Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | Supplementary Table 3A: Concentration of archaeal and bacterial lipid biomarkers, ratio of core vs intact polar lipids and average chain length of bacterial dietherglycerol lipids. 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_811268) |
| Range: | longitude = 57.278183 to 57.278183°E, latitude = -32.70567 to -32.70567°N, depth = 10.7 to 747.8m |
| Information: | Summary
| License
| ISO 19115
| Metadata
| Background
| Subset
| Data Access Form
| Files
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Zoom: ![[The graph you specified. Please be patient.]](https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_811268.png?longitude,latitude,Intact_polar_lipids_1G_2GGDGT&.draw=markers&.marker=5%7C5&.color=0x000000&.colorBar=%7C%7C%7C%7C%7C&.bgColor=0xffccccff)
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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, 747.8;
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";
}
Intact_polar_lipids_1G_2GGDGT {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 104.0;
String bcodmo_name "unknown";
String description "Intact polar lipids 1G-,2G-GDGT - mono, diglycosidic glycerol dialkyl glycerol tetraether";
String long_name "Intact Polar Lipids 1 G 2 GGDGT";
String units "picograms per gram (pg/g)";
}
Intact_polar_lipids_1G_2GAR {
Float32 _FillValue NaN;
Float32 actual_range 3.8, 1423.0;
String bcodmo_name "unknown";
String description "Intact polar lipids 1G-,2G-AR - mono,diglycosidic archaeol";
String long_name "Intact Polar Lipids 1 G 2 GAR";
String units "picograms per gram (pg/g)";
}
Core_lipids_core_GDGT {
Float32 _FillValue NaN;
Float32 actual_range 5.9, 780.0;
String bcodmo_name "unknown";
String description "Core lipids cire GDGT - glycerol dialkyl glycerol tetraethe";
String long_name "Core Lipids Core GDGT";
String units "picograms per gram (pg/g)";
}
Core_lipids_core_archaeol {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 3679.0;
String bcodmo_name "unknown";
String description "Core lipids core archaeik";
String long_name "Core Lipids Core Archaeol";
String units "picograms per gram (pg/g)";
}
Core_lipids_bacterial_diether_glyerol_lipids {
Float32 _FillValue NaN;
Float32 actual_range 1.0, 480.0;
String bcodmo_name "unknown";
String description "Core lipids bacterial diether glyerol lipids";
String long_name "Core Lipids Bacterial Diether Glyerol Lipids";
String units "picograms per gram (pg/g)";
}
G_GDGTs_core_GDGT {
Float32 _FillValue NaN;
Float32 actual_range 1.4, 99.0;
String bcodmo_name "unknown";
String description "G- glycerol dialkyl glycerol tetraethers/core glycerol dialkyl glycerol tetraethers";
String long_name "G GDGTs Core GDGT";
String units "picograms per gram (pg/g)";
}
GARs_core_ARs {
Float32 _FillValue NaN;
Float32 actual_range 0.0, 100.0;
String bcodmo_name "unknown";
String description "G- archaeols core archaeols";
String long_name "GARs Core ARs";
String units "picograms per gram (pg/g)";
}
Archaea_IPLcore {
Byte _FillValue 127;
Byte actual_range 4, 60;
String bcodmo_name "unknown";
String description "Archaea: Intact polar lipids/core";
String long_name "Archaea IPLcore";
String units "picograms per gram (pg/g)";
}
Bacteria_average_chain_length {
Float32 _FillValue NaN;
Float32 actual_range 30.3, 34.5;
String bcodmo_name "length";
String description "Average chain length Bacteria";
String long_name "Bacteria Average Chain Length";
String units "picograms per gram (pg/g)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson";
String acquisition_description
"Crushed core samples stored in falcon tubes at -80 \\u00b0C were first milled
for 10 min to a fine powder and subsequently extracted with a modified Bligh
and Dyer method after Sturt et al. (2004). Prior to milling and extraction of
each sample a procedure blank was performed. First a milling blank was
performed using combusted sea sand (fired at 450 \\u00b0C for 5 hrs) to clean
the mill and to limit cross-contamination of samples. Subsequently, this sea
sand was then transferred to geo-cleaned (rinsed three times with a mixture of
methanol, MeOH and dichloromethane, DCM) Teflon\\u00ae containers used for
extraction of the samples and solvent-extracted in the same manner as the
samples. For this, 100 ng of an internal standard (C46 GTGT) and ca. 50 mL of
a solvent mixture of DCM:MeOH:buffer (2:1:0.8, v/v) was added to the sample in
the Teflon\\u00ae container and ultrasonicated for 10 mins using a geo-cleaned
ultrasonic stick.
After ultrasonication, the samples were centrifuged (1750 rpm at 10 min) and
the supernatant was transferred to a fired separatory funnel. The samples were
extracted in four steps, for the first two steps a phosphate buffer (K2HPO4,
50 mM at pH 7.4) was used, in the second step the phosphate buffer was
replaced by 5 was used, in the second step the phosphate buffer was replaced
by 5 % trichloroacetic acid (50 g L-1 at pH 2), and in the last step only
DCM:MeOH (9:1, v/v) was used. Equal amounts of DCM and deionized MilliQ water
were added to the extract collected in the separatory funnel, the mixture was
shaken, and the organic phase was collected as the total lipid extract (TLE)
and blown to dryness under a gentle stream of nitrogen.
An aliquot of the TLE was analyzed via ultra-high-pressure liquid
chromatography (UHPLC) coupled to mass spectrometry (MS) on a Dionex Ultimate
3000RS UHPLC connected to an ABSciEX QTRAP4500 Triple Quadrupole/Ion Trap MS
(UHPLC-Triple Quad-MS) via a Turbolon electrospray ion source (ESI).
Separation of compounds was achieved on a Waters Acquity BEH C18 column (1.7
\\u03bcm, 2.1x150 mm) equipped with a guard column of the same material
following the protocol described in Klein et al. (2015). Compounds of interest
were screened for by using multiple reaction monitoring (MRM) and selected ion
monitoring (SIM) techniques after Klein et al. (2015). Concentrations of
lipids were determined relative to the internal C46 GTGT standard and were
corrected for individual response factors using commercially available
standards (diC16-DEG, archaeol) and isolated standards from cultures (GDGT-0,
1G-AR, 2G522AR, 1G-GDGT-0, 2G-GDGT-0). The presence of crenarchaeol was
confirmed by core GDGT analysis after Becker et al. (2013).
Briefly an aliquot of the TLE was analysed on Dionex Ultimate 3000RS UHPLC
connected to a Bruker maXis ultra-high resolution quadrupole time-of-flight
mass spectrometer, equipped with an APCI II source. Compounds were separated
using two aquity BEH HILIC amide columns (1.7 \\u03bcm, 2.1x300 mm) in tandem
maintained at 50 \\u00b0C, and n-hexane as eluent A and n528
hexane:isopropanol, 90:10, v:v as eluent B (REF). Drilling mud and extraction
blank contamination controls were also run for lipid biomarker analyses.";
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 3A: Lipid biomarkers ratio
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 "2020-05-13T15:50:57Z";
String date_modified "2020-07-08T20:32:38Z";
String defaultDataQuery "&time<now";
String doi "10.26008/1912/bco-dmo.811268.1";
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 747.8;
Float64 geospatial_vertical_min 10.7;
String geospatial_vertical_positive "down";
String geospatial_vertical_units "m";
String history
"2024-04-16T19:54:27Z (local files)
2024-04-16T19:54:27Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_811268.das";
String infoUrl "https://www.bco-dmo.org/dataset/811268";
String institution "BCO-DMO";
String instruments_0_acronym "HPLC";
String instruments_0_dataset_instrument_description "All membrane lipid analyses were performed at MARUM (Bremen, Germany) with an ultra-high-pressure liquid chromatography (UHPLC) coupled to mass spectrometry (MS) on a Dionex Ultimate 3000RS UHPLC connected to an ABSciEX QTRAP4500 Triple Quadrupole/Ion Trap MS (UHPLC-Triple Quad-MS) via a Turbolon electrospray ion source (ESI)";
String instruments_0_dataset_instrument_nid "811272";
String instruments_0_description "A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.";
String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB11/";
String instruments_0_instrument_name "High Performance Liquid Chromatograph";
String instruments_0_instrument_nid "506";
String instruments_1_acronym "Mass Spec";
String instruments_1_dataset_instrument_description "All membrane lipid analyses were performed at MARUM (Bremen, Germany) with an ultra-high-pressure liquid chromatography (UHPLC) coupled to mass spectrometry (MS) on a Dionex Ultimate 3000RS UHPLC connected to an ABSciEX QTRAP4500 Triple Quadrupole/Ion Trap MS (UHPLC-Triple Quad-MS) via a Turbolon electrospray ion source (ESI).";
String instruments_1_dataset_instrument_nid "811273";
String instruments_1_description "General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
String instruments_1_instrument_name "Mass Spectrometer";
String instruments_1_instrument_nid "685";
String keywords "archaea, Archaea_IPLcore, archaeol, ars, average, bacteria, Bacteria_average_chain_length, bacterial, bco, bco-dmo, biological, chain, chemical, core, Core_lipids_bacterial_diether_glyerol_lipids, Core_lipids_core_archaeol, Core_lipids_core_GDGT, data, dataset, depth, diether, dmo, erddap, G_GDGTs_core_GDGT, gar, gars, GARs_core_ARs, gdgt, gdgts, ggdgt, glyerol, intact, Intact_polar_lipids_1G_2GAR, Intact_polar_lipids_1G_2GGDGT, iplcore, latitude, length, lipids, longitude, management, oceanography, office, polar, preliminary, sample";
String license "https://www.bco-dmo.org/dataset/811268/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/811268";
Float64 Northernmost_Northing -32.70567;
String param_mapping "{'811268': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/811268/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 "Overview of archaeal and bacterial lipid biomarkers and cell counts. Concentration of archaeal and bacterial lipid biomarkers, ratio of core vs intact polar lipids and average chain length of bacterial dietherglycerol lipids. Samples taken on board of the R/V JOIDES Resolution between November 30, 2015 and January 30, 2016";
String title "Supplementary Table 3A: Concentration of archaeal and bacterial lipid biomarkers, ratio of core vs intact polar lipids and average chain length of bacterial dietherglycerol lipids.";
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.