Accessing BCO-DMO data
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BCO-DMO ERDDAP
Accessing BCO-DMO data |
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| Dataset Title: | [Sponge-Associated Microbial Communities (via 16S-V4 rRNA amplicon sequencing) Following Storm-Driven Flooding] - SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (2018) (RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_817436) |
| Information: | Summary
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| FGDC
| ISO 19115
| Metadata
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Attributes {
s {
Sample_Name {
String bcodmo_name "sample";
String description "Sample name";
String long_name "Sample Name";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Collection_Date_Start {
String bcodmo_name "date";
String description "Sample collection date (start of date range) in ISO 8601 format yyyy-mm-dd";
String long_name "Collection Date Start";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String source_name "Collection_Date_Start";
String time_precision "1970-01-01";
String units "unitless";
}
Collection_Date_End {
String bcodmo_name "date";
String description "Sample collection date (end of date range) in ISO 8601 format yyyy-mm-dd";
String long_name "Collection Date End";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/";
String time_precision "1970-01-01";
String units "unitless";
}
Depth_min {
Float32 _FillValue NaN;
Float32 actual_range 16.5, 28.0;
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Sample collection depth (minimum of depth range)";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String standard_name "depth";
String units "meters (m)";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 16.5, 28.0;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Sample collection depth (maxiumum of depth range)";
String ioos_category "Location";
String long_name "Depth";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/DEPH/";
String positive "down";
String standard_name "depth";
String units "m";
}
Bank {
String bcodmo_name "site_descrip";
String description "East or west bank of the Flower Garden Banks";
String long_name "Bank";
String units "unitless";
}
Species {
String bcodmo_name "taxon";
String description "Identification (taxonomic name or organism description)";
String long_name "Species";
String units "unitless";
}
SRA {
String bcodmo_name "accession number";
String description "Sequence Read Archive (SRA) accession number at NCBI";
String long_name "SRA";
String units "unitless";
}
Accession {
String bcodmo_name "accession number";
String description "BioSample accession number at NCBI";
String long_name "Accession";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range 27.8819, 27.9078;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Sample latitude";
String ioos_category "Location";
String long_name "Latitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LATX/";
String standard_name "latitude";
String units "degrees_north";
}
longitude {
String _CoordinateAxisType "Lon";
Float64 _FillValue NaN;
Float64 actual_range -93.62829, -93.6002;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Sample longitude";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String source_name "Long";
String standard_name "longitude";
String units "degrees_east";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Location:
East and West Banks of the Flower Garden Banks National Marine Sanctuary
(FGBNMS)\\u00a0
Sampling Events:\\u00a0
NOAA FGBNMS Cruise July 2016, NOAA FGBNMS Cruise August 2016
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018
Methodology:
V4-16S bacterial communities libraries were prepared and PE 250bp reads were
generated using Illumina MiSeq platform.\\u00a0
Sampling and analytical procedures:
Samples were flash frozen in liquid nitrogen and stored at -20\\u2103 until
further processing. DNA was extracted from 250 mg of sponge sample using the
Nucleospin Soil DNA extraction kit (Takara Bio) or the DNeasy PowerSoil DNA
extraction kit (QIAGEN).\\u00a0\\u00a0";
String awards_0_award_nid "746813";
String awards_0_award_number "OCE-1800914";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1800914";
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 "Daniel Thornhill";
String awards_0_program_manager_nid "722161";
String cdm_data_type "Other";
String comment
"Sponge-Associated Microbial Communities (via 16S-V4 rRNA amplicon sequencing) Following Storm-Driven Flooding
PI: Adrienne Simoes Correa
Data Version 1: 2020-07-23";
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 dataset_current_state "Final and no updates";
String date_created "2020-06-30T20:47:45Z";
String date_modified "2020-07-24T18:14:00Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.817436.1";
Float64 Easternmost_Easting -93.6002;
Float64 geospatial_lat_max 27.9078;
Float64 geospatial_lat_min 27.8819;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max -93.6002;
Float64 geospatial_lon_min -93.62829;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 28.0;
Float64 geospatial_vertical_min 16.5;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-11-23T17:18:33Z (local files)
2024-11-23T17:18:33Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_817436.html";
String infoUrl "https://www.bco-dmo.org/dataset/817436";
String institution "BCO-DMO";
String instruments_0_acronym "Automated Sequencer";
String instruments_0_dataset_instrument_nid "817437";
String instruments_0_description "General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.";
String instruments_0_instrument_name "Automated DNA Sequencer";
String instruments_0_instrument_nid "649";
String instruments_0_supplied_name "Illumina MiSeq Platform";
String keywords "accession, bank, bco, bco-dmo, biological, chemical, collection, Collection_Date_End, data, dataset, date, depth, Depth_max, Depth_min, dmo, end, erddap, latitude, longitude, management, name, oceanography, office, preliminary, sample, Sample_Name, species, sra, start, time";
String license "https://www.bco-dmo.org/dataset/817436/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/817436";
Float64 Northernmost_Northing 27.9078;
String param_mapping "{'817436': {'Lat': 'master - latitude', 'Depth_max': 'master - depth', 'Long': 'master - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/817436/parameters";
String people_0_affiliation "Rice University";
String people_0_person_name "Adrienne Simoes Correa";
String people_0_person_nid "713331";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "University of Houston";
String people_1_affiliation_acronym "UH-Clearlake";
String people_1_person_name "Lory Santiago-Vazquez";
String people_1_person_nid "746825";
String people_1_role "Co-Principal Investigator";
String people_1_role_type "originator";
String people_2_affiliation "Rice University";
String people_2_person_name "Amanda Shore";
String people_2_person_nid "817444";
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 "Amber D. York";
String people_3_person_nid "643627";
String people_3_role "BCO-DMO Data Manager";
String people_3_role_type "related";
String project "Rapid Reefs Harvey";
String projects_0_acronym "Rapid Reefs Harvey";
String projects_0_description
"NSF Award Abstract:
Coral reefs are ecologically and economically important ecosystems, and are threatened by a variety of global (climate change) and local (overfishing, pollution) stressors. Anthropogenic climate change is increasing the frequency and severity of storms, which can physically damage reef structures and reduce reef health through changes in seawater quality. In August of 2017, Hurricane Harvey caused widespread flooding in southeast Texas when it released more than 50 trillion liters of rain, which then accumulated along the Texas Shelf. This runoff is expected to impact nearby coral reefs in the Flower Garden Banks National Marine Sanctuary (FGBNMS, northwest Gulf of Mexico) via eddies and jets that transport coastal waters offshore. Findings from this project will allow managers to quickly predict whether extreme storm events are likely to induce reef mortality and ecosystem decline due to freshwater accumulation, by tracking of low salinity water masses coupled with microbial community characterization and metrics of coral health. These data are critical to managing coastal ecosystems, including the high coral cover reefs in the FGBNMS, and will help stakeholders (e.g., diving and fishing communities) plan for and minimize disruption to their livelihoods following these storms. Results will be communicated broadly across scientific arenas, in graduate and undergraduate education and training programs, and to the general public through outreach. The investigators have seven 7 square meter 2-D Reef Replicas from 2014 depicting representative FGBNMS reef bottoms, and will construct additional 2-D Reef Replicas from both banks following the arrival of Harvey runoff, allowing the public to directly experience and quantify the effects of Hurricane Harvey on local reefs using quadrats and identification guides. This project will also synergize with NSF REU programs at Boston University and Texas A&M University, providing transformative research experiences for undergraduates. One post-doctoral scholar, four graduate students, a technician and more than 5 undergraduates will be involved in all aspects of the research. All datasets will be made freely available to the public, and will serve as an important set of baselines for future lines of inquiry into the processes by which hurricanes and other extreme storms impact reef health.
Hurricanes and other extreme storm events can decimate coral reefs through wave-driven physical damage. Freshwater runoff from extreme storms is also potentially detrimental to reefs but has received comparatively less attention. This research will provide unprecedented resolution on how hurricanes and other extreme storm events may trigger cascading interactions among water chemistry, declines in metazoan health and shifts in their associated microbial communities, ultimately resulting in coral reef decline. The freshwater runoff initiated by Hurricane Harvey is likely to impact reefs within the FGBNMS, one of the few remaining coral-dominated reefs in the greater Caribbean. The effects of Harvey runoff will be compared to a previously documented storm-driven runoff event that was associated with invertebrate mortality on the same reef system. Sampling seawater chemistry, microbial communities (water column and benthic), and host gene expression and proteomics before, immediately after, and six months after Harvey runoff enters the FGBNMS will allow us to identify commonalities among large-scale freshwater runoff events and track the response of benthic invertebrate health, microbial community diversity, and the trajectory of reef community recovery or decline. The investigators will determine if changes in water chemistry induce pelagic microbial shifts, if microbial communities typically associated with corals and sponges are altered, and whether feedbacks occur between these potential drivers of benthic invertebrate mortality.";
String projects_0_end_date "2019-11";
String projects_0_geolocation "Flower Garden Banks National Marine Sanctuary, Northwest Gulf of Mexico";
String projects_0_name "RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities";
String projects_0_project_nid "746814";
String projects_0_start_date "2017-12";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing 27.8819;
String standard_name_vocabulary "CF Standard Name Table v55";
String summary
"To document the effects of storm-driven freshwater runoff on\\u00a0sponge-
associated microbiomes, we leveraged the heavy rainfall\\u00a0associated with
Tax Day Flooding (July 2016) and Hurricane Harvey\\u00a0(August 2017) to
characterize sponge-associated bacterial communities\\u00a0at five time points:
in July 2016 (at detection of the mortality\\u00a0event), one month after the
mortality event (August 2016), immediately\\u00a0after Hurricane Harvey
(September 2017), one month after Hurricane\\u00a0Harvey (October 2017), and
approximately one year following Hurricane\\u00a0Harvey (October 2018).
These data contain Sequence Read Archive (SRA) and BioSample accession numbers
associated with BioProject\\u00a0PRJNA605902
(see\\u00a0[https://www.ncbi.nlm.nih.gov/bioproject/605902](\\\\https://www.ncbi.nlm.nih.gov/bioproject/605902\\\\))\\u00a0at
The National Center for Biotechnology Information.";
String title "[Sponge-Associated Microbial Communities (via 16S-V4 rRNA amplicon sequencing) Following Storm-Driven Flooding] - SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (2018) (RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities)";
String version "1";
Float64 Westernmost_Easting -93.62829;
String xml_source "osprey2erddap.update_xml() v1.5";
}
}
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.