BCO-DMO ERDDAP
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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 PLoS ONE 11(1): e0147493.\ndoi:10.1371/journal.pone.0147493]\n \nImmediately following completion of the waterborne-transmission experiments\n(See Randall et al. 2016 PLoS ONE 11(1) attached), three each, of diseased,\nexposed, and healthy colonies of S. siderea were randomly selected for\nbacterial-community analyses, to determine whether potential bacterial\npathogens had transmitted to the exposed colonies. The nine coral colonies\nwere placed in individual, sterile whirl-paks at -80 degrees C and then were\ntransported on dry ice to Mote Marine Laboratory in Sarasota, Florida.\\u00a0\n \nTissue was removed from the skeleton of the preserved-coral colonies using a\nPaasche\\u00a0airbrush with 10 mL of sterile seawater. The tissue slurry was\ncollected in a sterile 50 mL Falcon\\u00ae tube and homogenized using a vortex.\nThe tissue homogenate was then spun down into a pellet using a centrifuge set\nat 10,000 rpm. The pellet was re-suspended in 2 mL of solution C1 and DNA was\nextracted using a Powersoil DNA extraction kit (MoBIO Laboratories Inc. Lot\n#PS14F19). Extracted DNA was then sent to MRDNA Laboratory\n([www.mrdnalab.com](\\\\\"http://www.mrdnalab.com\\\\\"), Shallowater, TX, USA) for\nIllumina\\u00a0sequencing (20,000 reads per assay) using the universal\nbacterial primers 27F/519R with a barcode on the forward primer. The 16S rRNA\ngene on the V1 \\u2013 V3 hypervariable region was amplified by applying a 30\ncycle polymerase chain reaction (PCR) with the HotStarTaq Plus Master Mix Kit\n(Qiagen, USA).\\u00a0 PCR was applied using the following protocol: (1) 94\ndegrees C for 3 minutes, (2) 28 cycles of: 94 degrees C for 30 seconds, 53\ndegrees C for 40 seconds, and 72 degrees C for 1 minute, and (3) a final\nelongation step at 72 degrees C for 5 minutes. After amplification, PCR\nproducts were confirmed in 2% agarose gels to determine the success of\namplification and the relative intensity of the bands. Multiple samples were\npooled together in equal proportions based on their molecular weight and DNA\nconcentrations. Pooled samples were purified using calibrated Ampure\\u00a0XP\nbeads. Then the pooled and purified PCR product was used to prepare DNA\nlibraries by following the Illumina\\u00a0TruSeq DNA library preparation\nprotocol. Sequencing was performed using the Illumina\\u00a0sequencing platform\nat MR DNA ([www.mrdnalab.com](\\\\\"http://www.mrdnalab.com\\\\\"), Shallowater, TX,\nUSA) following the manufacturer\\u2019s guidelines. Sequence data were\nprocessed using a standardized analysis pipeline.\\u00a0Briefly, sequences were\ninitially depleted of barcodes. Then sequences less than 150bp or with\nambiguous base calls were removed.\\u00a0Operational taxonomic units (OTUs)\nwere generated, and chimeras were removed using UCHIME\n[48].\\u00a0OTUs\\u00a0were defined by clustering at 3% divergence (i.e.,\nshowing 97% similarity) using a de novo method.\\u00a0Final OTUs were\ntaxonomically classified using BLASTn against the curated National Center for\nBiotechnology Information (NCBI) database and the Ribosomal Database Project\n(RDP). \\u00a0\n \nField collection:\n \nWonderland Reef, Florida (24.56028 N, 81.50127 W). Collections in July 2013.\n \nLaboratory experimentation:\\u00a0\n \nMote Marine Laboratory, Tropical Research Laboratory, Summerland Key, Florida\nfrom 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 (external link)
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 Pyrosequencing Metadata \n  R. van Woesik, PI \n  Version 2 September 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/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2016-09-06T22:07:04Z
attribute NC_GLOBAL date_modified String 2019-05-13T19:36:43Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.658322.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/658322 (external link)
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 658330
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 airbrush, bco, bco-dmo, biological, chemical, conc, data, dataset, date, date_DNA_extraction, date_sampled, date_tissue_airbrush, dmo, dna, DNA_conc, erddap, extraction, health, health_status, management, number, oceanography, office, preliminary, sample, sample_number, sampled, species, status, tissue
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/658322/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/658322 (external link)
attribute NC_GLOBAL param_mapping String {'658322': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/658322/parameters (external link)
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.\nThe 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).\nIntellectual merit\nThere 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.  \nBroader Impact\nThe 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 subsetVariables String date_DNA_extraction
attribute NC_GLOBAL summary String Health status and species of each coral sample taken in the Caribbean during 2013 (Contagious coral diseases project)
attribute NC_GLOBAL title String [Coral health status and DNA concentration] - Health status and species of each coral sample taken in the Caribbean during 2013 (Contagious coral diseases project) (Are coral diseases contagious?)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable species String
attribute species bcodmo_name String species
attribute species description String Species of coral sampled
attribute species long_name String Species
attribute species units String unitless
variable health_status String
attribute health_status bcodmo_name String status
attribute health_status description String Health status of coral sampled; description of disease exposure
attribute health_status long_name String Health Status
attribute health_status units String unitless
variable date_sampled String
attribute date_sampled bcodmo_name String date
attribute date_sampled description String Date coral was sampled; mm/dd/yy
attribute date_sampled long_name String Date Sampled
attribute date_sampled nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date_sampled units String unitless
variable date_tissue_airbrush String
attribute date_tissue_airbrush bcodmo_name String date
attribute date_tissue_airbrush description String Date airbrush was performed on sample; mm/dd/yy
attribute date_tissue_airbrush long_name String Date Tissue Airbrush
attribute date_tissue_airbrush nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date_tissue_airbrush units String unitless
variable date_DNA_extraction String
attribute date_DNA_extraction bcodmo_name String date
attribute date_DNA_extraction description String Date DNA was extracted from sample; mm/dd/yy
attribute date_DNA_extraction long_name String Date DNA Extraction
attribute date_DNA_extraction nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute date_DNA_extraction units String unitless
variable sample_number String
attribute sample_number bcodmo_name String sample
attribute sample_number description String Sample ID number
attribute sample_number long_name String Sample Number
attribute sample_number nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_number units String unitless
variable DNA_conc float
attribute DNA_conc _FillValue float NaN
attribute DNA_conc actual_range float 3.8, 32.5
attribute DNA_conc bcodmo_name String unknown
attribute DNA_conc description String Concentration of DNA
attribute DNA_conc long_name String DNA Conc
attribute DNA_conc units String ng mL -1

 
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