ERDDAP > info > bcodmo_dataset_811483

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
	set	data	graph		files	public	[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)		F   I   M	background			BCO-DMO	bcodmo_dataset_811483

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,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	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sterileartificial seawater (ASW) in a 8 mL serum vial with 90:5:5 N2:CO2:H2 headspace. 700 \u03bcL of each slurry was withdrawn with a sterile syringe to a 1.5 mL Eppendorf tube after setup but before sealing the vial; this sample served as T0, with triplicate 200 \u03bcL technical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.
attribute	NC_GLOBAL	awards_0_award_nid	String	709555
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1658031
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1658031
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	Supplementary Table 3B: Cell counts PI: Virginia Edgcomb Data Version 1: 2020-06-22
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	dataset_current_state	String	Final and no updates
attribute	NC_GLOBAL	date_created	String	2020-05-14T15:59:17Z
attribute	NC_GLOBAL	date_modified	String	2020-07-08T20:35:34Z
attribute	NC_GLOBAL	defaultDataQuery	String	&amp;time&lt;now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.811483.1
attribute	NC_GLOBAL	Easternmost_Easting	double	57.278183
attribute	NC_GLOBAL	geospatial_lat_max	double	-32.70567
attribute	NC_GLOBAL	geospatial_lat_min	double	-32.70567
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	57.278183
attribute	NC_GLOBAL	geospatial_lon_min	double	57.278183
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	747.7
attribute	NC_GLOBAL	geospatial_vertical_min	double	10.7
attribute	NC_GLOBAL	geospatial_vertical_positive	String	down
attribute	NC_GLOBAL	geospatial_vertical_units	String	m
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/811483
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Cell counts performed with a Zeiss Axio Imager M2 Epifluorescence microscope.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	813402
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	Zeiss Axio Imager M2 Epifluorescence microscope
attribute	NC_GLOBAL	instruments_1_acronym	String	sonicator
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Cell separation was performed through sonication with Diagenode Bioruptor sonication device.
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	813403
attribute	NC_GLOBAL	instruments_1_description	String	Instrument that applies sound energy to agitate particles in a sample.
attribute	NC_GLOBAL	instruments_1_instrument_name	String	ultrasonic cell disrupter
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	528691
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Diagenode Bioruptor
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Alkaline Phosphate activity was measured with a Spark 10M Multimode Microplate Reader (Tecan, Männedorf, Switzerland).
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	813418
attribute	NC_GLOBAL	instruments_2_description	String	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.
attribute	NC_GLOBAL	instruments_2_instrument_name	String	plate reader
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	528693
attribute	NC_GLOBAL	instruments_2_supplied_name	String	Spark 10M Multimode Microplate Reader
attribute	NC_GLOBAL	keywords	String	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
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/811483/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/811483
attribute	NC_GLOBAL	Northernmost_Northing	double	-32.70567
attribute	NC_GLOBAL	param_mapping	String	{'811483': {'Latitude': 'flag - latitude', 'Depth': 'flag - depth', 'Longitude': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/811483/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	WHOI
attribute	NC_GLOBAL	people_0_person_name	String	Virginia P. Edgcomb
attribute	NC_GLOBAL	people_0_person_nid	String	51284
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
attribute	NC_GLOBAL	people_1_person_name	String	Virginia P. Edgcomb
attribute	NC_GLOBAL	people_1_person_nid	String	51284
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Karen Soenen
attribute	NC_GLOBAL	people_2_person_nid	String	748773
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	Subseafloor Lower Crust Microbiology
attribute	NC_GLOBAL	projects_0_acronym	String	Subseafloor Lower Crust Microbiology
attribute	NC_GLOBAL	projects_0_description	String	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.
attribute	NC_GLOBAL	projects_0_end_date	String	2020-01
attribute	NC_GLOBAL	projects_0_geolocation	String	SW Indian Ridge, Indian Ocean
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: Delineating The Microbial Diversity and Cross-domain Interactions in The Uncharted Subseafloor Lower Crust Using Meta-omics and Culturing Approaches
attribute	NC_GLOBAL	projects_0_project_nid	String	709556
attribute	NC_GLOBAL	projects_0_start_date	String	2017-02
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	Southernmost_Northing	double	-32.70567
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	latitude,longitude
attribute	NC_GLOBAL	summary	String	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.
attribute	NC_GLOBAL	title	String	[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)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	57.278183
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Sample		String
attribute	Sample	bcodmo_name	String	sample
attribute	Sample	description	String	Sample ID
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	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	-32.70567, -32.70567
attribute	latitude	axis	String	Y
attribute	latitude	bcodmo_name	String	latitude
attribute	latitude	colorBarMaximum	double	90.0
attribute	latitude	colorBarMinimum	double	-90.0
attribute	latitude	description	String	Latitude, south is negative
attribute	latitude	ioos_category	String	Location
attribute	latitude	long_name	String	Latitude
attribute	latitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	latitude	standard_name	String	latitude
attribute	latitude	units	String	degrees_north
variable	longitude		double
attribute	longitude	_CoordinateAxisType	String	Lon
attribute	longitude	_FillValue	double	NaN
attribute	longitude	actual_range	double	57.278183, 57.278183
attribute	longitude	axis	String	X
attribute	longitude	bcodmo_name	String	longitude
attribute	longitude	colorBarMaximum	double	180.0
attribute	longitude	colorBarMinimum	double	-180.0
attribute	longitude	description	String	Longitude, west is negative
attribute	longitude	ioos_category	String	Location
attribute	longitude	long_name	String	Longitude
attribute	longitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	10.7, 747.7
attribute	depth	axis	String	Z
attribute	depth	bcodmo_name	String	depth
attribute	depth	colorBarMaximum	double	8000.0
attribute	depth	colorBarMinimum	double	-8000.0
attribute	depth	colorBarPalette	String	TopographyDepth
attribute	depth	description	String	Depth below seafloor
attribute	depth	ioos_category	String	Location
attribute	depth	long_name	String	Depth
attribute	depth	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/DEPH/
attribute	depth	positive	String	down
attribute	depth	standard_name	String	depth
attribute	depth	units	String	m
variable	Replicate_1		float
attribute	Replicate_1	_FillValue	float	NaN
attribute	Replicate_1	actual_range	float	8.77, 3000.0
attribute	Replicate_1	bcodmo_name	String	replicate
attribute	Replicate_1	description	String	Replicate 1
attribute	Replicate_1	long_name	String	Replicate 1
attribute	Replicate_1	units	String	cells per cubic centimeter (cells/cm3)
variable	Replicate_2		float
attribute	Replicate_2	_FillValue	float	NaN
attribute	Replicate_2	actual_range	float	17.5, 1740.0
attribute	Replicate_2	bcodmo_name	String	replicate
attribute	Replicate_2	description	String	Replicate 2
attribute	Replicate_2	long_name	String	Replicate 2
attribute	Replicate_2	units	String	cells per cubic centimeter (cells/cm3)
variable	Average		short
attribute	Average	_FillValue	short	32767
attribute	Average	actual_range	short	115, 1656
attribute	Average	bcodmo_name	String	mean
attribute	Average	description	String	Average number of cells
attribute	Average	long_name	String	Average
attribute	Average	units	String	cells per cubic centimeter (cells/cm3)
variable	Standard_Deviation		short
attribute	Standard_Deviation	_FillValue	short	32767
attribute	Standard_Deviation	actual_range	short	6, 1901
attribute	Standard_Deviation	bcodmo_name	String	standard deviation
attribute	Standard_Deviation	colorBarMaximum	double	50.0
attribute	Standard_Deviation	colorBarMinimum	double	0.0
attribute	Standard_Deviation	description	String	Standard deviation of average
attribute	Standard_Deviation	long_name	String	Standard Deviation
attribute	Standard_Deviation	units	String	cells per cubic centimeter (cells/cm3)
variable	AP_activity		float
attribute	AP_activity	_FillValue	float	NaN
attribute	AP_activity	actual_range	float	0.04, 2.3
attribute	AP_activity	bcodmo_name	String	unknown
attribute	AP_activity	description	String	Alkaline Phosphatase activity
attribute	AP_activity	long_name	String	AP Activity
attribute	AP_activity	units	String	picomole per gram per hour (pmol g-1 h-1)
variable	Time_of_AP_measurment		short
attribute	Time_of_AP_measurment	_FillValue	short	32767
attribute	Time_of_AP_measurment	actual_range	short	876, 3053
attribute	Time_of_AP_measurment	bcodmo_name	String	incubation time
attribute	Time_of_AP_measurment	description	String	Time of Alkaline Phosphatase measurements
attribute	Time_of_AP_measurment	long_name	String	Time Of AP Measurment
attribute	Time_of_AP_measurment	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/AZDRZZ01/
attribute	Time_of_AP_measurment	units	String	hours (Hr)

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.