Dataset title: 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 Dataset ID: doi:10.6073/pasta/6273598ee363e9d24f859804da904601 Dataset Creator Name: Jun Zhao Name: Willm Martens-Habbena Email: w.martenshabbena@ufl.edu Metadata Provider Organization: Florida Coastal Everglades LTER Address: Florida International University 11200 SW 8th Street, OE 148 Miami, FL 33199 USA Phone: 305-348-6054 Email: fcelter@fiu.edu URL: https://fcelter.fiu.edu 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 Geographic description: SRS1d West bounding coordinate: -80.654 East bounding coordinate: -80.654 North bounding coordinate: 25.7463 South bounding coordinate: 25.7463 Geographic description: SRS2 West bounding coordinate: -80.78520692 East bounding coordinate: -80.78520692 North bounding coordinate: 25.54972811 South bounding coordinate: 25.54972811 Geographic description: SRS3 West bounding coordinate: -80.85327617 East bounding coordinate: -80.85327617 North bounding coordinate: 25.46820617 South bounding coordinate: 25.46820617 Geographic description: SRS4 West bounding coordinate: -80.96431016 East bounding coordinate: -80.96431016 North bounding coordinate: 25.40976421 South bounding coordinate: 25.40976421 Geographic description: SRS5 West bounding coordinate: -81.03234716 East bounding coordinate: -81.03234716 North bounding coordinate: 25.37702258 South bounding coordinate: 25.37702258 Geographic description: SRS6 West bounding coordinate: -81.07794623 East bounding coordinate: -81.07794623 North bounding coordinate: 25.36462994 South bounding coordinate: 25.36462994 Geographic description: TS/Ph1b West bounding coordinate: -80.59027402 East bounding coordinate: -80.59027402 North bounding coordinate: 25.43857602 South bounding coordinate: 25.43857602 Geographic description: TS/Ph2 West bounding coordinate: -80.60690341 East bounding coordinate: -80.60690341 North bounding coordinate: 25.40357188 South bounding coordinate: 25.40357188 Geographic description: TS/Ph3 West bounding coordinate: -80.66271768 East bounding coordinate: -80.66271768 North bounding coordinate: 25.25240534 South bounding coordinate: 25.25240534 Geographic description: TS/Ph6a West bounding coordinate: -80.6490792 East bounding coordinate: -80.6490792 North bounding coordinate: 25.21418102 South bounding coordinate: 25.21418102 Geographic description: TS/Ph7a West bounding coordinate: -80.63910514 East bounding coordinate: -80.63910514 North bounding coordinate: 25.19080491 South bounding coordinate: 25.19080491 Geographic description: TS/Ph9 West bounding coordinate: -80.48978207 East bounding coordinate: -80.48978207 North bounding coordinate: 25.17692874 South bounding coordinate: 25.17692874 Geographic description: TS/Ph10 West bounding coordinate: -80.68097374 East bounding coordinate: -80.68097374 North bounding coordinate: 25.02476744 South bounding coordinate: 25.02476744 Geographic description: TS/Ph11 West bounding coordinate: -80.93798347 East bounding coordinate: -80.93798347 North bounding coordinate: 24.91293492 South bounding coordinate: 24.91293492 Temporal Coverage Start Date: 2019 End Date: 2020 Data Table 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 Data Format Number of Header Lines: 1 Attribute Orientation: column Field Delimiter: , Number of Records: Attributes Attribute Name: run Attribute Label: Run Attribute Definition: Run Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: run_link Attribute Label: Run link Attribute Definition: Run link Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: assay_type Attribute Label: Assay type Attribute Definition: Assay type Storage Type: string 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: bio_project Attribute Label: BioProject Attribute Definition: BioProject Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: biosample Attribute Label: BioSample Attribute Definition: BioSample Storage Type: string Measurement Scale: text 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: string Measurement Scale: text Missing Value Code: Attribute Name: datastore_provider Attribute Label: Datastore provider Attribute Definition: Datastore provider Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: datastore_region Attribute Label: Datastore region Attribute Definition: Datastore region Storage Type: string Measurement Scale: text 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: string Measurement Scale: text Missing Value Code: Attribute Name: env_local_scale Attribute Label: Environment local scale Attribute Definition: Environment local scale Storage Type: string 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: string Measurement Scale: text Missing Value Code: Attribute Name: experiment Attribute Label: Experiment Attribute Definition: Experiment Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: experiment_link Attribute Label: Experiment link Attribute Definition: Experiment link Storage Type: string Measurement Scale: text 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: text 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: text Missing Value Code: Attribute Name: geo_loc_name Attribute Label: Geographic location name Attribute Definition: Geographic location name Storage Type: string 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: string Measurement Scale: text Missing Value Code: Attribute Name: library_layout Attribute Label: Library layout Attribute Definition: Library layout Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: library_selection Attribute Label: Library selection Attribute Definition: Library selection Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: library_source Attribute Label: Library source Attribute Definition: Library source Storage Type: string Measurement Scale: text Missing Value Code: Attribute Name: organism Attribute Label: Organism Attribute Definition: Organism Storage Type: string Measurement Scale: text 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: text Missing Value Code: Attribute Name: SITENAME Attribute Label: Site name Attribute Definition: Site name/code Storage Type: string Measurement Scale: text 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 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. Dataset Keywords 16S rRNA ITS genes amplicon sequencing data inventory FCE LTER Florida Coastal Everglades LTER LTER GenBank genomics microbes fungi disturbance Maintenance 1265.1: Data inventory package created. Dataset Contact Name: Jun Zhao Name: Willm Martens-Habbena Email: w.martenshabbena@ufl.edu Position: Information Manager Organization: Florida Coastal Everglades LTER Address: Florida International University 11200 SW 8th Street, OE 148 Miami, FL 33199 USA Email: fcelter@fiu.edu URL: https://fcelter.fiu.edu