data

Metadata: 
  File identifier: 
      R4.x262.000-0021-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Lei Hu
      Organisation name: 
          Dauphin Island Sea Lab (DISL) / University Programs
      Position name: 
          Data Manager
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  2518617521
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  101 Bienville Blvd
              City: 
                  Dauphin Island
              Administrative area: 
                  Alabama
              Postal code: 
                  36528
              Country: 
                  USA
              Electronic mail address: 
                  lhu@disl.org
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2018-08-11T13:38:49+00:00
  Metadata standard name: 
      ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
  Metadata standard version: 
      ISO 19115-2:2009(E)
  Dataset URI: 
      https://data.gulfresearchinitiative.org/metadata/R4.x262.000:0021
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  Identification info: 
    Data identification: 
      Citation: 
        Citation: 
          Title: 
              Assessing the abundance of genes involved in the denitrification pathways collected in marsh and subtidal 
              unvegetated sediments at the Chandeleur Islands, July 2015 to February 2016
          Alternate title: 
          Date: 
            Date: 
              Date: 
                  2017-06-23
              Date type: 
                Date type code: 
                  publication
      Abstract: 
          Selected genes involved in nitrogen cycling were enumerated from sediment collected on the marsh platform as 
          well as from nearby subtidal unvegetated sediments in the Chandeleur Islands. Data were collected seasonally 
          from July 2015 to February 2016.
      Purpose: 
          The purpose of this study was to enumerate genes involved in denitrification in marsh and subtidal habitats 
          that were previously exposed to moderately levels of hydrocarbons.
      Status: 
        Progress code: 
          completed
      Point of contact: 
        Responsible party: 
          Individual name: 
              Patricia Sobecky
          Organisation name: 
              The University of Alabama / Department of Biological Sciences
          Position name: 
              Professor
          Contact info: 
            Contact: 
              Phone: 
                Telephone: 
                  Voice: 
                      2053481409
                  Facsimile: 
              Address: 
                Address: 
                  Delivery point: 
                      Box 870344
                  City: 
                      Tuscaloosa
                  Administrative area: 
                      Alabama
                  Postal code: 
                      35487
                  Country: 
                      USA
                  Electronic mail address: 
                      psobecky@ua.edu
          Role: 
            Role code: 
              pointOfContact
      Descriptive keywords: 
        Keywords: 
          Keyword: 
              sediments
          Keyword: 
              denitrification
          Keyword: 
              nitrogen cycling
          Type: 
            Keyword type code: 
              theme
      Descriptive keywords: 
        Keywords: 
          Keyword: 
              Chandeleur Islands
          Keyword: 
              Red Fish Point
          Keyword: 
              Gulf of Mexico
          Keyword: 
              Louisiana
          Type: 
            Keyword type code: 
              place
      Language: 
          eng; USA
      Topic category: 
        Topic category code: 
          environment
      Topic category: 
        Topic category code: 
          oceans
      Extent: 
        Extent: 
          Geographic element: 
            Geographic bounding box: 
              West bound longitude: 
                  -88.841188
              East bound longitude: 
                  -88.841188
              South bound latitude: 
                  29.862799
              North bound latitude: 
                  29.862799
          Geographic element: 
            BoundingPolygon: 
              Polygon: 
                gml:MultiPoint: 
                  gml:pointMember: 
                    Point: 
                      gml:pos: 
                        29.862799 -88.841188
          Temporal element: 
            Temporal extent: 
              Extent: 
                Time period: 
                  Description: 
                    ground condition
                  Begin date: 
                    2015-07-09
                  End date: 
                    2016-02-22
      Supplemental Information: 
          Date: month, day and year, Location: Location on the Map, Habitat: Marsh platform or subtidal unvegetated 
          sediments, Cores: replicate cores that were collected from each site, 16S (gene copies per gram): 16S 
          ribosomal (rRNA) in copies per gram sediment, napA (gene copies per gram): napA (nitrate reductase) gene 
          copies per gram sediment, norB (gene copies per gram): norB (nitric oxide reductase) gene copies per gram 
          sediment, nirS (gene copies per gram): nirS (nitrite reductase) gene copies per gram sediment, Latitude 
          Degrees: measured in degrees, Latitude Minutes: measured in minutes, Latitude Seconds: measured in seconds, 
          Longitude Degrees: measured in degrees, Longitude Minutes: measured in minutes, Longitude Seconds: measured 
          in seconds|Replicate cores were collected in the field and brought back to the laboratory where they were 
          set up for measurements of denitrification rates with the isotope pairing technique. At the termination of 
          the rate measurements the top 10cm of the cores were homogenized and frozen at -80oC for later analysis. DNA 
          was extracted in triplicate from 1 g sediment from each core with the FastDNATM Spin Kit for Soil (MP 
          Biomedicals) per the manufacturer’s protocol with the addition of two-minute ice incubations after the 
          homogenization and 4oC centrifugation steps. The triplicate extractions were pooled and purified using the 
          Zymoclean Gel DNA Recovery Kit (Zymo Research) and eluted with sterile milliQ water (total volume 50 µl). 
          DNA concentrations were measured via absorption at 260 nm using a NanoDrop ND-1000. Quantitative PCR (qPCR) 
          was performed to assess the abundance of three genes in the denitrification pathway: napA (nitrate 
          reductase), nirS (nitrite reductase), and norB (nitric oxide reductase). Total community abundance was 
          determined by qPCR of 16S ribosomal RNA (rRNA). Each reaction included Platinum SYBR Green qPCR supermix-UDG 
          with ROX (12.5 µL) (Invitrogen), 1 µL of forward and reverse primer (5 µM, IDT DNA technology), 0.5 µL MgCl2 
          (50 mM), and 5 ng of DNA template. The total reaction volume was adjusted to 25 µL with PCR grade water 
          (ThermoFisher). Following 2 min at 50ºC and activation of Platinum SYBR Green qPCR supermix-UDG with ROX at 
          95ºC for 10 min, thermal cycles consisted of (napA and nirS) 40 cycles of: 15 s at 95ºC (denaturation), 
          (norB) 30 cycles 15 s at 95ºC, 1 min at 60ºC elongation step, (16S) 30 cycles 15 s at 95oC, and 30 s at 
          72oC. Samples were run in duplicate on a 7000 Sequence Detection System (ABI Prism) with the primer 
          combinations, optimal annealing temperatures, and qPCR conditions detailed below. Primers and thermal 
          profiles (* denotes modified annealing temperature) used for PCR to generate standards and qPCR 
          quantification of different functional genes. Target gene: napA (qPCR) Primers: napA-1F; napA-1R Sequence(5’ 
          3’): GTY ATG GAR GAA AAA TTC AA; GAR CCG AAC ATG CCR AC References: Smith et al. (2007) Optimal Annealing 
          Temp.: 55 Celsius - 60 s Target gene: napA (PCR) Primers: napA V67 F; napA V67 R Sequence(5’ 3’): TAY TTY 
          YTN HSN AAR ATH ATG TAY GG; DAT NGG RTG CAT YTC NGC CAT RTT References: Flanagan et al. (1999) Optimal 
          Annealing Temp.: 55 Celsius - 30 s* Target gene: nirS (qPCR and PCR) Primers: nirScd3aF; nirS R3cd 
          Sequence(5’ 3’): GTS AAC GTS AAG GAR ACS GG; GAS TTC GGR TGS GTC TTG A References: Throback et al. (2004) 
          Optimal Annealing Temp.: 51 Celsius - 60 s Target gene: norB (qPCR and PCR) Primers: cnorB2F; cnorB6R 
          Sequence(5’ 3’): GAC AAG NNN TAC TGG TGG T; GAA NCC CCA NAC NCC NGC References: Geets et al. (2007) Optimal 
          Annealing Temp.: 50 Celsius - 60 s Target gene: 16S (PCR) Primers: 341F; 534R Sequence(5’ 3’): CCT ACG GGA 
          GGC AGC AG; ATT ACC GCG GCT GCT GGC A References: Bru et al. (2008) Optimal Annealing Temp.: 55 Celsius - 45 
          s Target gene: (q-PCR) Primers: N/A Sequence(5’ 3’): N/A References: López-Gutiérrez et al. (2004) Optimal 
          Annealing Temp.: 60 Celsius - 30 s Bru D, Martin-Laurent F, Philippot L. 2008. Quantification of the 
          Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an 
          Example. Applied and Environmental Microbiology 74:1660-1663. Flanagan DA, Gregory LG, Carter JP, 
          Karakas-Sen A, Richardson DJ & Spiro S. 1999. Detection of genes for periplasmic nitrate reductase in 
          nitrate respiring bacteria and in community DNA. Fems Microbiology Letters 177: 263-270. Geets J, de Cooman 
          M, Wittebolle L, Heylen K, Vanparys B, De Vos P, Verstraete W, & Boon N. 2007. Real-time PCR assay for the 
          simultaneous quantification of nitrifying and denitrifying bacteria in activated sludge. Applied Microbology 
          and Biotechnology 75:211-221. López-Gutiérrez JC, Henry S, Hallet S, Martin-Laurent F, Catroux G & Philippot 
          L. 2004. Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR. J 
          Microbiol Meth 57: 399-407. Smith, C. J., D.B. Nedwell, L.F. Dong, and A.M. Osborn. 2007. Diversity and 
          abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their 
          transcripts in estuarine sediments. App. Environ. Microbiol. 73: 3612-3622. Throbäck IN, Enwall K, Jarvis A, 
          Hallin S. 2004. Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of 
          denitrifying bacteria with DGGE. FEMS Microbiology Ecology 49:401-417.||||
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  Distribution info: 
    Distribution: 
      Distributor: 
        Distributor: 
          Distributor contact: 
            Responsible party: 
              Organisation name: 
                  Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC)
              Contact info: 
                Contact: 
                  Phone: 
                    Telephone: 
                      Voice: 
                          3618253604
                  Address: 
                    Address: 
                      Delivery point: 
                          6300 Ocean Drive
                      City: 
                          Corpus Christi
                      Administrative area: 
                          TX
                      Postal code: 
                          78412
                      Country: 
                          USA
                      Electronic mail address: 
                          griidc@gomri.org
                  Online Resource: 
                    Online Resource: 
                      Linkage: 
                        URL: 
                          https://data.gulfresearchinitiative.org
              Role: 
                Role code: 
                  distributor
          Distributor format: 
            Format: 
              Name: 
                  csv
              Version: 
                inapplicable
              File decompression technique: 
          Distributor transfer options: 
            Digital transfer options: 
              Transfer size: 
                  0.0065
              Online: 
                Online Resource: 
                  Linkage: 
                    URL: 
                      https://data.gulfresearchinitiative.org/data/R4.x262.000:0021
                  Protocol: 
                      https
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  Metadata maintenance: 
    Maintenance information: 
      Maintenance and update frequency: 
        unknown
      Maintenance note: 
          This ISO metadata record was automatically generated from information provided to GRIIDC for dataset: 
          R4.x262.000:0021 on 2018-12-13T00:08:26+00:00
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