Accessing BCO-DMO data
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BCO-DMO ERDDAP
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| Dataset Title: | [Geochemistry Summary] - Geochemistry summary data: single cell isotope incorporation of 1H, 2H, 12C14N, 12C15N, 12C12C, 12C13C ions from Chikyu- 337 (IODP 337) ( Determination of deep biosphere cell activity and identity utilizing the state of the art low-biomass, single cell techniques developed at JAMSTEC in their class 10,000 clean room) 
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| Institution: | BCO-DMO (Dataset ID: bcodmo_dataset_712761) |
| Information: | Summary
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Attributes {
s {
Order {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 1, 36;
String bcodmo_name "sample";
String description "Count of samples";
String long_name "Order";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Sample {
Int16 _FillValue 32767;
Int16 actual_range 6048, 6230;
String bcodmo_name "sample";
String description "Sample name/identifier";
String long_name "Sample";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P02/current/ACYC/";
String units "unitless";
}
Horizon {
String bcodmo_name "sample_descrip";
String description "IODP core name incubation originates from";
String long_name "Horizon";
String units "unitless";
}
Condition {
Byte _FillValue 127;
String _Unsigned "false";
Byte actual_range 35, 40;
String bcodmo_name "sample_descrip";
String description "Number code for Condition notes";
String long_name "Condition";
String units "unitless";
}
Autoclaved {
String bcodmo_name "sample_descrip";
String description "Autoclaved? Yes (Y) or No (N)";
String long_name "Autoclaved";
String units "unitless";
}
Amendment {
String bcodmo_name "sample_descrip";
String description "Amendments (what was added to the incubation )";
String long_name "Amendment";
String units "unitless";
}
cells_per_ml {
Float32 _FillValue NaN;
Float32 actual_range 2.68, 8066.36;
String bcodmo_name "abundance";
String description "Number of cells per milliliter of sample";
String long_name "Cells Per Ml";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "number/mL";
}
cells_per_cc_rock {
Int32 _FillValue 2147483647;
Int32 actual_range 25, 87953;
String bcodmo_name "abundance";
String description "Number of cells per cubic centimeter of sample";
String long_name "Cells Per Cc Rock";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "number/(cm^3)";
}
cells_per_g_rock {
Int32 _FillValue 2147483647;
Int32 actual_range 13, 70363;
String bcodmo_name "abundance";
String description "Number of cells per gram of rock";
String long_name "Cells Per G Rock";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P03/current/B070/";
String units "number/g";
}
Del_13C_DIC {
Float32 _FillValue NaN;
Float32 actual_range -16.19, 430.03;
String bcodmo_name "d13C_DIC";
String description "delta 13C DIC";
String long_name "Del 13 C DIC";
String nerc_identifier "https://vocab.nerc.ac.uk/collection/P01/current/D13CMIBX/";
String units "per mil";
}
mM_DIC {
Float32 _FillValue NaN;
Float32 actual_range 0.02, 2.31;
String bcodmo_name "DIC";
String description "Concentration of DIC in mM";
String long_name "M M DIC";
String units "milliMolar (mM)";
}
}
NC_GLOBAL {
String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
String acquisition_description
"SIP Incubation Preparation
IODP Expedition 337 operations commenced July 26 and continued through
September 30, 2012 on the D/V Chikyu. Utilizing riser drilling, a sedimentary
sequence was recovered down to 2466 m below seafloor (mbsf) at Hole C0020A (41
10' 36\\\" N, 142 12' 02\\\" E) in 1180 m water depth off the Shimokita Peninsula.
The drilled sequence transitioned from open marine (youngest; late Pliocene,
~5 Ma) to terrestrial (oldest; late Oligocene, ~30 Ma) with depth. Models for
maximum temperature reached by Expedition 337 coring report 63.7 degrees C.
Shipboard sedimentological, geochemical, and microbiological data and methods
are available through IODP publications. Additional coal petrography is
available in Gross et al.\\u00a0 A total of 52 incubation amendment conditions
were prepared onboard to interrogate a range of potential deep-biosphere
metabolic strategies, and then incubated back in the lab at temperatures
approximating that measured in situ. In this study, incubations from shale
(Core 8L4; 1606 mbsf; 37C incubation temperature), coal (Core 15R3; 1921 mbsf;
45C incubation temperature), and mixed (homogenized mixture from multiple
cores 19R1, 19R5, 19R7, 20R3, 23R6, 23R8, 24R3, 25R1, 25R2, and 25R3;
1950-1999 mbsf; 45C incubation temperature) with methanol and methylamine
substrate additions were analyzed. Age estimates of these samples are early to
middle Miocene. In situ temperatures ranged from 38C to 48C at these sample
depths with pressures ~30 MPa. Two coal beds were included in these
incubations: a shallower coal-only sample deposited under more marine-
influenced conditions (~1921 mbsf, core 15R3) and a deeper coal bed deposited
under more limnic conditions that was included in the mixed lithology sample
(~2000 mbsf, cores 24R3 and 25R1). Cores used for incubations were prepared by
removal of outer drill-fluid-contaminated layers by sterile ceramic knife as
soon as possible after core recovery and stored at 4C until incubation
preparation, while maintaining an anaerobic atmosphere during the entire
process.\\u00a0For preparation of the SIP incubations, the interior portion of
the core was manually crushed into cm-sized pieces under sterile, anaerobic
conditions and distributed evenly into sterile 50 ml glass vials with butyl
rubber stoppers and screw caps (Nichidenrika-Glass Co. Ltd.).\\u00a0 Vials were
flushed with argon and pressurized to 1 atm argon headspace. Sterile C-, N-,
and S-free media (1% PBS, 30 g/L NaCl, 12 g/L MgCl2, and 3 g/L KCl) was
prepared anaerobically with deuterated water (20 at. % 2H2O). 20 at. % 2H2O
was selected as the highest level of enrichment with little to no effect on
the activity of microorganisms in pure culture. Time point 1, time point 2,
and autoclaved treatments were prepared for each substrate condition. Time
point 1 incubations lasted for six months, while time point 2 and autoclaved
treatments were maintained at the in situ incubation temperature for 2.5
years. Due to low levels of activity ascertained from geochemical
measurements, all NanoSIMS analyses were conducted on time point 2 and
autoclaved samples. Amendments and incubation conditions for the methyl-
substrate subset analyzed in this study are provided in this
dataset.\\u00a0Equimolar amounts of substrate (30 umol C, 1.5 mM final; 3 umol
N, 0.15 mM final) were added across incubation conditions at 50 at. %
(Cambridge Isotopes). Hydrogen was added as 5 mL 100% H2 overpressure to
incubations (~15% H2 headspace). A full list of the additional incubation
conditions prepared onboard are listed in cruise Methods. Alkalinity (34.39
\\u2013 9.68 mM) ammonium (2.80 \\u2013 1.83 mM) concentrations from formation
fluid samples collected onboard exceed concentrations of C and N amendments.
Concentrations of methylamine (0.05 mM) and methanol (1 mM) measured from
lignite coal also suggest our substrate additions were environmentally
relevant. After 30 months of incubation (March 2014) all treatments were
sampled for geochemical analyses prior to preparation for NanoSIMS.\\u00a03 ml
of headspace gas was removed to a vial filled with 0.1 M NaOH for methane
analysis. About 1 ml of liquid was filtered through a 0.1 um 13 mm Whatman
Polycarbonate Nuclepore Track-Etched Membrane (110405) for DIC analysis. See
Supplemental Methods of Trembath-Reichert et al. for detailed description of
methane and DIC analyses.
Sample preparation for NanoSIMS analysis
To overcome technical challenges for NanoSIMS analysis of low biomass
samples, cell separation and fluorescence-activated cell sorting (FACS) were
used to directly concentrate cells in a small analysis area, ~1 to 0.5 sq.
mm.\\u00a0NanoSIMS samples were prepared from paraformaldehyde (PFA)-fixed cell
separates after 894 days of incubation. Cell preservation, separation,
enumeration, and FACS were all conducted in the clean booth and clean room
facilities at Kochi Institute for Core Sample Research, JAMSTEC. Half of the
solid and half of the liquid portion of each sample were fixed overnight in a
solution of 2% paraformaldehyde (PFA), 3 \\u00d7 phosphate buffered saline
(PBS).\\u00a0Samples were then subjected to two washes, incubating in 3 \\u00d7
PBS for 6 hrs and then 2 hrs, after each wash respectively. Samples were
centrifuged (3500 \\u00d7 g) and supernatant was decanted after each wash. PFA-
fixed samples were stored in 50 % ethanol : 3 \\u00d7 PBS. The other half of
the sample was preserved in glyTE (70% glycerol, 100mM Tris, 10mM EDTA;
Bigelow Single Cell Genomics Center preservation protocol) and frozen by cell
alive system (CAS) and stored at -80C. 1 ml liquid and ~1 g sediment chips
were subsampled by pipet and sterile cell culture loop, respectively, from the
PFA-fixed sample.\\u00a0Cell separation, microscopy, and sorting procedures
followed Morono et al., with the following modifications: 1) samples were
sonicated (Bioruptor UCD-250, COSMO BIO) in an ice bath for 20 cycles of 30
sec 200 W, 30 sec off, and 2) samples were incubated in hydrofluoric acid post
initial sonication, rather than after first density gradient
separation.\\u00a0Cell detection limit was determined by no-sample added
controls run in parallel with samples. Cells were stained with SYBR Green I
(1:40 dilution of SYBR Green in Tris (10 mM) \\u2013EDTA (1mM) (TE) and sorted
following the flow cytometry protocol of Morono et al. Sorted cells were
concentrated directly from the sorter onto NanoSIMS compatible 0.2 um
polycarbonate filters coated with indium tin oxide (ITO) as described in
Morono et al.\\u00a0and Inagaki et al. ITO coating on polycarbonate membranes
(Isopore GTBP02500 Millipore) was prepared by sputtering deposition technique
at Astellatech Co. Ltd. (Kanagawa, Japan).\\u00a0Scanning electron microscopy
(SEM) of the filters was done on a Zeiss 1550 VP Field Emission Scanning
Electron Microscope at the GPS Division Analytical Facility at Caltech and
SYBR stained cells were imaged with a BX51 epifluorescence microscope
(Olympus, Tokyo, Japan) using 20\\u00d7 (UPlanFL N) dry, 60\\u00d7 (PlanApo N),
and 100\\u00d7 (UPlanFL N) oil immersion objectives.";
String awards_0_award_nid "554980";
String awards_0_award_number "OCE-0939564";
String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564";
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
"NanoSIMS HCN - Geochemistry Summary
from IODP Expedition 337
PI: Elizabeth Trembath-Reichert
Version: 10 August 2017";
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 date_created "2017-08-11T19:32:16Z";
String date_modified "2019-08-02T15:46:44Z";
String defaultDataQuery "&time<now";
String doi "10.1575/1912/bco-dmo.712761.1";
String history
"2024-11-23T16:45:36Z (local files)
2024-11-23T16:45:36Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_712761.html";
String infoUrl "https://www.bco-dmo.org/dataset/712761";
String institution "BCO-DMO";
String instruments_0_dataset_instrument_description "SYBR stained cells were imaged with a BX51 epifluorescence microscope (Olympus, Tokyo, Japan).";
String instruments_0_dataset_instrument_nid "712769";
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 "BX51 epifluorescence microscope";
String instruments_1_dataset_instrument_description "Cell targets were identified (by SYBR stain) and marked on NanoSIMS membranes with a laser dissection microscope (LMD6000; Leica Microsystems) for ease of rediscovery on the NanoSIMS.";
String instruments_1_dataset_instrument_nid "712767";
String instruments_1_description "Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a \"light microscope\".";
String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB05/";
String instruments_1_instrument_name "Microscope-Optical";
String instruments_1_instrument_nid "708";
String instruments_1_supplied_name "LMD6000";
String instruments_2_acronym "SEM";
String instruments_2_dataset_instrument_description "Scanning electron microscopy (SEM) of the filters was done on a Zeiss 1550 VP Field Emission Scanning Electron Microscope at the GPS Division Analytical Facility at Caltech.";
String instruments_2_dataset_instrument_nid "712768";
String instruments_2_description "Scanning electron microscope";
String instruments_2_instrument_name "Scanning Electron Microscope";
String instruments_2_instrument_nid "637895";
String instruments_2_supplied_name "Zeiss 1550 VP Field Emission Scanning Electron Microscope";
String keywords "amendment, autoclaved, bco, bco-dmo, biological, cells, cells_per_cc_rock, cells_per_g_rock, cells_per_ml, chemical, condition, data, dataset, del, Del_13C_DIC, dic, dmo, erddap, horizon, management, mM_DIC, oceanography, office, order, per, preliminary, rock, sample";
String license "https://www.bco-dmo.org/dataset/712761/license";
String metadata_source "https://www.bco-dmo.org/api/dataset/712761";
String param_mapping "{'712761': {}}";
String parameter_source "https://www.bco-dmo.org/mapserver/dataset/712761/parameters";
String people_0_affiliation "California Institute of Technology";
String people_0_affiliation_acronym "Caltech";
String people_0_person_name "Elizabeth Trembath-Reichert";
String people_0_person_nid "672596";
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 BCO-DMO";
String people_1_person_name "Shannon Rauch";
String people_1_person_nid "51498";
String people_1_role "BCO-DMO Data Manager";
String people_1_role_type "related";
String project "Deep biosphere cell activity";
String projects_0_acronym "Deep biosphere cell activity";
String projects_0_description "IODP Expedition 337 set the record for deepest marine scientific drilling down to 2.4 kmbsf. This cruise also had the unique opportunity to retrieve deep cores from the Shimokita coal bed system in Japan with the aseptic and anaerobic conditions necessary to look for deep life. Onboard scientists prepared nearly 1,700 microbiology samples shared among five different countries to study life in the deep biosphere. Samples spanned over 1km in sampling depths and include representatives of shale, sandstone, and coal lithologies. Findings from previous IODP and deep mine expeditions suggest the genetic potential for methylotrophy in the deep subsurface, but it has yet to be observed in incubations. A subset of Expedition 337 anoxic incubations were prepared with a range of 13C-methyl substrates (methane, methylamine, and methanol) and maintained near in situ temperatures. To observe 13C methyl compound metabolism over time, we monitored the δ13C of the dissolved inorganic carbon and methane (by-products of methyl compound metabolism) over a period of 1.5 years. Our geochemical evidence suggests that the coal horizon incubated with 13C-methylamine showed the highest activity of all methyl incubations. Therefore, there are not only cells in the deeply buried terrigenous coal bed at Shimokita, but a microbial community that can be activated by methylotrophic compounds. Incubations showing the highest geochemical activity were prepared at the JAMSTEC Kochi Core Center for nanoSIMS analysis in March of 2015, and will be analyzed at Caltech in the coming months. This will allow us to observe if cells also incorporated the labeled methyl compounds into their body mass and provide another line of evidence that these substrates were used by the deep coalbed microbial community.";
String projects_0_end_date "2015-04";
String projects_0_geolocation "Hole C0020A (41°10′36″N, 142°12′02″E) Shimokita Peninsula.";
String projects_0_name "Determination of deep biosphere cell activity and identity utilizing the state of the art low-biomass, single cell techniques developed at JAMSTEC in their class 10,000 clean room";
String projects_0_project_nid "672592";
String projects_0_project_website "http://www.darkenergybiosphere.org/award/determination-of-deep-biosphere-cell-activity-and-identity-utilizing-the-state-of-the-art-low-biomass-single-cell-techniques-developed-at-jamstec-in-their-class-10000-clean-room/";
String projects_0_start_date "2015-03";
String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
String publisher_type "institution";
String sourceUrl "(local files)";
String standard_name_vocabulary "CF Standard Name Table v55";
String summary "Single cell isotope incorporation of 1H, 2H, 12C14N, 12C15N. 12C12C, 12C13C ions from samples collected on IODP Expedition 337.";
String title "[Geochemistry Summary] - Geochemistry summary data: single cell isotope incorporation of 1H, 2H, 12C14N, 12C15N, 12C12C, 12C13C ions from Chikyu-337 (IODP 337) ( Determination of deep biosphere cell activity and identity utilizing the state of the art low-biomass, single cell techniques developed at JAMSTEC in their class 10,000 clean room)";
String version "1";
String xml_source "osprey2erddap.update_xml() v1.3";
}
}
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.