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 At indicated dates, individual corals were visually assessed for bleaching.\nBleaching was noted for those corals paling or entirely lacking in\npigmentation.\\u00a0 A reference color card (Seibeck et al., 2006) was used as\na pigmentation reference. The normal level of pigmentation was C3 or darker\n(not bleached). Colors lighter than C3 were considered bleached. Using bone\ncutters, a small sub-apical piece was broken off of each coral. On the boat,\nsamples were transferred to CHAOS buffer (listed below) and extracted for DNA:\n \nChaos Buffer:\n \n4.5M Guanidinium thiocyanate  \n 2% N-lauroylsarcosine (sarcosyl)  \n 50mM EDTA  \n 25mM Tris-HCl, pH 7.5  \n 0.2% antifoam A (Sigma)  \n 0.1M b-mercaptoethanol (BME)\n \nBinding buffer (BB):\n \n6 M GuSCN 1 , (Guanidine Thiocyanate)  \n 20 mM EDTA pH 8.0  \n 10 mM Tris-HCl pH 7.5  \n 4% Triton X-100\n \nProtein wash buffer (PWB):\n \n70 mL of ethanol (96%) was thoroughly mixed with 26 mL of BB (stable at 20\ndeg\\u00a0C for1 week).\n \nWash buffer (WB):\n \nethanol (60%),  \n 50 mM NaCl  \n 10 mM Tris-HCl pH 7.4  \n 0.5 mM EDTA pH 8.0 (stored at -20 deg\\u00a0C)\n \n-Allow coral fragments to sit covered in CHAOS buffer in 1.5 - 2.0 mL tube for days- weeks.  \n -Pipet the Supernatant mixture into a silica spin column placed in a 2 ml\ncollection tube. Centrifuge at 6000 x g (8000 rpm) for 1 min. Discard flow-\nthrough. Repeat as needed to load entire sample.  \n -Add 700 ul PWB to column, and centrifuge for 1 min at 6000 x g (8000 rpm).\nDiscard flow-through.  \n -Repeat 2x (3 washes total).  \n -Add 700 ul WB to column and centrifuge for 1 min at 20,000 x g (14,000\nrpm). Discard flow-through.  \n -Repeat wash and centrifuge for 3 min at 20,000 x g (14,000 rpm) to dry the\nDNeasy membrane.  \n -Discard flow-through and collection tube.  \n -Place the spin column in a clean 1.5 ml or 2 ml microcentrifuge tube, and\npipet 100 ul 0.1x TE directly onto the spin column.  \n -Incubate at room temperature for 1 min, and then centrifuge for 1 min at\n6000 x g (8000 rpm) to elute.  \n (May repeat with another 100 ul of 0.1x TE).\n \nPurified DNA was sent to MR DNA in stillwater Texas for Illumina sequencing of\nthe cp-23S gene for Symbiodinium typing.
attribute NC_GLOBAL awards_0_award_nid String 637742
attribute NC_GLOBAL awards_0_award_number String OCE-1503483
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1503483 (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 David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL awards_1_award_nid String 637749
attribute NC_GLOBAL awards_1_award_number String OCE-1503430
attribute NC_GLOBAL awards_1_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1503430 (external link)
attribute NC_GLOBAL awards_1_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_1_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_1_funding_source_nid String 355
attribute NC_GLOBAL awards_1_program_manager String David L. Garrison
attribute NC_GLOBAL awards_1_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Symbiodinium community composition for individual A. cervicornis \n  M. Rodriguez-Lanetty, D. Lirman, and L. Richardson, PIs \n  Version 26 July 2017
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 2017-07-26T18:57:02Z
attribute NC_GLOBAL date_modified String 2019-03-20T20:10:32Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.709909.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/709909 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, bleaching, chemical, clonal, colony, data, dataset, disease, dmo, erddap, genet, genet_clonalPopulation_ID, individual, management, mortality, oceanography, office, population, preliminary, ramet, ramet_individualColony_ID, visit
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/709909/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/709909 (external link)
attribute NC_GLOBAL param_mapping String {'709909': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/709909/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Florida International University
attribute NC_GLOBAL people_0_affiliation_acronym String FIU
attribute NC_GLOBAL people_0_person_name String Dr Mauricio Rodriguez-Lanetty
attribute NC_GLOBAL people_0_person_nid String 516423
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 University of Miami Rosenstiel School of Marine and Atmospheric Science
attribute NC_GLOBAL people_1_affiliation_acronym String UM-RSMAS
attribute NC_GLOBAL people_1_person_name String Dr Diego Lirman
attribute NC_GLOBAL people_1_person_nid String 637751
attribute NC_GLOBAL people_1_role String Co-Principal Investigator
attribute NC_GLOBAL people_1_role_type String originator
attribute NC_GLOBAL people_2_affiliation String Florida International University
attribute NC_GLOBAL people_2_affiliation_acronym String FIU
attribute NC_GLOBAL people_2_person_name String Dr Laurie Richardson
attribute NC_GLOBAL people_2_person_nid String 637746
attribute NC_GLOBAL people_2_role String Co-Principal Investigator
attribute NC_GLOBAL people_2_role_type String originator
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 EMUCoReS
attribute NC_GLOBAL projects_0_acronym String EMUCoReS
attribute NC_GLOBAL projects_0_description String Description from NSF award abstract:\nCoral reefs are among the most biologically diverse and economically important ecosystems on the planet. However, coral reefs are in a state of global decline due to effects of climate change, disease outbreaks, and other stressors. Mass coral bleaching events, a breakdown of the association between corals and their symbiotic algae, are predicted to become more frequent and severe in response to climate change, and it is expected that subsequent disease outbreaks will become more common. Beginning in August 2014, nearly all coral species in the Florida Reef Tract have undergone severe bleaching, in some cases followed by coral mortality and/or disease outbreaks. This widespread, thermal-induced event presents a unique time-sensitive opportunity to explore the mechanisms underpinning the patterns of coral bleaching, disease, and recovery. The mechanisms linking patterns of bleaching, disease, mortality, and recovery remain relatively unexplored. This research will explore the influences that genotype combinations of host polyps, their algal symbionts, and associated bacterial have on bleaching/disease likelihood and recovery/mortality predisposition of coral specimens. By providing a mechanistic understanding of the processes that underlie coral bleaching and subsequent recovery this research will contribute to measures in support of preserving this invaluable natural resource. The study will further involve students from diverse backgrounds as well as provide project internship opportunities for high school students. A web based radio blog will disseminate project results and other relevant developments to the broad audiences\nMass coral bleaching events are predicted to become more frequent and severe in response to climate change, and it is expected that subsequent disease outbreaks will become more common. The lack of a baseline genetic datasets for coral holobionts prior to previous natural bleaching events has hindered our understanding of recovery patterns and physiological tolerance to thermal stress, also known as coral bleaching. An extensive pre-thermal stress baseline of genotypic identity of coral hosts, Symbiodinium, and associated bacterial community offers a unique opportunity to analyze changes associated with current bleaching event along the Florida coastline and to document holobiont compositions most and least resistant/resilient to bleaching and disease. Repeated sampling of the same coral colonies will allow the investigators to compare holobiont composition before, during and after bleaching of both healthy and diseased individuals. This bleaching event is a time-sensitive natural experiment to examine the dynamics of microbes (Symbiodinium and bacteria) associated with affected colonies, including their potential influence on disease susceptibility and resistance of reef corals. This effort would constitute the first time that high throughput sequencing of coral, Symbiodinium endosymbiont, and the coral-associated bacterial community genotypes are together used to explain patterns of disease, recovery, and mortality following natural bleaching. This study will likely change the way investigators study emerging wasting diseases of keystone species that define marine benthic communities.
attribute NC_GLOBAL projects_0_end_date String 2016-11
attribute NC_GLOBAL projects_0_geolocation String Florida Reef Tract (24.868358, -80.643495)
attribute NC_GLOBAL projects_0_name String RAPID: A hyper-thermal anomaly in the Florida Reef Tract: An opportunity to explore the mechanisms underpinning patterns of coral bleaching and disease
attribute NC_GLOBAL projects_0_project_nid String 637743
attribute NC_GLOBAL projects_0_start_date String 2014-12
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 Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS project)
attribute NC_GLOBAL title String [Symbiodinium community composition] - Symbiodinium community composition for individual A. cervicornis from Elliot Key, Florida during 2014 and 2015 (EMUCoReS project) (RAPID: A hyper-thermal anomaly in the Florida Reef Tract: An opportunity to explore the mechanisms underpinning patterns of coral bleaching and disease)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable genet_clonalPopulation_ID String
attribute genet_clonalPopulation_ID bcodmo_name String sample
attribute genet_clonalPopulation_ID description String Azexual clone identifier; A through X
attribute genet_clonalPopulation_ID long_name String Genet Clonal Population ID
attribute genet_clonalPopulation_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute genet_clonalPopulation_ID units String unitless
variable ramet_individualColony_ID byte
attribute ramet_individualColony_ID _FillValue byte 127
attribute ramet_individualColony_ID actual_range byte 1, 10
attribute ramet_individualColony_ID bcodmo_name String sample
attribute ramet_individualColony_ID description String Individual coral ID within each genet; 1 through 10
attribute ramet_individualColony_ID long_name String Ramet Individual Colony ID
attribute ramet_individualColony_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute ramet_individualColony_ID units String unitless
variable visit String
attribute visit bcodmo_name String month
attribute visit description String Month sampled: September 14; March 15; October 15
attribute visit long_name String Visit
attribute visit nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/MNTHXXXX/ (external link)
attribute visit units String unitless
variable bleaching String
attribute bleaching bcodmo_name String sample_descrip
attribute bleaching description String Presence or absence of bleaching categorically binned as bleaching, or healthy
attribute bleaching long_name String Bleaching
attribute bleaching units String unitless
variable disease String
attribute disease bcodmo_name String sample_descrip
attribute disease description String Presence or absence of disease categorically binned as: no disease; white band disease; or rapid tissue loss
attribute disease long_name String Disease
attribute disease units String unitless
variable mortality String
attribute mortality bcodmo_name String sample_descrip
attribute mortality description String Relative partial mortality categorically binned as; no mortality; partial mortality; mostly dead; or dead
attribute mortality long_name String Mortality
attribute mortality units String unitless

 
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