Table of Contents

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

For samples collected from the Florida Keys, U.S.A., sterile, 10 milliliter (mL) syringes were used to scrape/remove tissue from Montastraea cavernosa, Orbicella faveolata, Colpophyllia natans, Meandrina meandrites, and Pseudodiploria strigosa corals. For Siderastrea siderea corals collected from the Florida Keys, U.S.A., a sterile corer was used to scrape tissue off, which was captured in a sterile syringe. Coral tissues were transferred from the syringes to plastic tubes before transport on ice to the South Florida Regional Laboratory of the Florida Fish & Wildlife Conservation Commission's Fish and Wildlife Research Institute. There, coral tissues were flash frozen with liquid nitrogen before storage at -80 degrees Celsius (°C). DNA was extracted from samples using DNeasy PowerSoil Kits (QIAGEN, Germantown, MD, USA). 6 mL of coral tissue/mucus slurries were used for S. siderea, but 2 mL were used for all other species. Each slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. These methods are described by Clark et al. (2021).

For samples collected from the United States Virgin Islands, diseased and apparently healthy Porites astreoides, M. cavernosa, Orbicella annularis, S. siderea, C. natans, Diploria labyrinthiformis, M. meandrites, and P. strigosa corals were collected by divers on SCUBA via hammer and chisel. Fragments were stored in individual, sterile whirlpaks before being flash frozen in a charged liquid nitrogen dry shipper on the boat and subsequently stored at -80°C. All in situ samples (i.e., from both Florida, U.S.A., and the U.S. Virgin Islands) were sampled as sets of stony coral tissue loss disease-affected and apparently healthy conspecifics. Two samples were collected from each diseased coral: one adjacent to the gross tissue loss lesion and one from apparently healthy tissue on the same coral. One sample was collected from a nearby conspecific coral that was apparently healthy. Coral tissue was airbrushed from the flash-frozen fragments using phosphate buffered saline. Then, coral tissue slurry was centrifuged, and the supernatant was discarded to isolate a pellet of coral tissue/mucus. No more than 0.040 grams (g) of coral tissue was used for a DNA extraction using the ZymoBIOMICS DNA/RNA Miniprep Kit (ZymoResearch, Irvine, CA, USA).

Apparently healthy corals (C. natans, M. cavernosa, O. annularis, P. astreoides, P. strigosa, and S. siderea) for the stony coral tissue loss disease transmission experiment were originally collected from Rupert's Rock by divers on SCUBA via hammer and chisel. Corals were placed in separate, sealed bags before transport to the Center for Marine and Environmental Sciences in coolers with seawater. There, corals were halved with a sterilized chop saw or bandsaw and placed into shaded raceways for at least one week prior to the start of the experiment. One day before the start of the transmission experiment, healthy and diseased Diploria labyrinthiformis corals were collected from Rupert's Rock and Flat Cay, respectively, via hammer and chisel. These D. labyrinthiformis corals were placed in separate gallon bags and transported to the Center for Marine and Environmental Sciences. For the control treatment, one fragment each of C. natans, M. cavernosa, O. annularis, P. astreoides, P. strigosa, and S. siderea were randomly arranged around a central apparently healthy D. labyrinthiformis coral. For the disease treatment, corresponding fragments of each genet were randomly arranged around a central diseased D. labyrinthiformis coral. This was replicated eight times. Corals were examined twice daily. If a lesion was observed to actively expand for at least 12 hours, the fragment was removed from the experimental container and flash frozen in a charged dry shipper. After eight days, all remaining fragments were flash frozen. Methods for the transmission experiment are reported by Meiling et al. (2021), and DNA was extracted according to the in situ samples collected from the U.S. Virgin Islands, as described above.

The internal transcribed spacer-2 (ITS-2) region of Symbiodiniaceae rDNA was amplified from all extracted DNA using the SYM_Var primer pair (Hume et al., 2018): SYM_VAR_5.8SII (5'-GAATTGCAGAACTCCGTGAACC-3') and SYM_REV (5'-CGGGTTCWCTTGTYTGACTTCATGC-3'). PCR reagents included 2 microliters (µL) of DNA, 0.42 µL of forward and reverse primers, 15 µL of DNase/RNase-free water, and 17.5 µL of EconoTaq PLUS GREEN 2X Master Mix. After 10 minutes at 74°C, PCR conditions included 32 cycles of 94°C for 1 minute, 59°C for 1 minute, and 74°C for 2 minutes, followed by 74°C for 7 minutes. Sequencing was performed on an Illumina MiSeq PE300 platform at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA). These methods are described by Karrick et al. (in review).

Sequencing was performed on an Illumina MiSeq PE300 platform at Oregon State University's Center for Quantitative Life Sciences (OSU CQLS, Corvallis, OR, USA) with the ITS-2 rDNA SYM_Var primer pair. Raw fastq files were then uploaded to NCBI's Sequence Read Archive (SRA) under BioProjects PRJNA955224, PRJNA1230223, and PRJNA1375785.

Note that BioProject PRJNA1375785 will be made publicly available on or before 2027-01-01.

- Created a site list using the latitude and longitude coordinates from the data submitter.
- Imported the site list and the original data file, "metadata_sym_sctld_its2.csv", into the BCO-DMO system.
- Applied find/replace on "site" field, correcting spelling of "Perseverence" to "Perseverance".
- Joined the site list to the primary data file based on the site name, creating new columns for latitude and longitude.
- Applied conditional find/replace on row 27 only, replacing the value "z" in the site column with an empty/missing value. (This site name is unknown.)
- Saved the final file as "997771_v1_sctld-associated_symbiodiniaceae_its-2.csv".

NSF Award Abstract:
Marine diseases have devastating impacts on ocean ecosystems and this work will directly examine the framework for understanding disease transmission in the ocean. A team of ecologists, ocean connectivity and disease modelers, microbiologists, and coral immunologists (from the University of Virgin Islands (UVI), Louisiana State University (LSU), Rice University, University of Texas-Arlington and the Woods Hole Oceanographic Institution) will develop a model that predicts transmission of a devastating Caribbean coral disease that has the potential to impact the economic value of coral reefs, including those located in the U.S. This project will support multidisciplinary field and laboratory research experiences of graduate students at multiple minority-serving institutions, and will provide undergraduate students with hands-on training in modeling, ecological and molecular analysis techniques. UVI and LSU are in EPSCoR jurisdictions and have diverse student bodies, including numerous under-represented minority (URM) students. The research team will collaboratively provide URM students with research experiences in STEM fields. Project findings will be broadly communicated through virtual public programming, and through the Virgin Islands Coral Disease Advisory Committee with updates on the vicoraldisease.org website. A coral disease response workshop for the U.S. Virgin Islands will also be held, in which project results will be presented and used to support disease response planning.

Over the last four decades, marine diseases have decimated ecosystem engineers in marine coastal ecosystems, including the rocky intertidal, seagrasses and coral reefs. The pathogens driving these diseases have frequently been challenging to isolate, characterize and confirm, in part because they affect multiple host species and can spread by ocean currents, as well as through individual contact. Here, we propose a multi-scale epidemic model for studying marine disease that addresses both within-host and within-patch disease dynamics, and explicitly acknowledges the dispersal of pathogens between populations. Our interdisciplinary research team of ecologists, connectivity and disease modelers, microbiologists, and coral immunologists will integrate the largest set of predictors of marine disease spread to date: individual host species traits that allow for disease resistance or susceptibility, local transmission within communities that may have unique community structure, and hydrodynamic connectivity among susceptible communities. Modeling will be supported with rich data sets of within- and among-patch population characteristics and disease dynamics as well as molecular data on species-level disease responses. This project will advance knowledge of infectious diseases by integrating multidimensional scales and differential host susceptibilities into existing epidemiological models. This model will particularly advance the framework for studying marine diseases and has the potential to elucidate the transmission properties of a devastating Caribbean coral disease (stony coral tissue loss disease) that fits the most confounding and notorious hallmarks of marine diseases: infection of multiple hosts by an elusive pathogen.

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.