Health status and species of each coral sample taken in the Caribbean during 2013 (Contagious coral diseases project) (NCEI Accession 0278601)
This dataset contains biological and survey - biological data collected at Caribbean_nearshore during deployment vanWoesik_2012 at Caribbean nearshore: Mahahual, Mexico; Tuxpan, Mexico; Robet van; St. John; Wonderland Reef, Florida from 2013-07-21 to 2014-07-24. These data include species. The instruments used to collect these data include Airbrush. These data were collected by Dr Robert van Woesik of Florida Institute of Technology as part of the "Are coral diseases contagious? (Contagious coral diseases?)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2019-05-13.
The following is the text of the dataset description provided by BCO-DMO:
Health status and species of each sample taken.
Dataset Description:
Coral disease transmission experiments were completed for dark-spot syndrome on Siderastrea siderea and yellow-band disease on Orbicella faveolata, as described in Randall et al. 2016. Following experimentation, microbial communities were extracted from tissue samples to determine whether any potential pathogen may have transmitted from healthy to exposed corals. Microbial communities on healthy corals were compared with diseased corals to identify any potential pathogens.
Experimental diseased and healthy corals were sampled and their microbial communities were analyzed using 454 Illumina pyrosequencing of the amplified 16S rRNA gene on the V1-V3 hypervariable region.
The following is the text of the dataset description provided by BCO-DMO:
Health status and species of each sample taken.
Dataset Description:
Coral disease transmission experiments were completed for dark-spot syndrome on Siderastrea siderea and yellow-band disease on Orbicella faveolata, as described in Randall et al. 2016. Following experimentation, microbial communities were extracted from tissue samples to determine whether any potential pathogen may have transmitted from healthy to exposed corals. Microbial communities on healthy corals were compared with diseased corals to identify any potential pathogens.
Experimental diseased and healthy corals were sampled and their microbial communities were analyzed using 454 Illumina pyrosequencing of the amplified 16S rRNA gene on the V1-V3 hypervariable region.
Dataset Citation
- Cite as: van Woesik, Robert (2023). Health status and species of each coral sample taken in the Caribbean during 2013 (Contagious coral diseases project) (NCEI Accession 0278601). [indicate subset used]. NOAA National Centers for Environmental Information. Dataset. https://www.ncei.noaa.gov/archive/accession/0278601. Accessed [date].
Dataset Identifiers
ISO 19115-2 Metadata
gov.noaa.nodc:0278601
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Ordering Instructions | Contact NCEI for other distribution options and instructions. |
Distributor |
NOAA National Centers for Environmental Information +1-301-713-3277 NCEI.Info@noaa.gov |
Dataset Point of Contact |
NOAA National Centers for Environmental Information ncei.info@noaa.gov |
Coverage Description | Caribbean nearshore: Mahahual, Mexico; Tuxpan, Mexico; Robet van; St. John; Wonderland Reef, Florida |
Time Period | 2013-07-21 to 2014-07-24 |
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Data Presentation Form | Digital table - digital representation of facts or figures systematically displayed, especially in columns |
Dataset Progress Status | Complete - production of the data has been completed Historical archive - data has been stored in an offline storage facility |
Data Update Frequency | As needed |
Supplemental Information | Acquisition Description: [Adapted from: Randall et al. 2016 PLoS ONE 11(1): e0147493. doi:10.1371/journal.pone.0147493] Immediately following completion of the waterborne-transmission experiments (See Randall et al. 2016 PLoS ONE 11(1) attached), three each, of diseased, exposed, and healthy colonies of S. siderea were randomly selected for bacterial-community analyses, to determine whether potential bacterial pathogens had transmitted to the exposed colonies. The nine coral colonies were placed in individual, sterile whirl-paks at -80 degrees C and then were transported on dry ice to Mote Marine Laboratory in Sarasota, Florida. Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche airbrush with 10 mL of sterile seawater. The tissue slurry was collected in a sterile 50 mL Falcon® tube and homogenized using a vortex. The tissue homogenate was then spun down into a pellet using a centrifuge set at 10,000 rpm. The pellet was re-suspended in 2 mL of solution C1 and DNA was extracted using a Powersoil DNA extraction kit (MoBIO Laboratories Inc. Lot #PS14F19). Extracted DNA was then sent to MRDNA Laboratory (, Shallowater, TX, USA) for Illumina sequencing (20,000 reads per assay) using the universal bacterial primers 27F/519R with a barcode on the forward primer. The 16S rRNA gene on the V1 – V3 hypervariable region was amplified by applying a 30 cycle polymerase chain reaction (PCR) with the HotStarTaq Plus Master Mix Kit (Qiagen, USA). PCR was applied using the following protocol: (1) 94 degrees C for 3 minutes, (2) 28 cycles of: 94 degrees C for 30 seconds, 53 degrees C for 40 seconds, and 72 degrees C for 1 minute, and (3) a final elongation step at 72 degrees C for 5 minutes. After amplification, PCR products were confirmed in 2% agarose gels to determine the success of amplification and the relative intensity of the bands. Multiple samples were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads. Then the pooled and purified PCR product was used to prepare DNA libraries by following the Illumina TruSeq DNA library preparation protocol. Sequencing was performed using the Illumina sequencing platform at MR DNA (, Shallowater, TX, USA) following the manufacturer’s guidelines. Sequence data were processed using a standardized analysis pipeline. Briefly, sequences were initially depleted of barcodes. Then sequences less than 150bp or with ambiguous base calls were removed. Operational taxonomic units (OTUs) were generated, and chimeras were removed using UCHIME [48]. OTUs were defined by clustering at 3% divergence (i.e., showing 97% similarity) using a de novo method. Final OTUs were taxonomically classified using BLASTn against the curated National Center for Biotechnology Information (NCBI) database and the Ribosomal Database Project (RDP). Field collection: Wonderland Reef, Florida (24.56028 N, 81.50127 W). Collections in July 2013. Laboratory experimentation: Mote Marine Laboratory, Tropical Research Laboratory, Summerland Key, Florida from 10 July – 14 August 2013. |
Purpose | This dataset is available to the public for a wide variety of uses including scientific research and analysis. |
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Data Center keywords | NODC COLLECTING INSTITUTION NAMES THESAURUS NODC SUBMITTING INSTITUTION NAMES THESAURUS Global Change Master Directory (GCMD) Data Center Keywords |
Platform keywords | BCO-DMO Platform Names |
Instrument keywords | BCO-DMO Standard Instruments Originator Instrument Names |
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Project keywords | BCO-DMO Standard Projects Provider Deployment IDs Provider Funding Award Information |
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Last Modified: 2024-05-31T15:15:28Z
For questions about the information on this page, please email: ncei.info@noaa.gov
For questions about the information on this page, please email: ncei.info@noaa.gov