ERDDAP > info > bcodmo_dataset_684323

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
	set	data	graph		files	public	Direct counts (flow cytometry) on microbes obtained by Niskin bottle and pressure-retaining sampler from the Leggo Lander on R/V Falkor cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014		I   M	background			BCO-DMO	bcodmo_dataset_684323

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	This data set is associated with PI Douglas Bartlett (NSF OCE-1536776) and Schmidt Ocean Institute R/V Falkor cruise FK141215. The cruise occurred December 15-21, 2014 in the Challenger Deep within the territorial waters of the Federated States of Micronesia. During this cruise the Leggo lander was deployed multiple times and drops 1 and 3 recovered seawater samples that were analyzed. Additional details can be found at: [https://schmidtocean.org/cruise /expanding-mariana-trench-perspectives/](\\"https://schmidtocean.org/cruise /expanding-mariana-trench-perspectives/\\") and [https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep- cruise-2014/](\\"https://scripps.ucsd.edu/labs/dbartlett/contact/challenger- deep-cruise-2014/\\") Leggo Lander Drop 1: Time (in Guam) deployed/recovered: December 16, 9:00/19:26. Position at deployment: 11\u00b0 21.9836 N 142\u00b0 25.9533 E, middle section of the Challenger Deep. Greatest depth of dive: approximately ~10,900 m. In situ temperature on seafloor: 2.6\u00b0C. Notes: This drop recovered seawater samples from about a meter off the seafloor.\u00a0This included a 3 L\u00a0Niskin bottle of seawater and ~ 150 mls of seawater collected in a pressure-retaining seawater sampler.\u00a0The PRS sampler held more than 81% of the in situ pressure.\u00a0 Flow Cytometry: Direct counts (flow cytometry) on the microbes obtained in the Leggo drop 1 Niskin bottle and the Leg drop 1 pressure-retaining sampler.\u00a0Samples were fixed with ~1% PFA and frozen. Later samples were removed from the -80 freezer and thawed in the dark. The Attune was started and a Performance Test was run with the \"Performance Tracking Beads\"\u00a0to check that all lasers and filters were working, and that voltages were correct. Cleaning and decontamination was also done using the Attune Wash solution and MilliQ water. Random samples selected from Logan's samples were run using Instrument Settings in the Attune software. This allows for real-time adjustments of voltages and thresholds in the different channels to get the best resolution for that day\u2019s run as well as allows for quantification of instrument noise for a given day. Once samples were thawed, 300 uL of each sample was loaded into a 96-well U-bottom plate. 3 uL of Invitrogen Sybr-green stain (diluted to 100x in MilliQ water) was then added to each well. The plate then incubated in the dark for 30 minutes before being run. The Sybr-green stain stains any DNA within a cell which then fluoresces when passing the BL1 channel laser, allowing for counts of cells. Once instrument settings were determined for the day, the plate was loaded into the NxT autosampler and the run was started. Samples were run at \"Standard\" sensitivity at 100 uL/min for a total volume of 250 uL. Counts were delayed for 15 seconds to avoid any noise or dilution that can occur when sample starts being sipped. Once entire plate was run, I used the Attune software to correct for noise and gate various populations within the samples. Note: Leggo1 is the first drop of the Leggo Lander and the values reflect the flow cytometric cell counts from its 2 liter Niskin bottle. Leggo1_PRS_day_2 is the flow cytometric cell count obtained from the pressure retaining sampler used on the first Leggo drop, following incubation in ice water for about 36 hours after recovery. Colony Identification: Data from the identification of bacteria cultured from the Leggo drop 1 and 3 Niskin bottles are available as a [supplemental file](\\"https://datadocs .bco- dmo.org/docs/bartlett/mariana_perspectives/data_docs/colony_identification.txt\\") (.txt).\u00a0These identifications were performed using standard methods associated with PCR amplification of the 16S rRNA gene followed by dideoxy sequencing at Retrogen Inc.\u00a0\u00a0
attribute	NC_GLOBAL	awards_0_award_nid	String	675559
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1536776
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1536776
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	Flow cytometry PI: Douglas Bartlett (UCSD) Version: 13 March 2017 Notes: Leggo1 is the first drop of the Leggo Lander and the values reflect the flow cytometric cell counts from its 2 liter Niskin bottle. Leggo1_PRS_day_2 is the flow cytometric cell count obtained from the pressure retaining sampler used on the first Leggo drop, following incubation in ice water for about 36 hours after recovery.
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	2017-03-14T18:19:38Z
attribute	NC_GLOBAL	date_modified	String	2020-01-21T21:07:29Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.684323.1
attribute	NC_GLOBAL	Easternmost_Easting	double	142.432555
attribute	NC_GLOBAL	geospatial_lat_max	double	11.36639
attribute	NC_GLOBAL	geospatial_lat_min	double	11.36639
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	142.432555
attribute	NC_GLOBAL	geospatial_lon_min	double	142.432555
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/684323
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	684330
attribute	NC_GLOBAL	instruments_0_description	String	A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	413
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Niskin bottle
attribute	NC_GLOBAL	instruments_1_acronym	String	Flow Cytometer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	684332
attribute	NC_GLOBAL	instruments_1_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_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB37/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Flow Cytometer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	660
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	684329
attribute	NC_GLOBAL	instruments_2_description	String	The "Leggo Lander" is a lander system that primarily relies on syntactic foam for buoyancy and uses iridium GPS, radio signal, strobe light and flag for surface recovery, and acoustics for underwater monitoring and instrument control. The lander has a timer with 5 control settings for various operations. It routinely measures pressure (depth) throughout its dive and temperature on the seafloor. The lander payloads include a pressure-retaining seawater sampler plus 2 liter Niskin bottle, and a camera/battery/light system that also includes a 30 liter Niskin bottle and a sea cucumber trap. With the camera payload it travels down or up the water column at about 39 meters per minute (~ 4.5 hours for a descent to the Challenger Deep at ~10,920 m). (Description obtained from the R/V Falkor FK141215 post-cruise report (PDF))
attribute	NC_GLOBAL	instruments_2_instrument_name	String	Leggo Lander
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	684302
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, cells, cells_per_mL, chemical, data, dataset, date, deploy, dmo, drop, drop_name, erddap, iso, ISO_DateTime_recover, latitude, longitude, management, name, oceanography, office, per, preliminary, recover, time
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/684323/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/684323
attribute	NC_GLOBAL	Northernmost_Northing	double	11.36639
attribute	NC_GLOBAL	param_mapping	String	{'684323': {'lat': 'flag - latitude', 'lon': 'flag - longitude', 'ISO_DateTime_deploy': 'flag - time'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/684323/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of California-San Diego
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UCSD-SIO
attribute	NC_GLOBAL	people_0_person_name	String	Douglas Bartlett
attribute	NC_GLOBAL	people_0_person_nid	String	675562
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	Mariana Perspectives
attribute	NC_GLOBAL	projects_0_acronym	String	Mariana Perspectives
attribute	NC_GLOBAL	projects_0_description	String	Award Abstract from NSF: The deepest portion of the ocean is present in ocean trenches, whose steep walls descend from approximately 4 miles down to depths that in some cases are close to 7 miles below the seawater surface. At these locations Earth's crust is recycled. Perhaps not surprisingly given their remoteness, deep ocean trenches are the least understood habitats in the ocean. The researchers participating in this project are working to characterize the microbes present in two of the deepest trenches present on Earth, both in the Pacific Ocean, the Kermadec Trench located north of New Zealand, and the Mariana Trench, located east and south of the island of Guam. Most of the Mariana Trench is located within the United States Mariana Trench Marine National Monument. Relatively little is known about the diversity and adaptations of the microorganisms in deep ocean trenches. An unknown fraction of the microbes present have descended from shallow waters above and are unlikely to participate in any nutrient cycles in the deep sea. Others are adapted to near freezing temperatures and up to pressures greater than 10e7 kilograms per square meter (16,000 pounds per square inch). These latter microbes perform important roles recycling organic matter. But who are they? This project is contributing to the training of diverse undergraduate and graduate students participating in research, additional undergraduate students learning about microbes inhabiting extreme environments in a web-based class, and additional graduate students and postdoctoral scientists participating in an advanced training course being offered in Antarctica. Experiments being performed include direct counts of prokaryotes and viruses in seawater and sediments, analyses of the abundance and phylogenetic breadth of culturable heterotrophic bacteria at a range of pressures, measurements of bacterial community species diversity and richness both within and across seawater and sediment samples, as well as within and across the two trench systems, measurements of microbial activity as a function of pressure and the identification of high pressure-active cells. The data generated from these analyses are being integrated into the results of additional chemical, geological and biological measurements performed by others as a part of the National Science Foundation funded Hadal Ecosystems Studies Project. Two of the working hypotheses are that prokaryote numbers and diversity are generally positively correlated with surface productivity and proximity to the trench axis and that bacterial taxa exist which are endemic to specific trenches, present in multiple trenches and more widely distributed in deep-sea environments.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-08
attribute	NC_GLOBAL	projects_0_geolocation	String	Challenger Deep, Mariana Trench
attribute	NC_GLOBAL	projects_0_name	String	Patterns of Microbial Community Structure Within and Between Hadal Environments
attribute	NC_GLOBAL	projects_0_project_nid	String	675560
attribute	NC_GLOBAL	projects_0_start_date	String	2015-09
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	11.36639
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	time,ISO_DateTime_recover,latitude,longitude
attribute	NC_GLOBAL	summary	String	Direct counts (flow cytometry) on the microbes obtained in the Leggo drop 1 Niskin bottle and the Leg drop 1 pressure-retaining sampler.
attribute	NC_GLOBAL	time_coverage_end	String	2014-12-16T09:00:00Z
attribute	NC_GLOBAL	time_coverage_start	String	2014-12-16T09:00:00Z
attribute	NC_GLOBAL	title	String	Direct counts (flow cytometry) on microbes obtained by Niskin bottle and pressure-retaining sampler from the Leggo Lander on R/V Falkor cruise FK141215 in the Challenger Deep, Mariana Trench in December 2014
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	142.432555
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	drop_name		String
attribute	drop_name	bcodmo_name	String	sample
attribute	drop_name	description	String	Name of the lander drop
attribute	drop_name	long_name	String	Drop Name
attribute	drop_name	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	drop_name	units	String	unitless
variable	cells_per_mL		double
attribute	cells_per_mL	_FillValue	double	NaN
attribute	cells_per_mL	actual_range	double	14306.66667, 184064.6667
attribute	cells_per_mL	bcodmo_name	String	abundance
attribute	cells_per_mL	description	String	Number of cells per milliliter (mL)
attribute	cells_per_mL	long_name	String	Cells Per M L
attribute	cells_per_mL	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P03/current/B070/
attribute	cells_per_mL	units	String	cells/mL
variable	time		double
attribute	time	_CoordinateAxisType	String	Time
attribute	time	actual_range	double	1.4187204E9, 1.4187204E9
attribute	time	axis	String	T
attribute	time	bcodmo_name	String	ISO_DateTime_Local
attribute	time	description	String	Date and time (local Guam time zone) of lander deployment; formatted to ISO 8601 standard.
attribute	time	ioos_category	String	Time
attribute	time	long_name	String	ISO Date Time Deploy
attribute	time	source_name	String	ISO_DateTime_deploy
attribute	time	standard_name	String	time
attribute	time	time_origin	String	01-JAN-1970 00:00:00
attribute	time	time_precision	String	1970-01-01T00:00:00Z
attribute	time	units	String	seconds since 1970-01-01T00:00:00Z
variable	ISO_DateTime_recover		String
attribute	ISO_DateTime_recover	bcodmo_name	String	ISO_DateTime_Local
attribute	ISO_DateTime_recover	description	String	Date and time (local Guam time zone) of lander recovery; formatted to ISO 8601 standard.
attribute	ISO_DateTime_recover	long_name	String	ISO Date Time Recover
attribute	ISO_DateTime_recover	time_precision	String	1970-01-01T00:00:00Z
attribute	ISO_DateTime_recover	units	String	unitless
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	11.36639, 11.36639
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 lander deployment
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	142.432555, 142.432555
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 lander deployment
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.