ERDDAP > info > bcodmo_dataset_814713

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	Intracellular sulfonate metabolites measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics		I   M	background			BCO-DMO	bcodmo_dataset_814713

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	Pure cultures of bacteria and phytoplankton were grown in artificial seawater medium, and cells were collected during mid-to-late exponential phase by gentle filtration onto 0.2 micron Durapore filters. All filters were flash frozen in liquid nitrogen and stored at -80 degrees Celsius until further processing. Frozen filters of cells and media blanks were extracted and analyzed using a targeted liquid chromatography-mass spectrometry-based metabolomics method according to the protocols in Boysen and Heal et al., 2018. Briefly, metabolites were extracted using a modified Bligh\u2013Dyer extraction using 1:1 methanol/water (aqueous phase) and dichloromethane (organic phase). Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole with both reverse-phase and hydrophilic interaction liquid chromatography (HILIC). Taurine, isethionate, sulfolactate, and cysteate were quantified using isotopically-labeled internal standards that were added prior to extraction. DHPS was quantified by generating standard addition curves. Instruments: Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole (TQS) with electrospray ionization (ESI) in selected reaction monitoring mode (SRM) with polarity switching. SRM conditions for each compound (collision energy, cone voltage, precursor, and product ions) were optimized by infusion of each metabolite standard. For most metabolites, two SRM transitions were selected based on maximum peak areas. All chromatographic separations were carried out on a Waters Acquity I-Class UPLC (Waters Corporation, Milford, MA).
attribute	NC_GLOBAL	awards_0_award_nid	String	718130
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1521564
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1521564
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	Elizabeth L. Rom
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	682003
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Sulfonates in plankton cultures PI: Bryndan P. Durham Version date: 10 June 2020
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	2020-06-10T14:53:27Z
attribute	NC_GLOBAL	date_modified	String	2020-06-10T20:25:53Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.814713.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/814713
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Mass Spec
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Targeted metabolomics data were generated using a Waters Xevo TQ-S triple quadrupole with both reverse-phase and hydrophilic interaction liquid chromatography (HILIC).
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	814730
attribute	NC_GLOBAL	instruments_0_description	String	General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB16/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Mass Spectrometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	685
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Waters Xevo TQ-S triple quadrupole
attribute	NC_GLOBAL	keywords	String	acid, bco, bco-dmo, biological, cells, cells_filtered, chemical, cysteic, cysteic_acid, data, dataset, dhps, dmo, erddap, filtered, isethionic, isethionic_acid, management, oceanography, office, organism, preliminary, replicate, sulfolactate, taurine
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/814713/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/814713
attribute	NC_GLOBAL	param_mapping	String	{'814713': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/814713/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Washington
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UW
attribute	NC_GLOBAL	people_0_person_name	String	Bryndan P. Durham
attribute	NC_GLOBAL	people_0_person_nid	String	718133
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	Sulfonate Cycling
attribute	NC_GLOBAL	projects_0_acronym	String	Sulfonate Cycling
attribute	NC_GLOBAL	projects_0_description	String	NSF Award Abstract: Information in the form of chemicals and energy flows constantly through complex networks of marine microbes. In the surface ocean, sunlight and atmospheric carbon dioxide are captured by autotrophic unicellular phytoplankton and transformed into a vast pool of organic matter that microbes use as metabolic currencies and signaling molecules to form the basis for different trading alliances. Several little-known sulfonate compounds have recently been identified as key currencies underlying marine bacterial-phytoplankton mutualisms and appear to be widespread in coastal communities. In this project, the fellow will investigate the prevalence and role of sulfonates in marine microbial interactions and their resulting impact on the Earth's biogeochemistry. With sponsor Dr. E. Virginia Armbrust at the University of Washington, the fellow will advance professionally through interdisciplinary training in microbial ecology and marine biogeochemistry. Broadening participation activities include mentorship of an undergraduate and development of an outreach program for a local minority-serving high school where students will conduct classroom laboratory exercises using microbiological and bioinformatics concepts. Sulfonates are produced and degraded by several important phytoplankton and heterotrophic bacterial taxa, respectively. Yet, these compounds represent a poorly understood component of the marine organic matter pool. To the extent that sulfonates account for an unquantified flux of carbon and sulfur that supports mutualisms between bacteria and phytoplankton, sulfonates represent cryptic missing links in both carbon and sulfur transformations in the ocean. In this study, the fellow will use laboratory-based approaches to examine physiological and ecological controls on sulfonate production in model phytoplankton species and field-based approaches to examine taxonomically driven dynamics of sulfonate pools in the coastal waters of Puget Sound and surrounding North Pacific. Specifically, the fellow will perform metabolic profiling of model sulfonate-producing phytoplankton taxa (Aim I) and measure spatiotemporal gradients and turnover rates of sulfonates in the ocean environment using targeted in situ metabolite surveys (II) and stable isotope incubations (III), respectively, together with transcriptomics-based identification of marine microbes that control the fate of sulfonate-derived carbon (IV). The planned experiments will provide the first intensive characterization of sulfonates in the environment in terms of their contribution to the marine organic matter pool, their taxonomically driven spatiotemporal dynamics, and their roles in ocean ecosystem interdependencies.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-06
attribute	NC_GLOBAL	projects_0_geolocation	String	University of Washington
attribute	NC_GLOBAL	projects_0_name	String	OCE-PRF Track 1 (Broadening Participation): Cryptic Sulfonate Cycling between Marine Phytoplankton and Heterotrophic Bacterioplankton
attribute	NC_GLOBAL	projects_0_project_nid	String	718131
attribute	NC_GLOBAL	projects_0_start_date	String	2015-07
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	Intracellular sulfonate metabolites were measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics. These data have been published in Durham et al. (2019). Raw data are available at Metabolomics Workbench under Project ID PR000797.
attribute	NC_GLOBAL	title	String	Intracellular sulfonate metabolites measured in a variety of eukaryotic and prokaryotic phytoplankton and heterotrophic bacteria using liquid chromatography-mass spectrometry-based metabolomics
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Organism		String
attribute	Organism	bcodmo_name	String	taxon
attribute	Organism	description	String	name and strain number
attribute	Organism	long_name	String	Organism
attribute	Organism	units	String	unitless
variable	replicate		String
attribute	replicate	bcodmo_name	String	replicate
attribute	replicate	description	String	biological replicate
attribute	replicate	long_name	String	Replicate
attribute	replicate	units	String	unitless
variable	cells_filtered		String
attribute	cells_filtered	bcodmo_name	String	number
attribute	cells_filtered	description	String	number of cells extracted
attribute	cells_filtered	long_name	String	Cells Filtered
attribute	cells_filtered	units	String	unitless
variable	DHPS		float
attribute	DHPS	_FillValue	float	NaN
attribute	DHPS	actual_range	float	88.442, 3247.047
attribute	DHPS	bcodmo_name	String	unknown
attribute	DHPS	description	String	sulfonate
attribute	DHPS	long_name	String	DHPS
attribute	DHPS	units	String	amol per cell
variable	cysteic_acid		float
attribute	cysteic_acid	_FillValue	float	NaN
attribute	cysteic_acid	actual_range	float	1.0E-4, 126.71
attribute	cysteic_acid	bcodmo_name	String	unknown
attribute	cysteic_acid	description	String	sulfonate
attribute	cysteic_acid	long_name	String	Cysteic Acid
attribute	cysteic_acid	units	String	amol per cell
variable	sulfolactate		float
attribute	sulfolactate	_FillValue	float	NaN
attribute	sulfolactate	actual_range	float	0.002, 14.931
attribute	sulfolactate	bcodmo_name	String	unknown
attribute	sulfolactate	description	String	sulfonate
attribute	sulfolactate	long_name	String	Sulfolactate
attribute	sulfolactate	units	String	amol per cell
variable	isethionic_acid		double
attribute	isethionic_acid	_FillValue	double	NaN
attribute	isethionic_acid	actual_range	double	8.164, 45919.871
attribute	isethionic_acid	bcodmo_name	String	unknown
attribute	isethionic_acid	description	String	sulfonate
attribute	isethionic_acid	long_name	String	Isethionic Acid
attribute	isethionic_acid	units	String	amol per cell
variable	taurine		float
attribute	taurine	_FillValue	float	NaN
attribute	taurine	actual_range	float	4.0E-4, 15245.64
attribute	taurine	bcodmo_name	String	unknown
attribute	taurine	description	String	sulfonate
attribute	taurine	long_name	String	Taurine
attribute	taurine	units	String	amol per cell

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.