ERDDAP > info > bcodmo_dataset_767141

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	Limits of detection and qPCR efficiencies from cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017		I   M	background			BCO-DMO	bcodmo_dataset_767141

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	Nutrient analysis Nutrient samples were filtered through 0.22\u00a0\u03bcm pore size Durapore\u00a0GVWP filters (Millipore Sigma) and frozen at\u00a0\u221220_C immediately\u00a0after collection, then stored at\u00a0\u221280_C until analysis.\u00a0Dissolved nitrate (NO3\u00a0\u2212), nitrite (NO2\u00a0\u2212), phosphate (PO4\u00a03\u2212), and\u00a0silicate (SiO4\u00a04\u2212) were measured using a Bran and Luebbe AA3\u00a0autoanalyzer as described previously (Wilkerson et al. 2015).\u00a0Ammonium and urea were measured manually using the\u00a0phenolhypochlorite method (Sol\u00f3rzano 1969) and the diacetylmonoxime\u00a0method (Rahmatullah and Boyde 1980; Mulvenna\u00a0and Savidge 1992), respectively.\u00a0 Oxidation rate measurements\u00a0 We used 15N-labeled substrates (98\u201399% 15N, Cambridge\u00a0Isotope Laboratories) to measure the oxidation of N supplied\u00a0as NH4+, urea, 1,2-diaminoethane (DAE), 1,3-diaminopropane\u00a0(DAP), 1,4-diaminobutane (putrescine, PUT), L-glutamic acid\u00a0(GLU), and L-arginine (ARG). 15N oxidation from NH4+, urea,\u00a0PUT, and GLU were measured extensively, whereas 15N oxidation\u00a0from DAE, DAP, and ARG was only measured at a subset\u00a0of stations (Supporting Information Table S1). GLU and ARG\u00a0were included as a control for remineralization, as their central\u00a0roles in microbial metabolism leads to rapid catabolism and\u00a0NH4\u00a0+ regeneration (Hollibaugh 1978; Goldman et al. 1987).\u00a0PUT was used in routine assessments of the oxidation of\u00a0polyamine-N because it is one of the most consistently detected\u00a0polyamines in seawater (Nishibori et al. 2001a, 2003; Lu\u00a0et al. 2014; Liu et al. 2015). Although spermine and spermidine\u00a0are also common in seawater, 15N-labeled stocks of these polyamines\u00a0were not commercially available. We measured the oxidation\u00a0of N from DAE and DAP to investigate the effect of\u00a0aliphatic chain length (which affects pKa) on oxidation rate.\u00a0 Duplicate seawater samples contained in 1-liter polycarbonate\u00a0or 250 mL high density polyethylene (HDPE) bottles\u00a0wrapped with aluminum foil (to exclude light) were\u00a0amended with 10\u201350 nM 15N-labeled substrate. Marsh\u00a0Landing samples were then placed in an incubator held at\u00a0in situ temperature in the dark. Samples taken at the Skidaway\u00a0dock were placed in a mesh bag and immersed at the\u00a0sea surface at the sampling site. Samples collected at sea\u00a0were incubated in a tank of flowing surface seawater or in an\u00a0incubator held at 18\u00a0C in the dark. Incubation bottles were sampled\u00a0for 15N analysis immediately after substrate addition and\u00a0again after a period of ~ 24 h. 15N samples were subsampled into\u00a050 mL polypropylene centrifuge tubes, frozen at\u00a0\u221220_C, and\u00a0stored at\u00a0\u221280_C until analysis. The 15N/14N ratios of the NO3\u00a0\u2212\u00a0plus NO2\u00a0\u2212\u00a0(NOX) pools (\u03b415NNOx) in the samples were measured\u00a0using the bacterial denitrifier method to convert NOX to nitrous\u00a0oxide (N2O; Sigman et al. 2001). The\u00a0\u03b415N values of the N2O\u00a0produced were measured using a Finnigan MAT-252 isotope\u00a0ratio mass spectrometer coupled with a modified GasBench II interface (Casciotti et al. 2002; Beman et al. 2011; McIlvin\u00a0and Casciotti 2011). Oxidation rates were calculated using an\u00a0endpoint model (Beman et al. 2011; Damashek et al. 2016).\u00a0Since the substrates used were uniformly labeled with 15N, the\u00a0amount of the N added as the 15N spike (in\u00a0\u03bcM) was multiplied\u00a0by the number of moles of 15N per mole of substrate, which\u00a0assumes that all of the N atoms have equal probability of being\u00a0oxidized. This is likely true for urea, DAE, DAP, and PUT, which\u00a0are symmetrical molecules, but not likely to be true for ARG,\u00a0which contains 4 N atoms (one in the\u00a0\u03b1-amino position and\u00a0three in the guanidine structure of its R-group). Abiotic oxidation\u00a0of organic N was assessed by measuring 15NOX production\u00a0following 15N amendment and incubation of 0.22\u00a0\u03bcm filtered\u00a0seawater (as described above), and potential metabolism of\u00a0DON by the denitrifying bacteria used to convert NOX to N2O\u00a0was checked by adding 15N-labeled substrates into the bacterial\u00a0cultures prior to mass spectrometry.\u00a0 We were unable to measure the in situ concentrations of\u00a0the individual components of DON used in oxidation experiments,\u00a0other than urea. Based on previous measurements\u00a0made in the SAB (Lu et al. 2014; Liu et al. 2015), we assumed\u00a0concentrations of 1 nM and 0.25 nM for DAE, DAP and PUT,\u00a0and 10 nM and 5 nM for GLU and ARG, at inshore and\u00a0mid-shelf /shelf-break/oceanic stations, respectively. Rates of\u00a0polyamine and amino acid oxidation reported below should\u00a0therefore be considered potential rates, as amendments as low\u00a0as 10\u201350 nM are likely to increase substrate concentrations\u00a0substantially above in situ. Initial substrate 15N activity was\u00a0calculated using isotope mass balance using the known concentration\u00a0and 15N activity of the labeled substrates added\u00a0and assuming the concentrations described above and natural\u00a0abundance 15N activity (i.e., 0.3663 atom% 15N).\u00a0
attribute	NC_GLOBAL	awards_0_award_nid	String	757586
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1537995
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1537995
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	awards_1_award_nid	String	757590
attribute	NC_GLOBAL	awards_1_award_number	String	OCE-1538677
attribute	NC_GLOBAL	awards_1_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538677
attribute	NC_GLOBAL	awards_1_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_1_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_1_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_1_program_manager	String	Henrietta N Edmonds
attribute	NC_GLOBAL	awards_1_program_manager_nid	String	51517
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Limits of detection and qPCR efficiencies from cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017 PI: James T. Hollibaugh Version: 2019-05-08
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	2019-05-08T16:37:45Z
attribute	NC_GLOBAL	date_modified	String	2019-06-21T18:13:39Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.767141.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/767141
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	IR Mass Spec
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	The δ15N values of the N2O produced were measured using a Finnigan MAT-252 isotope ratio mass spectrometer coupled with a modified GasBench II interface
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	767198
attribute	NC_GLOBAL	instruments_0_description	String	The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).
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	Isotope-ratio Mass Spectrometer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	469
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Finnigan MAT-252 isotope ratio mass spectrometer
attribute	NC_GLOBAL	instruments_1_acronym	String	Bran Luebbe AA3 AutoAnalyzer
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	Dissolved nitrate (NO3 −), nitrite (NO2 −), phosphate (PO4 3−), and silicate (SiO4 4−) were measured using a Bran and Luebbe AA3 autoanalyzer as described previously (Wilkerson et al. 2015).
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	767197
attribute	NC_GLOBAL	instruments_1_description	String	Bran Luebbe AA3 AutoAnalyzer See the description from the manufacturer.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB04/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Bran Luebbe AA3 AutoAnalyzer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	700
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Bran and Luebbe AA3 autoanalyzer
attribute	NC_GLOBAL	instruments_2_acronym	String	qPCR
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	All reactions (25 μL total volume) were run in triplicate on a C1000 Touch Thermal Cycler equipped with a CFX96 Real-Time System (Bio- Rad), using either the iTaq Universal Green SYBR Mix (Bio-Rad) or the Platinum qPCR SuperMix-UDG (Thermo Fisher).
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	767199
attribute	NC_GLOBAL	instruments_2_description	String	An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).
attribute	NC_GLOBAL	instruments_2_instrument_name	String	qPCR Thermal Cycler
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	707569
attribute	NC_GLOBAL	instruments_2_supplied_name	String	C1000 Touch Thermal Cycler
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, biological, chemical, conditions, cycling, Cycling_conditions, data, dataset, detection, dmo, efficiency, erddap, forward, Forward_primer, limit, Limit_of_Detection_sample, Limit_of_Detection_template, management, number, Number_plates_run, oceanography, office, parameters, pcr, plates, preliminary, primer, probe, qPCR_Parameters, reference, reverse, Reverse_primer, run, sample, template
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/767141/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/767141
attribute	NC_GLOBAL	param_mapping	String	{'767141': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/767141/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	Dr James T. Hollibaugh
attribute	NC_GLOBAL	people_0_person_nid	String	662307
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 Hawaii
attribute	NC_GLOBAL	people_1_person_name	String	Brian N. Popp
attribute	NC_GLOBAL	people_1_person_nid	String	51093
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	DON Oxidation
attribute	NC_GLOBAL	projects_0_acronym	String	DON Oxidation
attribute	NC_GLOBAL	projects_0_description	String	NSF Abstract: Nitrogen is an essential nutrient for phytoplankton that often limits primary production in the ocean, and its availability therefore plays a key role in global ocean productivity. The amounts and form in which nitrogen exist are controlled by microorganisms. One microorganism-mediated process is known as nitrification, which oxidizes ammonia or ammonium to nitrite and nitrite to nitrate, nitrate being the bioavailable form of nitrogen. While this is the well-accepted process of nitrification, preliminary results strongly suggest that a nitrogen-containing compound know as polyamine nitrogen may be directly converted by some microorganisms to nitrate. However, the importance of this process for global biogeochemical nitrogen cycling is unknown. The goal of this study is to evaluate the biogeochemical significance of direct oxidation of polyamine nitrogen, as a model organic nitrogen compound, to nitrification compared to canonical nitrification of ammonia. The project will result in training a postdoctoral researcher and provide opportunities for undergraduates to gain hands-on experience with research on microbial geochemistry and coastal ecosystem processes. Project personnel will also work with the Georgia Coastal Ecosystems Long-Term Ecological Research program to engage a K-12 science teacher in the project. Ammonia oxidation is a key step in the process of converting fixed nitrogen to dinitrogen gas and thus is central to the global nitrogen cycle and to removing excess fixed nitrogen from coastal waters with high concentrations of nutrients. Recent research has shown that Thaumarchaeota play a major role in ammonia oxidation in the ocean. Experiments with enrichment cultures and coastal water samples where ammonia oxidizing archaea are the dominant ammonia oxidizers, show that some forms of organic nitrogen may be oxidized directly to nitrogen oxides without first being regenerated as ammonium. Of the substrates tested, polyamine and particularly putrescine nitrogen appear to be oxidized directly to nitrogen oxides, while amino acid and urea nitrogen is first regenerated as ammonium and then oxidized. The investigators will examine this process in detail over three years using enrichment cultures and experiments conducted with coastal bacterioplankton. Specifically, they will aim to better understand 1) the consequences of this novel process to ocean geochemistry, 2) the fate of the carbon present in polyamines, 3) what organisms are responsible for the direct oxidation, and 4) the chemical characteristics of the organic nitrogen compounds accessible to direct oxidation.
attribute	NC_GLOBAL	projects_0_end_date	String	2018-11
attribute	NC_GLOBAL	projects_0_geolocation	String	Coastal waters and the South Atlantic Bight continental shelf from Savannah GA out to the shelf break (SAV 17-16, UNOLS STR _104733, Marsden Grid 117, Navy Ops NA06), coastal waters around Sapelo Island, Georgia USA
attribute	NC_GLOBAL	projects_0_name	String	Collaborative Research: Direct Oxidation of Organic Nitrogen by Marine Ammonia Oxidizing Organisms
attribute	NC_GLOBAL	projects_0_project_nid	String	757587
attribute	NC_GLOBAL	projects_0_start_date	String	2015-12
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	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	summary	String	This dataset contains the results of analyses related to ammonia oxidation rates, including oxidation rates of 15N supplied as ammonia, urea, 1,2 diamino ethane, 1,3 diamino propane, 1,4 diamino butane (putrescine), arginine and glutamate. Ancillary data including nutrient concentrations and the abundance of ammonia- and nitrite-oxidizing microorganisms are also reported. The samples analyzed to produce the dataset were collected off the coast of Georgia, USA. Most data were collected on one cruise in August 2017, incidental data from 2011, 2013 and 2016 are also reported.
attribute	NC_GLOBAL	title	String	Limits of detection and qPCR efficiencies from cruise SAV 17-16 in the South Atlantic Bight aboard the R/V Savannah from 2011 to 2017
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	qPCR_Parameters		String
attribute	qPCR_Parameters	bcodmo_name	String	unknown
attribute	qPCR_Parameters	description	String	qPCR parameters
attribute	qPCR_Parameters	long_name	String	Q PCR Parameters
attribute	qPCR_Parameters	units	String	unitless
variable	Probe		String
attribute	Probe	bcodmo_name	String	unknown
attribute	Probe	description	String	Probe. All probes contained a 5' FAM tag and a 3' BHQ1 quencher.
attribute	Probe	long_name	String	Probe
attribute	Probe	units	String	unitless
variable	Forward_primer		String
attribute	Forward_primer	bcodmo_name	String	unknown
attribute	Forward_primer	description	String	forward primer
attribute	Forward_primer	long_name	String	Forward Primer
attribute	Forward_primer	units	String	unitless
variable	Reverse_primer		String
attribute	Reverse_primer	bcodmo_name	String	unknown
attribute	Reverse_primer	description	String	reverse primer
attribute	Reverse_primer	long_name	String	Reverse Primer
attribute	Reverse_primer	units	String	unitless
variable	Cycling_conditions		String
attribute	Cycling_conditions	bcodmo_name	String	unknown
attribute	Cycling_conditions	description	String	Cycling conditions
attribute	Cycling_conditions	long_name	String	Cycling Conditions
attribute	Cycling_conditions	units	String	unitless
variable	Efficiency		float
attribute	Efficiency	_FillValue	float	NaN
attribute	Efficiency	actual_range	float	92.8, 102.0
attribute	Efficiency	bcodmo_name	String	unknown
attribute	Efficiency	description	String	efficiency (%)
attribute	Efficiency	long_name	String	Efficiency
attribute	Efficiency	units	String	unitless
variable	Limit_of_Detection_template		float
attribute	Limit_of_Detection_template	_FillValue	float	NaN
attribute	Limit_of_Detection_template	actual_range	float	2.8, 9.9
attribute	Limit_of_Detection_template	bcodmo_name	String	unknown
attribute	Limit_of_Detection_template	description	String	Limit of detection of template
attribute	Limit_of_Detection_template	long_name	String	Limit Of Detection Template
attribute	Limit_of_Detection_template	units	String	copies per microliter of template
variable	Limit_of_Detection_sample		String
attribute	Limit_of_Detection_sample	bcodmo_name	String	unknown
attribute	Limit_of_Detection_sample	description	String	Limit of detection of sample
attribute	Limit_of_Detection_sample	long_name	String	Limit Of Detection Sample
attribute	Limit_of_Detection_sample	units	String	copies per liter of sample
variable	Number_plates_run		byte
attribute	Number_plates_run	_FillValue	byte	127
attribute	Number_plates_run	actual_range	byte	2, 5
attribute	Number_plates_run	bcodmo_name	String	unknown
attribute	Number_plates_run	colorBarMaximum	double	100.0
attribute	Number_plates_run	colorBarMinimum	double	0.0
attribute	Number_plates_run	description	String	number of plates run
attribute	Number_plates_run	long_name	String	Number Plates Run
attribute	Number_plates_run	units	String	count
variable	Reference		String
attribute	Reference	bcodmo_name	String	unknown
attribute	Reference	description	String	citation for values
attribute	Reference	long_name	String	Reference
attribute	Reference	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.