ERDDAP > info > bcodmo_dataset_641495

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	[Prochlorococcus_narB] - The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008 (Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph)		F   I   M	background			BCO-DMO	bcodmo_dataset_641495

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	Sample processing and analyses are detailed in the publications listed below. Briefly, 100ml of seawater was collected onto 25mm dia polycarbonate filters (0.22um pore size), rinsed with Tris-buffered saline, flash frozen in liquid N2, and stored at -80C until extraction. DNA was extracted using a combination of 5min of bead beating and 15min heat lysis at 95C. Extracted DNA was used as template of quantitative PCR reactions using primers specifically designed to target the narB gene from the HLII and LLI clades of Prochlorococcus. Standard curves used for quantitation of field data were derived from DNA extracted from defined cell numbers of cultured representatives of each clade.
attribute	NC_GLOBAL	awards_0_award_nid	String	54649
attribute	NC_GLOBAL	awards_0_award_number	String	DBI-0424599
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0424599
attribute	NC_GLOBAL	awards_0_funder_name	String	National Science Foundation
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	350
attribute	NC_GLOBAL	awards_1_award_nid	String	522893
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1153588
attribute	NC_GLOBAL	awards_1_data_url	String	http://nsf.gov/awardsearch/showAward?AWD_ID=1153588
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	50534
attribute	NC_GLOBAL	awards_2_award_nid	String	522915
attribute	NC_GLOBAL	awards_2_award_number	String	GBMF495
attribute	NC_GLOBAL	awards_2_data_url	String	http://www.moore.org/grants/list/GBMF495
attribute	NC_GLOBAL	awards_2_funder_name	String	Gordon and Betty Moore Foundation
attribute	NC_GLOBAL	awards_2_funding_acronym	String	GBMF
attribute	NC_GLOBAL	awards_2_funding_source_nid	String	361
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Two year time series Prochlorococcus with narB gene at HOT and BATS sites S. Chisholm, PI P. Berube, Contact
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	2016-03-30T20:21:47Z
attribute	NC_GLOBAL	date_modified	String	2018-11-16T20:45:44Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.641735
attribute	NC_GLOBAL	Easternmost_Easting	double	-64.1667
attribute	NC_GLOBAL	geospatial_lat_max	double	31.6667
attribute	NC_GLOBAL	geospatial_lat_min	double	22.75
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-64.1667
attribute	NC_GLOBAL	geospatial_lon_min	double	-158.0
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	200.0
attribute	NC_GLOBAL	geospatial_vertical_min	double	1.0
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/641495
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Flow Cytometer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	from Becton Dickinson, Franklin Lakes, NJ, USA
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	644814
attribute	NC_GLOBAL	instruments_0_description	String	Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells. (from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB37/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Flow Cytometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	660
attribute	NC_GLOBAL	instruments_0_supplied_name	String	influx flow cytometer
attribute	NC_GLOBAL	keywords	String	abundance, altimetry, bco, bco-dmo, biological, chemical, cruiseid, data, dataset, date, day, depth, deviation, dmo, erddap, gene, laboratory, latitude, longitude, management, month, oceanography, office, preliminary, sal, satellite, sigma, sigma_0, site, standard, standard_deviation, temperature, year, yrday, yrday_gmt
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/641495/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/641495
attribute	NC_GLOBAL	Northernmost_Northing	double	31.6667
attribute	NC_GLOBAL	param_mapping	String	{'641495': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/641495/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Massachusetts Institute of Technology
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	MIT-Dept CEE
attribute	NC_GLOBAL	people_0_person_name	String	Sallie W. Chisholm
attribute	NC_GLOBAL	people_0_person_nid	String	50605
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	Massachusetts Institute of Technology
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	MIT-Dept CEE
attribute	NC_GLOBAL	people_1_person_name	String	Paul Berube
attribute	NC_GLOBAL	people_1_person_nid	String	522886
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	Ms Dicky Allison
attribute	NC_GLOBAL	people_2_person_nid	String	50382
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	Prochloro_ecology
attribute	NC_GLOBAL	projects_0_acronym	String	Prochloro_ecology
attribute	NC_GLOBAL	projects_0_description	String	Extracted from the NSF award abstract: First discovered in 1988, Prochlorococcus is now recognized as the most abundant photosynthetic cell in the oceans and is responsible for a significant fraction of global primary productivity. Arguably one of the best studied marine microorganisms to date, Prochlorococcus is well-developed as a model system for advancing our understanding of microbial ecology. It is comprised of a collection of genetically and physiologically distinct populations that co-exist and are differentially distributed along quantifiable gradients of light, temperature, and inorganic nutrients. Early physiological studies using cultured isolates indicated that this group of cyanobacteria was unable to assimilate nitrate, typically the most abundant inorganic nitrogen source in the open ocean. This observation was supported by the first 12 genome sequences of Prochlorococcus which all lacked the genes necessary for nitrate assimilation. The lack of these genes in Prochlorococcus was puzzling given that closely related, and co-occurring, Synechococcus cells have them, and that nitrogen availability can be a significant limiting factor for primary production in marine ecosystems. Our understanding changed in 2009 with the discovery of nitrate assimilation genes in wild Prochlorococcus genomes and the isolation of an axenic strain capable of growth on nitrate (unpublished data). This discovery has lead to the overarching questions that are the subject of this project: - What subset of the Prochlorococcus meta-population in the wild contains nitrate assimilation genes and how do the dynamics of this sub-population vary in time and space? - What features of the environment select for cells with this functional trait?  - Is the phylogeny of Prochlorococcus nitrate assimilation genes better correlated with the local environment or the overall 16S-23S ITS phylogeny of Prochlorococcus? - Do the genomes of cells that contain nitrate assimilation genes share specific features? What do they tell us about what other environmental variables influence the fitness of nitrate-assimilating cells? - What are the physiological tradeoffs underlying the loss or gain of assimilation genes in particular strains? These questions will be addressed using an integrative cross-scale approach to characterize nitrate assimilation by Prochlorococcus at the population, cellular, and genomic levels. Specifically, the distribution and abundance of nitrate assimilating Prochlorococcus will be measured at two contrasting open ocean time-series stations (HOT and BATS), and along a longitudinal gradient in the Atlantic (AMT). The PI will examine the regulation of nitrate assimilation, the kinetics of growth on nitrate, and the ability of Prochlorococcus to compete with Synechococcus under nitrogen limiting conditions. Further, they will use a culture independent single cell genomics approach to assess the phylogenetic diversity of nitrate assimilation genes within the genomic context of several ribotypes. These studies will advance our understanding the biogeography of functional traits in microbes, how it is shaped by selection, and the role of intra-species functional diversity in the overall population dynamics of Prochlorococcus.
attribute	NC_GLOBAL	projects_0_end_date	String	2016-01
attribute	NC_GLOBAL	projects_0_geolocation	String	BATS station (31.7 N 64.2 W) and HOT station ALOHA (22.75 N 158 W)
attribute	NC_GLOBAL	projects_0_name	String	Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph
attribute	NC_GLOBAL	projects_0_project_nid	String	522910
attribute	NC_GLOBAL	projects_0_start_date	String	2012-02
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	22.75
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	Two year time series of the abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans. The goal was to collect long-term, high-resolution data on the temporal and spatial variability of Prochlorococcus narB genotypes belonging to the HLII and LLI clades. The abundance of Prochlorococcus cells containing narB for each of these clades was determined by quantitative PCR at 12 depths every month from October 2005 to December 2007 at two locations: BATS location (5 nautical mile radius around 31 40'N, 64 10'W) and HOT Station ALOHA (5 nautical mile radius around 22 45'N, 158 00' W). These field samples are a subset of those utilized in the \Prochlorococcus HOT/BATS\ dataset ([https://www.bco-dmo.org/dataset/3381](\\http://www.bco- dmo.org/dataset/3381\\)). These data are reported and described in: Berube, P. M., Coe, A., Roggensack, S. E., & Chisholm, S. W. (2015). Temporal dynamics of Prochlorococcuscells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans. Limnology and Oceanography, 61(2), 482\u2013495. doi:10.1002/lno.10226
attribute	NC_GLOBAL	title	String	[Prochlorococcus_narB] - The abundance of Prochlorococcus cells containing the nitrate reductase gene (narB) at the HOT and BATS sites in the Pacific and Atlantic Oceans between October 2005 and January 2008 (Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-158.0
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	gene		String
attribute	gene	bcodmo_name	String	unknown
attribute	gene	description	String	nitrate reductase gene (narB) in one of two clades (HLII and LLI)
attribute	gene	long_name	String	Gene
attribute	gene	units	String	text
variable	site		String
attribute	site	bcodmo_name	String	site
attribute	site	description	String	Location of the measurement at one of two sites located at the HOT and BATS sites
attribute	site	long_name	String	Site
attribute	site	units	String	text
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	22.75, 31.6667
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; north is positive
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	-158.0, -64.1667
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; east is positive
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	cruiseid		float
attribute	cruiseid	_FillValue	float	NaN
attribute	cruiseid	actual_range	float	174.0, 230.0
attribute	cruiseid	bcodmo_name	String	cruiseid
attribute	cruiseid	description	String	The cruise identification
attribute	cruiseid	long_name	String	Cruiseid
attribute	cruiseid	units	String	numeric
variable	year		short
attribute	year	_FillValue	short	32767
attribute	year	actual_range	short	2005, 2008
attribute	year	bcodmo_name	String	year
attribute	year	description	String	Year the measurement was taken in YYYY format
attribute	year	long_name	String	Year
attribute	year	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/
attribute	year	units	String	unitless
variable	month		byte
attribute	month	_FillValue	byte	127
attribute	month	actual_range	byte	1, 12
attribute	month	bcodmo_name	String	month_gmt
attribute	month	description	String	Month the measurement was taken
attribute	month	long_name	String	Month
attribute	month	units	String	mm
variable	day		byte
attribute	day	_FillValue	byte	127
attribute	day	actual_range	byte	2, 31
attribute	day	bcodmo_name	String	day
attribute	day	description	String	Day the measurement was taken
attribute	day	long_name	String	Day
attribute	day	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/DAYXXXXX/
attribute	day	units	String	dd
variable	date		String
attribute	date	bcodmo_name	String	date
attribute	date	description	String	Date the sample was taken
attribute	date	long_name	String	Date
attribute	date	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	date	units	String	mm/dd/yy
variable	yrday_gmt		int
attribute	yrday_gmt	_FillValue	int	2147483647
attribute	yrday_gmt	actual_range	int	118886400, 191894400
attribute	yrday_gmt	bcodmo_name	String	yrday_gmt
attribute	yrday_gmt	description	String	The year day the sample was taken with 1 meaning January 1
attribute	yrday_gmt	long_name	String	Yrday Gmt
attribute	yrday_gmt	units	String	decimal number
variable	abundance		float
attribute	abundance	_FillValue	float	NaN
attribute	abundance	actual_range	float	0.65, 133000.0
attribute	abundance	bcodmo_name	String	abundance
attribute	abundance	description	String	Abundance of HLII or LLI clade Prochlorococcus cells containing the narB gene
attribute	abundance	long_name	String	Abundance
attribute	abundance	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P03/current/B070/
attribute	abundance	units	String	cells/milliliter
variable	temp		float
attribute	temp	_FillValue	float	NaN
attribute	temp	actual_range	float	15.76415, 27.9653
attribute	temp	bcodmo_name	String	temperature
attribute	temp	description	String	Temperature at the sample location
attribute	temp	long_name	String	Temperature
attribute	temp	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/
attribute	temp	units	String	degrees centigrade
variable	sal		float
attribute	sal	_FillValue	float	NaN
attribute	sal	actual_range	float	34.4049, 36.8736
attribute	sal	bcodmo_name	String	sal
attribute	sal	description	String	Salinity measured at the sample location
attribute	sal	long_name	String	Sal
attribute	sal	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/PSALST01/
attribute	sal	units	String	PSS-78
variable	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	1.0, 200.0
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 at which the sample was taken
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	sigma_0		float
attribute	sigma_0	_FillValue	float	NaN
attribute	sigma_0	actual_range	float	22.843, 26.448
attribute	sigma_0	bcodmo_name	String	sigma_0
attribute	sigma_0	description	String	Potential density
attribute	sigma_0	long_name	String	Sigma 0
attribute	sigma_0	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/SIGTPR01/
attribute	sigma_0	units	String	kilograms/cubic meter
variable	standard_deviation		float
attribute	standard_deviation	_FillValue	float	NaN
attribute	standard_deviation	actual_range	float	0.118, 29500.0
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 the abundance measurements
attribute	standard_deviation	long_name	String	Standard Deviation
attribute	standard_deviation	units	String	cells/milliliter

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.