ERDDAP > info > bcodmo_dataset_749412

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	[Geltrap micrographs] - Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017 (Collaborative Research: EAGER: Particle- specific DNA sequencing to directly observe ecological mechanisms of the biological pump)		F   I   M	background			BCO-DMO	bcodmo_dataset_749412

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,.odvTxt
attribute	NC_GLOBAL	acquisition_description	String	The NBST carried 4 collection tubes with a diameter of 12 cm (Valdes and Price 2000). The STST included 5 frames (KC Denmark) clipped onto a surface- tethered, free drifting array line at increasing depths and each frame carried 4, 7 cm diameter collection tubes. The WW trap consisted of one, 4-tube trap frame (KC Denmark) tethered by a bungee below the profiling component of the WW array.\u00a0 To prepare tubes for deployment, seawater was collected from a depth of 150 m using a CTD rosette and pumped through a 1 \u03bcm filter cartridge. Trap tubes were filled with filtered water overlying a jar containing a polyacrylamide gel layer (Durkin et al. 2015). Trap platforms were deployed for between 1 day and 3.5 days (see Trap Deployment Log).\u00a0 Identically prepared tubes were incubated in parallel onboard the ship to serve as process blanks. Upon recovery, collection tubes were allowed to settle for at least 1 hour before the overlying water was siphoned off.\u00a0 Jars containing polyacrylamide gel were removed from trap tubes and the remaining overlying water was carefully pipetted off the gel.\u00a0 Gels were stored at 4 degrees C and imaged within the following 2 days before being stored at -80 degrees C.\u00a0 Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.\u00a0 Particles collected in gel layers during EN572 and EN581 were imaged under brightfield illumination.\u00a0 Particles collected in gel layers during FK170124 were imaged under both brightfield and oblique illumination, producing two separate sets of images for each sample.\u00a0 EN572 gel layers were imaged with a transparent grid to assist in tracking gel location during imaging. The grid was not used when imaging samples collected during subsequent cruises because the pronounced grid lines complicated image analysis. All gel layers were imaged at 4 increasing magnifications, though the combination of magnifications varied by cruise: at 7x, 20x, 40x, and 115x for EN572 samples, at 7x, 20x, 40x, and 80x for EN581 samples, and at 7x, 20x, 50x, and 115x for FK170124 samples. At magnifications greater than 7x, multiple focal planes within a field of view were imaged to capture particles embedded in different depths of the gel layer.\u00a0 The number of focal planes imaged was consistent across all fields of view for a given magnification but varied across cruises due to variation in gel thickness and particle types present. To determine whether measured particle properties changed if gel layers are frozen, samples collected during FK170124 were thawed after being stored for approximately 1 year at -80\u00a0 degrees C and imaged again under both brightfield and oblique illumination.
attribute	NC_GLOBAL	awards_0_award_nid	String	675295
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1703664
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1703664
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	Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017 PI: Colleen Durkin Version: 2019-10-18
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	2018-11-07T17:55:41Z
attribute	NC_GLOBAL	date_modified	String	2020-07-15T15:47:38Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.749412.1
attribute	NC_GLOBAL	Easternmost_Easting	double	151.903
attribute	NC_GLOBAL	geospatial_lat_max	double	39.88133333
attribute	NC_GLOBAL	geospatial_lat_min	double	22.329
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	151.903
attribute	NC_GLOBAL	geospatial_lon_min	double	-71.09866667
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/749412
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	camera
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	749428
attribute	NC_GLOBAL	instruments_0_description	String	All types of photographic equipment including stills, video, film and digital systems.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/311/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Camera
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	520
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Luminera Infinity 2 microscope camera
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16)
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	749427
attribute	NC_GLOBAL	instruments_1_description	String	Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB05/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Microscope-Optical
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	708
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Olympus SZX16 Stereomicroscope
attribute	NC_GLOBAL	keywords	String	additional, Additional_Trap_Label, bco, bco-dmo, biological, chemical, cruise, data, dataset, date, days, deploy, Deploy_Date_UTC, Deploy_Time_UTC, deployment, Deployment_Duration_days, depth, dmo, duration, erddap, label, latitude, longitude, management, oceanography, office, platform, preliminary, recover, recover_date_time, Recover_Date_UTC, Recover_Latitude, Recover_Longitude, Recover_Time_UTC, time, trap, Trap_Platform
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/749412/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/749412
attribute	NC_GLOBAL	Northernmost_Northing	double	39.88133333
attribute	NC_GLOBAL	param_mapping	String	{'749412': {'Deploy_Latitude': 'flag - latitude', 'deploy_date_time': 'flag - time', 'Deploy_Longitude': 'flag - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/749412/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	Moss Landing Marine Laboratories
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	MLML
attribute	NC_GLOBAL	people_0_person_name	String	Colleen Durkin
attribute	NC_GLOBAL	people_0_person_nid	String	675299
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	Skidmore College
attribute	NC_GLOBAL	people_1_person_name	String	Margaret L. Estapa
attribute	NC_GLOBAL	people_1_person_nid	String	644830
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	University of Rhode Island
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	URI-GSO
attribute	NC_GLOBAL	people_2_person_name	String	Melissa Omand
attribute	NC_GLOBAL	people_2_person_nid	String	675309
attribute	NC_GLOBAL	people_2_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_2_role_type	String	originator
attribute	NC_GLOBAL	people_3_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_3_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_3_person_name	String	Mathew Biddle
attribute	NC_GLOBAL	people_3_person_nid	String	708682
attribute	NC_GLOBAL	people_3_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_3_role_type	String	related
attribute	NC_GLOBAL	project	String	EAGER DNA BioPump
attribute	NC_GLOBAL	projects_0_acronym	String	EAGER DNA BioPump
attribute	NC_GLOBAL	projects_0_description	String	Text from the NSF award abstract: Carbon is fixed into organic matter by phytoplankton growing in the surface ocean, and is naturally sequestered in the ocean interior when particles and organisms sink: a process called the "biological pump." Because of its recognized influence on the global carbon cycle, ocean scientists have studied the biological pump for decades. However, we still do not have a sufficient understanding of the underlying processes to accurately quantify and predict carbon cycling. Much of this uncertainty stems from an inability to directly link specific plankton in the surface ocean with the types of particles sinking out of the surface ocean. To address this missing link in biological pump research, this work will directly observe how plankton are transported out of the surface ocean using novel, particle-specific observational approaches embedded within an interdisciplinary field program that will finely resolve upper ocean plankton groups and the resulting amount of sinking carbon across space and in time. The genetic identity of organisms within different types of sinking particles will be determined by sequencing the genetic contents of individually collected particles. This new application of a molecular method will definitively link surface plankton with sinking particles at five locations across the Pacific Ocean. This work has the potential to transform our understanding of the biological pump by identifying previously unknown links between surface ecosystems and sinking carbon particles. Because this work is embedded within an interdisciplinary field program, including biogeochemical modelers and remote sensing scientists, these data will feed directly into new models of the biological pump, improving our ability to quantify and predict carbon uptake by the ocean. This project will train 1 graduate student and at least 2 undergraduate researchers. Findings will be communicated to the non-scientific public through blogs, videos, and the public communication channels of participating institutions. Accurate prediction of the global carbon cycle requires an understanding of the specific processes that link surface plankton communities and sinking particulate carbon flux (export) out of the surface ocean, but current methodological paradigms in biological pump research do not directly observe these processes. This project will comprehensively determine who is exported from the surface ocean and how using new, particle-resolving optical and molecular techniques embedded within a sampling scheme that characterizes export events at high time and space resolution. The investigation suggests that different plankton types in the surface waters are transported out of the surface ocean by distinct export pathways, and that an understanding of these connections is critical knowledge for global carbon cycle modeling. If successful, this work has the potential to transform our conceptual understanding of the biological pump by directly identifying mechanisms that link surface plankton with particle export, without relying on bulk sampling schemes and large-scale correlation analysis. Particle export environments will be studied at five open ocean locations during a cruise from Hawaii to Seattle in January-February 2017. The surface plankton communities will be characterized by a combination of satellite observations, sensors attached to a free-drifting, continuously profiling WireWalker, an in situ holographic camera, microscopy, and by sequencing 18S and 16S rRNA gene fragments. Exported particles will simultaneously be captured by various specialized sediment traps and their characteristics will be directly related to their sources in the surface community by identifying the genetic contents of individual particle types. Individual particles will be isolated from gel layers and the 16S and 18S rRNA gene fragments will be amplified and sequenced. This work would, for the first time, combine molecular approaches with particle-specific observations to enable simultaneous identification of both which organisms are exported and the processes responsible for their export.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-11
attribute	NC_GLOBAL	projects_0_geolocation	String	Eastern Pacific
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump
attribute	NC_GLOBAL	projects_0_project_nid	String	675296
attribute	NC_GLOBAL	projects_0_start_date	String	2016-12
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	22.329
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017
attribute	NC_GLOBAL	time_coverage_end	String	2017-02-13T17:48Z
attribute	NC_GLOBAL	time_coverage_start	String	2015-11-04T11:03Z
attribute	NC_GLOBAL	title	String	[Geltrap micrographs] - Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017 (Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-71.09866667
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	Cruise		String
attribute	Cruise	bcodmo_name	String	cruise_id
attribute	Cruise	description	String	Cruise identifier
attribute	Cruise	long_name	String	Cruise
attribute	Cruise	units	String	unitless
variable	Trap_Platform		String
attribute	Trap_Platform	bcodmo_name	String	platform
attribute	Trap_Platform	description	String	trap identifier
attribute	Trap_Platform	long_name	String	Trap Platform
attribute	Trap_Platform	units	String	unitless
variable	Additional_Trap_Label		String
attribute	Additional_Trap_Label	bcodmo_name	String	unknown
attribute	Additional_Trap_Label	description	String	additional trap label
attribute	Additional_Trap_Label	long_name	String	Additional Trap Label
attribute	Additional_Trap_Label	units	String	unitless
variable	Depth		short
attribute	Depth	_FillValue	short	32767
attribute	Depth	actual_range	short	50, 200
attribute	Depth	bcodmo_name	String	depth_trap
attribute	Depth	colorBarMaximum	double	8000.0
attribute	Depth	colorBarMinimum	double	-8000.0
attribute	Depth	colorBarPalette	String	TopographyDepth
attribute	Depth	description	String	depth of trap
attribute	Depth	long_name	String	Depth
attribute	Depth	standard_name	String	depth
attribute	Depth	units	String	meters
variable	Deployment_Duration_days		float
attribute	Deployment_Duration_days	_FillValue	float	NaN
attribute	Deployment_Duration_days	actual_range	float	1.042, 3.41
attribute	Deployment_Duration_days	bcodmo_name	String	duration
attribute	Deployment_Duration_days	description	String	deployment duration
attribute	Deployment_Duration_days	long_name	String	Deployment Duration Days
attribute	Deployment_Duration_days	units	String	days
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	22.329, 39.88133333
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	deployment 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	source_name	String	Deploy_Latitude
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	-71.09866667, 151.903
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	deployment 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	source_name	String	Deploy_Longitude
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	Deploy_Date_UTC		String
attribute	Deploy_Date_UTC	bcodmo_name	String	date
attribute	Deploy_Date_UTC	description	String	date of deployment in UTC following ISO-8601 convention
attribute	Deploy_Date_UTC	long_name	String	Deploy Date UTC
attribute	Deploy_Date_UTC	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	Deploy_Date_UTC	units	String	unitless
variable	Deploy_Time_UTC		String
attribute	Deploy_Time_UTC	bcodmo_name	String	time
attribute	Deploy_Time_UTC	description	String	Time of deployment in UTC following ISO-8601 convention
attribute	Deploy_Time_UTC	long_name	String	Deploy Time UTC
attribute	Deploy_Time_UTC	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/
attribute	Deploy_Time_UTC	units	String	unitless
variable	Recover_Latitude		double
attribute	Recover_Latitude	_FillValue	double	NaN
attribute	Recover_Latitude	actual_range	double	21.592, 39.94433333
attribute	Recover_Latitude	bcodmo_name	String	latitude
attribute	Recover_Latitude	colorBarMaximum	double	90.0
attribute	Recover_Latitude	colorBarMinimum	double	-90.0
attribute	Recover_Latitude	description	String	recover latitude with positive values indicating North
attribute	Recover_Latitude	long_name	String	Latitude
attribute	Recover_Latitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	Recover_Latitude	standard_name	String	latitude
attribute	Recover_Latitude	units	String	decimal degrees
variable	Recover_Longitude		double
attribute	Recover_Longitude	_FillValue	double	NaN
attribute	Recover_Longitude	actual_range	double	-71.092106, 151.779
attribute	Recover_Longitude	bcodmo_name	String	longitude
attribute	Recover_Longitude	colorBarMaximum	double	180.0
attribute	Recover_Longitude	colorBarMinimum	double	-180.0
attribute	Recover_Longitude	description	String	recover longitude with negative values indicating West
attribute	Recover_Longitude	long_name	String	Longitude
attribute	Recover_Longitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	Recover_Longitude	standard_name	String	longitude
attribute	Recover_Longitude	units	String	decimal degrees
variable	Recover_Date_UTC		String
attribute	Recover_Date_UTC	bcodmo_name	String	date
attribute	Recover_Date_UTC	description	String	date of recover in UTC following ISO-8601 convention
attribute	Recover_Date_UTC	long_name	String	Recover Date UTC
attribute	Recover_Date_UTC	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/
attribute	Recover_Date_UTC	units	String	unitless
variable	Recover_Time_UTC		String
attribute	Recover_Time_UTC	bcodmo_name	String	time
attribute	Recover_Time_UTC	description	String	Time of recover in UTC following ISO-8601 convention
attribute	Recover_Time_UTC	long_name	String	Recover Time UTC
attribute	Recover_Time_UTC	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/
attribute	Recover_Time_UTC	units	String	unitless
variable	time		double
attribute	time	_CoordinateAxisType	String	Time
attribute	time	actual_range	double	1.44663498E9, 1.48700808E9
attribute	time	axis	String	T
attribute	time	bcodmo_name	String	ISO_DateTime_UTC
attribute	time	description	String	deployment date and time following ISO-8901 convention
attribute	time	ioos_category	String	Time
attribute	time	long_name	String	Deploy Date Time
attribute	time	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/
attribute	time	source_name	String	deploy_date_time
attribute	time	standard_name	String	time
attribute	time	time_origin	String	01-JAN-1970 00:00:00
attribute	time	time_precision	String	1970-01-01T00:00Z
attribute	time	units	String	seconds since 1970-01-01T00:00:00Z
variable	recover_date_time		String
attribute	recover_date_time	bcodmo_name	String	ISO_DateTime_UTC
attribute	recover_date_time	description	String	recover date and time following ISO-8901 convention
attribute	recover_date_time	long_name	String	Recover Date Time
attribute	recover_date_time	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/DTUT8601/
attribute	recover_date_time	time_precision	String	1970-01-01T00:00Z
attribute	recover_date_time	units	String	unitless

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.