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Inventory of soil prokaryotic and fungal microbiome (via 16S rRNA gene amplicons and ITS sequencing) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, February 2019 - October 2020


At a Glance


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Authors: Jun Zhao, Willm Martens-Habbena
Time period: 2019-01-01 to 2020-12-31
Package id: knb-lter-fce.1265.1

How to cite:
Zhao, J., W. Martens-Habbena. 2024. Inventory of soil prokaryotic and fungal microbiome (via 16S rRNA gene amplicons and ITS sequencing) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, February 2019 - October 2020. Environmental Data Initiative. https://doi.org/10.6073/pasta/6273598ee363e9d24f859804da904601. Dataset accessed 2024-05-01.

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 saltwater exposure, leading to change in soil microbial communities and many important biogeochemical processes. Given the high spatial and temporal heterogeneity in coastal wetlands, especially in tropical or subtropical climates characterized by seasonal temperature, precipitation, and tidal fluctuations, it remains unclear which environmental factors influence the compositions of soil microbial communities in wetlands affected by varying degrees of sea-water intrusion. To address this, a two-year survey was conducted on microbial community structure in submerged surface soils from 14 wetland sites across the Florida Everglades, representing three major ecosystem types, i.e. freshwater marshes, mangrove forests, and seagrass meadows. Bulk surface soil samples of each site were collected from February 2019 to October 2020 to cover dry and wet seasons. In addition to bulk soil samples, soil cores were collected from each site in August 2020 to assess vertical gradients of microbial communities. The dataset contains amplicon sequencing data of 16S rRNA gene (both bulk soil and soil cores) and ITS gene (only the bulk soil). The 2019 to 2020 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 PRJNA804243 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804243), PRJNA804246 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804246), and PRJNA804228 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA804228).
    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
    SRS1d
    N: 25.7463, S: 25.7463, E: -80.654, W: -80.654

    SRS2
    N: 25.54972811, S: 25.54972811, E: -80.78520692, W: -80.78520692

    SRS3
    N: 25.46820617, S: 25.46820617, E: -80.85327617, W: -80.85327617

    SRS4
    N: 25.40976421, S: 25.40976421, E: -80.96431016, W: -80.96431016

    SRS5
    N: 25.37702258, S: 25.37702258, E: -81.03234716, W: -81.03234716

    SRS6
    N: 25.36462994, S: 25.36462994, E: -81.07794623, W: -81.07794623

    TS/Ph1b
    N: 25.43857602, S: 25.43857602, E: -80.59027402, W: -80.59027402

    TS/Ph2
    N: 25.40357188, S: 25.40357188, E: -80.60690341, W: -80.60690341

    TS/Ph3
    N: 25.25240534, S: 25.25240534, E: -80.66271768, W: -80.66271768

    TS/Ph6a
    N: 25.21418102, S: 25.21418102, E: -80.6490792, W: -80.6490792

    TS/Ph7a
    N: 25.19080491, S: 25.19080491, E: -80.63910514, W: -80.63910514

    TS/Ph9
    N: 25.17692874, S: 25.17692874, E: -80.48978207, W: -80.48978207

    TS/Ph10
    N: 25.02476744, S: 25.02476744, E: -80.68097374, W: -80.68097374

    TS/Ph11
    N: 24.91293492, S: 24.91293492, E: -80.93798347, W: -80.93798347

  • Attributes
    • Data Table:   Table containing an inventory of datasets accessible through NCBI related to this project.
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      Average spot length
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      Average spot length
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      Attribute Name:
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      Attribute Label:
      Bases
      Attribute Definition:
      Bases
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      Measurement Scale:
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      Attribute Name:
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      Attribute Label:
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      BioProject
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      Attribute Name:
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      Attribute Label:
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      Attribute Name:
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      Attribute Label:
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      BioSample link
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      Attribute Name:
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      Attribute Label:
      BioSample model
      Attribute Definition:
      BioSample model
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      Attribute Name:
      bytes
      Attribute Label:
      Bytes
      Attribute Definition:
      Bytes
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      Measurement Scale:
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      Attribute Name:
      center_name
      Attribute Label:
      Center name
      Attribute Definition:
      Center name
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      collection_date
      Attribute Label:
      Collection date
      Attribute Definition:
      Date of collection
      Storage Type:
      dateTime
      Measurement Scale:
      Missing Value Code:
       

      Attribute Name:
      consent
      Attribute Label:
      Consent
      Attribute Definition:
      Consent
      Storage Type:
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      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
      Datastore filetype
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      Datastore filetype
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      Attribute Name:
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      Attribute Label:
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      Datastore provider
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      Attribute Name:
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      Attribute Label:
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      Attribute Definition:
      Datastore region
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      depth
      Attribute Label:
      Depth
      Attribute Definition:
      Depth or depth range of sample collected
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      env_broad_scale
      Attribute Label:
      Environment broad scale
      Attribute Definition:
      Environment broad scale
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      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
      Environment local scale
      Attribute Definition:
      Environment local scale
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      env_medium
      Attribute Label:
      Environment medium
      Attribute Definition:
      Environment medium (terms from the EnvO ontology)
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      experiment
      Attribute Label:
      Experiment
      Attribute Definition:
      Experiment
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
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      Experiment link
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      Attribute Name:
      geo_loc_name_country
      Attribute Label:
      Geographic location country name
      Attribute Definition:
      Geographic location country name
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      geo_loc_name_country_continent
      Attribute Label:
      Geographic location continent
      Attribute Definition:
      Geographic location continent
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      geo_loc_name
      Attribute Label:
      Geographic location name
      Attribute Definition:
      Geographic location name
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      instrument
      Attribute Label:
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      Attribute Definition:
      Instrument
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      latitude
      Attribute Label:
      Latitude
      Attribute Definition:
      Latitude, WGS84 datum
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      Missing Value Code:
       

      Attribute Name:
      longitude
      Attribute Label:
      Longitude
      Attribute Definition:
      Longitude, WGS84 datum
      Storage Type:
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      Measurement Scale:
      Units: degree
      Number Type: real
      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
      Library name
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      Library name
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
      Library layout
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      Library layout
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
      Library selection
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      Library selection
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
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      Library source
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      Measurement Scale:
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      Attribute Name:
      organism
      Attribute Label:
      Organism
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      Organism
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      platform
      Attribute Label:
      Platform
      Attribute Definition:
      Platform
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      release_date
      Attribute Label:
      Release date
      Attribute Definition:
      Release date
      Storage Type:
      dateTime
      Measurement Scale:
      Missing Value Code:
       

      Attribute Name:
      create_date
      Attribute Label:
      Creation date
      Attribute Definition:
      Creation date
      Storage Type:
      dateTime
      Measurement Scale:
      Missing Value Code:
       

      Attribute Name:
      version
      Attribute Label:
      Version
      Attribute Definition:
      Version
      Storage Type:
      float
      Measurement Scale:
      Units: dimensionless
      Number Type: real
      Missing Value Code:
       

      Attribute Name:
      sample_name
      Attribute Label:
      Sample name
      Attribute Definition:
      Sample name
      Storage Type:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      sra_study
      Attribute Label:
      SRA study
      Attribute Definition:
      SRA study
      Storage Type:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      SITENAME
      Attribute Label:
      Site name
      Attribute Definition:
      Site name/code
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       


  • Methods
    Method Step

    Description
    Site description: Soil and sediment samples were collected as part of the Florida Coastal Everglades (FCE) Long Term Ecological Research (LTER) program from the 14 main long-term monitoring sites along the two major water flow paths of the Everglades, Shark River Slough (SRS) and Taylor Slough/Panhandle (TS/Ph). The sampling sites represent three major ecosystem types, i.e. freshwater marshes (SRS1–SRS3 and TS/Ph1–TS/Ph3, respectively), mangrove forests (SRS4–SRS6 and TS/Ph 6–TS/Ph7) and the seagrass meadows located in Florida Bay (TS/Ph9–TS/Ph11). More detailed descriptions of the sampling locations and site metadata can be found at previous studies (Chen et al., 2013; Childers et al., 2006).
    References:
    Chen, M., Maie, N., Parish, K., & Jaffé, R. (2013). Spatial and temporal variability of dissolved organic matter quantity and composition in an oligotrophic subtropical coastal wetland. Biogeochemistry, 115, 167–183.
    Childers, D.L., Boyer, J.N., Davis, S.E., Madden, C.J., Rudnick, D.T., & Sklar, F.H. (2006). Relating precipitation and water management to nutrient concentrations in the oligotrophic "upside-down" estuaries of the Florida Everglades. Limnology and Oceanography, 51 (1, part 2), 602–616.


    Method Step

    Description
    Soil collection: Bulk surface soil samples of each site (~ 0–10 cm) were collected from February 2019 to October 2020 to cover dry and wet seasons. Samples were immediately placed on ice and transported to laboratory. The samples were stored at −20 °C until further molecular biological analysis. In addition to bulk soil samples, three replicate soil cores of ~90 mm depth (TS7, ~70 mm) were collected from each site in August 2020, to assess vertical gradients of microbial communities within the soil or sediment column. Soil cores were closed with rubber stoppers, transported back to the laboratory on ice, and immediately sliced into 9-mm sections, resulting in a total of 8–10 soil section samples for each core. Each sliced soil section was well mixed to homogenize, and 4–5 representative depths (0–9 mm, 18–27 mm, 36–45 mm, 54–63 mm and 72–81 mm) from each soil core were selected for molecular biological analysis.


    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: DNA concentrations were normalized to ~10 ng/μL and the 16S rRNA- and ITS genes were amplified using primer pair 515f-926r (Parada et al., 2016; Quince et al., 2011) and ITS1f-ITS2 (Gardes and Bruns, 1993; White et al., 1990), respectively, fused with specific adaptors following Earth Microbiome protocol (Thompson et al., 2017). The PCR amplification, library construction (2 × 250 bp) and sequencing of the amplicons were performed on an Illumina NovaSeq instrument at Novogene, Sacramento, CA following standard procedures.
    References:
    Gardes, M., & Bruns, T.D. (1993). ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology, 2(2), 113–118
    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.
    Quince, C., Lanzen, A., Davenport, R.J., & Turnbaugh, P.J. (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.
    Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., et al., 2017. A communal catalogue reveals Earth's multiscale microbial diversity. Nature, 551, 457–463
    White, T.J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M.A., Gelfand, D.H., Sninsky, J.J., White, T.J. (Eds.), PCR Protocols: A Guide to Methods and Applications. Academic Press, London, pp. 315–322.


  • Distribution and Intellectual Rights
    Online distribution
    https://pasta.lternet.edu/package/data/eml/knb-lter-fce/1265/1/ece6461dd211e27aed235ec4448f0cf7
    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, ITS genes, amplicon sequencing, data inventory, FCE LTER, Florida Coastal Everglades LTER, LTER, GenBank, genomics, microbes, fungi, disturbance
  • Data Table and Format
    Data Table:  Table containing an inventory of datasets accessible through NCBI related to this project.

    Entity Name:
    FCE1265_microbiome_data_inventory
    Entity Description:
    Table containing an inventory of datasets accessible through NCBI related to this project.
    Object Name:
    FCE1265_microbiome_data_inventory.csv
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    461