ERDDAP > info > bcodmo_dataset_712761

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[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)		I   M	background			BCO-DMO	bcodmo_dataset_712761

The Dataset's Variables and Attributes

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 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.
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
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 from IODP Expedition 337 PI: Elizabeth Trembath-Reichert 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/
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
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/
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/
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/712761
attribute	NC_GLOBAL	param_mapping	String	{'712761': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/712761/parameters
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/
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/
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/
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/
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/
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/
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/
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)

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.