ERDDAP > info > bcodmo_dataset_658340

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 mail	Institution	Dataset ID
	set	data			files	public	[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?)		I   M	background			BCO-DMO	bcodmo_dataset_658340

The Dataset's Variables and Attributes

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. 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.
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	Bacteria Mapping Data R. van Woesik, PI 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/
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
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/658340
attribute	NC_GLOBAL	param_mapping	String	{'658340': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/658340/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	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/
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

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.