Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [Sample numbers and associated data for bacteria sequence mapping] - Sample numbers, barcode information, primer information and project name from bacteria samples collected in the Caribbean during 2013 (Contagious coral diseases project) (Are coral diseases contagious?) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_658340) |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Files
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Attributes {
s {
project_name {
String bcodmo_name "project";
String description "Project name";
String long_name "Project Name";
String units "unitless";
}
linker_primer_sequence {
String bcodmo_name "sequence";
String description "Primer information";
String long_name "Linker Primer Sequence";
String units "unitless";
}
sample_id {
String bcodmo_name "sample";
String description "Sample ID number";
String long_name "Sample Id";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
barcode_sequence {
String bcodmo_name "sequence";
String description "Barcode information";
String long_name "Barcode Sequence";
String units "unitless";
}
barcode_name {
String bcodmo_name "sequence";
String description "Barcode name";
String long_name "Barcode Name";
String units "unitless";
}
description {
String bcodmo_name "brief_desc";
String description "Description; same as sample ID";
String long_name "Description";
String units "unitless";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String 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.\\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.";
String awards_0_award_nid "562562";
String awards_0_award_number "OCE-1219804";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1219804";
String awards_0_funder_name "NSF Division of Ocean Sciences";
String awards_0_funding_acronym "NSF OCE";
String awards_0_funding_source_nid "355";
String awards_0_program_manager "Michael E. Sieracki";
String awards_0_program_manager_nid "50446";
String cdm_data_type "Other";
String comment
"Bacteria Mapping Data
R. van Woesik, PI
Version 2 September 2016";
String Conventions "COARDS, CF-1.6, ACDD-1.3";
String creator_email "info@bco-dmo.org";
String creator_name "BCO-DMO";
String creator_type "institution";
String creator_url "https://www.bco-dmo.org/";
String data_source "extract_data_as_tsv version 2.3 19 Dec 2019";
String date_created "2016-09-06T22:14:14Z";
String date_modified "2019-05-13T19:19:15Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.658340.1";
String history
"2024-12-03T17:29:44Z (local files)
2024-12-03T17:29:44Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_658340.html";
String infoUrl "https://www.bco-dmo.org/dataset/658340";
String institution "BCO-DMO";
String instruments_0_acronym "Airbrush";
String instruments_0_dataset_instrument_description "Tissue was removed from the skeleton of the preserved-coral colonies using a Paasche airbrush with 10 mL of sterile seawater";
String instruments_0_dataset_instrument_nid "658348";
String instruments_0_description "Device for spraying liquid by means of compressed air.";
String instruments_0_instrument_name "Airbrush";
String instruments_0_instrument_nid "657881";
String instruments_0_supplied_name "Paasche airbrush";
String keywords "barcode, barcode_name, barcode_sequence, bco, bco-dmo, biological, chemical, data, dataset, description, dmo, erddap, linker, linker_primer_sequence, management, name, oceanography, office, preliminary, primer, project, project_name, sample, sample_id, sequence";
String license "https://www.bco-dmo.org/dataset/658340/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/658340";
String param_mapping "{'658340': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/658340/parameters";
String people_0_affiliation "Florida Institute of Technology";
String people_0_affiliation_acronym "FIT";
String people_0_person_name "Robert van Woesik";
String people_0_person_nid "562565";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Florida Institute of Technology";
String people_1_affiliation_acronym "FIT";
String people_1_person_name "Dr Carly J. Randall";
String people_1_person_nid "657875";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Florida Institute of Technology";
String people_2_affiliation_acronym "FIT";
String people_2_person_name "Robert van Woesik";
String people_2_person_nid "562565";
String people_2_role "Contact";
String people_2_role_type "related";
String people_3_affiliation "Woods Hole Oceanographic Institution";
String people_3_affiliation_acronym "WHOI BCO-DMO";
String people_3_person_name "Hannah Ake";
String people_3_person_nid "650173";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Contagious coral diseases?";
String projects_0_acronym "Contagious coral diseases?";
String projects_0_description
"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.";
String projects_0_end_date "2016-05";
String projects_0_geolocation "Caribbean";
String projects_0_name "Are coral diseases contagious?";
String projects_0_project_nid "562563";
String projects_0_start_date "2012-06";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "project_name,linker_primer_sequence";
String summary "Sample numbers, barcode information, primer information and project name from bacteria samples collected in the Caribbean during 2013 (Contagious coral diseases project)";
String title "[Sample numbers and associated data for bacteria sequence mapping] - Sample numbers, barcode information, primer information and project name from bacteria samples collected in the Caribbean during 2013 (Contagious coral diseases project) (Are coral diseases contagious?)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
Data Access Protocol (DAP) and its
selection constraints.
The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.
Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names,
followed by a collection of
constraints (e.g., variable<value),
each preceded by '&' (which is interpreted as "AND").
For details, see the tabledap Documentation.