vibrio spp. levels within oyster tissue will be measured at the trial start (pre-handling), after handling procedures (post-tumbling and desiccation) and after 5, 7, and 14 days of resubmergence to test for statistically significant reductions in Vibrio spp. concentrations. Statistical analysis will follow methods of published resubmergence studies (Pruente et al., 2021 & 2022).
    8. The project team is dedicated to producing data that meet FDA and state sanitation (SC-DHEC) standards which may be utilized to inform policy change. This requires that experimental methods and sample analyses comply with NSSP protocol. The SC-DHEC Shellfish Sanitation Specialist will lead the development and submission of a Vibrio Technical Assistance and Research Request in year 1 of the project, for samples to be analyzed and Vibrio data to be provided by the certified GCSL Vibrio Lab. The private FDA facility incurs the costs of and conducts Vibrio spp. analyses based on external requests that are evaluated by the FDA and the ISSC (entities who manage the NSSP) on a case by case basis. The project team has consulted with the GCSL - Vibrio lab to inform the experimental design, to discuss analysis request timelines, and will continue correspondence to align on experimental sampling protocols and sample shipping methods.
  3. Continually engage with a PAC of public health, environmental and fisheries managers, and industry experts at state and federal levels throughout the development, implementation, and dissemination of the proposed work to maximize the use of the data in guiding public health requirements for off-bottom aquaculture:
    1. A PAC of experts will be convened as a resource for the industry and project team to call on throughout the project, and will be beneficial for sharing concerns and in continuing to build trust between the aquaculture industry and management agencies. Participants will include but are not limited to decision makers, such as state SC-DHEC shellfish sanitation managers, regional FDA shellfish specialists, SCDNR shellfish managers, SC Shellfish Growers Association, and Consortium specialists; as well as federal entities as the USDA FDA health officials.
    2. The PAC will convene for Consortium facilitated meetings iteratively throughout the project duration to share updates and progress. Concluding the project, the PAC will gather for a final meeting to determine best practices moving forward to implement project outcomes. Results will be provided to SC-DHEC responsible bodies for regulating aquaculture sanitation in South Carolina to inform science-based management decisions.
  4. Conduct an analysis of the policy process to translate results into policy recommendations, following the completion of data collection:
    1. The objective will include an assessment of current aquaculture policies and produce recommendations for ways forward on how to better integrate science into the policymaking processes. Included in this analysis will be an assessment of how typical science-to-policy change timelines align with expected climate change impact timelines in South Carolina, as well as interviews and deliberative discussions with key stakeholders. PI Nowlin, along with a graduate student will complete this work. The policy process analysis is another way for the project to undertake a whole-systems approach by addressing socio-political parameters in addition to ecological (g., Vibrio spp. levels) and economic parameters (evaluating different resubmergence times).
    2. A network analysis of decision-makers and other stakeholders will be developed through semi-structured interviews and surveys of those involved with aquaculture policy. An understanding of the decision-making network structure can highlight the key players and decision points as well as the connections between decision-making and implementation.
    3. This project will use network analysis to highlight points where the connections between science and policymaking could be enhanced. Based on this analysis we will develop recommendations for how to improve the integration of science and policymaking, particularly in the context of a changing climate which will necessitate a policy process more responsive to rapidly changing conditions and knowledge. In addition, the network analysis will be used to produce guidelines for scientists interested in engaging in the policy process.
  5. Conduct education and outreach efforts to disseminate project results and best management practices to the South Carolina aquaculture industry:
    1. The Consortium shellfish aquaculture specialist will lead education and outreach activities targeted toward the oyster aquaculture industry, the public, and research and management entities. The outreach plan below elaborates specific activities that will be completed for each target audience. This will result in dissemination of project results through printed and digital fact sheets, best management practices guides, as well as educational research symposiums. All of which will create long-lasting content that can be accessible through the Consortium’s digital platforms for years to come and used in future education and training efforts.
Research results and discussion:

Project Update March 2024:

The S.C. Sea Grant Consortium (Consortium) hosted a kickoff meeting in April 2023 including the research team from the South Carolina Department of Natural Resources (SCDNR), participating shellfish farmers, and the South Carolina Department of Health and Environmental Control (SCDHEC). Principal Investigator Pedigo engaged a wide variety of experts during year 1 of the project in addition to the project team including those who have conducted similar oyster cage resubmergence focused studies in other states, and engaging the Food and Drug Administration (FDA) lab in Dauphin Island, AL well in advance to set up logistics for shipping samples in years 2 and 3 of the project. A Vibrio Assistance Review Board (VARB) request to FDA was submitted by SCDHEC on behalf of this project in August 2023. The project team submitted clarifying comments to FDA in September 2023 and January 2024.

All participating farmers have set aside stocked oyster cages for the study, with the oysters growing to market size throughout year 1 of the project. These oysters will then be ready to be sampled in summer 2024. Regular project team meetings were held throughout year 1 to refine the sampling, temperature control, and shipping protocols; and to establish field logistics. Three field teams have been established in order to sample from all three farms on the same day. A practice trial with all the field teams at a Lowcountry Oyster Co. lease site was held in February 2024 to get a better feel for the field logistics. 

Participation Summary
4 Farmers participating in research


Educational approach:

The educational approach used in this project is one of co-production, with a public-private partnership. Field sampling and temperature protocols are established based on typical industry practices and FDA regulations. 

In terms of student workforce development, funds have included in years 2 and 3 to hire graduate students and interns. A job post is slated for release in March 2024 for a graduate student to work on the project. Interviews are currently being held for Minorities in Aquaculture Interns for summer of 2024, to be placed on shellfish farms in South Carolina: https://www.scseagrant.org/minorities-in-aquaculture-internship-program/ 

Principal Investigator Pedigo hosted a contingent of Southern SARE representatives on a field trip to Charleston, SC. Fifty-three (53) Southern SARE representatives and stakeholders attended a presentation about the project at the SCDNR Marine Resources Research Institute, and received a tour of the marine lab, including tanks where fish are reared for research purposes for application to the aquaculture and fishing industries

Educational & Outreach Activities

5 Consultations
1 On-farm demonstrations
3 Webinars / talks / presentations
1 Workshop field days

Participation Summary:

4 Farmers participated
53 Ag professionals participated
Education/outreach description:

The Consortium provides science-based information on issues and opportunities to enhance the social and economic well-being of our coastal citizens, while ensuring the optimal use and conservation of our coastal and marine resources through extension, outreach, and education activities. The experimental research and policy analysis conducted in objectives 1-4 will provide science information as well as best recommendations for applying the results to inform policy. To extend project outcomes, PI Pedigo, the Shellfish Aquaculture Specialist with the Consortium, will lead the development of outreach plans and products for sharing project results, educating end users, and providing information for further research and/or implementation at state, regional, and national levels.

During outreach efforts, entities involved within our whole systems approach will be targeted to ensure that appropriate end users are engaged and receive project results. End users include the participating target audience, which is the oyster farming industry, first and foremost. This also includes SC-DHEC and the FDA officials, entities pertinent to enacting policy change, and students at South Carolina universities. Additional target audiences to direct outreach efforts include the seafood consuming public, and on a regional and national scale, researchers, regulators, and the broader Sea Grant community.

Oyster Farming Industry Outreach Efforts

This project will engage the South Carolina oyster farming industry in outreach initiatives throughout the project, not only during dissemination of results. To carry out this project in collaboration with oyster farmers, PI Pedigo will work to maintain transparency and good-standing relationships between the farmers and management agencies (SCDNR and SC-DHEC) by facilitating communication, creating Memorandum of Understanding (MOU) working agreements, and will engage with the participating farmers to plan, gather input, and share updates. Involving farmers in this work also necessitates that compensation is provided. All participating farmers will receive reimbursement for their time, will be provided gear used in the trials, will be compensated for oysters used in trials, and their voices will be heard through involvement in advisory committee meetings.

To extend project outcomes to the whole oyster aquaculture industry in South Carolina, an industry-focused symposium will take place. The event will include presentations of current research with a focus on this project, resulting in an information exchange with the aquaculture industry. Oral presentations will be shared by graduate students as well as the project team. Depending on the ability to inform policy change, the symposium will include status updates and next steps from SC-DHEC Shellfish Sanitation officials. In addition, the event may offer facilitated panel discussions to document needs for advancing and maintaining sustainability of the South Carolina Aquaculture industry. As an added benefit, the symposium will provide an opportunity for the industry, management agencies, students, and researchers to interact and network.

Materials for the oyster aquaculture industry will include a guide to detail South Carolina shellfish aquaculture best management practices, based on project results. The document will include, but will not be limited to a project overview, research outcomes, and technical information for adapting new practices to operations if data support a policy change. The Consortium currently hosts a suite of shellfish aquaculture resources in an Aquaculture Toolkit on the Consortium’s website (https://www.scseagrant.org/aquaculture-toolkit/). These tools provide information for navigating processes to enter the industry as well as provide information for existing growers. The best management practice guide will be added to the Consortium’s Aquaculture Toolkit, which is readily accessible, and is hosted on a trusted platform.

To maintain a healthy and efficiently functioning operation, there is a need to keep detailed records of farm operations. As a component of the best management practices guide, the Consortium will also work with oyster farmers to refine an inventory log sheet. Necessary components of the inventory include documenting environmental conditions, seed importation and planting, mortality, farm handling (e.g., desiccation and tumbling), as well as growth rates. Once refined, a log sheet template will be available in digital form and print form. For digital access, the inventory sheet will be added to the Consortium’s aquaculture toolkit. For print form, the Consortium has budgeted to provide each oyster farmer in South Carolina with waterproof inventory books to use for record keeping.

Outreach Efforts to Inform the Regional Oyster Farming Industry

Materials for the broader oyster farming community include publications and presentations by the project investigators to extend results at regional and national levels. Research findings will be shared with the aquaculture community during at least one annual meeting such as Oyster South (https://www.oystersouth.com/our-mission). Manuscripts will be submitted to aquaculture and public health journals, such as Aquaculture Research and the Journal of Food Protection. Consortium Specialists will leverage existing aquaculture networks to share challenges, opportunities, results, and lessons learned from the project with other Sea Grant programs such as regional “Aqua chats” and the National Sea Grant Aquaculture Research Symposium.

Information generated from the project will be pertinent for state shellfish sanitation officials in South Carolina and southeast states, as well as FDA officials. SC-DHEC Shellfish Sanitation officials will share results of the study with the FDA, other state shellfish control authorities, industry stakeholders, and the ISSC through regional meetings, conferences, and work group committees. In consultation with the FDA, South Carolina will utilize study data to assist in facilitating regulation changes if results from the study affirms shortening time frames would not pose a risk to public health.

An expected product, which is applicable to local and regional oyster farmers, shellfish managers, and researchers is a guide with recommendations for conducting applied research that also integrates guidelines from the network analysis.

Student Support

A graduate student will be supported by the Consortium to assist with farm engagement and carrying out experimental trials. The student will be provided with the opportunity to conduct a thesis project as part of the applied aquaculture research, and will also be able to enhance their aquaculture technical skills by being immersed in field research and interacting with industry members. An additional graduate student will be supported by the College of Charleston and PI, Nowlin to assist with conducting surveys to develop the policy analysis, leading to a thesis project concentrated toward political science. Students will have the opportunity to develop a thesis and publishable manuscripts to add to resubmergence and aquaculture policy literature. The Consortium has a long history of training graduate students for successful environmental careers. Additionally, project investigators have a wide knowledge and experience mentoring students.

Funding is also included for four summer internships as part of the Consortium’s partnership with the nonprofit Minorities in Aquaculture (MIA). The Consortium and MIA successfully piloted this internship program in the summer of 2022, providing paid hands-on opportunities on three different SC shellfish farms (https://www.scseagrant.org/new-internship-program-promotes-diversity-in-aquaculture-industry) to three students of color enrolled at universities in South Carolina. Securing support to continue this successful program will help enhance diversity within the aquaculture sector in the southeast.

Seafood Consuming Public Outreach Efforts

We intend to use the Consortium’s website and social media to reach local communities as well as regional and national audiences, in extending factsheets for bivalve shellfish consumers. We expect that at least 3-5 informational documents will be produced through this project by the Consortium’s communications team with engagement with the project team. Fact sheets will focus on elevating and educating seafood consumers on the source of their shellfish products, highlight aquaculture practices, and will elaborate when it is safe to consume certain types of shellfish. For instance, triploid aquaculture oysters may be consumed year round whereas wild harvest oysters are only safe to eat within a season (typically October to May). The Consortium Shellfish Aquaculture Specialist will partner with and leverage existing SCDNR and SC-DHEC outreach programs to share information. This may include opportunities to exhibit oyster aquaculture techniques at the Port Royal Sound Foundation, 501(c)(3) non-profit, to promote sustainable aquaculture.

Through leveraging the expertise of the Consortium’s Coastal Public Information Coordinator, informational videos and feature stories will also be created to highlight ongoing project efforts, summarize results, and share benefits associated with farming oysters in South Carolina estuaries. These materials will be shared through the Consortium’s website and social media platforms.

Information Products

    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.