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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\n \nNutrient samples were filtered through 0.22\\u00a0\\u03bcm pore size\nDurapore\\u00a0GVWP filters (Millipore Sigma) and frozen at\\u00a0\\u221220_C\nimmediately\\u00a0after collection, then stored at\\u00a0\\u221280_C until\nanalysis.\\u00a0Dissolved nitrate (NO3\\u00a0\\u2212), nitrite (NO2\\u00a0\\u2212),\nphosphate (PO4\\u00a03\\u2212), and\\u00a0silicate (SiO4\\u00a04\\u2212) were\nmeasured using a Bran and Luebbe AA3\\u00a0autoanalyzer as described previously\n(Wilkerson et al. 2015).\\u00a0Ammonium and urea were measured manually using\nthe\\u00a0phenolhypochlorite method (Sol\\u00f3rzano 1969) and the\ndiacetylmonoxime\\u00a0method (Rahmatullah and Boyde 1980; Mulvenna\\u00a0and\nSavidge 1992), respectively.\\u00a0\n \nOxidation rate measurements\\u00a0\n \nWe used 15N-labeled substrates (98\\u201399% 15N, Cambridge\\u00a0Isotope\nLaboratories) to measure the oxidation of N supplied\\u00a0as NH4+, urea,\n1,2-diaminoethane (DAE), 1,3-diaminopropane\\u00a0(DAP), 1,4-diaminobutane\n(putrescine, PUT), L-glutamic acid\\u00a0(GLU), and L-arginine (ARG). 15N\noxidation from NH4+, urea,\\u00a0PUT, and GLU were measured extensively,\nwhereas 15N oxidation\\u00a0from DAE, DAP, and ARG was only measured at a\nsubset\\u00a0of stations (Supporting Information Table S1). GLU and\nARG\\u00a0were included as a control for remineralization, as their\ncentral\\u00a0roles in microbial metabolism leads to rapid catabolism\nand\\u00a0NH4\\u00a0+ regeneration (Hollibaugh 1978; Goldman et al.\n1987).\\u00a0PUT was used in routine assessments of the oxidation\nof\\u00a0polyamine-N because it is one of the most consistently\ndetected\\u00a0polyamines in seawater (Nishibori et al. 2001a, 2003; Lu\\u00a0et\nal. 2014; Liu et al. 2015). Although spermine and spermidine\\u00a0are also\ncommon in seawater, 15N-labeled stocks of these polyamines\\u00a0were not\ncommercially available. We measured the oxidation\\u00a0of N from DAE and DAP\nto investigate the effect of\\u00a0aliphatic chain length (which affects pKa)\non oxidation rate.\\u00a0\n \nDuplicate seawater samples contained in 1-liter polycarbonate\\u00a0or 250 mL\nhigh density polyethylene (HDPE) bottles\\u00a0wrapped with aluminum foil (to\nexclude light) were\\u00a0amended with 10\\u201350 nM 15N-labeled substrate.\nMarsh\\u00a0Landing samples were then placed in an incubator held at\\u00a0in\nsitu temperature in the dark. Samples taken at the Skidaway\\u00a0dock were\nplaced in a mesh bag and immersed at the\\u00a0sea surface at the sampling\nsite. Samples collected at sea\\u00a0were incubated in a tank of flowing\nsurface seawater or in an\\u00a0incubator held at 18\\u00a0C in the dark.\nIncubation bottles were sampled\\u00a0for 15N analysis immediately after\nsubstrate addition and\\u00a0again after a period of ~ 24 h. 15N samples were\nsubsampled into\\u00a050 mL polypropylene centrifuge tubes, frozen\nat\\u00a0\\u221220_C, and\\u00a0stored at\\u00a0\\u221280_C until analysis. The\n15N/14N ratios of the NO3\\u00a0\\u2212\\u00a0plus NO2\\u00a0\\u2212\\u00a0(NOX)\npools (\\u03b415NNOx) in the samples were measured\\u00a0using the bacterial\ndenitrifier method to convert NOX to nitrous\\u00a0oxide (N2O; Sigman et al.\n2001). The\\u00a0\\u03b415N values of the N2O\\u00a0produced were measured using\na Finnigan MAT-252 isotope\\u00a0ratio mass spectrometer coupled with a\nmodified GasBench II interface (Casciotti et al. 2002; Beman et al. 2011;\nMcIlvin\\u00a0and Casciotti 2011). Oxidation rates were calculated using\nan\\u00a0endpoint model (Beman et al. 2011; Damashek et al. 2016).\\u00a0Since\nthe substrates used were uniformly labeled with 15N, the\\u00a0amount of the N\nadded as the 15N spike (in\\u00a0\\u03bcM) was multiplied\\u00a0by the number of\nmoles of 15N per mole of substrate, which\\u00a0assumes that all of the N atoms\nhave equal probability of being\\u00a0oxidized. This is likely true for urea,\nDAE, DAP, and PUT, which\\u00a0are symmetrical molecules, but not likely to be\ntrue for ARG,\\u00a0which contains 4 N atoms (one in the\\u00a0\\u03b1-amino\nposition and\\u00a0three in the guanidine structure of its R-group). Abiotic\noxidation\\u00a0of organic N was assessed by measuring 15NOX\nproduction\\u00a0following 15N amendment and incubation of 0.22\\u00a0\\u03bcm\nfiltered\\u00a0seawater (as described above), and potential metabolism\nof\\u00a0DON by the denitrifying bacteria used to convert NOX to N2O\\u00a0was\nchecked by adding 15N-labeled substrates into the bacterial\\u00a0cultures\nprior to mass spectrometry.\\u00a0\n \nWe were unable to measure the in situ concentrations of\\u00a0the individual\ncomponents of DON used in oxidation experiments,\\u00a0other than urea. Based\non previous measurements\\u00a0made in the SAB (Lu et al. 2014; Liu et al.\n2015), we assumed\\u00a0concentrations of 1 nM and 0.25 nM for DAE, DAP and\nPUT,\\u00a0and 10 nM and 5 nM for GLU and ARG, at inshore and\\u00a0mid-shelf\n/shelf-break/oceanic stations, respectively. Rates of\\u00a0polyamine and amino\nacid oxidation reported below should\\u00a0therefore be considered potential\nrates, as amendments as low\\u00a0as 10\\u201350 nM are likely to increase\nsubstrate concentrations\\u00a0substantially above in situ. Initial substrate\n15N activity was\\u00a0calculated using isotope mass balance using the known\nconcentration\\u00a0and 15N activity of the labeled substrates added\\u00a0and\nassuming the concentrations described above and natural\\u00a0abundance 15N\nactivity (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 (external link)
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 (external link)
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  \n  PI: James T. Hollibaugh \n  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/ (external link)
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 (external link)
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/ (external link)
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\nSee the description from the manufacturer.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB04/ (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/767141 (external link)
attribute NC_GLOBAL param_mapping String {'767141': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/767141/parameters (external link)
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:\nNitrogen 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.\nAmmonia 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

 
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