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Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing


At a Glance


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Authors: Ulrich Stingl, Chang Jae Choi
Time period: 2017-01-01 to 2022-12-31
Package id: knb-lter-fce.1247.3

How to cite:
Stingl, U., C. Choi. 2024. Inventory of High-resolution phylogenetic profiles of the planktonic microbial communities (via 16S and 18S rRNA gene amplicons) from Shark River Slough and Taylor Slough, Everglades National Park (FCE LTER), Florida, USA, 2017 - ongoing. Environmental Data Initiative. https://doi.org/10.6073/pasta/5b35f07c8f4c77dd05897907c6f77765. Dataset accessed 2024-05-01.

Geographic Coverage


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Detailed Metadata


  • Dataset Abstract
    Planktonic microbial communities mediate many vital biogeochemical processes in wetland ecosystems, yet compared to other aquatic ecosystems, like oceans, lakes, rivers, or estuaries, they remain relatively underexplored. Our study site, the Florida Everglades (USA)—a vast iconic wetland consisting of a slow-moving system of shallow rivers connecting freshwater marshes with coastal mangrove forests and seagrass meadows—is a highly threatened model ecosystem for studying salinity and nutrient gradients, as well as the effects of sea level rise and saltwater intrusion. This dataset provides the first high-resolution phylogenetic profiles of planktonic bacterial and eukaryotic microbial communities (using 16S and 18S rRNA gene amplicons) from these environments. The dataset contains 16S and 18S rRNA data from 2017, and contains 16S rRNA data for monthly (2019) and quarterly water samples (2020-ongoing). The 2017 data are published in Laas et al. 2022. A detailed list of sequence data and their accession numbers in GenBank is provided and will be updated as more data are published.

    This data package is an inventory of sequence read archive (SRA) entries available through GenBank BioProject PRJNA525456 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA525456) and BioProject PRJNA1018945 (at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1018945).
    This data package is associated with the following publication:
    Laas, P., Ugarelli, K., Travieso, R., Stumpf, S., Gaiser, E. E., Kominoski, J. S., & Stingl, U. (2022). Water column microbial communities vary along salinity gradients in the Florida Coastal Everglades wetlands. Microorganisms, 10(2), 215. https://doi.org/10.3390/microorganisms10020215
    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/Ph1a
    N: 25.42388762, S: 25.42388762, E: -80.59029790000001, W: -80.59029790000001

    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/Ph8
    N: 25.23269749, S: 25.23269749, E: -80.52455665, W: -80.52455665

    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.
      Attribute Name:
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      Run
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      Run
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      Measurement Scale:
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      Attribute Name:
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      Attribute Label:
      Run link
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      Run link
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      assay_type
      Attribute Label:
      Assay type
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      Assay type
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      avg_spot_len
      Attribute Label:
      Average spot length
      Attribute Definition:
      Average spot length
      Storage Type:
      float
      Measurement Scale:
      Units: dimensionless
      Number Type: real
      Missing Value Code:
       

      Attribute Name:
      bases
      Attribute Label:
      Bases
      Attribute Definition:
      Bases
      Storage Type:
      integer
      Measurement Scale:
      Units: dimensionless
      Number Type: integer
      Missing Value Code:
       

      Attribute Name:
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      Attribute Label:
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      Attribute Definition:
      BioProject
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      Attribute Name:
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      Attribute Label:
      BioSample
      Attribute Definition:
      BioSample
      Storage Type:
      string
      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      biosample_link
      Attribute Label:
      BioSample link
      Attribute Definition:
      BioSample link
      Storage Type:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      biosample_model
      Attribute Label:
      BioSample model
      Attribute Definition:
      BioSample model
      Storage Type:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      bytes
      Attribute Label:
      Bytes
      Attribute Definition:
      Bytes
      Storage Type:
      integer
      Measurement Scale:
      Units: byte
      Number Type: integer
      Missing Value Code:
       

      Attribute Name:
      center_name
      Attribute Label:
      Center name
      Attribute Definition:
      Center name
      Storage Type:
      string
      Measurement Scale:
      text
      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:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      datastore_filetype
      Attribute Label:
      Datastore filetype
      Attribute Definition:
      Datastore filetype
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      datastore_provider
      Attribute Label:
      Datastore provider
      Attribute Definition:
      Datastore provider
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      datastore_region
      Attribute Label:
      Datastore region
      Attribute Definition:
      Datastore region
      Storage Type:
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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:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      env_broad_scale
      Attribute Label:
      Environment broad scale
      Attribute Definition:
      Environment broad scale
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      env_local_scale
      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
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      experiment_link
      Attribute Label:
      Experiment link
      Attribute Definition:
      Experiment link
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      geo_loc_name_country
      Attribute Label:
      Geographic location country name
      Attribute Definition:
      Geographic location country name
      Storage Type:
      string
      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
      Storage Type:
      string
      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:
      text
      Missing Value Code:
       

      Attribute Name:
      instrument
      Attribute Label:
      Instrument
      Attribute Definition:
      Instrument
      Storage Type:
      string
      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      latitude
      Attribute Label:
      Latitude
      Attribute Definition:
      Latitude, WGS84 datum
      Storage Type:
      decimal
      Measurement Scale:
      Units: degree
      Number Type: real
      Missing Value Code:
       

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

      Attribute Name:
      library_name
      Attribute Label:
      Library name
      Attribute Definition:
      Library name
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      library_layout
      Attribute Label:
      Library layout
      Attribute Definition:
      Library layout
      Storage Type:
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      Measurement Scale:
      text
      Missing Value Code:
       

      Attribute Name:
      library_selection
      Attribute Label:
      Library selection
      Attribute Definition:
      Library selection
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      library_source
      Attribute Label:
      Library source
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      Library source
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      organism
      Attribute Label:
      Organism
      Attribute Definition:
      Organism
      Storage Type:
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      Measurement Scale:
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      Missing Value Code:
       

      Attribute Name:
      platform
      Attribute Label:
      Platform
      Attribute Definition:
      Platform
      Storage Type:
      string
      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:
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      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
    Sample collection:
    Two liters of surface water samples were obtained by grab sampling in sterile acid-washed bottles. Samples were kept on ice until filtration and were processed within 12 h.


    Method Step

    Description
    Collection of microbial biomass: The microbial communities were separated during filtration into two size fractions using 5 µm (>5 µm fraction) and 0.22 µm (0.22 µm–5 µm fraction) nitrocellulose membranes (MF-Millipore, Darmstadt, Germany).


    Method Step

    Description
    DNA extractions: DNA extractions were carried out with the Qiagen PowerWater Kit following the manufacturer’s recommended protocol (Qiagen, Hilden, Germany). DNA sequence data was generated using Illumina paired-end sequencing (151 bp × 12 bp × 151 bp MiSeq run) at the Environmental Sample Preparation and Sequencing Facility at Argonne National Laboratory (Lemont, IL, USA).


    Method Step

    Description
    PCR and sequencing: DNA extracts were used as templates for the amplification of the V4 hypervariable region of the 16S rRNA gene (515F-806R primer pair) and V9 hypervariable region of the 18S rRNA gene (1389F-EukB primer pair). In addition, primers contained sequencer adapter sequences and the reverse amplification primer also contained a twelve-base barcode sequence for multiplexing. Each 25-µL PCR reaction contained 9.5 µL of MO BIO PCR Water (Certified DNA-Free), 12.5 µL of QuantaBio’s AccuStart II PCR ToughMix (2× concentration, 1× final), 1 µL Forward Primer (5 µM concentration, 200 pM final), 1 µL Golay barcode tagged Reverse Primer (5 µM concentration, 200 pM final), and 1 µL of template DNA. The PCR conditions to amplify the 16S rRNA gene were as follows: 94 °C for 3 min to denature the DNA, with 35 cycles at 94 °C for 45 s, 50 °C for 60 s, and 72 °C for 90 s; final extension of 10 min at 72 °C to ensure complete amplification. The PCR conditions to amplify the 18S rRNA gene were as follows: 94 °C for 3 min to denature the DNA, with 35 cycles at 94 °C for 45 s, 57 °C for 60 s, and 72 °C for 90 s; final extension of 10 min at 72 °C. Amplicons were then quantified using PicoGreen (Invitrogen, Waltham, MA, USA) and a plate reader (Infinite 200 PRO, Tecan). Once quantified, volumes of each of the products were pooled into a single tube so that each amplicon is represented in equimolar amounts. This pool was then cleaned up using AMPure XP Beads (Beckman Coulter, Brea, CA, USA), and afterwards quantified using a fluorometer (Qubit, Invitrogen). After quantification, the molarity of the pool was determined and diluted to 2 nM, denatured, and diluted to a final concentration of 6.75 pM with a 10% PhiX spike for sequencing on an Illumina MiSeq.


  • Distribution and Intellectual Rights
    Online distribution
    https://pasta.lternet.edu/package/data/eml/knb-lter-fce/1247/3/ce29c2df1921ad55a4b6c98a64032b58
    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, 18S rRNA, amplicon sequencing, data inventory, LTER, FCE LTER, Florida Coastal Everglades LTER, microbes, genomics, disturbance
  • Data Table and Format
    Data Table:  Table containing an inventory of datasets accessible through NCBI related to this project.

    Entity Name:
    FCE1247_metagenomic_data_inventory
    Entity Description:
    Table containing an inventory of datasets accessible through NCBI related to this project.
    Object Name:
    FCE1247_metagenomic_data_inventory.csv
    Number of Header Lines:
    1
    Attribute Orientation:
    column
    Field Delimiter:
    ,
    Number of Records:
    125