ERDDAP > info > bcodmo_dataset_753343

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	[ESP 2016 Seq] - Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016. (Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere)		F   I   M	background			BCO-DMO	bcodmo_dataset_753343

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	The Environmental Sample Processor (ESP) filtered seawater sequentially through 5.0 um and 0.2 um pore size polyvinylidene fluoride filters. Seawater was evacuated from filters and followed twice with a 2 minute incubation with 1 ml of RNAlater\u2122. RNAlater was evacuated, and filters were stored in the ESP until they were transferred to -80 C upon instrument recovery.\u00a0 Grab samples for sequencing while the ESP was not deployed were taken using Niskin bottles that collected seawater at the same depth and location of the ESP. Water was transferred to a low-density polyethylene cubitainer and maintained at ambient temperature until return to lab within 30 min. Seawater was filtered as above with vacuum filtration and preserved immediately in liquid nitrogen and transferred to -80 C. Single-cell sequencing: Seawater was transferred directly from the Niskin bottle to a 50 ml Falcon tube and placed on ice until brought back to lab. Each sampling day, 3 x 1 ml of seawater was preserved in cryovials using 100 ul of glyTe (5 ml glycerol, 3 ml Milli-Q H2O, 1 ml 100 x TE pH 8.0, 0.2 um filter sterilized after mixing the above, and stored in -20 C freezer). Preserved samples were then placed in a -80 C freezer. Samples were processed and sequenced at JGI
attribute	NC_GLOBAL	awards_0_award_nid	String	541254
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1342694
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1342694
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	Metagenomic, metatranscriptomic, and single cell sequencing data from the Fall 2016 ESP deployment in Monterey Bay, CA PI: Mary Ann Moran Version: 2020-03-10
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	2019-01-22T20:12:37Z
attribute	NC_GLOBAL	date_modified	String	2020-04-01T17:17:54Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.753343.2
attribute	NC_GLOBAL	Easternmost_Easting	double	-121.901
attribute	NC_GLOBAL	geospatial_lat_max	double	36.835
attribute	NC_GLOBAL	geospatial_lat_min	double	36.835
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-121.901
attribute	NC_GLOBAL	geospatial_lon_min	double	-121.901
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/753343
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	keywords	String	accession, analysis, Analysis_Project_Name, assembly, Assembly_Method, bases, bco, bco-dmo, bio, biological, biome, chemical, collection, Collection_Date, contigs, data, dataset, date, dmo, env, env_biome, env_feature, env_material, erddap, feature, filtered, geo, geo_loc_name, gold, GOLD_Project_ID, instrument, jgi, JGI_Contigs_Link, JGI_Project_ID, JGI_Sample_ID, JGI_Sequencing_Project_ID, JGI_Sequencing_Project_Name, latitude, Latitude_and_Longitude, link, loc, longitude, management, material, method, mode, name, ncbi, NCBI_BioProject_Accession, NCBI_BioSample_Accession, NCBI_Project_ID, NCBI_SRA_Accession_ID, oceanography, office, preliminary, project, run, sample, Sample_Name, sea, seawater, sequencing, Sequencing_Run_Mode, sra, total, Total_Bases, type, volume, Volume_Seawater_Filtered, water
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/753343/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/753343
attribute	NC_GLOBAL	Northernmost_Northing	double	36.835
attribute	NC_GLOBAL	param_mapping	String	{'753343': {'lat': 'flag - latitude', 'lon': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/753343/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Georgia
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UGA
attribute	NC_GLOBAL	people_0_person_name	String	Mary Ann Moran
attribute	NC_GLOBAL	people_0_person_nid	String	51592
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	University of Georgia
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UGA
attribute	NC_GLOBAL	people_1_person_name	String	Brent Nowinski
attribute	NC_GLOBAL	people_1_person_nid	String	662396
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
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	Mathew Biddle
attribute	NC_GLOBAL	people_2_person_nid	String	708682
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	OceanSulfurFluxBact
attribute	NC_GLOBAL	projects_0_acronym	String	OceanSulfurFluxBact
attribute	NC_GLOBAL	projects_0_description	String	Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling. The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation. This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-12
attribute	NC_GLOBAL	projects_0_name	String	Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
attribute	NC_GLOBAL	projects_0_project_nid	String	541255
attribute	NC_GLOBAL	projects_0_start_date	String	2014-01
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	36.835
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	latitude,longitude
attribute	NC_GLOBAL	summary	String	These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.
attribute	NC_GLOBAL	title	String	[ESP 2016 Seq] - Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016. (Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere)
attribute	NC_GLOBAL	version	String	2
attribute	NC_GLOBAL	Westernmost_Easting	double	-121.901
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	GOLD_Project_ID		String
attribute	GOLD_Project_ID	bcodmo_name	String	accession number
attribute	GOLD_Project_ID	description	String	Accession number at DOE JGI IMG database: https://img.jgi.doe.gov
attribute	GOLD_Project_ID	long_name	String	GOLD Project ID
attribute	GOLD_Project_ID	units	String	unitless
variable	Analysis_Project_Name		String
attribute	Analysis_Project_Name	bcodmo_name	String	project
attribute	Analysis_Project_Name	description	String	Name of sequencing project
attribute	Analysis_Project_Name	long_name	String	Analysis Project Name
attribute	Analysis_Project_Name	units	String	unitless
variable	Type		String
attribute	Type	bcodmo_name	String	sample_descrip
attribute	Type	description	String	Material type sequenced
attribute	Type	long_name	String	Type
attribute	Type	units	String	unitless
variable	Assembly_Method		String
attribute	Assembly_Method	bcodmo_name	String	sampling_method
attribute	Assembly_Method	description	String	assembly method
attribute	Assembly_Method	long_name	String	Assembly Method
attribute	Assembly_Method	units	String	unitless
variable	Collection_Date		String
attribute	Collection_Date	bcodmo_name	String	date
attribute	Collection_Date	description	String	collection date of samples
attribute	Collection_Date	long_name	String	Collection Date
attribute	Collection_Date	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	Collection_Date	units	String	unitless
variable	Instrument		String
attribute	Instrument	bcodmo_name	String	instrument
attribute	Instrument	description	String	instrument
attribute	Instrument	long_name	String	Instrument
attribute	Instrument	units	String	unitless
variable	JGI_Contigs_Link		String
attribute	JGI_Contigs_Link	bcodmo_name	String	unknown
attribute	JGI_Contigs_Link	description	String	JGI Contigs Link
attribute	JGI_Contigs_Link	long_name	String	JGI Contigs Link
attribute	JGI_Contigs_Link	units	String	unitless
variable	JGI_Project_ID		int
attribute	JGI_Project_ID	_FillValue	int	2147483647
attribute	JGI_Project_ID	actual_range	int	1174504, 1190880
attribute	JGI_Project_ID	bcodmo_name	String	unknown
attribute	JGI_Project_ID	description	String	JGI Project ID
attribute	JGI_Project_ID	long_name	String	JGI Project ID
attribute	JGI_Project_ID	units	String	unitless
variable	JGI_Sample_ID		int
attribute	JGI_Sample_ID	_FillValue	int	2147483647
attribute	JGI_Sample_ID	actual_range	int	166736, 178378
attribute	JGI_Sample_ID	bcodmo_name	String	sample
attribute	JGI_Sample_ID	description	String	JGI Sample ID
attribute	JGI_Sample_ID	long_name	String	JGI Sample ID
attribute	JGI_Sample_ID	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	JGI_Sample_ID	units	String	unitless
variable	JGI_Sequencing_Project_ID		int
attribute	JGI_Sequencing_Project_ID	_FillValue	int	2147483647
attribute	JGI_Sequencing_Project_ID	actual_range	int	1174680, 1190883
attribute	JGI_Sequencing_Project_ID	bcodmo_name	String	unknown
attribute	JGI_Sequencing_Project_ID	description	String	JGI Sequencing Project ID
attribute	JGI_Sequencing_Project_ID	long_name	String	JGI Sequencing Project ID
attribute	JGI_Sequencing_Project_ID	units	String	unitless
variable	JGI_Sequencing_Project_Name		String
attribute	JGI_Sequencing_Project_Name	bcodmo_name	String	unknown
attribute	JGI_Sequencing_Project_Name	description	String	JGI Sequencing Project Name
attribute	JGI_Sequencing_Project_Name	long_name	String	JGI Sequencing Project Name
attribute	JGI_Sequencing_Project_Name	units	String	unitless
variable	Latitude_and_Longitude		String
attribute	Latitude_and_Longitude	bcodmo_name	String	unknown
attribute	Latitude_and_Longitude	description	String	Latitude and Longitude
attribute	Latitude_and_Longitude	long_name	String	Longitude
attribute	Latitude_and_Longitude	standard_name	String	longitude
attribute	Latitude_and_Longitude	units	String	unitless
variable	NCBI_BioProject_Accession		String
attribute	NCBI_BioProject_Accession	bcodmo_name	String	unknown
attribute	NCBI_BioProject_Accession	description	String	NCBI BioProject Accession
attribute	NCBI_BioProject_Accession	long_name	String	NCBI Bio Project Accession
attribute	NCBI_BioProject_Accession	units	String	unitless
variable	NCBI_BioSample_Accession		String
attribute	NCBI_BioSample_Accession	bcodmo_name	String	unknown
attribute	NCBI_BioSample_Accession	description	String	NCBI BioSample Accession
attribute	NCBI_BioSample_Accession	long_name	String	NCBI Bio Sample Accession
attribute	NCBI_BioSample_Accession	units	String	unitless
variable	NCBI_Project_ID		int
attribute	NCBI_Project_ID	_FillValue	int	2147483647
attribute	NCBI_Project_ID	actual_range	int	467720, 511331
attribute	NCBI_Project_ID	bcodmo_name	String	unknown
attribute	NCBI_Project_ID	description	String	NCBI Project ID
attribute	NCBI_Project_ID	long_name	String	NCBI Project ID
attribute	NCBI_Project_ID	units	String	unitless
variable	NCBI_SRA_Accession_ID		String
attribute	NCBI_SRA_Accession_ID	bcodmo_name	String	unknown
attribute	NCBI_SRA_Accession_ID	description	String	NCBI SRA Accession ID
attribute	NCBI_SRA_Accession_ID	long_name	String	NCBI SRA Accession ID
attribute	NCBI_SRA_Accession_ID	units	String	unitless
variable	Sample_Name		String
attribute	Sample_Name	bcodmo_name	String	sample
attribute	Sample_Name	description	String	sample name
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	Sequencing_Run_Mode		String
attribute	Sequencing_Run_Mode	bcodmo_name	String	unknown
attribute	Sequencing_Run_Mode	description	String	sequencing run mode
attribute	Sequencing_Run_Mode	long_name	String	Sequencing Run Mode
attribute	Sequencing_Run_Mode	units	String	unitless
variable	Total_Bases		String
attribute	Total_Bases	bcodmo_name	String	unknown
attribute	Total_Bases	description	String	total bases
attribute	Total_Bases	long_name	String	Total Bases
attribute	Total_Bases	units	String	unitless
variable	Volume_Seawater_Filtered		float
attribute	Volume_Seawater_Filtered	_FillValue	float	NaN
attribute	Volume_Seawater_Filtered	actual_range	float	73.5, 1000.0
attribute	Volume_Seawater_Filtered	bcodmo_name	String	vol_filt
attribute	Volume_Seawater_Filtered	description	String	Volume Seawater Filtered
attribute	Volume_Seawater_Filtered	long_name	String	Volume Seawater Filtered
attribute	Volume_Seawater_Filtered	units	String	milliliters (mL)
variable	env_biome		String
attribute	env_biome	bcodmo_name	String	unknown
attribute	env_biome	description	String	environmental biome
attribute	env_biome	long_name	String	Env Biome
attribute	env_biome	units	String	unitless
variable	env_feature		String
attribute	env_feature	bcodmo_name	String	unknown
attribute	env_feature	description	String	environmental feature
attribute	env_feature	long_name	String	Env Feature
attribute	env_feature	units	String	unitless
variable	env_material		String
attribute	env_material	bcodmo_name	String	unknown
attribute	env_material	description	String	environmental material
attribute	env_material	long_name	String	Env Material
attribute	env_material	units	String	unitless
variable	geo_loc_name		String
attribute	geo_loc_name	bcodmo_name	String	unknown
attribute	geo_loc_name	description	String	location name
attribute	geo_loc_name	long_name	String	Geo Loc Name
attribute	geo_loc_name	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	36.835, 36.835
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 with positive values indicating North
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	-121.901, -121.901
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 with negative values indicating West
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

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.