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 Bacteria Mapping Data \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 2016-09-06T22:14:14Z
attribute NC_GLOBAL date_modified String 2019-05-13T19:19:15Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.658340.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/658340 (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 658348
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 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/658340/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/658340 (external link)
attribute NC_GLOBAL param_mapping String {'658340': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/658340/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 project_name,linker_primer_sequence
attribute NC_GLOBAL summary String Sample numbers, barcode information, primer information and project name from bacteria samples collected in the Caribbean during 2013 (Contagious coral diseases project)
attribute NC_GLOBAL title String [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?)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable project_name String
attribute project_name bcodmo_name String project
attribute project_name description String Project name
attribute project_name long_name String Project Name
attribute project_name units String unitless
variable linker_primer_sequence String
attribute linker_primer_sequence bcodmo_name String sequence
attribute linker_primer_sequence description String Primer information
attribute linker_primer_sequence long_name String Linker Primer Sequence
attribute linker_primer_sequence units String unitless
variable sample_id String
attribute sample_id bcodmo_name String sample
attribute sample_id description String Sample ID number
attribute sample_id long_name String Sample Id
attribute sample_id nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute sample_id units String unitless
variable barcode_sequence String
attribute barcode_sequence bcodmo_name String sequence
attribute barcode_sequence description String Barcode information
attribute barcode_sequence long_name String Barcode Sequence
attribute barcode_sequence units String unitless
variable barcode_name String
attribute barcode_name bcodmo_name String sequence
attribute barcode_name description String Barcode name
attribute barcode_name long_name String Barcode Name
attribute barcode_name units String unitless
variable description String
attribute description bcodmo_name String brief_desc
attribute description description String Description; same as sample ID
attribute description long_name String Description
attribute description units String unitless

 
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