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Inventory of soil prokaryotic microbiome (via 16S based on rRNA gene amplicons) in freshwater and brackish water marshes following saltwater intrusion along Shark River Slough boundary, Everglades National Park (FCE LTER), Florida, USA, September 2018


At a Glance


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Authors: Jun Zhao, Willm Martens-Habbena
Time period: 2018-01-01 to 2018-12-31
Package id: knb-lter-fce.1264.1

How to cite:
Zhao, J., W. Martens-Habbena. 2024. Inventory of soil prokaryotic microbiome (via 16S based on rRNA gene amplicons) in freshwater and brackish water marshes following saltwater intrusion along Shark River Slough boundary, Everglades National Park (FCE LTER), Florida, USA, September 2018. Environmental Data Initiative. https://doi.org/10.6073/pasta/04d96a23b5e5dc8dba846f3a40a0f427. Dataset accessed 2024-04-30.

Geographic Coverage


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Detailed Metadata


  • Dataset Abstract
    Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in microbial communities and related ecological services. Soil prokaryotes play a fundamental role in regulating important biogeochemical processes in coastal wetland ecosystem. Yet, it is still difficult to predict how soil prokaryotic communities respond to the saltwater exposure because of poorly understood prokaryotic sensitivity within complex wetland soil microbial communities, as well as the high heterogeneity of wetland soils and saltwater exposure. To address this, a four-year experimental simulation of saltwater intrusion in a pristine freshwater site and a previously saltwater-impacted site was conducted. The saltwater addition started in October 2014 on a monthly basis and continued through October 2018. The dataset contains amplicon sequencing date of 16S rRNA gene obtained from saltwater-exposed soils and unmanipulated native soils in both sites (collected in September 2018). The 2018 data are published in Zhao et al. 2023. A detailed list of sequence data and their accession numbers in GenBank is provided, and data collection is complete.
    This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA804545 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804545).
    This data package is associated with the following publication:
    Zhao, J., Chakrabarti, S., Chambers, R., Weisenhorn, P., Travieso, R., Stumpf, S., Standen, E., Briceno, H., Troxler, T., Gaiser, E., Kominoski, J., Dhillon, B., & Martens-Habbena, W. (2023). Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands. Science of The Total Environment, 858, 159865. https://doi.org/10.1016/j.scitotenv.2022.159865
    Instead of citing this package, which is an inventory, please cite the original GenBank data or journal article, as appropriate. Citation guidance for the journal article is available on the respective publisher's website.
  • Geographic Coverage
    Bounding Coordinates
    Freshwater marsh site
    N: 25.43, S: 25.43, E: -80.83, W: -80.83

    Brackish water marsh site
    N: 25.22, S: 25.22, E: -80.83, W: -80.83

  • Attributes
    • Data Table:   Table containing an inventory of datasets accessible through NCBI related to this project
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  • Methods
    Method Step

    Description
    Soil samples from saltwater-exposed soils and unmanipulated native soils from both sites were collected in September 2018.


    Method Step

    Description
    DNA extraction: Soil samples were homogenized using sterile mortar and pestle before total DNA extraction using DNeasy PowerSoil Kit (QIAGEN) following manufacturer's instruction including bead-beating twice for 30 s at 4.5 m/s in a FastPrep-24 bead beater (MP Biomedical, Irvine, CA). DNA was dissolved in 50 μL molecular biology grade water and stored at −20 °C before use.


    Method Step

    Description
    PCR and sequencing: PCR amplification using primer pair 515F-806R (Apprill et al., 2015; Parada et al., 2016), library preparation (2 × 150 bp) and sequencing on an Illumina MiSeq instrument was conducted at Argonne National Laboratory, Chicago, Illinois, following the standard pipeline.

    References:
    Apprill, A., McNally, S., Parsons, R., & Weber, L. (2015). Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton. Aquatic Microbial Ecology, 75(2), 129-137.

    Parada, A. E., Needham, D. M., & Fuhrman, J. A. (2016). Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environmental microbiology, 18(5), 1403-1414.


  • Distribution and Intellectual Rights
    Online distribution
    https://pasta.lternet.edu/package/data/eml/knb-lter-fce/1264/1/744b4c32aee0e2e3423a83573b2e3641
    Intellectual Rights
    This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

  • Keywords
    16S rRNA, amplicon sequencing, Saltwater intrusion simulation, GenBank, data inventory, FCE LTER, Florida Coastal Everglades LTER, LTER, genomics, microbes, disturbance
  • Data Table and Format
    Data Table:  Table containing an inventory of datasets accessible through NCBI related to this project

    Entity Name:
    FCE1264_microbiome_data_inventory
    Entity Description:
    Table containing an inventory of datasets accessible through NCBI related to this project
    Object Name:
    FCE1264_microbiome_data_inventory.csv
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    25