Community composition of ammonia oxidizing bacteria in Louisiana salt marshes three years after the Deepwater Horizon oil spill (2013)

Coastal Waters Consortium (CWC)

DOI:
10.7266/N7SF2T4H
 
UDI:
R1.x139.143:0060
Last Update:
Oct 11 2016 15:28 UTC
 
Dataset Author(s):
Bernhard, Anne
Point of Contact:
Bernhard, Anne E.
Connecticut College / Department of Biology
Box 5213 211 New London Hall, 270 Mohegan Ave.
New London, Connecticut  06320
USA
aeber@conncoll.edu
Funding Source:
RFP-I
Data Collection Period:
2013-03-01 to 2013-10-01

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Bernhard, Anne. 2016. Community composition of ammonia oxidizing bacteria in Louisiana salt marshes three years after the Deepwater Horizon oil spill (2013). Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7SF2T4H

Abstract:

This dataset contains relative abundances (%) of terminal restriction fragments of the ammonia monooxygenase genes (amoA) from ammonia-oxidizing betaproteobacteria (AOB). Data are from sediments collected from 12 marshes in Terrebonne Bay (TB), western Barataria Bay (WB), and Port Sulfur in eastern Barataria Bay (PS), LA. In each region, we sampled two oiled marshes and two unoiled marshes. At each marsh, we collected 5-cm deep soil cores along a 20-m transect from the marsh edge and collecting soil samples every 5 m. All sites were samples in May, July, and September 2013, with an additional sampling date in March 2013 at the TB sites.

Purpose:

This dataset was developed as part of a research project investigating the effects of the Deepwater Horizon oil spill on salt marsh biogeochemistry and microbial ecology. This particular project was directed to determine: 1) if there was a significant impact on community composition of ammonia-oxidizing betaproteobacterial communities; and 2) if there were spatial (regional, within marsh) or temporal patterns in their distribution.

Theme Keywords:

amoA, salt marsh, sediment, TRFLP, ammonia-oxidizing bacteria, community composition

File Format:

Excel Spreadsheet

Filename:

AOB_TRFLP_2013.xlsx (63.45 KB)

Dataset Downloads:

4

Community composition of ammonia oxidizing bacteria in Louisiana salt marshes three years after the Deepwater Horizon oil spill (2013)



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R1.x139.143-0060-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Anne E. Bernhard
      Organisation name: 
          Connecticut College / Department of Biology
      Position name: 
          Professor
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  8604392580
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  Box 5213
                  211 New London Hall, 270 Mohegan Ave.
              City: 
                  New London
              Administrative area: 
                  Connecticut
              Postal code: 
                  06320
              Country: 
                  USA
              Electronic mail address: 
                  aeber@conncoll.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2021-05-04T20:04:56+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/R1.x139.143:0060
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Identification info: Data identification: Citation: Citation: Title: Community composition of ammonia oxidizing bacteria in Louisiana salt marshes three years after the Deepwater Horizon oil spill (2013) Alternate title: Date: Date: Date: 2016-03-16 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/N7SF2T4H title: DOI doi:10.7266/N7SF2T4H Abstract: This dataset contains relative abundances (%) of terminal restriction fragments of the ammonia monooxygenase genes (amoA) from ammonia-oxidizing betaproteobacteria (AOB). Data are from sediments collected from 12 marshes in Terrebonne Bay (TB), western Barataria Bay (WB), and Port Sulfur in eastern Barataria Bay (PS), LA. In each region, we sampled two oiled marshes and two unoiled marshes. At each marsh, we collected 5-cm deep soil cores along a 20-m transect from the marsh edge and collecting soil samples every 5 m. All sites were samples in May, July, and September 2013, with an additional sampling date in March 2013 at the TB sites. Purpose: This dataset was developed as part of a research project investigating the effects of the Deepwater Horizon oil spill on salt marsh biogeochemistry and microbial ecology. This particular project was directed to determine: 1) if there was a significant impact on community composition of ammonia-oxidizing betaproteobacterial communities; and 2) if there were spatial (regional, within marsh) or temporal patterns in their distribution. Status: Progress code: completed Point of contact: Responsible party: Individual name: Anne E. Bernhard Organisation name: Connecticut College / Department of Biology Position name: Professor Contact info: Contact: Phone: Telephone: Voice: 8604392580 Facsimile: Address: Address: Delivery point: Box 5213 211 New London Hall, 270 Mohegan Ave. City: New London Administrative area: Connecticut Postal code: 06320 Country: USA Electronic mail address: aeber@conncoll.edu Role: Role code: principalInvestigator Descriptive keywords: Keywords: Keyword: amoA Keyword: salt marsh Keyword: sediment Keyword: TRFLP Keyword: ammonia-oxidizing bacteria Keyword: community composition Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: Barataria Bay Keyword: Louisiana Keyword: Gulf of Mexico Keyword: Terrebonne Bay Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Bernhard, Anne. 2016. Community composition of ammonia oxidizing bacteria in Louisiana salt marshes three years after the Deepwater Horizon oil spill (2013). Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7SF2T4H Resource constraints: title: CC0 License Legal constraints: Use constraints: Restriction code: licenceUnrestricted Other constraints: This information is released under the Creative Commons license - No Rights Reserved - CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/). The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Resource constraints: title: Liability and Warranty Legal constraints: Other constraints: All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be submitted by an individual who represents and warrants that s/he has sufficient rights to be able to make the content available under a CC0 waiver. There is no warranty (expressed or implied) to these materials, their title, accuracy, non-infringement of third party rights, or fitness for any particular purpose, including the performance or results you may obtain from their use. Use these materials at your own risk. Under no circumstances shall GRIIDC be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use or the inability to use either this website or the materials available via this website. If you are dissatisfied with any website feature, content, or terms of use, your sole and exclusive remedy is to discontinue use. Aggregation Info: AggregateInformation: Aggregate Data Set Name: title: Related Publication Citation Citation: Title: Bernhard, A. E., Chelsky, A., Giblin, A. E., & Roberts, B. J. (2019). Influence of Local and Regional Drivers on Spatial and Temporal Variation of Ammonia‐Oxidizing Communities in Gulf of Mexico Salt Marshes. Environmental Microbiology Reports. doi:10.1111/1758-2229.12802 Date: inapplicable Aggregate Data Set Identifier: title: Related Publication DOI Identifier: Code: Anchor: xlink: https://dx.doi.org/10.1111/1758-2229.12802 title: DOI doi:10.1111/1758-2229.12802 Association Type: Association type code: crossReference Language: eng; USA Topic category: Topic category code: biota Topic category: Topic category code: inlandWaters Extent: Extent: Geographic element: Geographic bounding box: West bound longitude: -90.60494 East bound longitude: -89.75 South bound latitude: 29.26584 North bound latitude: 29.4742 Geographic element: BoundingPolygon: Polygon: gml:MultiPoint: gml:pointMember: Point: gml:pos: 29.29297 -90.60494 gml:pointMember: Point: gml:pos: 29.2915 -90.60282 gml:pointMember: Point: gml:pos: 29.30449 -90.56582 gml:pointMember: Point: gml:pos: 29.2964 -90.54979 gml:pointMember: Point: gml:pos: 29.28895 -90.04267 gml:pointMember: Point: gml:pos: 29.26584 -90.02486 gml:pointMember: Point: gml:pos: 29.2801 -89.97583 gml:pointMember: Point: gml:pos: 29.27653 -89.97535 gml:pointMember: Point: gml:pos: 29.4608 -89.875 gml:pointMember: Point: gml:pos: 29.4508 -89.75 gml:pointMember: Point: gml:pos: 29.4458 -89.8761 gml:pointMember: Point: gml:pos: 29.4742 -89.8564 Temporal element: Temporal extent: Extent: Time period: Description: ground condition Begin date: 2013-03-01 End date: 2013-10-01 Supplemental Information: Region- identifies the region (TB for Terrebonne Bay, WB for western Barataria Bay, PS for Port Sulfur) Site - four sites within each region Plot number - four plots at each site that are increasing distance from marsh edge (1 = 5 m, 2 = 10 m, 3 = 15 m, 4 = 20 m) oil status- oiled indicates sites that received Macondo oil AOB# - represents the different TRFs (terminal restriction fragments) detected and their relative abundance (%) TB 1 29.29297 -90.604939 TB 2 29.2915 -90.602824 TB3 29.304486 -90.565818 TB 4 29.2964 -90.549793 WB 1 29.288949 -90.042667 WB 2 29.265837 -90.024864 WB 3 29.2801 -89.975833 WB 4 29.276533 -89.97535 PS 3A 29.4608 -89.8750 PS 5 29.4508 -89.7500 PS 6 29.4458 -89.8761 PS 7 29.4742 -89.8564 |Community composition was measured using TRFLP analysis of the betaproteobacterial amoA genes using primers amoA-1F and amoA-2RTC. Each TRF represents a population of AOB.|Samples were analyzed at the Cornell University Life Sciences Core Laboratories Center using an Applied Biosystems 3730xl DNA Analyzer.|||
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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: Excel Spreadsheet Version: inapplicable File decompression technique: Distributor transfer options: Digital transfer options: Transfer size: 0.0634 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R1.x139.143:0060 Protocol: https Name: Data Landing Page Description: GRIIDC dataset landing page Function: Online function code: information
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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: R1.x139.143:0060 on 2021-09-23T18:09:43-05:00
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