Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
  • BCO-DMO Processing Description
• Related Publications
• Parameters
• Instruments
• Project Information
• Funding

The surveys were conducted at various shallow depths (3-, 4-, 10-, 15-meters (m)) in the reefs Turrumote 2, Romero, Guilligan Is, Guanica Bay, Cayo Coral, and Punta Guanica. These reefs are located in southwestern Puerto Rico (approx. lat. 17.8849, long. -67.01546, depth 3-15 m).

The methodology used in the field was the line transect method. The length of each line was 10 m.

Five haphazardly placed, 10-m long permanent, linear/band transects were set up in each of at least three depth intervals (0-5, 7-12, and > 15 m) in several localities prior to the arrival of the disease. They were surveyed before the epizootic event started, to estimate initial live coral cover, during the peak of the event to estimate disease prevalence and species impacted, and again after the disease arrested to estimate impact at the population and community levels.

The linear distance (in centimeters (cm)) of each different substrate (live coral colonies, sponges, zoanthids, crustose coralline algae, etc.) under the tape was measured along each ten-meter-long transect. Relative cover (as a percent (%)) for each substrate in each transect was calculated and added up for each transect. The overall and average percent cover for each biological group and substrate was then estimated for each depth and each locality. Variability in live coral cover across depth intervals in each reef and locality, and among localities will be compared before, during, and after the SCTLD epizootic event.

All coral colonies were checked for health status (healthy, SCTLD infected, other diseases, and bleaching) along a band transect (10 x 2 m (20 sqm) marked by the linear tape. Proportions of colonies in each health category will be calculated for each depth, locality, and over time. Variability in the temporal dynamics of SCTLD prevalence for each foundational, susceptible species impacted will be assessed across depth intervals within each locality, across localities, and over time.

Instrumentation:
Besides the individual diving equipment and an underwater camera, no special instruments were needed to collect the live coral cover. A fiberglass graduated 30-m long tape, a PVC pipe (1-m long), a slate, underwater paper, and pencils were the materials used. Additionally, we had HOBO temp loggers (ONSET Corp.) in several localities, which will provide seasonal/annual variability and the number of days/weeks with higher-than-normal water temperatures.

Identification of benthic species was done by the diver in situ. Most of the survey data has been entered into Excel spreadsheets and edited for errors. We still have to finish a couple of localities to then run the analyses with parametric and multivariate analyses to assess significant variability and changes in live coral cover, disease prevalence, biodiversity, and the impact of the disease at the population and community levels.

- Converted the species code list to CSV format and imported the file into the BCO-DMO system.
- Imported original file "RAW-DATA-GUANICA-REEFS-2018-2020-EW-REV-jan25.xlsx" into the BCO-DMO system.
- Converted dates to YYYY-MM-DD format.
- Converted latitude and longitude values from degrees and decimal minutes to decimal degrees; rounded values to 5 decimal places.
- Renamed fields to comply with BCO-DMO naming conventions.
- Made the following changes for consistent formatting/use of codes:
-- Replaced "Turf" with "TUR" in the "Group" column.
-- Replaced "OCT" and "Oct" with "Octocoral" in the "Genera" column.
-- Replaced "SPO" and "Spo" with "Sponge" in the "Genera" column.
-- Replaced "Turf+Sand" with "Turf and sand" in the "Genera" column.
-- Replaced "OCT" and "oct" with "Oct" in the "Species" column.
-- Replaced "Romero2" with "Romero 2" in the "Locality" column.
- For rows where "Genera" = "Palythoa", and "Species" = "Pame", changed "Pame" to "Pcar".
- Corrected the species code list so "Pcar" = "Palythoa caribaeorum".
- Joined the species code list to the primary data file, creating a new column "Species_name".
- Renamed the original "Species" column to "Species_code".
- Saved the final file as "958181_v1_reef_surveys_2018_2020.csv".

Location: The study will be carried out in reefs off La Parguera Natural Reserve, on the south-west coast of Puerto Rico. Facilities are located within the Reserve, so we have quick and easy access to the reefs for collections and surveys. Caribbean Sea, Southwest Puerto Rico,  Lat. 17.8849 Long. -67.01546

NSF Award Abstract:
Modern coral reefs are the result of thousands of years of growth and development, but their demise is occurring at alarming rates around the World. In the Caribbean alone, over 60% of live coral cover has been lost in many reefs in just 30-40 years. Consequently, their ecological and economic benefits to coastal communities are also declining. Disease outbreaks and more intense and frequent bleaching (loss of the microalgae in coral tissues) events associated with increasing water temperatures are some of the main factors for coral reef mass mortalities. The highly infectious and deadly Scleractinian Coral Tissue Loss Disease (SCTLD), first identified in 2014 in Florida, is quickly moving through the Caribbean causing extensive mortalities across important reef-building corals. Current research is focused in after-infection events to identify the pathogen and characterize the signs, patterns and consequences of SCTLD transmission. This study investigates coral tissues and the coral-associated bacteria communities before, during and after the infection has occurred in reefs in Puerto Rico. The societal broader impact of the project relates to the significant ecosystem services provided by coral reefs, which are threatened by SCTLD. The project will also support training of a graduate student.

Questions about etiological variability and the temporal dynamics of the microbiome in SCTLD-affected coral species remain unanswered. Specifically, this proposal addresses the following questions: (1) What are the changes in the microbiome composition and abundances of the susceptible coral species when infected with SCTLD? (2) What is the variability in virulence, prevalence and mortality within and amongst species in different phases of the infection and in different habitats? The research site is in La Parguera Natural Reserve, southwest Puerto Rico, where the research team has characterized and monitored several reefs and environmental conditions from the shore to the shelf edge since 2003. This project includes surveys of permanent transects and molecular characterization of tissue/mucus samples, and microbial communities within those, collected from healthy colonies of two to three of the most susceptible coral species (i.e., Meandrina meandrites, M. jacksoni and Orbicella faveolata) and colonies of two resistant species (i.e., Montastraea cavernosa, Porites astreoides) at the long-term monitoring site. The expected arrival of SCTLD to Puerto Rico in Fall 2019, offers the team of researchers a unique window of opportunity to capture reef biological conditions before, during and after infection to complement other research efforts to better understand the ecological dynamics, prevalence and consequences of this new deadly coral disease.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.