Marine Ecosystem Health

Coral Reef & Molecular Ecology


J. Voss

Principal Investigator

Joshua D. Voss. Ph.D.
Assistant Research Professor


Coral reef communities are not just exquisitely beautiful, they are extremely important both ecologically and economically. Highly productive and biodiverse coral reefs protect our coastlines from erosion, provide essential habitat, and are integral in global nutrient cycling. In addition, corals support a worldwide multi-billion dollar diving and tourism industry. However, the ecological and societal benefits imparted by these reefs are seriously threatened. Coral reefs are experiencing a recent period of severe decline due to emerging coral diseases, climate change, fisheries exploitation, and land-based sources of pollution.

The Coral Reef & Molecular Ecology Lab integrates experimental and field monitoring approaches with advanced molecular techniques to better understand coral ecosystems. Our primary goals are to:

  • Identify and characterize coral reef resources
  • Determine the links between environment conditions, coral stressors, and reef health
  • Create diagnostic molecular tools and protocols that can be used to assess coral health
  • Track and predict the impacts of coral stressors on reef ecosystems
  • Train researchers and students in advanced molecular techniques for quantifying coral health
  • Provide data and information to improve management strategies for marine ecosystems


Current projects

Exploration, Habitat Characterization, and Coral Health Assessment in Flower Garden Banks National Marine Sanctuary

The Flower Garden Banks National Marine Sanctuary (FGBNMS) is comprised of unique shelf-edge coral reef habitats in the northwest Gulf of Mexico (GOM). To develop enhanced management strategies and to understand potential impacts from stressors such as climate change, fishing, disease, or oil spills, comprehensive ecological baseline data are required. Our collaborative approach and complementary methods include SCUBA, technical diving, fish acoustics sonar, and remotely operated vehicles (ROVs) to survey benthic and fish communities among five habitat types: coral reef cap, deep reef, algal nodules, coralline algae, and soft bottom. This project will provide detailed mapping and characterization of the habitat and community structure on shallow and mesophotic coral reefs in FGB. Likewise the project will establish baseline fish community data for FGB to assess potential impacts from a proposed experimental fisheries closure. Ongoing work will integrate data among the survey methods and incorporate molecular approaches to understand coral stress and connectivity in the FGBNMS and elsewhere in the GOM. This project builds into our larger Mesophotic Coral Reef initiative in the Cooperative Institute for Ocean Exploration, Research, and Technology. 

Partners: Flower Garden Banks National Marine Sanctuary (Emma Hickerson, Marissa Nuttall, G.P. Schmahl), NOAA NCCOS (Randy Clark, Chris Taylor, Greg Piniak), UNCW Undersea Vehicles Program (Lance Horn), John Reed

Funding: Cooperative Institute for Ocean Exploration, Research, and Technology, NOAA Coral Reef Conservation Program, NOAA Sanctuaries


Estuarine Impacts on St. Lucie Reef: Determining the effects of changing resource management on Florida’s northernmost coral reef

Save Our Seas plate


This research is funded by proceeds from Florida's Save Our Seas specialty license plate.


Development of sound management strategies is critical for conserving and protecting vital coral reef communities in South Florida. Successful strategies require an improved understanding the effects of coastal anthropogenic activities, including community development, freshwater management, and release of potential pollutants. This project specifically addresses the effects of management activities in the St. Lucie Estuary and the resulting water quality impacts on downstream coral and algal communities located on St. Lucie Reef. This state park protected reef represents the known northern limit of many tropical benthic coral reef species and serves as habitat for numerous fish species of both commercial and recreational importance. The overarching goal of this research is to provide data and information for enhanced adaptive management in ongoing and proposed regional restoration and conservation efforts including the Comprehensive Everglades Restoration Plan.

Partners: Florida Fish and Wildlife Conservation Commission (Jeff Beal), St. Lucie Inlet State Park (Charles Jabaly), Dennis Hanisak

Funding: Florida State Wildlife Grant, FWC, Robertson Coral Reef Program, Save Our Seas Florida specialty license plate sales, River Branch Foundation


Molecular diagnostics of coral exposed to oil and dispersants: a holobiont approach to investigate potential effects on the host corals, symbiotic algae, and mucus associated microbial communities

The overall goal of this project is an integrated assessment of oil and dispersant impacts on Florida’s reef-building corals. A combination of ex situ exposure experiments, advanced molecular techniques, and in situ monitoring at potentially affected sites provide complimentary data on the potential effects of oil and dispersant. The goals of this project are to: 1) adapt our coral-stress microarray to include genetic biomarkers indicative of oil/ dispersant exposure, 2) determine the potential effects of Deepwater Horizon oil and dispersants on coral health at molecular, organismal, population, and community levels, 3) identify damage to corals due to oil/dispersant exposure including both mortality and sublethal stresses, 4) determine chronic impacts of oil on coral health and the potential for recovery and resilience in affected habitats. A coral and zooxanthellae toxicant-stress microarray has been developed to identify genetic profiles indicative of exposure to crude oil, dispersants, or a combination of the contaminants. This project will also use bacterial community profiling to identify changes in the microbial communities of corals in response to oil and dispersants and to predict the effects of these changes on coral resilience. Both of these techniques will be combined with ongoing surveys of coral reef health at established Coral Reef Evaluation and Monitoring Project (CREMP) sites in the Florida Keys National Marine Sanctuary.

Partners: Sara Edge (PI), Florida Fish and Wildlife Conservation Commission (Kate Semon Lunz, Rob Ruzicka), Mote Tropical Marine Laboratory (Erich Bartels), Tonya Shearer (Georgia Tech)


Assessing Disease Susceptibility, Resistance, and Resilience in Caribbean Corals

Coral diseases have dramatically increased over the past four decades, with documented increases in the number of described diseases, geographic ranges, number of host species, and overall incidence. This project combines in situ monitoring data on coral disease prevalence, recurrence, and severity with targeted ex situ factorial experiments to understand why some coral species or individual colonies succumb to disease while others survive. Black band disease and two Caribbean coral species, Montastraea cavernosa and M. faveolata, are being used as models to investigate a number of complete research questions. For example, is susceptibility to disease determined by coral and zooxanthellae genotypes or driven primarily by environmental conditions? Are corals exposed to disease more like to be resistant during subsequent exposures? Can we predict which corals are most likely to survive (or) during disease outbreaks? Perhaps most important, can we alter management strategies to mitigate losses of corals to disease? Techniques to identify disease resistant/resilient corals would be particularly advantageous for coral restoration efforts. Ecological disease data have been collected throughout the Caribbean while ex situ experiments have been focused in the Florida Keys and Lee Stocking Island, Bahamas.

Partners: Mote Tropical Marine Laboratory (Erich Bartels), Sara Edge

Funding: Mote Protect Our Reef Grant Program, Robertson Coral Reef Program, River Branch Foundation   


CIOERT Mesophotic Coral Reefs

In shallow waters (< 20 m) of the Caribbean Region, a coral decline of 80% over the last 30 years has been documented. Mesophotic reefs deeper than 30 m are a largely unknown frontier and appear to be healthier than shallow water reefs. They are habitats of commercially important fish species and source of coral larvae for recruitment and potential recovery of the shallower reef areas. The overall scope of work envisioned for the mesophotic reef project reflects the need to conduct broad surveys to understand the large scale dimensions of mesophotic reefs (e.g., geomorphological structure and forcing, biodiversity and biogeography, geographic connectivity) coupled with detailed work at selected sites to understand the functioning of mesophotic reefs (e.g., connectivity to shallow reefs, dynamics and life histories, effects of anthropogenic stress and climate change, historical development and their support of fisheries resources and endangered species). The primary goal of this project is to characterize mesophotic reef ecosystems across a large spatial scale, ranging from the U.S Caribbean (Puerto Rico and U.S. Virgin Islands) to the Gulf of Mexico (Flower Gardens and adjacent deep-water banks that are prospective MPA sites), and including new shelf-edge MPA sites off the southeastern