BCO-DMO ERDDAP
Accessing BCO-DMO data |
log in
Brought to you by BCO-DMO |
Grid DAP Data | Sub- set | Table DAP Data | Make A Graph | W M S | Source Data Files | Acces- sible | Title | Sum- mary | FGDC, ISO, Metadata | Back- ground Info | RSS | E | Institution | Dataset ID |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
data | graph | files | public | [Coral pyrosequencing data] - Microbial communities of corals analyzed using 454 Illumina pyrosequencing from Wonderland Reef, Florida in 2013 (Are coral diseases contagious?) | I M | background | BCO-DMO | bcodmo_dataset_657866 |
Row Type | Variable Name | Attribute Name | Data Type | Value |
---|---|---|---|---|
attribute | NC_GLOBAL | access_formats | String | .htmlTable,.csv,.json,.mat,.nc,.tsv |
attribute | NC_GLOBAL | acquisition_description | String | [Adapted from: Randall et al. 2016] Immediately following completion of the waterborne-transmission experiments (See Randall et al. 2016), 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.\u00a0 Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche\u00a0airbrush with 10 mL of sterile seawater. The tissue slurry was collected in a sterile 50 mL Falcon\u00ae 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 ([www.mrdnalab.com](\\"http://www.mrdnalab.com\\"), Shallowater, TX, USA) for Illumina\u00a0sequencing (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 \u2013 V3 hypervariable region was amplified by applying a 30 cycle polymerase chain reaction (PCR) with the HotStarTaq Plus Master Mix Kit (Qiagen, USA).\u00a0 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\u00a0XP beads. Then the pooled and purified PCR product was used to prepare DNA libraries by following the Illumina\u00a0TruSeq DNA library preparation protocol. Sequencing was performed using the Illumina\u00a0sequencing platform at MR DNA ([www.mrdnalab.com](\\"http://www.mrdnalab.com\\"), Shallowater, TX, USA) following the manufacturer\u2019s guidelines. Sequence data were processed using a standardized analysis pipeline.\u00a0Briefly, sequences were initially depleted of barcodes. Then sequences less than 150bp or with ambiguous base calls were removed.\u00a0Operational taxonomic units (OTUs) were generated, and chimeras were removed using UCHIME [48].\u00a0OTUs\u00a0were defined by clustering at 3% divergence (i.e., showing 97% similarity) using a de novo method.\u00a0Final OTUs were taxonomically classified using BLASTn against the curated National Center for Biotechnology Information (NCBI) database and the Ribosomal Database Project (RDP). \u00a0 Field collection: Wonderland Reef, Florida (24.56028 N, 81.50127 W). Collections in July 2013. Laboratory experimentation:\u00a0 Mote Marine Laboratory, Tropical Research Laboratory, Summerland Key, Florida from 10 July \u2013 14 August 2013. |
attribute | NC_GLOBAL | awards_0_award_nid | String | 562562 |
attribute | NC_GLOBAL | awards_0_award_number | String | OCE-1219804 |
attribute | NC_GLOBAL | awards_0_data_url | String | http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1219804 |
attribute | NC_GLOBAL | awards_0_funder_name | String | NSF Division of Ocean Sciences |
attribute | NC_GLOBAL | awards_0_funding_acronym | String | NSF OCE |
attribute | NC_GLOBAL | awards_0_funding_source_nid | String | 355 |
attribute | NC_GLOBAL | awards_0_program_manager | String | Michael E. Sieracki |
attribute | NC_GLOBAL | awards_0_program_manager_nid | String | 50446 |
attribute | NC_GLOBAL | cdm_data_type | String | Other |
attribute | NC_GLOBAL | comment | String | Coral Diseases - Counts and Percentages R. van Woesik Version 26 August 2016 |
attribute | NC_GLOBAL | Conventions | String | COARDS, CF-1.6, ACDD-1.3 |
attribute | NC_GLOBAL | creator_email | String | info at bco-dmo.org |
attribute | NC_GLOBAL | creator_name | String | BCO-DMO |
attribute | NC_GLOBAL | creator_type | String | institution |
attribute | NC_GLOBAL | creator_url | String | https://www.bco-dmo.org/ |
attribute | NC_GLOBAL | data_source | String | extract_data_as_tsv version 2.3 19 Dec 2019 |
attribute | NC_GLOBAL | date_created | String | 2016-08-30T20:04:04Z |
attribute | NC_GLOBAL | date_modified | String | 2019-06-11T14:54:02Z |
attribute | NC_GLOBAL | defaultDataQuery | String | &time<now |
attribute | NC_GLOBAL | doi | String | 10.1575/1912/bco-dmo.657866.1 |
attribute | NC_GLOBAL | infoUrl | String | https://www.bco-dmo.org/dataset/657866 |
attribute | NC_GLOBAL | institution | String | BCO-DMO |
attribute | NC_GLOBAL | instruments_0_acronym | String | Airbrush |
attribute | NC_GLOBAL | instruments_0_dataset_instrument_description | String | Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche airbrush with 10 mL of sterile seawater |
attribute | NC_GLOBAL | instruments_0_dataset_instrument_nid | String | 657882 |
attribute | NC_GLOBAL | instruments_0_description | String | Device for spraying liquid by means of compressed air. |
attribute | NC_GLOBAL | instruments_0_instrument_name | String | Airbrush |
attribute | NC_GLOBAL | instruments_0_instrument_nid | String | 657881 |
attribute | NC_GLOBAL | instruments_0_supplied_name | String | Paasche airbrush |
attribute | NC_GLOBAL | keywords | String | bco, bco-dmo, biological, chemical, d13, D13U, D1L, D1U, d22, D22L, D22U, d27, D27U, D3L, D3U, D4U, data, dataset, dmo, erddap, level, management, measurement, oceanography, office, organism, preliminary, taxon, taxon_level, u, y11, Y11U, y23, Y23L, Y23U, y26, Y26U, y27, Y27U, Y4L, Y4U, Y9L, Y9U |
attribute | NC_GLOBAL | license | String | https://www.bco-dmo.org/dataset/657866/license |
attribute | NC_GLOBAL | metadata_source | String | https://www.bco-dmo.org/api/dataset/657866 |
attribute | NC_GLOBAL | param_mapping | String | {'657866': {}} |
attribute | NC_GLOBAL | parameter_source | String | https://www.bco-dmo.org/mapserver/dataset/657866/parameters |
attribute | NC_GLOBAL | people_0_affiliation | String | Florida Institute of Technology |
attribute | NC_GLOBAL | people_0_affiliation_acronym | String | FIT |
attribute | NC_GLOBAL | people_0_person_name | String | Robert van Woesik |
attribute | NC_GLOBAL | people_0_person_nid | String | 562565 |
attribute | NC_GLOBAL | people_0_role | String | Principal Investigator |
attribute | NC_GLOBAL | people_0_role_type | String | originator |
attribute | NC_GLOBAL | people_1_affiliation | String | Florida Institute of Technology |
attribute | NC_GLOBAL | people_1_affiliation_acronym | String | FIT |
attribute | NC_GLOBAL | people_1_person_name | String | Dr Carly J. Randall |
attribute | NC_GLOBAL | people_1_person_nid | String | 657875 |
attribute | NC_GLOBAL | people_1_role | String | Contact |
attribute | NC_GLOBAL | people_1_role_type | String | related |
attribute | NC_GLOBAL | people_2_affiliation | String | Florida Institute of Technology |
attribute | NC_GLOBAL | people_2_affiliation_acronym | String | FIT |
attribute | NC_GLOBAL | people_2_person_name | String | Robert van Woesik |
attribute | NC_GLOBAL | people_2_person_nid | String | 562565 |
attribute | NC_GLOBAL | people_2_role | String | Contact |
attribute | NC_GLOBAL | people_2_role_type | String | related |
attribute | NC_GLOBAL | people_3_affiliation | String | Woods Hole Oceanographic Institution |
attribute | NC_GLOBAL | people_3_affiliation_acronym | String | WHOI BCO-DMO |
attribute | NC_GLOBAL | people_3_person_name | String | Hannah Ake |
attribute | NC_GLOBAL | people_3_person_nid | String | 650173 |
attribute | NC_GLOBAL | people_3_role | String | BCO-DMO Data Manager |
attribute | NC_GLOBAL | people_3_role_type | String | related |
attribute | NC_GLOBAL | project | String | Contagious coral diseases? |
attribute | NC_GLOBAL | projects_0_acronym | String | Contagious coral diseases? |
attribute | NC_GLOBAL | projects_0_description | String | 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. 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). Intellectual merit 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. Broader Impact 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. |
attribute | NC_GLOBAL | projects_0_end_date | String | 2016-05 |
attribute | NC_GLOBAL | projects_0_geolocation | String | Caribbean |
attribute | NC_GLOBAL | projects_0_name | String | Are coral diseases contagious? |
attribute | NC_GLOBAL | projects_0_project_nid | String | 562563 |
attribute | NC_GLOBAL | projects_0_start_date | String | 2012-06 |
attribute | NC_GLOBAL | publisher_name | String | Biological and Chemical Oceanographic Data Management Office (BCO-DMO) |
attribute | NC_GLOBAL | publisher_type | String | institution |
attribute | NC_GLOBAL | sourceUrl | String | (local files) |
attribute | NC_GLOBAL | standard_name_vocabulary | String | CF Standard Name Table v55 |
attribute | NC_GLOBAL | summary | String | Microbial communities of corals analyzed using 454 Illumina pyrosequencing from Wonderland Reef, Florida in 2013 |
attribute | NC_GLOBAL | title | String | [Coral pyrosequencing data] - Microbial communities of corals analyzed using 454 Illumina pyrosequencing from Wonderland Reef, Florida in 2013 (Are coral diseases contagious?) |
attribute | NC_GLOBAL | version | String | 1 |
attribute | NC_GLOBAL | xml_source | String | osprey2erddap.update_xml() v1.3 |
variable | organism | String | ||
attribute | organism | bcodmo_name | String | species |
attribute | organism | description | String | the category of organism which the analysis was organised by |
attribute | organism | long_name | String | Organism |
attribute | organism | units | String | unitless |
variable | measurement | String | ||
attribute | measurement | bcodmo_name | String | sample_descrip |
attribute | measurement | description | String | indication of whether percentage or count of specific taxonomy found on coral is described |
attribute | measurement | long_name | String | Measurement |
attribute | measurement | units | String | unitless |
variable | taxon_level | String | ||
attribute | taxon_level | bcodmo_name | String | taxon |
attribute | taxon_level | description | String | taxonomic level for which percentages and counts are described |
attribute | taxon_level | long_name | String | Taxon Level |
attribute | taxon_level | units | String | unitless |
variable | taxon | String | ||
attribute | taxon | bcodmo_name | String | taxon |
attribute | taxon | description | String | taxonomy for which percentages and counts are described |
attribute | taxon | long_name | String | Taxon |
attribute | taxon | units | String | unitless |
variable | D4U | float | ||
attribute | D4U | _FillValue | float | NaN |
attribute | D4U | actual_range | float | 0.0, 96023.0 |
attribute | D4U | bcodmo_name | String | treatment |
attribute | D4U | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = healthy |
attribute | D4U | long_name | String | D4 U |
attribute | D4U | units | String | percent or count |
variable | D13U | float | ||
attribute | D13U | _FillValue | float | NaN |
attribute | D13U | actual_range | float | 0.0, 49332.0 |
attribute | D13U | bcodmo_name | String | treatment |
attribute | D13U | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = healthy |
attribute | D13U | long_name | String | D13 U |
attribute | D13U | units | String | percent or count |
variable | D27U | float | ||
attribute | D27U | _FillValue | float | NaN |
attribute | D27U | actual_range | float | 0.0, 77301.0 |
attribute | D27U | bcodmo_name | String | treatment |
attribute | D27U | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = healthy |
attribute | D27U | long_name | String | D27 U |
attribute | D27U | units | String | percent or count |
variable | Y11U | float | ||
attribute | Y11U | _FillValue | float | NaN |
attribute | Y11U | actual_range | float | 0.0, 74193.0 |
attribute | Y11U | bcodmo_name | String | treatment |
attribute | Y11U | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = healthy |
attribute | Y11U | long_name | String | Y11 U |
attribute | Y11U | units | String | percent or count |
variable | Y26U | float | ||
attribute | Y26U | _FillValue | float | NaN |
attribute | Y26U | actual_range | float | 0.0, 55471.0 |
attribute | Y26U | bcodmo_name | String | treatment |
attribute | Y26U | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = healthy |
attribute | Y26U | long_name | String | Y26 U |
attribute | Y26U | units | String | percent or count |
variable | Y27U | float | ||
attribute | Y27U | _FillValue | float | NaN |
attribute | Y27U | actual_range | float | 0.0, 61122.0 |
attribute | Y27U | bcodmo_name | String | treatment |
attribute | Y27U | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = healthy |
attribute | Y27U | long_name | String | Y27 U |
attribute | Y27U | units | String | percent or count |
variable | D1L | float | ||
attribute | D1L | _FillValue | float | NaN |
attribute | D1L | actual_range | float | 0.0, 52628.0 |
attribute | D1L | bcodmo_name | String | treatment |
attribute | D1L | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = exposed to dark-spot syndrome |
attribute | D1L | long_name | String | D1 L |
attribute | D1L | units | String | percent or count |
variable | D3L | float | ||
attribute | D3L | _FillValue | float | NaN |
attribute | D3L | actual_range | float | 0.0, 97019.0 |
attribute | D3L | bcodmo_name | String | treatment |
attribute | D3L | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = exposed to dark-spot syndrome |
attribute | D3L | long_name | String | D3 L |
attribute | D3L | units | String | percent or count |
variable | D22L | float | ||
attribute | D22L | _FillValue | float | NaN |
attribute | D22L | actual_range | float | 0.0, 33162.0 |
attribute | D22L | bcodmo_name | String | treatment |
attribute | D22L | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = exposed to dark-spot syndrome |
attribute | D22L | long_name | String | D22 L |
attribute | D22L | units | String | percent or count |
variable | Y4L | float | ||
attribute | Y4L | _FillValue | float | NaN |
attribute | Y4L | actual_range | float | 0.0, 50980.0 |
attribute | Y4L | bcodmo_name | String | treatment |
attribute | Y4L | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = exposed to yellow-band disease |
attribute | Y4L | long_name | String | Y4 L |
attribute | Y4L | units | String | percent or count |
variable | Y23L | float | ||
attribute | Y23L | _FillValue | float | NaN |
attribute | Y23L | actual_range | float | 0.0, 49217.0 |
attribute | Y23L | bcodmo_name | String | treatment |
attribute | Y23L | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = exposed to yellow-band disease |
attribute | Y23L | long_name | String | Y23 L |
attribute | Y23L | units | String | percent or count |
variable | Y9L | float | ||
attribute | Y9L | _FillValue | float | NaN |
attribute | Y9L | actual_range | float | 0.0, 84128.0 |
attribute | Y9L | bcodmo_name | String | treatment |
attribute | Y9L | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = exposed to yellow-band disease |
attribute | Y9L | long_name | String | Y9 L |
attribute | Y9L | units | String | percent or count |
variable | D1U | float | ||
attribute | D1U | _FillValue | float | NaN |
attribute | D1U | actual_range | float | 0.0, 42555.0 |
attribute | D1U | bcodmo_name | String | treatment |
attribute | D1U | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = diseased with dark-spot syndrome |
attribute | D1U | long_name | String | D1 U |
attribute | D1U | units | String | percent or count |
variable | D3U | float | ||
attribute | D3U | _FillValue | float | NaN |
attribute | D3U | actual_range | float | 0.0, 63847.0 |
attribute | D3U | bcodmo_name | String | treatment |
attribute | D3U | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = diseased with dark-spot syndrome |
attribute | D3U | long_name | String | D3 U |
attribute | D3U | units | String | percent or count |
variable | D22U | float | ||
attribute | D22U | _FillValue | float | NaN |
attribute | D22U | actual_range | float | 0.0, 57417.0 |
attribute | D22U | bcodmo_name | String | treatment |
attribute | D22U | description | String | percent or count found on sample; coral species = Siderastrea siderea; health status = diseased with dark-spot syndrome |
attribute | D22U | long_name | String | D22 U |
attribute | D22U | units | String | percent or count |
variable | Y4U | float | ||
attribute | Y4U | _FillValue | float | NaN |
attribute | Y4U | actual_range | float | 0.0, 67964.0 |
attribute | Y4U | bcodmo_name | String | treatment |
attribute | Y4U | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = diseased with yellow-band disease |
attribute | Y4U | long_name | String | Y4 U |
attribute | Y4U | units | String | percent or count |
variable | Y23U | float | ||
attribute | Y23U | _FillValue | float | NaN |
attribute | Y23U | actual_range | float | 0.0, 63779.0 |
attribute | Y23U | bcodmo_name | String | treatment |
attribute | Y23U | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = diseased with yellow-band disease |
attribute | Y23U | long_name | String | Y23 U |
attribute | Y23U | units | String | percent or count |
variable | Y9U | float | ||
attribute | Y9U | _FillValue | float | NaN |
attribute | Y9U | actual_range | float | 0.0, 12861.0 |
attribute | Y9U | bcodmo_name | String | treatment |
attribute | Y9U | description | String | percent or count found on sample; coral species = Orbicella faveolata; health status = diseased with yellow-band disease |
attribute | Y9U | long_name | String | Y9 U |
attribute | Y9U | units | String | percent or count |
The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.