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
attribute NC_GLOBAL acquisition_description String SIP Incubation Preparation  \n IODP Expedition 337 operations commenced July 26 and continued through\nSeptember 30, 2012 on the D/V Chikyu. Utilizing riser drilling, a sedimentary\nsequence was recovered down to 2466 m below seafloor (mbsf) at Hole C0020A (41\n10' 36\\\" N, 142 12' 02\\\" E) in 1180 m water depth off the Shimokita Peninsula.\nThe drilled sequence transitioned from open marine (youngest; late Pliocene,\n~5 Ma) to terrestrial (oldest; late Oligocene, ~30 Ma) with depth. Models for\nmaximum temperature reached by Expedition 337 coring report 63.7 degrees C.\nShipboard sedimentological, geochemical, and microbiological data and methods\nare available through IODP publications. Additional coal petrography is\navailable in Gross et al.\\u00a0 A total of 52 incubation amendment conditions\nwere prepared onboard to interrogate a range of potential deep-biosphere\nmetabolic strategies, and then incubated back in the lab at temperatures\napproximating that measured in situ. In this study, incubations from shale\n(Core 8L4; 1606 mbsf; 37C incubation temperature), coal (Core 15R3; 1921 mbsf;\n45C incubation temperature), and mixed (homogenized mixture from multiple\ncores 19R1, 19R5, 19R7, 20R3, 23R6, 23R8, 24R3, 25R1, 25R2, and 25R3;\n1950-1999 mbsf; 45C incubation temperature) with methanol and methylamine\nsubstrate additions were analyzed. Age estimates of these samples are early to\nmiddle Miocene. In situ temperatures ranged from 38C to 48C at these sample\ndepths with pressures ~30 MPa. Two coal beds were included in these\nincubations: a shallower coal-only sample deposited under more marine-\ninfluenced conditions (~1921 mbsf, core 15R3) and a deeper coal bed deposited\nunder more limnic conditions that was included in the mixed lithology sample\n(~2000 mbsf, cores 24R3 and 25R1). Cores used for incubations were prepared by\nremoval of outer drill-fluid-contaminated layers by sterile ceramic knife as\nsoon as possible after core recovery and stored at 4C until incubation\npreparation, while maintaining an anaerobic atmosphere during the entire\nprocess.\\u00a0For preparation of the SIP incubations, the interior portion of\nthe core was manually crushed into cm-sized pieces under sterile, anaerobic\nconditions and distributed evenly into sterile 50 ml glass vials with butyl\nrubber stoppers and screw caps (Nichidenrika-Glass Co. Ltd.).\\u00a0 Vials were\nflushed with argon and pressurized to 1 atm argon headspace. Sterile C-, N-,\nand S-free media (1% PBS, 30 g/L NaCl, 12 g/L MgCl2, and 3 g/L KCl) was\nprepared anaerobically with deuterated water (20 at. % 2H2O). 20 at. % 2H2O\nwas selected as the highest level of enrichment with little to no effect on\nthe activity of microorganisms in pure culture. Time point 1, time point 2,\nand autoclaved treatments were prepared for each substrate condition. Time\npoint 1 incubations lasted for six months, while time point 2 and autoclaved\ntreatments were maintained at the in situ incubation temperature for 2.5\nyears. Due to low levels of activity ascertained from geochemical\nmeasurements, all NanoSIMS analyses were conducted on time point 2 and\nautoclaved samples. Amendments and incubation conditions for the methyl-\nsubstrate subset analyzed in this study are provided in this\ndataset.\\u00a0Equimolar amounts of substrate (30 umol C, 1.5 mM final; 3 umol\nN, 0.15 mM final) were added across incubation conditions at 50 at. %\n(Cambridge Isotopes). Hydrogen was added as 5 mL 100% H2 overpressure to\nincubations (~15% H2 headspace). A full list of the additional incubation\nconditions prepared onboard are listed in cruise Methods. Alkalinity (34.39\n\\u2013 9.68 mM) ammonium (2.80 \\u2013 1.83 mM) concentrations from formation\nfluid samples collected onboard exceed concentrations of C and N amendments.\nConcentrations of methylamine (0.05 mM) and methanol (1 mM) measured from\nlignite coal also suggest our substrate additions were environmentally\nrelevant. After 30 months of incubation (March 2014) all treatments were\nsampled for geochemical analyses prior to preparation for NanoSIMS.\\u00a03 ml\nof headspace gas was removed to a vial filled with 0.1 M NaOH for methane\nanalysis. About 1 ml of liquid was filtered through a 0.1 um 13 mm Whatman\nPolycarbonate Nuclepore Track-Etched Membrane (110405) for DIC analysis. See\nSupplemental Methods of Trembath-Reichert et al. for detailed description of\nmethane and DIC analyses.\n \nSample preparation for NanoSIMS analysis  \n To overcome technical challenges for NanoSIMS analysis of low biomass\nsamples, cell separation and fluorescence-activated cell sorting (FACS) were\nused to directly concentrate cells in a small analysis area, ~1 to 0.5 sq.\nmm.\\u00a0NanoSIMS samples were prepared from paraformaldehyde (PFA)-fixed cell\nseparates after 894 days of incubation. Cell preservation, separation,\nenumeration, and FACS were all conducted in the clean booth and clean room\nfacilities at Kochi Institute for Core Sample Research, JAMSTEC. Half of the\nsolid and half of the liquid portion of each sample were fixed overnight in a\nsolution of 2% paraformaldehyde (PFA), 3 \\u00d7 phosphate buffered saline\n(PBS).\\u00a0Samples were then subjected to two washes, incubating in 3 \\u00d7\nPBS for 6 hrs and then 2 hrs, after each wash respectively. Samples were\ncentrifuged (3500 \\u00d7 g) and supernatant was decanted after each wash. PFA-\nfixed samples were stored in 50 % ethanol : 3 \\u00d7 PBS. The other half of\nthe sample was preserved in glyTE (70% glycerol, 100mM Tris, 10mM EDTA;\nBigelow Single Cell Genomics Center preservation protocol) and frozen by cell\nalive system (CAS) and stored at -80C. 1 ml liquid and ~1 g sediment chips\nwere subsampled by pipet and sterile cell culture loop, respectively, from the\nPFA-fixed sample.\\u00a0Cell separation, microscopy, and sorting procedures\nfollowed Morono et al., with the following modifications: 1) samples were\nsonicated (Bioruptor UCD-250, COSMO BIO) in an ice bath for 20 cycles of 30\nsec 200 W, 30 sec off, and 2) samples were incubated in hydrofluoric acid post\ninitial sonication, rather than after first density gradient\nseparation.\\u00a0Cell detection limit was determined by no-sample added\ncontrols run in parallel with samples. Cells were stained with SYBR Green I\n(1:40 dilution of SYBR Green in Tris (10 mM) \\u2013EDTA (1mM) (TE) and sorted\nfollowing the flow cytometry protocol of Morono et al. Sorted cells were\nconcentrated directly from the sorter onto NanoSIMS compatible 0.2 um\npolycarbonate filters coated with indium tin oxide (ITO) as described in\nMorono et al.\\u00a0and Inagaki et al. ITO coating on polycarbonate membranes\n(Isopore GTBP02500 Millipore) was prepared by sputtering deposition technique\nat Astellatech Co. Ltd. (Kanagawa, Japan).\\u00a0Scanning electron microscopy\n(SEM) of the filters was done on a Zeiss 1550 VP Field Emission Scanning\nElectron Microscope at the GPS Division Analytical Facility at Caltech and\nSYBR stained cells were imaged with a BX51 epifluorescence microscope\n(Olympus, Tokyo, Japan) using 20\\u00d7 (UPlanFL N) dry, 60\\u00d7 (PlanApo N),\nand 100\\u00d7 (UPlanFL N) oil immersion objectives.
attribute NC_GLOBAL awards_0_award_nid String 554980
attribute NC_GLOBAL awards_0_award_number String OCE-0939564
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward?AWD_ID=0939564 (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 David L. Garrison
attribute NC_GLOBAL awards_0_program_manager_nid String 50534
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String NanoSIMS HCN - Geochemistry Summary \n  from IODP Expedition 337 \n PI: Elizabeth Trembath-Reichert \n Version: 10 August 2017
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 2017-08-11T19:32:16Z
attribute NC_GLOBAL date_modified String 2019-08-02T15:46:44Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.712761.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/712761 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_dataset_instrument_description String SYBR stained cells were imaged with a BX51 epifluorescence microscope (Olympus, Tokyo, Japan).
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 712769
attribute NC_GLOBAL instruments_0_description String 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.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB06/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Microscope-Fluorescence
attribute NC_GLOBAL instruments_0_instrument_nid String 695
attribute NC_GLOBAL instruments_0_supplied_name String BX51 epifluorescence microscope
attribute NC_GLOBAL instruments_1_dataset_instrument_description String 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.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 712767
attribute NC_GLOBAL instruments_1_description String 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\".
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB05/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Microscope-Optical
attribute NC_GLOBAL instruments_1_instrument_nid String 708
attribute NC_GLOBAL instruments_1_supplied_name String LMD6000
attribute NC_GLOBAL instruments_2_acronym String SEM
attribute NC_GLOBAL instruments_2_dataset_instrument_description String 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.
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 712768
attribute NC_GLOBAL instruments_2_description String Scanning electron microscope
attribute NC_GLOBAL instruments_2_instrument_name String Scanning Electron Microscope
attribute NC_GLOBAL instruments_2_instrument_nid String 637895
attribute NC_GLOBAL instruments_2_supplied_name String Zeiss 1550 VP Field Emission Scanning Electron Microscope
attribute NC_GLOBAL keywords String 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
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/712761/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/712761 (external link)
attribute NC_GLOBAL param_mapping String {'712761': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/712761/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String California Institute of Technology
attribute NC_GLOBAL people_0_affiliation_acronym String Caltech
attribute NC_GLOBAL people_0_person_name String Elizabeth Trembath-Reichert
attribute NC_GLOBAL people_0_person_nid String 672596
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 BCO-DMO
attribute NC_GLOBAL people_1_person_name String Shannon Rauch
attribute NC_GLOBAL people_1_person_nid String 51498
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String Deep biosphere cell activity
attribute NC_GLOBAL projects_0_acronym String Deep biosphere cell activity
attribute NC_GLOBAL projects_0_description String 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.
attribute NC_GLOBAL projects_0_end_date String 2015-04
attribute NC_GLOBAL projects_0_geolocation String Hole C0020A (41°10′36″N, 142°12′02″E) Shimokita Peninsula.
attribute NC_GLOBAL projects_0_name String 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
attribute NC_GLOBAL projects_0_project_nid String 672592
attribute NC_GLOBAL projects_0_project_website String 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/ (external link)
attribute NC_GLOBAL projects_0_start_date String 2015-03
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 standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Single cell isotope incorporation of 1H, 2H, 12C14N, 12C15N. 12C12C, 12C13C ions from samples collected on IODP Expedition 337.
attribute NC_GLOBAL title String [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)
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Order byte
attribute Order _FillValue byte 127
attribute Order actual_range byte 1, 36
attribute Order bcodmo_name String sample
attribute Order description String Count of samples
attribute Order long_name String Order
attribute Order nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Order units String unitless
variable Sample short
attribute Sample _FillValue short 32767
attribute Sample actual_range short 6048, 6230
attribute Sample bcodmo_name String sample
attribute Sample description String Sample name/identifier
attribute Sample long_name String Sample
attribute Sample nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Sample units String unitless
variable Horizon String
attribute Horizon bcodmo_name String sample_descrip
attribute Horizon description String IODP core name incubation originates from
attribute Horizon long_name String Horizon
attribute Horizon units String unitless
variable Condition byte
attribute Condition _FillValue byte 127
attribute Condition actual_range byte 35, 40
attribute Condition bcodmo_name String sample_descrip
attribute Condition description String Number code for Condition notes
attribute Condition long_name String Condition
attribute Condition units String unitless
variable Autoclaved String
attribute Autoclaved bcodmo_name String sample_descrip
attribute Autoclaved description String Autoclaved? Yes (Y) or No (N)
attribute Autoclaved long_name String Autoclaved
attribute Autoclaved units String unitless
variable Amendment String
attribute Amendment bcodmo_name String sample_descrip
attribute Amendment description String Amendments (what was added to the incubation )
attribute Amendment long_name String Amendment
attribute Amendment units String unitless
variable cells_per_ml float
attribute cells_per_ml _FillValue float NaN
attribute cells_per_ml actual_range float 2.68, 8066.36
attribute cells_per_ml bcodmo_name String abundance
attribute cells_per_ml description String Number of cells per milliliter of sample
attribute cells_per_ml long_name String Cells Per Ml
attribute cells_per_ml nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute cells_per_ml units String number/mL
variable cells_per_cc_rock int
attribute cells_per_cc_rock _FillValue int 2147483647
attribute cells_per_cc_rock actual_range int 25, 87953
attribute cells_per_cc_rock bcodmo_name String abundance
attribute cells_per_cc_rock description String Number of cells per cubic centimeter of sample
attribute cells_per_cc_rock long_name String Cells Per Cc Rock
attribute cells_per_cc_rock nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute cells_per_cc_rock units String number/(cm^3)
variable cells_per_g_rock int
attribute cells_per_g_rock _FillValue int 2147483647
attribute cells_per_g_rock actual_range int 13, 70363
attribute cells_per_g_rock bcodmo_name String abundance
attribute cells_per_g_rock description String Number of cells per gram of rock
attribute cells_per_g_rock long_name String Cells Per G Rock
attribute cells_per_g_rock nerc_identifier String https://vocab.nerc.ac.uk/collection/P03/current/B070/ (external link)
attribute cells_per_g_rock units String number/g
variable Del_13C_DIC float
attribute Del_13C_DIC _FillValue float NaN
attribute Del_13C_DIC actual_range float -16.19, 430.03
attribute Del_13C_DIC bcodmo_name String d13C_DIC
attribute Del_13C_DIC description String delta 13C DIC
attribute Del_13C_DIC long_name String Del 13 C DIC
attribute Del_13C_DIC nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/D13CMIBX/ (external link)
attribute Del_13C_DIC units String per mil
variable mM_DIC float
attribute mM_DIC _FillValue float NaN
attribute mM_DIC actual_range float 0.02, 2.31
attribute mM_DIC bcodmo_name String DIC
attribute mM_DIC description String Concentration of DIC in mM
attribute mM_DIC long_name String M M DIC
attribute mM_DIC units String milliMolar (mM)

 
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