ERDDAP > info > bcodmo_dataset_719487

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	[EN556 bulk peptidase hydrolysis rates - plate reader] - Hydrolysis rates from bulk samples, plate reader results from RV/Endeavor EN556, 2015 (Patterns of activities project) (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?)		I   M	background			BCO-DMO	bcodmo_dataset_719487

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	Seawater was transferred to 20 L carboys that were rinsed three times with water from the sampling depth and then filled with seawater from a single Niskin bottle, using silicone tubing that had been acid washed then rinsed with distilled water prior to use. From each carboy, water was dispensed into smaller glass containers that were cleaned and pre-rinsed three times with water from the carboy prior to dispensing. This water was used to measure cell counts, bacterial productivity, and the activities of polysaccharide hydrolases, peptidases, and glucosidases. A separate glass Duran bottle was filled with seawater from the carboy and sterilized in an autoclave for 20-30 minutes to serve as a killed control for microbial activity measurements. Two substrates, -glucose and -glucose linked to a 4-methylumbelliferyl (MUF) fluorophore, were used to measure glucosidase activities. Five substrates linked to a 7-amido-4-methyl coumarin (MCA) fluorophore, one amino acid \u2013 leucine \u2013 and four oligopeptides \u2013 the chymotrypsin substrates alanine-alanine-phenylalanine (AAF) and alanine-alanine-proline-phenylalanine (AAPF), and the trypsin substrates glutamine-alanine-arginine (QAR) and phenylalanine-serine-arginine (FSR) \u2013 were used to measure exo- and endo- acting peptidase activities, respectively. Hydrolysis rates of the substrates were measured as an increase in fluorescence as the fluorophore was hydrolyzed from the substrate over time [as in Hoppe, 1993; Obayashi and Suzuki, 2005]. Incubations with the seven low molecular weight substrates were set up in a 96-well plate. For each substrate, triplicate wells were filled with a total volume of 200 L seawater for experimental incubations; triplicate wells were filled with 200 L autoclaved seawater for killed control incubations. Substrate was added at saturating concentrations. A saturation curve was determined with surface water from each station to determine saturating concentrations of substrate. The saturating concentration was identified as the lowest tested concentration of substrate at which additional substrate did not yield higher rates of hydrolysis. Fluorescence was measured over 24-48 hours incubation time with a plate reader (TECAN spectrafluor plus; 360 nm excitation, 460 emission), with time points taken every 4-6 hours. Hydrolysis rates were calculated from the rate of increase of fluorescence in the incubation over time relative to a set of standards of known concentration of fluorophore. Scripts to calculate hydrolysis rates and produce the figures shown here are available in the associated Github repository [Hoarfrost, 2017]. The potential of the seawater microbial community to hydrolyze six high- molecular-weight polysaccharides (arabinogalactan, chondroitin sulfate, fucoidan, laminarin, pullulan, and xylan) was investigated in surface and bottom water. For each substrate, three 50 mL falcon tubes were filled with seawater and one 50 mL falcon tube was filled with autoclaved seawater to serve as a killed control. Substrate was added at 3.5 \u03bcM monomer- equivalent concentrations, except for fucoidan, which was added at 5 \u03bcM concentrations (a higher concentration was necessary for sufficient fluorescence signal). Two 50 mL falcon tubes \u2013 one with seawater and one with autoclaved seawater \u2013 with no added substrate served as blank controls. Incubations were stored in the dark at as close to in situ temperature as possible. Subsamples of the incubations were collected at time zero, and at six subsequent time points (t1-t6): 2 days, 5 days, 10 days, 17 days, 30 days, and 42 days. At each time point, 2 mL of seawater was collected from the 50 mL falcon tube using a sterile syringe, filtered through a 0.2 \u03bcm pore size syringe filter, and stored frozen until processing.
attribute	NC_GLOBAL	awards_0_award_nid	String	712358
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1332881
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1332881
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	Henrietta N Edmonds
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	51517
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Hydrolysis rates from bulk samples, plate reader results: EN556 C. Arnosti (UNC) version: 2017-11-16
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	2017-11-17T15:23:29Z
attribute	NC_GLOBAL	date_modified	String	2020-05-13T14:03:00Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.719487.1
attribute	NC_GLOBAL	geospatial_vertical_max	double	4574.0
attribute	NC_GLOBAL	geospatial_vertical_min	double	1.0
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/719487
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Niskin bottle
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Used to collect water for large volume mesocosm experiments
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	719493
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	30 liter Niskin bottles
attribute	NC_GLOBAL	instruments_1_acronym	String	Fluorometer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	719494
attribute	NC_GLOBAL	instruments_1_description	String	A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/113/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Fluorometer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	484
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	719495
attribute	NC_GLOBAL	instruments_2_description	String	Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: https://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
attribute	NC_GLOBAL	instruments_2_instrument_name	String	plate reader
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	528693
attribute	NC_GLOBAL	instruments_2_supplied_name	String	TECAN spectrafluor plus
attribute	NC_GLOBAL	keywords	String	average, bco, bco-dmo, biological, cast, chemical, cruise, cruise_id, data, dataset, depth, depth_m, depth_no, dev, dmo, erddap, management, oceanography, office, preliminary, profiler, rate, rep1, rep1_rate, rep2, rep2_rate, rep3, rep3_rate, salinity, salinity-temperature-depth, station, std, std_dev, substrate, temperature
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/719487/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/719487
attribute	NC_GLOBAL	param_mapping	String	{'719487': {'depth_m': 'master - depth'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/719487/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of North Carolina at Chapel Hill
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UNC-Chapel Hill
attribute	NC_GLOBAL	people_0_person_name	String	Carol Arnosti
attribute	NC_GLOBAL	people_0_person_nid	String	661940
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	Patterns of activities
attribute	NC_GLOBAL	projects_0_acronym	String	Patterns of activities
attribute	NC_GLOBAL	projects_0_description	String	NSF Award Abstract: Heterotrophic microbial communities are key players in the marine carbon cycle, transforming and respiring organic carbon, regenerating nutrients, and acting as the final filter in sediments through which organic matter passes before long-term burial. Microbially-driven carbon cycling in the ocean profoundly affects the global carbon cycle, but key factors determining rates and locations of organic matter remineralization are unclear. In this study, researchers from the University of North Carolina at Chapel Hill will investigate the ability of pelagic microbial communities to initiate the remineralization of polysaccharides and proteins, which together constitute a major pool of organic matter in the ocean. Results from this study will be predictive on a large scale regarding the nature of the microbial response to organic matter input, and will provide a mechanistic framework for interpreting organic matter reactivity in the ocean. Broader Impacts: This study will provide scientific training for undergraduate and graduate students from underrepresented groups. The project will also involve German colleagues, thus strengthening international scientific collaboration.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-07
attribute	NC_GLOBAL	projects_0_geolocation	String	Atlantic Ocean, Arctic Ocean, Pacific Ocean, Greenland
attribute	NC_GLOBAL	projects_0_name	String	Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?
attribute	NC_GLOBAL	projects_0_project_nid	String	712359
attribute	NC_GLOBAL	projects_0_start_date	String	2013-08
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	subsetVariables	String	cruise_id
attribute	NC_GLOBAL	summary	String	This dataset includes polysaccharide hydrolysis rates to measure microbial enzyme activities and bacterial productivity, from bulk samples, plate reader results from RV/Endeavor EN556, 2015.
attribute	NC_GLOBAL	title	String	[EN556 bulk peptidase hydrolysis rates - plate reader] - Hydrolysis rates from bulk samples, plate reader results from RV/Endeavor EN556, 2015 (Patterns of activities project) (Latitudinal and depth-related contrasts in enzymatic capabilities of pelagic microbial communities: Predictable patterns in the ocean?)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	cruise_id		String
attribute	cruise_id	bcodmo_name	String	cruise_id
attribute	cruise_id	description	String	cruise identifier
attribute	cruise_id	long_name	String	Cruise Id
attribute	cruise_id	units	String	unitless
variable	station		byte
attribute	station	_FillValue	byte	127
attribute	station	actual_range	byte	1, 8
attribute	station	bcodmo_name	String	station
attribute	station	description	String	station number
attribute	station	long_name	String	Station
attribute	station	units	String	unitless
variable	cast		byte
attribute	cast	_FillValue	byte	127
attribute	cast	actual_range	byte	1, 13
attribute	cast	bcodmo_name	String	cast
attribute	cast	description	String	cast number
attribute	cast	long_name	String	Cast
attribute	cast	units	String	unitless
variable	depth_no		String
attribute	depth_no	bcodmo_name	String	depth_comment
attribute	depth_no	description	String	depth description: sequence of depths sampled with 1 is surface and higher numbers at greater depths
attribute	depth_no	long_name	String	Depth
attribute	depth_no	standard_name	String	depth
attribute	depth_no	units	String	unitless
variable	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	1.0, 4574.0
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	actual depth at which water collected
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
variable	substrate		String
attribute	substrate	bcodmo_name	String	unknown
attribute	substrate	description	String	substrates for measurement of enzymatic activities: a-glu = alpha glucosidase: 4-methylumbelliferyl-a-D-glucopyranoside; b-glu = beta glucosidase: 4-methylumbelliferyl-beta-D-glucopyranoside; L = leucine aminopeptidase (L-leucine-7-amido-4 MCA); AAF = chymotrypsin activity: ala-ala-phe-MCA; AAPF = chymotrypsin activity: N-succinyl-ala-ala-pro-phe-MCA; QAR = trypsin activity: Boc-gln-ala-arg-MCA; FSR = trypsin activity: N-t-boc-phe-ser-arg-MCA
attribute	substrate	long_name	String	Substrate
attribute	substrate	units	String	unitless
variable	rep1_rate		float
attribute	rep1_rate	_FillValue	float	NaN
attribute	rep1_rate	actual_range	float	0.0, 127.93
attribute	rep1_rate	bcodmo_name	String	unknown
attribute	rep1_rate	description	String	replicate 1 of enzymatic hydrolysis rate
attribute	rep1_rate	long_name	String	Rep1 Rate
attribute	rep1_rate	units	String	nanomol monosaccharide/liter/hour
variable	rep2_rate		float
attribute	rep2_rate	_FillValue	float	NaN
attribute	rep2_rate	actual_range	float	0.0, 88.86
attribute	rep2_rate	bcodmo_name	String	unknown
attribute	rep2_rate	description	String	replicate 2 of enzymatic hydrolysis rate
attribute	rep2_rate	long_name	String	Rep2 Rate
attribute	rep2_rate	units	String	nanomol monosaccharide/liter/hour
variable	rep3_rate		float
attribute	rep3_rate	_FillValue	float	NaN
attribute	rep3_rate	actual_range	float	0.0, 85.03
attribute	rep3_rate	bcodmo_name	String	unknown
attribute	rep3_rate	description	String	replicate 3 of enzymatic hydrolysis rate
attribute	rep3_rate	long_name	String	Rep3 Rate
attribute	rep3_rate	units	String	nanomol monosaccharide/liter/hour
variable	average		float
attribute	average	_FillValue	float	NaN
attribute	average	actual_range	float	0.0, 80.0
attribute	average	bcodmo_name	String	unknown
attribute	average	description	String	average of the 3 hydrolysis rates
attribute	average	long_name	String	Average
attribute	average	units	String	nanomol monosaccharide/liter/hour
variable	std_dev		float
attribute	std_dev	_FillValue	float	NaN
attribute	std_dev	actual_range	float	0.0, 53.23
attribute	std_dev	bcodmo_name	String	unknown
attribute	std_dev	description	String	standard deviation of the 3 hydrolysis rates
attribute	std_dev	long_name	String	Std Dev
attribute	std_dev	units	String	nanomol monosaccharide/liter/hour

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.