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,.esriCsv,.geoJson,.odvTxt
attribute NC_GLOBAL acquisition_description String Materials and Methods\n \nSampling. Sampling occurred from July 22-24, 2017 and coincided with the\nspring tides. A new moon occurred on July 23 at 5:45 (EST). While St. John\ntidal cycles are typically semidiurnal, during spring tide the tide cycle is\ndiurnal. Sampling time points coincided with the low, flood, high, and ebb\ntides over a 48 hour (hr) window, resulting in 8 total sampling time points.\nSamples were collected \\u00b11 hr from the designated time point, placed on\nice, and processed within two hours of collection. Samples from nine locations\nacross Lameshur Bay and Fish Bay on the south shore of St. John, U.S. Virgin\nIslands represented coral reef, seagrass bed and mangrove biomes. The Lameshur\nBay mangrove location included two distinct sampling sites: an inland area\nthat was only submerged and sampled during high tide and an outlet area that\nwas always submerged and sampled at each time point. The majority of sampling\nsites were within the boundaries of the Virgin Islands National Park, which is\nlargely undeveloped except for a small research station. The Fish Bay\nmangrove, Fish Bay seagrass, and Ditliff reef sites are outside the boundary\nof the park, and the land surrounding Fish Bay is inhabited.\n \nAt all sites, a CTD (Castaway, SonTek, San Diego, CA, USA) was deployed from\nthe surface to the bottom depth in reef and seagrass seawater, and single\npoint measurements were collected from mangrove seawater, to capture the\ntemperature and salinity at each timepoint over the course of the 48 hr\nsampling window. Only temperature and salinity at the surface of the cast was\nused for analysis. Samples for inorganic nutrients were collected by filling\n30ml of surface seawater into acid-washed and seawater-rinsed vials (HDPE,\nNalgene), followed by freezing to 20C. Seawater (875\\u00b5l) was transferred\nto a 2ml cryovial (Corning) for analysis of microbial abundances and fixed to\na final concentration of 1% paraformaldehyde (Electron Microscopy Sciences),\nallowed to fix for 20 min at 4C, then flash-frozen in an LN2 dry shipper. To\ncapture seawater microbial communities, acid-washed 4L bottles (LDPE, Nalgene,\nThermoFisher Scientific, Waltham, MA, USA) were rinsed three times with\nseawater prior to collection of 3L of surface seawater. The specific 4L bottle\nused for a site at the first timepoint remained consistent across all sampling\ntimepoints, and the bottles were rinsed with freshwater between uses.\nFollowing collection, 1L of seawater was pumped using a Masterflex peristaltic\npump (Cole-Palmer, Vernon Hills, IL, USA) through Masterflex silicone tubing\n(L/S, platinum-cured, #96410-24 size, Cole-Parmer) to rinse the tubing. The\nremaining 2L of seawater was filtered through a 0.22\\u00b5m Supor filter\n(25mm; Pall, Ann Arbor, MI, USA). For the mangrove and seagrass sites, 2L\ncould not always be filtered completely and therefore 0.3 - 2L and 1.2 - 2L of\nwater was filtered through the membrane, respectively. For the coral reef\nsites, 1.5 - 2L passed through the filter membrane. All filters were placed\ninto 2ml cryovials (Corning, Corning, NY, USA) and flash-frozen in a liquid\nnitrogen dry shipper until returned to Woods Hole, MA and placed at 80C.\n \nFlow cytometry and Nutrient analyses. Samples for microbial abundance were\nanalyzed at the University of Hawaii with an EPICS Altra flow cytometry\n(Beckman Coulter Life Sciences, Inc, Indianapolis, IN) as described in Furby\net al (Furby et al. 2014), with some modifications. Briefly, to obtain\nconcentrations of cyanobacteria (Prochlorococcus and Synechococcus) and\neukaryotic phytoplankton (picoeukaryotes), an unstained aliquot was run on the\ninstrument and excited by visible wavelengths. To enumerate unpigmented cells,\nwhich is a proxy for heterotrophic bacteria and archaea (Marie et al. 1997),\nan aliquot was stained with a Hoechst DNA stain and run on the flow cytometer\nwith excitation at 488nm. The number of cells per ml was estimated following\nanalysis of fluorescence spectra using FlowJo software (v 6.4.7, Tree Star,\nInc., Ashland, OR, USA).\n \nSamples for nutrient analysis were analyzed at Oregon State University using\nmethods described in Furby et al. (Furby et al. 2014) to measure dissolved\nconcentrations (\\u00b5M) of phosphate, ammonium, nitrite, nitrite + nitrate,\nand silicate.\n \nDNA Extraction, PCR amplification, and Sequencing. DNA was extracted from the\nfilters using a sucrose-EDTA lysis method similar to Santoro et al. (Santoro\net al. 2010) that combines lysis with filter column purification. Briefly, the\n25mm filter was subjected to physical and chemical lysis using 0.1mm glass\nbeads (Lysing Matrix B, MP Biomedicals, Irvine, CA, USA), sucrose-EDTA lysis\nbuffer (0.75M Sucrose, 20mM EDTA, 400mM NaCl, 50 mM Tris) and 10% sodium\ndodecyl sulfate (Teknova, Hollister, CA, USA), followed by a proteinase-K\ndigestion (20 mg/ml Promega, Madison, WI, USA). Lysate was then purified using\nthe DNeasy Blood and Tissue Kit (Qiagen, Germantown, MD, USA) spin column\nfilters. Purified DNA was fluorometrically quantified using a high sensitivity\ndsDNA assay on a Qubit 2.0 fluorometer (ThermoFisher Scientific).\n \nSample DNA was diluted 1:100 in UV-sterilized PCR-grade H2O and 1\\u00b5l was\nused in a PCR reaction. Barcoded primers recommended by the Earth Microbiome\nProject, 515FY and 806RB, were used to amplify the V4 region of the SSU rRNA\ngene in bacteria and archaea (Apprill et al. 2015, Parada et al. 2016).\nTriplicate 25\\u00b5l reactions contained 1.25 units of GoTaq DNA Polymerase\n(Promega, Madison, WI, USA), 0.2\\u00b5M forward and reverse primers, 0.2mM\ndeoxynucleoside triphosphate (dNTP) mix (Promega), 2.5mM MgCl2, 5\\u00b5l GoTaq\n5X colorless flexi buffer (Promega), and nuclease-free water. The reactions\nwere run on a Bio-Rad Thermocycler (Hercules, CA, USA) using the following\ncriteria: denaturation at 95C for 2 min; 28C cycles of 95C for 20 s, 55C for\n15 s, and 72C for 5 min; and extension at 72C for 10 min. Successful\namplification was verified by running 5\\u00b5l of product on a 1% agarose-TBE\ngel stained with SYBR Safe gel stain (Invitrogen, Carlsbad, CA, USA).\nTriplicate PCR products were pooled and purified using the MinElute PCR\npurification kit (Qiagen). Concentration of purified products was quantified\nusing the high sensitivity dsDNA assay on the Qubit 2.0 fluorometer\n(ThermoFisher Scientific). Barcoded PCR products were diluted to equal\nconcentrations and pooled for sequencing. Samples were shipped to the Georgia\nGenomics and Bioinformatics Core at the University of Georgia for sequencing\non an Illumina MiSeq using paired-end 250bp sequencing.\n \nData analysis. All sequence processing and data analysis was performed in R\nStudio (v 1.1.463) running R (v 3.4.0, 2017-04-21). Sequence reads were\ninspected for quality, filtered, trimmed, and dereplicated in the DADA2 R\npackage (v.1.10.0) (Callahan et al. 2016). Specific filtering parameters used\nincluded the following: truncLen = c(240, 200), maxN = 0, maxEE = c(2,2),\nrm.phix = TRUE, and compress = TRUE. DADA2 was then used to generate amplicon\nsequence variants (ASVs) and remove chimeras. Taxonomy was assigned in DADA2\nusing the SILVA SSU rRNA database down to the species level where applicable\n(v.132, (Quast et al. 2012)). ASV counts in each sample were transformed to\nrelative abundance for further data analysis.\n \nTo understand the variability in microbial communities over time at all sites,\nBray-Curtis dissimilarity was calculated between each sample in the R package\nvegan (v2.5.4) (Oksanen et al. 2019) and illustrated using non-metric\nmultidimensional scaling (NMDS) in the R package, ggplot2 (v3.2.1) (Wickham\n2016). Environmental vectors that significantly associated (cutoff p<0.01)\nwith the ordination were produced using the function envfit() in the vegan R\npackage. Pairwise dissimilarity was plotted to represent the range of\ndissimilarity in microbial communities over 48 hrs at each site. A higher\naverage dissimilarity would suggest that the site experiences more variable\nmicrobial communities than a site with a lower average dissimilarity. A\nKruskal-Wallis test was used to examine if there is a significant difference\nbetween sites (significance level p<0.05). To determine which pairs of sites\nhad significantly different dissimilarities, a pairwise Wilcoxon Rank Sum test\nwas used with a Benjamini-Hochberg correction for multiple testing and a\ncutoff of 0.05.\n \nDifferential abundance (DA) and of ASVs in relation to the tide was evaluated\nat mangrove sites using the corncob R package (v0.1.0) (Martin et al. 2019).\nThe following analyses were conducted on a subset of the data representing\nmangrove communities. All ASV relative abundances were modeled in corncob\nusing a logit-link for mean and dispersion. DA was modeled as a linear\nfunction of sea level (a continuous covariate that is representative of the\ntide cycle) while controlling for differential variance and the effect of site\nand day or night on DA. Controlling for the effect of day or night was\nimperative because over the 48 hr period low and flood tide only occurred\nduring the day and high and low tide only occurred during dusk and night,\nrespectively. The parametric Wald test was used to test the hypotheses that\nthe relative abundance or variance of a given ASV changed significantly with\nrespect to sea level and the Benjamini-Hochberg false discovery rate (FDR)\ncorrection was applied to account for multiple comparisons, with the cutoff at\n0.05.
attribute NC_GLOBAL awards_0_award_nid String 746195
attribute NC_GLOBAL awards_0_award_number String OCE-1736288
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1736288 (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 Daniel Thornhill
attribute NC_GLOBAL awards_0_program_manager_nid String 722161
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Tidal study of seawater microbial communities \n  PI: Amy Apprill \n  Data Version 1: 2019-12-09
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 2019-12-06T16:55:52Z
attribute NC_GLOBAL date_modified String 2019-12-12T20:24:25Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.783679.1
attribute NC_GLOBAL Easternmost_Easting double -64.72223
attribute NC_GLOBAL geospatial_lat_max double 18.32065
attribute NC_GLOBAL geospatial_lat_min double 18.30964
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -64.72223
attribute NC_GLOBAL geospatial_lon_min double -64.76453
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL geospatial_vertical_max double 0.3
attribute NC_GLOBAL geospatial_vertical_min double 0.3
attribute NC_GLOBAL geospatial_vertical_positive String down
attribute NC_GLOBAL geospatial_vertical_units String m
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/783679 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String CTD
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 783835
attribute NC_GLOBAL instruments_0_description String The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column.  The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or  radiometers.  It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.  This instrument designation is used when specific make and model are not known.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/130/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String CTD profiler
attribute NC_GLOBAL instruments_0_instrument_nid String 417
attribute NC_GLOBAL instruments_0_supplied_name String CTD (Castaway, SonTek, San Diego, CA, USA)
attribute NC_GLOBAL instruments_1_acronym String Fluorometer
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 783845
attribute NC_GLOBAL instruments_1_description String A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/113/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Fluorometer
attribute NC_GLOBAL instruments_1_instrument_nid String 484
attribute NC_GLOBAL instruments_1_supplied_name String Qubit 2.0 fluorometer (ThermoFisher Scientific)
attribute NC_GLOBAL instruments_2_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Samples were shipped to the Georgia Genomics and Bioinformatics Core at the University of Georgia for sequencing on an Illumina MiSeq using paired-end 250bp sequencing
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 783846
attribute NC_GLOBAL instruments_2_description String 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.
attribute NC_GLOBAL instruments_2_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_2_instrument_nid String 649
attribute NC_GLOBAL instruments_2_supplied_name String Illumina MiSeq
attribute NC_GLOBAL instruments_3_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 783836
attribute NC_GLOBAL instruments_3_description String Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.\n(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)
attribute NC_GLOBAL instruments_3_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_3_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_3_instrument_nid String 660
attribute NC_GLOBAL instruments_3_supplied_name String EPICS Altra flow cytometry (Beckman Coulter Life Sciences, Inc, Indianapolis, IN)
attribute NC_GLOBAL keywords String accession, ammonia, ammonium, bco, bco-dmo, bio, biological, biome, cells, chemical, chemistry, collection, Collection_Date, Collection_Depth, Collection_Time, concentration, data, dataset, date, density, depth, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, Earth Science > Oceans > Salinity/Density > Salinity, Earth Science > Oceans > Sea Surface Topography > Sea Surface Height, erddap, height, instrument, iso, latitude, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, mass_concentration_of_silicate_in_sea_water, model, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, n02, name, ncbi, NCBI_BioProject_accession_number, NCBI_BioSample_accession_number, nh4, nitrate, Nitrate_Nitrite, nitrite, no3, number, ocean, oceanography, oceans, office, phosphate, picoeukaryotes, po4, practical, preliminary, prochlorococcus, project, salinity, sample, Sample_ID, Sample_type, science, sea, sea_surface_height, sea_water_practical_salinity, seawater, sequencing, Sequencing_Instrument_model, Sequencing_Strategy, Sequencing_strategy, silicate, site, Site_Depth, Site_Name, strategy, surface, synechococcus, temperature, tide, Tide_Height, time, Time_elapsed_between_tide_timepoint_and_collection, topography, type, unpigmented, Unpigmented_cells, water
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/783679/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/783679 (external link)
attribute NC_GLOBAL Northernmost_Northing double 18.32065
attribute NC_GLOBAL param_mapping String {'783679': {'Latitude': 'master - latitude', 'Collection_Depth': 'master - depth', 'Longitude': 'master - longitude', 'ISO_DateTime_UTC': 'master - time'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/783679/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_0_affiliation_acronym String WHOI
attribute NC_GLOBAL people_0_person_name String Amy Apprill
attribute NC_GLOBAL people_0_person_nid String 553489
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 Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI
attribute NC_GLOBAL people_1_person_name String Cynthia Becker
attribute NC_GLOBAL people_1_person_nid String 784315
attribute NC_GLOBAL people_1_role String Student
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Amber York
attribute NC_GLOBAL people_2_person_nid String 643627
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Coral Exometabolomes
attribute NC_GLOBAL projects_0_acronym String Coral Exometabolomes
attribute NC_GLOBAL projects_0_description String NSF abstract:\nCoral reefs are some of the most diverse and productive ecosystems in the ocean. Globally, reefs have declined in stony (reef-building) coral abundance due to environmental variations, and in the Caribbean this decline has coincided with an increase in octocoral (soft coral) abundance. This phase shift occurring on Caribbean reefs may be impacting the interactions between the sea floor and water column and particularly between corals and picoplankton. Picoplankton are the microorganisms in the water column that utilize organic matter released from corals to support their growth. These coral-picoplankton interactions are relatively unstudied, but could have major implications for reef ecology and coral health. This project will take place in the U.S. territory of the Virgin Islands (USVI) and will produce the first detailed knowledge about the chemical diversity and composition of organic matter released from diverse stony coral and octocoral species. This project will advance our understanding of coral reef microbial ecology by allowing us to understand how different coral metabolites impact picoplankton growth and dynamics over time. The results from this project will be made publically accessible in a freely available online magazine, and USVI minority middle and high school students will be exposed to a lesson about chemical-biological interactions on coral reefs through established summer camps. This project will also contribute to the training of USVI minority undergraduates as well as a graduate student.\nCoral exometabolomes, which are the sum of metabolic products of the coral together with its microbiome, are thought to structure picoplankton communities in a species-specific manner. However, a detailed understanding of coral exometabolomes, and their influences on reef picoplankton, has not yet been obtained. This project will utilize controlled aquaria-based experiments with stony corals and octocorals, foundational species of Caribbean reef ecosystems, to examine how the exometabolomes of diverse coral species differentially influence the reef picoplankton community. Specifically, this project will capitalize on recent developments in mass spectrometry-based metabolomics to define the signature exometabolomes of ecologically important and diverse stony corals and octocorals. Secondly, this project will determine how the exometabolomes of these corals vary with factors linked to coral taxonomy as well as the coral-associated microbiome (Symbiodinium algae, bacteria and archaea). With this new understanding of coral exometabolomes, the project will then apply a stable isotope probe labeling approach to the coral exometabolome and will examine if and how (through changes in growth and activity) the seawater picoplankton community incorporates coral exometabolomes from different coral species over time. This project will advance our ability to evaluate the role that coral exometabolomes play in contributing to benthic-picoplankton interactions on changing Caribbean reefs.
attribute NC_GLOBAL projects_0_end_date String 2020-09
attribute NC_GLOBAL projects_0_geolocation String U.S. Virgin Islands
attribute NC_GLOBAL projects_0_name String Signature exometabolomes of Caribbean corals and influences on reef picoplankton
attribute NC_GLOBAL projects_0_project_nid String 746196
attribute NC_GLOBAL projects_0_start_date String 2017-10
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 Southernmost_Northing double 18.30964
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String NCBI_BioProject_accession_number,Sample_type,Sequencing_Strategy,Sequencing_Instrument_model
attribute NC_GLOBAL summary String Data from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in 2017.  These data include tidal height, depth, temperature, salinity, Prochlorococcus counts, Synechococcus counts, Picoeukaryote abundances, nutrient concentrations at accession numbers for sequences at The National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA).
attribute NC_GLOBAL time_coverage_end String 2017-07-24T10:43:00Z
attribute NC_GLOBAL time_coverage_start String 2017-07-22T15:55:00Z
attribute NC_GLOBAL title String [Tidal study of seawater microbial communities] - Flow cytometry and nutrient analyses data from a tidal study over 48 hours of mangrove, seagrass, and seawater from the US Virgin Islands in July of 2017 (Signature exometabolomes of Caribbean corals and influences on reef picoplankton)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -64.76453
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Sample_ID String
attribute Sample_ID bcodmo_name String sample
attribute Sample_ID description String Sample identifier
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 NCBI_BioProject_accession_number String
attribute NCBI_BioProject_accession_number bcodmo_name String accession number
attribute NCBI_BioProject_accession_number description String BioProject accession number for the NCBI Sequence read archive
attribute NCBI_BioProject_accession_number long_name String NCBI Bio Project Accession Number
attribute NCBI_BioProject_accession_number units String unitless
variable NCBI_BioSample_accession_number String
attribute NCBI_BioSample_accession_number bcodmo_name String accession number
attribute NCBI_BioSample_accession_number description String BioSample accession number for the NCBI Sequence read archive
attribute NCBI_BioSample_accession_number long_name String NCBI Bio Sample Accession Number
attribute NCBI_BioSample_accession_number units String unitless
variable Sample_type String
attribute Sample_type bcodmo_name String sample_descrip
attribute Sample_type description String Sample type as reported to NCBI for sequence upload
attribute Sample_type long_name String Sample Type
attribute Sample_type units String unitless
variable Sequencing_Strategy String
attribute Sequencing_Strategy bcodmo_name String brief_desc
attribute Sequencing_Strategy description String Describes what type of sequencing library preparation we did
attribute Sequencing_Strategy long_name String Sequencing Strategy
attribute Sequencing_Strategy units String unitless
variable Sequencing_Instrument_model String
attribute Sequencing_Instrument_model bcodmo_name String brief_desc
attribute Sequencing_Instrument_model description String This is the model type of sequencer used for the dataset uploaded to NCBI
attribute Sequencing_Instrument_model long_name String Sequencing Instrument Model
attribute Sequencing_Instrument_model units String unitless
variable Sequencing_strategy String
attribute Sequencing_strategy bcodmo_name String brief_desc
attribute Sequencing_strategy description String This is a more detailed description of how we sequenced. This is included in the methods in more depth.
attribute Sequencing_strategy long_name String Sequencing Strategy
attribute Sequencing_strategy units String unitless
variable Site_Name String
attribute Site_Name bcodmo_name String site
attribute Site_Name description String This is the local name of the site where samples were collected
attribute Site_Name long_name String Site Name
attribute Site_Name units String unitless
variable Biome String
attribute Biome bcodmo_name String site_descrip
attribute Biome description String This is a qualitative assessment of the type of ecosystem
attribute Biome long_name String Biome
attribute Biome units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 18.30964, 18.32065
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String Latitude
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude double
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -64.76453, -64.72223
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String Longitude
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable Collection_Date String
attribute Collection_Date bcodmo_name String date_local
attribute Collection_Date description String Local date when samples were collected (UTC-4)
attribute Collection_Date long_name String Collection Date
attribute Collection_Date time_precision String 1970-01-01
attribute Collection_Date units String unitless
variable Collection_Time String
attribute Collection_Time bcodmo_name String time_local
attribute Collection_Time description String Local time when samples were collected (UTC-4)
attribute Collection_Time long_name String Collection Time
attribute Collection_Time units String unitless
variable time double
attribute time _CoordinateAxisType String Time
attribute time actual_range double 1.5007389E9, 1.50089298E9
attribute time axis String T
attribute time bcodmo_name String ISO_DateTime_UTC
attribute time description String ISO Datetime (UTC) when samples were collected in ISO 8601:2004(E) format yyyy-mm-ddTHH:MM:SSZ
attribute time ioos_category String Time
attribute time long_name String ISO Date Time UTC
attribute time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/ (external link)
attribute time source_name String ISO_DateTime_UTC
attribute time standard_name String time
attribute time time_origin String 01-JAN-1970 00:00:00
attribute time time_precision String 1970-01-01T00:00:00Z
attribute time units String seconds since 1970-01-01T00:00:00Z
variable Tide String
attribute Tide bcodmo_name String tide
attribute Tide description String Qualitative description of the tide level during the sample timepoint
attribute Tide long_name String Tide
attribute Tide units String unitless
variable Tide_Height float
attribute Tide_Height _FillValue float NaN
attribute Tide_Height actual_range float -0.042, 0.401
attribute Tide_Height bcodmo_name String height
attribute Tide_Height colorBarMaximum double 2.0
attribute Tide_Height colorBarMinimum double -2.0
attribute Tide_Height description String Tide height corresponding to verified mean low low water  (MLLW), as taken from the NOAA station 9751381 in Lameshur Bay, USVI.
attribute Tide_Height long_name String Sea Surface Height
attribute Tide_Height units String meters (m)
variable Time_elapsed_between_tide_timepoint_and_collection byte
attribute Time_elapsed_between_tide_timepoint_and_collection _FillValue byte 127
attribute Time_elapsed_between_tide_timepoint_and_collection actual_range byte 0, 58
attribute Time_elapsed_between_tide_timepoint_and_collection bcodmo_name String time_elapsed
attribute Time_elapsed_between_tide_timepoint_and_collection colorBarMaximum double 2.0
attribute Time_elapsed_between_tide_timepoint_and_collection colorBarMinimum double -2.0
attribute Time_elapsed_between_tide_timepoint_and_collection description String Time that elapsed between the designated collection timepoint and when the sample was actually collected during the time series.
attribute Time_elapsed_between_tide_timepoint_and_collection long_name String Sea Surface Height
attribute Time_elapsed_between_tide_timepoint_and_collection nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ELTMZZZZ/ (external link)
attribute Time_elapsed_between_tide_timepoint_and_collection units String minutes
variable depth double
attribute depth _CoordinateAxisType String Height
attribute depth _CoordinateZisPositive String down
attribute depth _FillValue double NaN
attribute depth actual_range double 0.3, 0.3
attribute depth axis String Z
attribute depth bcodmo_name String depth
attribute depth description String Collection depth of all samples
attribute depth ioos_category String Location
attribute depth long_name String Collection Depth
attribute depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute depth positive String down
attribute depth standard_name String depth
attribute depth units String m
variable Site_Depth float
attribute Site_Depth _FillValue float NaN
attribute Site_Depth actual_range float 0.2, 12.2
attribute Site_Depth bcodmo_name String depth
attribute Site_Depth description String Approximate depth of the collection site. Generally taken from the CTD cast.
attribute Site_Depth long_name String Site Depth
attribute Site_Depth nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute Site_Depth units String meters (m)
variable Temperature float
attribute Temperature _FillValue float NaN
attribute Temperature actual_range float 27.84, 34.4
attribute Temperature bcodmo_name String temperature
attribute Temperature description String Temperature of seawater as taken from the CastAway CTD (SonTek)
attribute Temperature long_name String Temperature
attribute Temperature nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute Temperature units String degrees Celsius (ºC)
variable Salinity float
attribute Salinity _FillValue float NaN
attribute Salinity actual_range float 34.52, 37.38
attribute Salinity bcodmo_name String sal
attribute Salinity colorBarMaximum double 37.0
attribute Salinity colorBarMinimum double 32.0
attribute Salinity description String Salinity of seawater as taken from the CastAway CTD (SonTek)
attribute Salinity long_name String Sea Water Practical Salinity
attribute Salinity nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/ (external link)
attribute Salinity units String Practical Salinity Units (PSU)
variable Prochlorococcus int
attribute Prochlorococcus _FillValue int 2147483647
attribute Prochlorococcus actual_range int 0, 197086
attribute Prochlorococcus bcodmo_name String cell_concentration
attribute Prochlorococcus description String Prochlorococcus cell counts as determined by flow cytometry
attribute Prochlorococcus long_name String Prochlorococcus
attribute Prochlorococcus units String cells per milliliter (cells/ml)
variable Synechococcus int
attribute Synechococcus _FillValue int 2147483647
attribute Synechococcus actual_range int 1547, 95963
attribute Synechococcus bcodmo_name String cell_concentration
attribute Synechococcus description String Synechococcus cell counts as determined by flow cytometry
attribute Synechococcus long_name String Synechococcus
attribute Synechococcus units String cells per milliliter (cells/ml)
variable Picoeukaryotes short
attribute Picoeukaryotes _FillValue short 32767
attribute Picoeukaryotes actual_range short 844, 6441
attribute Picoeukaryotes bcodmo_name String cell_concentration
attribute Picoeukaryotes description String Picoeukaryote abundances as determined by flow cytometry
attribute Picoeukaryotes long_name String Picoeukaryotes
attribute Picoeukaryotes units String cells per milliliter (cells/ml)
variable Unpigmented_cells int
attribute Unpigmented_cells _FillValue int 2147483647
attribute Unpigmented_cells actual_range int 366483, 4500000
attribute Unpigmented_cells bcodmo_name String cell_concentration
attribute Unpigmented_cells description String unpigmented cells as determined by flow cytometry of Hoescht stained cells.
attribute Unpigmented_cells long_name String Unpigmented Cells
attribute Unpigmented_cells units String cells per milliliter (cells/ml)
variable Phosphate float
attribute Phosphate _FillValue float NaN
attribute Phosphate actual_range float 0.157, 0.553
attribute Phosphate bcodmo_name String PO4
attribute Phosphate description String Phosphate concentrations in seawater
attribute Phosphate long_name String Mass Concentration Of Phosphate In Sea Water
attribute Phosphate units String micromolar (µM)
variable Silicate float
attribute Silicate _FillValue float NaN
attribute Silicate actual_range float 1.7, 9.1
attribute Silicate bcodmo_name String SiOH_4
attribute Silicate description String Silicate concentrations in seawater
attribute Silicate long_name String Mass Concentration Of Silicate In Sea Water
attribute Silicate units String micromolar (µM)
variable Nitrate_Nitrite float
attribute Nitrate_Nitrite _FillValue float NaN
attribute Nitrate_Nitrite actual_range float -0.01, 1.17
attribute Nitrate_Nitrite bcodmo_name String NO3_NO2
attribute Nitrate_Nitrite colorBarMaximum double 50.0
attribute Nitrate_Nitrite colorBarMinimum double 0.0
attribute Nitrate_Nitrite description String Nitrate and Nitrite concentrations in seawater
attribute Nitrate_Nitrite long_name String Mole Concentration Of Nitrate In Sea Water
attribute Nitrate_Nitrite units String micromolar (µM)
variable Nitrite float
attribute Nitrite _FillValue float NaN
attribute Nitrite actual_range float 0.01, 0.26
attribute Nitrite bcodmo_name String NO2
attribute Nitrite colorBarMaximum double 1.0
attribute Nitrite colorBarMinimum double 0.0
attribute Nitrite description String Nitrite concentrations in seawater
attribute Nitrite long_name String Mole Concentration Of Nitrite In Sea Water
attribute Nitrite nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/ (external link)
attribute Nitrite units String micromolar (µM)
variable Ammonium float
attribute Ammonium _FillValue float NaN
attribute Ammonium actual_range float 0.02, 2.94
attribute Ammonium bcodmo_name String Ammonium
attribute Ammonium colorBarMaximum double 5.0
attribute Ammonium colorBarMinimum double 0.0
attribute Ammonium description String Ammonium concentrations in seawater
attribute Ammonium long_name String Mole Concentration Of Ammonium In Sea Water
attribute Ammonium nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/ (external link)
attribute Ammonium units String micromolar (µM)

 
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