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Dataset Title:  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
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_767141)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Files | Make a graph
Variable ?   Optional
Constraint #1 ?
Constraint #2 ?
   Minimum ?
   Maximum ?
 qPCR_Parameters (unitless) ?          "Bacterial 16S rRNA"    "WCB amoA"
 Probe (unitless) ?          "NaN"    "WCB-amoA-P; CCAAAG..."
 Forward_primer (unitless) ?          "Arch-amoAFB; CATCC..."    "WCA-amoA-F; ACACCA..."
 Reverse_primer (unitless) ?          "GI_554R; CTGTAGGCC..."    "WCB-amoA-R; AAYGCA..."
 Cycling_conditions (unitless) ?          "94 C 15 m 50 cycl..."    "95 C 10 m 40 cycl..."
 Efficiency (unitless) ?          92.8    102.0
 Limit_of_Detection_template (copies per microliter of template) ?          2.8    9.9
 Limit_of_Detection_sample (copies per liter of sample) ?          "270-1100"    "920-7000"
 Number_plates_run (count) ?          2    5
 Reference (unitless) ?          "Mincer et al. 2007"    "Suzuki et al. 2000"
Server-side Functions ?
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The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  qPCR_Parameters {
    String bcodmo_name "unknown";
    String description "qPCR parameters";
    String long_name "Q PCR Parameters";
    String units "unitless";
  Probe {
    String bcodmo_name "unknown";
    String description "Probe. All probes contained a 5' FAM tag and a 3' BHQ1 quencher.";
    String long_name "Probe";
    String units "unitless";
  Forward_primer {
    String bcodmo_name "unknown";
    String description "forward primer";
    String long_name "Forward Primer";
    String units "unitless";
  Reverse_primer {
    String bcodmo_name "unknown";
    String description "reverse primer";
    String long_name "Reverse Primer";
    String units "unitless";
  Cycling_conditions {
    String bcodmo_name "unknown";
    String description "Cycling conditions";
    String long_name "Cycling Conditions";
    String units "unitless";
  Efficiency {
    Float32 _FillValue NaN;
    Float32 actual_range 92.8, 102.0;
    String bcodmo_name "unknown";
    String description "efficiency (%)";
    String long_name "Efficiency";
    String units "unitless";
  Limit_of_Detection_template {
    Float32 _FillValue NaN;
    Float32 actual_range 2.8, 9.9;
    String bcodmo_name "unknown";
    String description "Limit of detection of template";
    String long_name "Limit Of Detection Template";
    String units "copies per microliter of template";
  Limit_of_Detection_sample {
    String bcodmo_name "unknown";
    String description "Limit of detection of sample";
    String long_name "Limit Of Detection Sample";
    String units "copies per liter of sample";
  Number_plates_run {
    Byte _FillValue 127;
    Byte actual_range 2, 5;
    String bcodmo_name "unknown";
    Float64 colorBarMaximum 100.0;
    Float64 colorBarMinimum 0.0;
    String description "number of plates run";
    String long_name "Number Plates Run";
    String units "count";
  Reference {
    String bcodmo_name "unknown";
    String description "citation for values";
    String long_name "Reference";
    String units "unitless";
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"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";
    String awards_0_award_nid "757586";
    String awards_0_award_number "OCE-1537995";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1537995";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "Henrietta N Edmonds";
    String awards_0_program_manager_nid "51517";
    String awards_1_award_nid "757590";
    String awards_1_award_number "OCE-1538677";
    String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1538677";
    String awards_1_funder_name "NSF Division of Ocean Sciences";
    String awards_1_funding_acronym "NSF OCE";
    String awards_1_funding_source_nid "355";
    String awards_1_program_manager "Henrietta N Edmonds";
    String awards_1_program_manager_nid "51517";
    String cdm_data_type "Other";
    String comment 
"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";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv version 2.3  19 Dec 2019";
    String date_created "2019-05-08T16:37:45Z";
    String date_modified "2019-06-21T18:13:39Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.767141.1";
    String history 
"2022-01-23T05:32:20Z (local files)
2022-01-23T05:32:20Z https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_767141.html";
    String infoUrl "https://www.bco-dmo.org/dataset/767141";
    String institution "BCO-DMO";
    String instruments_0_acronym "IR Mass Spec";
    String instruments_0_dataset_instrument_description "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";
    String instruments_0_dataset_instrument_nid "767198";
    String instruments_0_description "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).";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB16/";
    String instruments_0_instrument_name "Isotope-ratio Mass Spectrometer";
    String instruments_0_instrument_nid "469";
    String instruments_0_supplied_name "Finnigan MAT-252 isotope ratio mass spectrometer";
    String instruments_1_acronym "Bran Luebbe AA3 AutoAnalyzer";
    String instruments_1_dataset_instrument_description "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).";
    String instruments_1_dataset_instrument_nid "767197";
    String instruments_1_description 
"Bran Luebbe AA3 AutoAnalyzer
See the description from the manufacturer.";
    String instruments_1_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/LAB04/";
    String instruments_1_instrument_name "Bran Luebbe AA3 AutoAnalyzer";
    String instruments_1_instrument_nid "700";
    String instruments_1_supplied_name "Bran and Luebbe AA3 autoanalyzer";
    String instruments_2_acronym "qPCR";
    String instruments_2_dataset_instrument_description "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).";
    String instruments_2_dataset_instrument_nid "767199";
    String instruments_2_description "An instrument for quantitative polymerase chain reaction (qPCR), also known as real-time polymerase chain reaction (Real-Time PCR).";
    String instruments_2_instrument_name "qPCR Thermal Cycler";
    String instruments_2_instrument_nid "707569";
    String instruments_2_supplied_name "C1000 Touch Thermal Cycler";
    String keywords "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";
    String license "https://www.bco-dmo.org/dataset/767141/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/767141";
    String param_mapping "{'767141': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/767141/parameters";
    String people_0_affiliation "University of Georgia";
    String people_0_affiliation_acronym "UGA";
    String people_0_person_name "Dr James T. Hollibaugh";
    String people_0_person_nid "662307";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "University of Hawaii";
    String people_1_person_name "Brian N. Popp";
    String people_1_person_nid "51093";
    String people_1_role "Co-Principal Investigator";
    String people_1_role_type "originator";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Mathew Biddle";
    String people_2_person_nid "708682";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "DON Oxidation";
    String projects_0_acronym "DON Oxidation";
    String projects_0_description 
"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.";
    String projects_0_end_date "2018-11";
    String projects_0_geolocation "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";
    String projects_0_name "Collaborative Research: Direct Oxidation of Organic Nitrogen by Marine Ammonia Oxidizing Organisms";
    String projects_0_project_nid "757587";
    String projects_0_start_date "2015-12";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "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.";
    String title "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";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";


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