ERDDAP > info > bcodmo_dataset_782301

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	[Synechococcus accessions] - NCBI accessions for raw genomic sequence data of 11 new isolates of marine Synechococcus from Naragansett Bay, July 2017 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients)		F   I   M	background			BCO-DMO	bcodmo_dataset_782301

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	Natural seawater was enriched for photoautotrophs and split into multiple temperatures for two weeks. After the enrichment period, Synechococcus was isolated from each temperature. Each isolate's thermal niche was measured through a series of lab experiments and sequenced. The culture of each isolate was filtered onto 0.22 um PES filters and genomic DNA extracted using Qiagen\u2019s (CA) DNeasy Power Soil Extraction kit. Sequencing was done by Novogene (Beijing, China) on an Illumina 1500 making 2x150 pe reads.
attribute	NC_GLOBAL	awards_0_award_nid	String	712792
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1638804
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1638804
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	Michael E. Sieracki
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50446
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Synechococcus accessions NCBI accessions for genomic sequence data of 11 new isolates of marine Synechococcus PI: D. Hutchins (USC) version date: 2019-11-20
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	2019-11-21T13:15:23Z
attribute	NC_GLOBAL	date_modified	String	2020-03-09T12:47:21Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.782301.1
attribute	NC_GLOBAL	Easternmost_Easting	double	-71.4
attribute	NC_GLOBAL	geospatial_lat_max	double	41.47
attribute	NC_GLOBAL	geospatial_lat_min	double	41.47
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-71.4
attribute	NC_GLOBAL	geospatial_lon_min	double	-71.4
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	0.0
attribute	NC_GLOBAL	geospatial_vertical_min	double	0.0
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/782301
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Sequencing was done by Novogene (Beijing, China) on an Illumina 1500 making 2x150 pe reads.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	782307
attribute	NC_GLOBAL	instruments_0_description	String	General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Illumina 1500
attribute	NC_GLOBAL	keywords	String	accession, bco, bco-dmo, biological, chemical, data, dataset, depth, dmo, erddap, isolate, latitude, longitude, management, name, oceanography, office, organism, preliminary, sample, Sample_Name, spuid, tax, Tax_ID
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/782301/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/782301
attribute	NC_GLOBAL	Northernmost_Northing	double	41.47
attribute	NC_GLOBAL	param_mapping	String	{'782301': {'Lat': 'flag - latitude', 'Depth': 'flag - depth', 'Long': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/782301/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Southern California
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	USC
attribute	NC_GLOBAL	people_0_person_name	String	David A. Hutchins
attribute	NC_GLOBAL	people_0_person_nid	String	51048
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	Nancy Copley
attribute	NC_GLOBAL	people_1_person_nid	String	50396
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	Phytoplankton Community Responses
attribute	NC_GLOBAL	projects_0_acronym	String	Phytoplankton Community Responses
attribute	NC_GLOBAL	projects_0_description	String	NSF Award Abstract: Photosynthetic marine microbes, phytoplankton, contribute half of global primary production, form the base of most aquatic food webs and are major players in global biogeochemical cycles. Understanding their community composition is important because it affects higher trophic levels, the cycling of energy and elements and is sensitive to global environmental change. This project will investigate how phytoplankton communities respond to two major global change stressors in aquatic systems: warming and changes in nutrient availability. The researchers will work in two marine systems with a long history of environmental monitoring, the temperate Narragansett Bay estuary in Rhode Island and a subtropical North Atlantic site near Bermuda. They will use field sampling and laboratory experiments with multiple species and varieties of phytoplankton to assess the diversity in their responses to different temperatures under high and low nutrient concentrations. If the diversity of responses is high within species, then that species may have a better chance to adapt to rising temperatures and persist in the future. Some species may already be able to grow at high temperatures; consequently, they may become more abundant as the ocean warms. The researchers will incorporate this response information in mathematical models to predict how phytoplankton assemblages would reorganize under future climate scenarios. Graduate students and postdoctoral associates will be trained in diverse scientific approaches and techniques such as shipboard sampling, laboratory experiments, genomic analyses and mathematical modeling. The results of the project will be incorporated into K-12 teaching, including an advanced placement environmental science class for underrepresented minorities in Los Angeles, data exercises for rural schools in Michigan and disseminated to the public through an environmental journalism institute based in Rhode Island. Predicting how ecological communities will respond to a changing environment requires knowledge of genetic, phylogenetic and functional diversity within and across species. This project will investigate how the interaction of phylogenetic, genetic and functional diversity in thermal traits within and across a broad range of species determines the responses of marine phytoplankton communities to rising temperature and changing nutrient regimes. High genetic and functional diversity within a species may allow evolutionary adaptation of that species to warming. If the phylogenetic and functional diversity is higher across species, species sorting and ecological community reorganization is likely. Different marine sites may have a different balance of genetic and functional diversity within and across species and, thus, different contribution of evolutionary and ecological responses to changing climate. The research will be conducted at two long-term time series sites in the Atlantic Ocean, the Narragansett Bay Long-Term Plankton Time Series and the Bermuda Atlantic Time Series (BATS) station. The goal is to assess intra- and inter-specific genetic and functional diversity in thermal responses at contrasting nutrient concentrations for a representative range of species in communities at the two sites in different seasons, and use this information to parameterize eco-evolutionary models embedded into biogeochemical ocean models to predict responses of phytoplankton communities to projected rising temperatures under realistic nutrient conditions. Model predictions will be informed by and tested with field data, including the long-term data series available for both sites and in community temperature manipulation experiments. This project will provide novel information on existing intraspecific genetic and functional thermal diversity for many ecologically and biogeochemically important phytoplankton species, estimate generation of new genetic and functional diversity in evolution experiments, and develop and parameterize novel eco-evolutionary models interfaced with ocean biogeochemical models to predict future phytoplankton community structure. The project will also characterize the interaction of two major global change stressors, warming and changing nutrient concentrations, as they affect phytoplankton diversity at functional, genetic, and phylogenetic levels. In addition, the project will develop novel modeling methodology that will be broadly applicable to understanding how other types of complex ecological communities may adapt to a rapidly warming world.
attribute	NC_GLOBAL	projects_0_end_date	String	2020-09
attribute	NC_GLOBAL	projects_0_geolocation	String	Narragansett Bay, RI and Bermuda, Bermuda Atlantic Time-series Study (BATS)
attribute	NC_GLOBAL	projects_0_name	String	Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients
attribute	NC_GLOBAL	projects_0_project_nid	String	712787
attribute	NC_GLOBAL	projects_0_start_date	String	2016-10
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	41.47
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	Organism,Tax_ID,latitude,longitude,depth
attribute	NC_GLOBAL	summary	String	NCBI accessions for raw genomic sequence data of 11 new isolates of marine Synechococcus from Naragansett Bay.
attribute	NC_GLOBAL	title	String	[Synechococcus accessions] - NCBI accessions for raw genomic sequence data of 11 new isolates of marine Synechococcus from Naragansett Bay, July 2017 (Dimensions: Collaborative Research: Genetic, functional and phylogenetic diversity determines marine phytoplankton community responses to changing temperature and nutrients)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-71.4
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Accession		String
attribute	Accession	bcodmo_name	String	accession number
attribute	Accession	description	String	NCBI accession number
attribute	Accession	long_name	String	Accession
attribute	Accession	units	String	unitless
variable	Sample_Name		String
attribute	Sample_Name	bcodmo_name	String	sample
attribute	Sample_Name	description	String	sample description
attribute	Sample_Name	long_name	String	Sample Name
attribute	Sample_Name	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	Sample_Name	units	String	unitless
variable	SPUID		String
attribute	SPUID	bcodmo_name	String	sample
attribute	SPUID	description	String	sample description
attribute	SPUID	long_name	String	SPUID
attribute	SPUID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	SPUID	units	String	unitless
variable	Organism		String
attribute	Organism	bcodmo_name	String	taxon
attribute	Organism	description	String	taxonomic genus of sample
attribute	Organism	long_name	String	Organism
attribute	Organism	units	String	unitless
variable	Tax_ID		short
attribute	Tax_ID	_FillValue	short	32767
attribute	Tax_ID	actual_range	short	1129, 1129
attribute	Tax_ID	bcodmo_name	String	taxon_code
attribute	Tax_ID	description	String	taxonomic identifier code
attribute	Tax_ID	long_name	String	Tax ID
attribute	Tax_ID	units	String	unitless
variable	Isolate		String
attribute	Isolate	bcodmo_name	String	taxon_code
attribute	Isolate	description	String	isolate identifier
attribute	Isolate	long_name	String	Isolate
attribute	Isolate	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	41.47, 41.47
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 of sample collection; 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	-71.4, -71.4
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 of sample collection; north 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	source_name	String	Long
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	0.0, 0.0
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 of sample collection
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

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.