Developing Rapid Remote Assessments of Oyster Reef Health and Biodiversity (2019-2020)


Oysters are ecosystem engineers that provide critical habitat for fishes and invertebrates. Oyster reefs protect shorelines, filter water and sequester carbon. Globally, oyster reefs have experienced precipitous declines, with an estimated 85% decrease in stocks in the last 130 years.

Current assessment methods for restoration and conservation of remaining oyster stocks are costly, time-intensive, dependent on weather conditions and sea state and destructive to existing habitat. Novel methods and the integration of technologies such as passive acoustic monitoring and aerial imagery can help produce robust, rapid, cost-effective methods to assess oyster reef ecosystem health, habitat health and biodiversity.

Project Description

This Bass Connections project team will develop, assess and improve tools for coastal conservation practices. The team has four research aims:

  1. Improve on drone-based assessments for population metrics in coastal ecosystems. Building on the research of the previous Bass Connections project team, the 2019-2020 team will assess the efficacy of this methodology in North Carolina oyster reefs. This work will deploy unmanned aerial systems (UAS, or drones) to capture detailed multiband imagery and reef structure.
  2. Use passive acoustic monitoring to assess similar structural reef measurements that are often associated with reef health. Team members will collect passive acoustic recordings over the course of one year and determine which acoustic parameters (e.g., sound pressure levels, acoustic complexity indices, spectral characteristics of the soundscape and counting snapping shrimp snaps) are best suited to provide rapid appraisals of reef structure.
  3. Develop acoustic metrics to assess abundance and biodiversity in fishes and invertebrates. The team will use the aforementioned acoustic parameters and measure fish abundance and diversity using fish traps and gill nets. Team members will also measure invertebrate abundance biodiversity using quadrat surveys, soil cores and autonomous reef monitoring structures (ARMS).
  4. Calculate differences in soundscapes measured by pressure versus particle motion to assess whether one is more suitable than the other for soundscape metrics. Team members will deploy a particle motion sensor synchronized with a pressure-sensing hydrophone at one site and compare the soundscape recordings between the two recording methods. Using the previously obtained biological and physical survey data, the team will determine whether sound pressure or particle motion is more sensitive to differences in population and community structure.

Anticipated Outputs

Dissemination of research progress and outcomes on project blog and website; peer-reviewed papers for publication; oral and poster presentations (including at Benthic Ecology Meeting)


Fall 2019 – Summer 2020

  • Fall 2019: First and second sampling trip; deploy hydrophones and ARMS; conduct initial spatial surveys and traditional ecological surveys; begin sampling and data processing from first deployment
  • Spring 2020: Third sampling trip; continue deployments, sampling and data processing; attend Benthic Ecology Meeting in Wilmington, NC
  • Summer 2020: Final sampling trip; complete data processing and analysis; prepare manuscripts

Team Outputs to Date

Alexandra E. DiGiacomo, Clara N. Bird, Virginia G. Pan, Kelly Dobroski, Claire Atkins-Davis, David W. Johnston. "Modeling Salt Marsh Vegetation Height Using Unoccupied Aircraft Systems and Structure from Motion." 2020. Remote Sens 12(14):2333. 

Tools for Conserving Coastal Ecosystems (Fortin Foundation Bass Connections Virtual Showcase 2020)

Project team site

What Are ARMS?

This Team in the News

Meet the Members of the 2019-2020 Bass Connections Student Advisory Council

See earlier related team, Developing Rapid, Cost-effective Methods for Evaluating Coastal Biodiversity and Resilience (2018-2019).


Image: Oyster Reef, by Lia McLaughlin/U.S. Fish and Wildlife Service Northeast Region, public domain

Oyster reef.

Team Leaders

  • Jason Dinh, Trinity-Biology-Ph.D. Student
  • Douglas Nowacek, Nicholas School of the Environment-Marine Science and Conservation
  • Julianna Renzi, Nicholas School of Environment-Marine Science & Conservation-Ph.D. Student
  • Justin Ridge, Nicholas School of the Environment-Marine Science and Conservation

/graduate Team Members

  • Molly Bruce, Juris Doctor, Master of Environmental Management, Coastal Environmental Management

/undergraduate Team Members

  • Eve Adelson
  • Catherine Bailey, Biology (BS), Theater Studies (AB2)
  • Melissa Baldino, Biology (BS), Environmental Sci/Policy (AB2)
  • Avery Indermaur, Environmental Sciences (BS)
  • Haynes Lynch

/yfaculty/staff Team Members

  • David Johnston, Nicholas School of the Environment-Marine Science and Conservation
  • Brian Silliman, Nicholas School of the Environment-Marine Science and Conservation