http://lod.bco-dmo.org/id/dataset/658298
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-09-06
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Experimental data from coral disease analysis in raw form for sequencing collected in the Caribbean during 2012 (Contagious coral diseases project)
2016-09-06
publication
2016-09-06
revision
BCO-DMO Linked Data URI
2016-09-06
creation
http://lod.bco-dmo.org/id/dataset/658298
Robert van Woesik
Florida Institute of Technology
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: van Woesik, R. (2016) Experimental data from coral disease analysis in raw form for sequencing collected in the Caribbean during 2012 (Contagious coral diseases project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2016-09-06 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/658298 [access date]
Experimental data from coral disease analysis in raw form for sequencing. Dataset Description: <p>This dataset contains the raw information for the sequencing.&nbsp; This is the “SFF” file which is the 454 binary data.&nbsp; The fasta (FNA) and QUAL (quality) files have the typical extension (.fna and .qual). These are the text versions of the sequence data and quality scores.</p>
<ol>
<li>–full.fasta, -full.qual
<ol style="list-style-type:lower-alpha">
<li>These files contain the raw sequence data information and still have primers and barcodes</li>
</ol>
</li>
<li>–pr.fasta, -pr.qual
<ol style="list-style-type:lower-alpha">
<li>Sequencing information without primers and barcodes used in our analysis. The sample names from which each sequence is derived is encoded in the definition line of each sequence.</li>
</ol>
</li>
</ol>
<p>Coral disease transmission experiments were completed for dark-spot syndrome on Sidereastrea siderea&nbsp;and yellow-band disease on Orbicella faveolata, as described in Randall et al. 2016.&nbsp;Following experimentation, microbial communities were extracted from tissue samples to determine whether any&nbsp;potential pathogen may have transmitted from healthy to exposed corals. Microbial communities on healthy corals&nbsp;were compared with diseased corals to identify any potential pathogens.</p>
<p>Experimental diseased and healthy corals were sampled and their microbial communities were analyzed using 454 Illumina pyrosequencing&nbsp;of the amplified 16S rRNA gene on the V1-V3&nbsp;hypervariable region.</p> Methods and Sampling: <p>[Adapted from: Randall et al. 2016&nbsp;<em>PLoS ONE</em>&nbsp;11(1): e0147493. doi:10.1371/journal.pone.0147493]</p>
<p>Immediately following completion of the waterborne-transmission experiments (See Randall et al. 2016&nbsp;<em>PLoS ONE</em>11(1) attached), three each, of diseased, exposed, and healthy colonies of&nbsp;<em>S. siderea</em>&nbsp;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.&nbsp;</p>
<p>Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche&nbsp;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 (<a href="http://www.mrdnalab.com/" style="margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration: none; color: rgb(0, 102, 153);">www.mrdnalab.com</a>, Shallowater, TX, USA) for Illumina&nbsp;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).&nbsp; 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&nbsp;XP beads. Then the pooled and purified PCR product was used to prepare DNA libraries by following the Illumina&nbsp;TruSeq DNA library preparation protocol. Sequencing was performed using the Illumina&nbsp;sequencing platform at MR DNA (<a href="http://www.mrdnalab.com/" style="margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration: none; color: rgb(0, 102, 153);">www.mrdnalab.com</a>, Shallowater, TX, USA) following the manufacturer’s guidelines. Sequence data were processed using a standardized analysis pipeline.&nbsp;Briefly, sequences were initially depleted of barcodes. Then sequences less than 150bp or with ambiguous base calls were removed.&nbsp;Operational taxonomic units (OTUs) were generated, and chimeras were removed using UCHIME [48].&nbsp;OTUs&nbsp;were defined by clustering at 3% divergence (i.e., showing 97% similarity) using a de novo method.&nbsp;Final OTUs were taxonomically classified using BLASTn against the curated National Center for Biotechnology Information (NCBI) database and the Ribosomal Database Project (RDP). &nbsp;</p>
<p><strong>Field collection:</strong></p>
<p>Wonderland Reef, Florida (24.56028 N, 81.50127 W). Collections in July 2013.</p>
<p><strong>Laboratory experimentation:&nbsp;</strong></p>
<p>Mote Marine Laboratory, Tropical Research Laboratory, Summerland Key, Florida from 10 July – 14 August 2013.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1219804 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1219804
completed
Robert van Woesik
Florida Institute of Technology
321-674-7475
150 West University Blvd
Melbourne
FL
32901-6975
USA
rvw@fit.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Paasche airbrush
theme
None, User defined
Airbrush
instrument
BCO-DMO Standard Instruments
vanWoesik_2012
service
Deployment Activity
Caribbean nearshore: Mahahual, Mexico; Tuxpan, Mexico; Robet van; St. John; Wonderland Reef, Florida
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Are coral diseases contagious?
https://osprey.bco-dmo.org/project/562563
Are coral diseases contagious?
<p>Diseases are one of the greatest threats to corals in the Caribbean. Yet, very little is known about marine diseases in general and coral diseases in particular. Although some pathogens have been acknowledged, identifying coral pathogens has proven difficult and evasive. Presently, coral diseases are assumed to be both infectious and contagious, suggesting that infection is caused by pathogens being passed from colony to colony through a vector. However, few studies have tested this assumption. Spatial epidemiology, or disease mapping, can provide insight into whether diseases cluster and follow a contagious-disease model. In this study we will take a two tiered approach. First, we will use a hierarchical sampling design to test whether coral diseases follow a contagious-disease model over two spatial scales in the Caribbean. We will also undertake this study in locations with and without a recent history of frequent thermal stress to test the alternate hypothesis that coral diseases are not infectious and contagious but are instead the result of compromised coral hosts that have undergone thermal stress. Second, we will undertake transmission experiments to examine whether coral diseases are indeed transmissible.</p>
<p>The research will take place in the Caribbean, at four locations: (1) Mahahual, Mexico (latitude 18"42’N, longitude 87"42’W) and (2) Tuxpan, Mexico (latitude 21"01’N, longitude 97"11'W), (3) Bocas del Toro, Panama (latitude 9"12’N, longitude 82"09’W) and (4) St. John, United States Virgin Islands (USVI) (latitude 18"18’N, longitude 64"45’W).</p>
<p><strong>Intellectual merit</strong></p>
<p>There is a certain urgency to identify coral diseases, predict their prevalence, and determine whether they are infectious and contagious or non-communicable. By understanding the etiology of coral diseases, we can determine whether human intervention will help reduce their prevalence. Without understanding these processes, we will merely continue to measure disease, continue to look for pathogens that may not exist, and watch coral populations continue to deteriorate. Although microbes play a role in disease infection, many coral diseases might not be transmissible. Therefore, we may need to incorporate environmental threshold parameters, which may be more likely the underlying mechanisms driving coral-disease dynamics. The results will have important implications for modeling diseases and predicting contemporary and future coral disease outbreaks. </p>
<p><strong>Broader Impact</strong></p>
<p>The underlying assumption of most disease models is contagion, which is the transmission of pathogens from infected to susceptible hosts. This study will examine this basic assumption. If it turns out that coral diseases are a consequence of a two-step process, and the corals that are tolerant to temperature stress are also resistant to diseases, then making predictions based on temperature trends will be transformational, especially in rapidly warming, yet heterogeneous, oceans. The study will train students in the field of spatial epidemiology of coral diseases.</p>
Contagious coral diseases?
largerWorkCitation
project
eng; USA
oceans
Caribbean nearshore: Mahahual, Mexico; Tuxpan, Mexico; Robet van; St. John; Wonderland Reef, Florida
2016-09-06
Caribbean
0
BCO-DMO catalogue of parameters from Experimental data from coral disease analysis in raw form for sequencing collected in the Caribbean during 2012 (Contagious coral diseases project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
59163811
https://datadocs.bco-dmo.org/file/jAW81oVIYxO7M0/mapping_pr1.txt
mapping_pr1.txt
Sequencing information without primers and barcodes used in our analysis. The sample names from which each sequence is derived is encoded in the definition line of each sequence.
download
65004163
https://datadocs.bco-dmo.org/file/WWAqVMvizr1NAK/mapping_pr2.txt
mapping_pr2.txt
Sequencing information without primers and barcodes used in our analysis. The sample names from which each sequence is derived is encoded in the definition line of each sequence.
download
744878909
https://datadocs.bco-dmo.org/file/5AoLPOxHgpgLV4/sequences_full.fasta
sequences_full.fasta
These files contain the raw sequence data information and still haveprimers and barcodes.
download
1193869312
https://datadocs.bco-dmo.org/file/7DqXRQwsQ0Wvvq/sequences_full.qual
sequences_full.qual
These files contain the raw sequence data information and still haveprimers and barcodes.
download
https://osprey.bco-dmo.org/dataset/658298/data/download
download
onLine
dataset
<p>[Adapted from: Randall et al. 2016&nbsp;<em>PLoS ONE</em>&nbsp;11(1): e0147493. doi:10.1371/journal.pone.0147493]</p>
<p>Immediately following completion of the waterborne-transmission experiments (See Randall et al. 2016&nbsp;<em>PLoS ONE</em>11(1) attached), three each, of diseased, exposed, and healthy colonies of&nbsp;<em>S. siderea</em>&nbsp;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.&nbsp;</p>
<p>Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche&nbsp;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 (<a href="http://www.mrdnalab.com/" style="margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration: none; color: rgb(0, 102, 153);">www.mrdnalab.com</a>, Shallowater, TX, USA) for Illumina&nbsp;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).&nbsp; 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&nbsp;XP beads. Then the pooled and purified PCR product was used to prepare DNA libraries by following the Illumina&nbsp;TruSeq DNA library preparation protocol. Sequencing was performed using the Illumina&nbsp;sequencing platform at MR DNA (<a href="http://www.mrdnalab.com/" style="margin: 0px; padding: 0px; border: 0px; font-style: inherit; font-variant: inherit; font-weight: inherit; font-stretch: inherit; font-size: inherit; line-height: inherit; font-family: inherit; vertical-align: baseline; text-decoration: none; color: rgb(0, 102, 153);">www.mrdnalab.com</a>, Shallowater, TX, USA) following the manufacturer’s guidelines. Sequence data were processed using a standardized analysis pipeline.&nbsp;Briefly, sequences were initially depleted of barcodes. Then sequences less than 150bp or with ambiguous base calls were removed.&nbsp;Operational taxonomic units (OTUs) were generated, and chimeras were removed using UCHIME [48].&nbsp;OTUs&nbsp;were defined by clustering at 3% divergence (i.e., showing 97% similarity) using a de novo method.&nbsp;Final OTUs were taxonomically classified using BLASTn against the curated National Center for Biotechnology Information (NCBI) database and the Ribosomal Database Project (RDP). &nbsp;</p>
<p><strong>Field collection:</strong></p>
<p>Wonderland Reef, Florida (24.56028 N, 81.50127 W). Collections in July 2013.</p>
<p><strong>Laboratory experimentation:&nbsp;</strong></p>
<p>Mote Marine Laboratory, Tropical Research Laboratory, Summerland Key, Florida from 10 July – 14 August 2013.</p>
from Deployment: vanWoesik_2012 <p>Caribbean Region, 4 locations (5-15 m depth):</p>
<p>1) Mahahual, Mexico; 18.7 N, 87.7 W</p>
<p>2) Tuxpan, Mexico; 21.0 to 21.5 N, 97.2 W </p>
<p>3) St. John, U.S. Virgin Islands; 18.3 N, 64.7 W</p>
<p>4) Bocas del Toro, Panama; 9.3 N, 82.2 W</p>
Specified by the Principal Investigator(s)
<p><span style="color:rgb(0, 0, 0); font-family:helvetica,arial,sans-serif; font-size:14.4px">Please see the methods described above and in Randall et al. 2016 for data processing.&nbsp;</span></p>
<p><strong>Data Management Office Notes:</strong></p>
<p>- Links created to direct the user to the&nbsp;original file generated by PI.<br />
- Data files linked are unaltered.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Paasche airbrush
Paasche airbrush
PI Supplied Instrument Name: Paasche airbrush PI Supplied Instrument Description:Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche airbrush with 10 mL of sterile seawater Instrument Name: Airbrush Instrument Short Name:Airbrush Instrument Description: Device for spraying liquid by means of compressed air.
Deployment: vanWoesik_2012
vanWoesik_2012
Caribbean_nearshore
shoreside
Caribbean_nearshore
shoreside