Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [IODP360 - Replicate Cell Counts] - Supplementary Table 3B: Replicate cell counts for the 11 samples and alkaline phosphatase activity measurements available for any of the 11 samples (Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_811483) |
| Information: | Summary
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| ISO 19115
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Attributes {
s {
Sample {
String bcodmo_name "sample";
String description "Sample ID";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
latitude {
String _CoordinateAxisType "Lat";
Float64 _FillValue NaN;
Float64 actual_range -32.70567, -32.70567;
String axis "Y";
String bcodmo_name "latitude";
Float64 colorBarMaximum 90.0;
Float64 colorBarMinimum -90.0;
String description "Latitude, south is negative";
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 57.278183, 57.278183;
String axis "X";
String bcodmo_name "longitude";
Float64 colorBarMaximum 180.0;
Float64 colorBarMinimum -180.0;
String description "Longitude, west is negative";
String ioos_category "Location";
String long_name "Longitude";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P09/current/LONX/";
String standard_name "longitude";
String units "degrees_east";
}
depth {
String _CoordinateAxisType "Height";
String _CoordinateZisPositive "down";
Float64 _FillValue NaN;
Float64 actual_range 10.7, 747.7;
String axis "Z";
String bcodmo_name "depth";
Float64 colorBarMaximum 8000.0;
Float64 colorBarMinimum -8000.0;
String colorBarPalette "TopographyDepth";
String description "Depth below seafloor";
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";
}
Replicate_1 {
Float32 _FillValue NaN;
Float32 actual_range 8.77, 3000.0;
String bcodmo_name "replicate";
String description "Replicate 1";
String long_name "Replicate 1";
String units "cells per cubic centimeter (cells/cm3)";
}
Replicate_2 {
Float32 _FillValue NaN;
Float32 actual_range 17.5, 1740.0;
String bcodmo_name "replicate";
String description "Replicate 2";
String long_name "Replicate 2";
String units "cells per cubic centimeter (cells/cm3)";
}
Average {
Int16 _FillValue 32767;
Int16 actual_range 115, 1656;
String bcodmo_name "mean";
String description "Average number of cells";
String long_name "Average";
String units "cells per cubic centimeter (cells/cm3)";
}
Standard_Deviation {
Int16 _FillValue 32767;
Int16 actual_range 6, 1901;
String bcodmo_name "standard deviation";
Float64 colorBarMaximum 50.0;
Float64 colorBarMinimum 0.0;
String description "Standard deviation of average";
String long_name "Standard Deviation";
String units "cells per cubic centimeter (cells/cm3)";
}
AP_activity {
Float32 _FillValue NaN;
Float32 actual_range 0.04, 2.3;
String bcodmo_name "unknown";
String description "Alkaline Phosphatase activity";
String long_name "AP Activity";
String units "picomole per gram per hour (pmol g-1 h-1)";
}
Time_of_AP_measurment {
Int16 _FillValue 32767;
Int16 actual_range 876, 3053;
String bcodmo_name "incubation time";
String description "Time of Alkaline Phosphatase measurements";
String long_name "Time Of AP Measurment";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/AZDRZZ01/";
String units "hours (Hr)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Alkaline phosphatase (AP) activity was measured using the fluorogenic
substrate 4-methylumbelliferyl phosphate (MUF-P) (Sigma-Aldrich, St. Louis,
MO) and its reference standard, methylumbelliferone (MUF). Fluorescence was
measured using black, flat bottom, 96-well microplates in a Spark 10M
Multimode Microplate Reader (Tecan, M\\u00e4nnedorf, Switzerland). Fluorescence
of MUF is greatest at pH 10, therefore 25 \\u03bcL of 0.4 M NaOH was added to
the wells (final concentration 40 mM) to be read. 25 \\u03bcL of 1M EDTA was
added as well (100 mM final concentration) to prevent precipitation of c 439
arbonate from sampled veins.
Fluorescence was measured with an excitation wavelength of 380 nm and emission
of 454 nm for all substrates and standards. One cm3 powdered rock was mixed
with 5 cm3 of sterileartificial seawater (ASW) in a 8 mL serum vial with
90:5:5 N2:CO2:H2 headspace. 700 \\u03bcL of each slurry was withdrawn with a
sterile syringe to a 1.5 mL Eppendorf tube after setup but before sealing the
vial; this sample served as T0, with triplicate 200 \\u03bcL technical
replicates. These 700 \\u03bcL samples were briefly centrifuged (60 sec. at
2500 rpm) and the supernatant used for the T0 analyses.
Two additional samples were taken using the same methods as for T0 after at
least 2 weeks and then again after 4-6 weeks to generate a slope of activity.
Incubations were kept at 10\\u02daC, the inferred in situ temperature, for the
duration of each assay. Autoclaved, powderized rock from each of the samples
was tested to determine the amount of fluorophore adsorbance to rock powder.
Adsorbance was found to behave in a systematic manner, resulting in a straight
line when comparing fluorescence standards in artificial seawater (ASW) alone
with fluorescence standards plus rock powder in ASW, although this
relationship was found to be different when measured at 4 hours versus days
later. Therefore, a correction factor for adsorbance was applied to the enzyme
data for the initial measurement (t0, y=1.90x-676), taken <2 hours after
experiment initiation, versus the second and third measurements (t1 and t2, y
= 4.64x - 303), taken days to weeks later. Negative controls consisting of the
same ASW used for the sample incubations plus substrate, but no sample, were
consistently below detection. The limit of quantification for the AP assay,
defined as 3X the standard deviation of the blank, was 0.0242 pmol cm-3 rock
hour-1 based on analysis of eight blanks.";
String awards_0_award_nid "709555";
String awards_0_award_number "OCE-1658031";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1658031";
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 "David L. Garrison";
String awards_0_program_manager_nid "50534";
String cdm_data_type "Other";
String comment
"Supplementary Table 3B: Cell counts
PI: Virginia Edgcomb
Data Version 1: 2020-06-22";
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 "2020-05-14T15:59:17Z";
String date_modified "2020-07-08T20:35:34Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.811483.1";
Float64 Easternmost_Easting 57.278183;
Float64 geospatial_lat_max -32.70567;
Float64 geospatial_lat_min -32.70567;
String geospatial_lat_units "degrees_north";
Float64 geospatial_lon_max 57.278183;
Float64 geospatial_lon_min 57.278183;
String geospatial_lon_units "degrees_east";
Float64 geospatial_vertical_max 747.7;
Float64 geospatial_vertical_min 10.7;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-12-21T15:36:42Z (local files)
2024-12-21T15:36:42Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_811483.html";
String infoUrl "https://www.bco-dmo.org/dataset/811483";
String institution "BCO-DMO";
String instruments_0_dataset_instrument_description "Cell counts performed with a Zeiss Axio Imager M2 Epifluorescence microscope.";
String instruments_0_dataset_instrument_nid "813402";
String instruments_0_description "Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB06/";
String instruments_0_instrument_name "Microscope-Fluorescence";
String instruments_0_instrument_nid "695";
String instruments_0_supplied_name "Zeiss Axio Imager M2 Epifluorescence microscope";
String instruments_1_acronym "sonicator";
String instruments_1_dataset_instrument_description "Cell separation was performed through sonication with Diagenode Bioruptor sonication device.";
String instruments_1_dataset_instrument_nid "813403";
String instruments_1_description "Instrument that applies sound energy to agitate particles in a sample.";
String instruments_1_instrument_name "ultrasonic cell disrupter";
String instruments_1_instrument_nid "528691";
String instruments_1_supplied_name "Diagenode Bioruptor";
String instruments_2_dataset_instrument_description "Alkaline Phosphate activity was measured with a Spark 10M Multimode Microplate Reader (Tecan, Männedorf, Switzerland).";
String instruments_2_dataset_instrument_nid "813418";
String instruments_2_description "Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: https://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.";
String instruments_2_instrument_name "plate reader";
String instruments_2_instrument_nid "528693";
String instruments_2_supplied_name "Spark 10M Multimode Microplate Reader";
String keywords "activity, AP_activity, average, bco, bco-dmo, biological, chemical, data, dataset, depth, deviation, dmo, erddap, latitude, longitude, management, measurment, oceanography, office, preliminary, replicate, Replicate_1, Replicate_2, sample, standard, Standard_Deviation, time, Time_of_AP_measurment";
String license "https://www.bco-dmo.org/dataset/811483/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/811483";
Float64 Northernmost_Northing -32.70567;
String param_mapping "{'811483': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/811483/parameters";
String people_0_affiliation "Woods Hole Oceanographic Institution";
String people_0_affiliation_acronym "WHOI";
String people_0_person_name "Virginia P. Edgcomb";
String people_0_person_nid "51284";
String people_0_role "Principal Investigator";
String people_0_role_type "originator";
String people_1_affiliation "Woods Hole Oceanographic Institution";
String people_1_affiliation_acronym "WHOI";
String people_1_person_name "Virginia P. Edgcomb";
String people_1_person_nid "51284";
String people_1_role "Contact";
String people_1_role_type "related";
String people_2_affiliation "Woods Hole Oceanographic Institution";
String people_2_affiliation_acronym "WHOI BCO-DMO";
String people_2_person_name "Karen Soenen";
String people_2_person_nid "748773";
String people_2_role "BCO-DMO Data Manager";
String people_2_role_type "related";
String project "Subseafloor Lower Crust Microbiology";
String projects_0_acronym "Subseafloor Lower Crust Microbiology";
String projects_0_description
"NSF abstract:
The lower ocean crust has remained largely unexplored and represents one of the last frontiers for biological exploration on Earth. Preliminary data indicate an active subsurface biosphere in samples of the lower oceanic crust collected from Atlantis Bank in the SW Indian Ocean as deep as 790 m below the seafloor. Even if life exists in only a fraction of the habitable volume where temperatures permit and fluid flow can deliver carbon and energy sources, an active lower oceanic crust biosphere would have implications for deep carbon budgets and yield insights into microbiota that may have existed on early Earth. This is all of great interest to other research disciplines, educators, and students alike. A K-12 education program will capitalize on groundwork laid by outreach collaborator, A. Martinez, a 7th grade teacher in Eagle Pass, TX, who sailed as outreach expert on Drilling Expedition 360. Martinez works at a Title 1 school with ~98% Hispanic and ~2% Native American students and a high number of English Language Learners and migrants. Annual school visits occur during which the project investigators present hands on-activities introducing students to microbiology, and talks on marine microbiology, the project, and how to pursue science related careers. In addition, monthly Skype meetings with students and PIs update them on project progress. Students travel to the University of Texas Marine Science Institute annually, where they get a campus tour and a 3-hour cruise on the R/V Katy, during which they learn about and help with different oceanographic sampling approaches. The project partially supports two graduate students, a Woods Hole undergraduate summer student, the participation of multiple Texas A+M undergraduate students, and 3 principal investigators at two institutions, including one early career researcher who has not previously received NSF support of his own.
Given the dearth of knowledge of the lower oceanic crust, this project is poised to transform our understanding of life in this vast environment. The project assesses metabolic functions within all three domains of life in this crustal biosphere, with a focus on nutrient cycling and evaluation of connections to other deep marine microbial habitats. The lower ocean crust represents a potentially vast biosphere whose microbial constituents and the biogeochemical cycles they mediate are likely linked to deep ocean processes through faulting and subsurface fluid flow. Atlantis Bank represents a tectonic window that exposes lower oceanic crust directly at the seafloor. This enables seafloor drilling and research on an environment that can transform our understanding of connections between the deep subseafloor biosphere and the rest of the ocean. Preliminary analysis of recovered rocks from Expedition 360 suggests the interaction of seawater with the lower oceanic crust creates varied geochemical conditions capable of supporting diverse microbial life by providing nutrients and chemical energy. This project is the first interdisciplinary investigation of the microbiology of all 3 domains of life in basement samples that combines diversity and \"meta-omics\" analyses, analysis of nutrient addition experiments, high-throughput culturing and physiological analyses of isolates, including evaluation of their ability to utilize specific carbon sources, Raman spectroscopy, and lipid biomarker analyses. Comparative genomics are used to compare genes and pathways relevant to carbon cycling in these samples to data from published studies of other deep-sea environments. The collected samples present a rare and time-sensitive opportunity to gain detailed insights into microbial life, available carbon and energy sources for this life, and of dispersal of microbiota and connections in biogeochemical processes between the lower oceanic crust and the overlying aphotic water column.
About the study area:
The International Ocean Discovery Program (IODP) Expedition 360 explored the lower crust at Atlantis Bank, a 12 Ma oceanic core complex on the ultraslow-spreading SW Indian Ridge. This oceanic core complex represents a tectonic window that exposes lower oceanic crust and mantle directly at the seafloor, and the expedition provided an unprecedented opportunity to access this habitat in the Indian Ocean.";
String projects_0_end_date "2020-01";
String projects_0_geolocation "SW Indian Ridge, Indian Ocean";
String projects_0_name "Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches";
String projects_0_project_nid "709556";
String projects_0_start_date "2017-02";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
Float64 Southernmost_Northing -32.70567;
String standard_name_vocabulary "CF Standard Name Table v55";
String subsetVariables "latitude,longitude";
String summary "Supplementary Table 3B: Overview of archaeal and bacterial lipid biomarkers and cell counts. Replicate cell counts for the 11 samples and alkaline phosphatase activity measurements available for any of the 11 samples. Samples were taken on board of the JOIDES Resolution between November 30, 2015 and January 30, 2016 in the SW Indian Ridge.";
String title "[IODP360 - Replicate Cell Counts] - Supplementary Table 3B: Replicate cell counts for the 11 samples and alkaline phosphatase activity measurements available for any of the 11 samples (Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches)";
String version "1";
Float64 Westernmost_Easting 57.278183;
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.