Dataset title: 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 Dataset ID: doi:10.6073/pasta/04d96a23b5e5dc8dba846f3a40a0f427 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 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 Geographic description: Freshwater marsh site West bounding coordinate: -80.83 East bounding coordinate: -80.83 North bounding coordinate: 25.43 South bounding coordinate: 25.43 Geographic description: Brackish water marsh site West bounding coordinate: -80.83 East bounding coordinate: -80.83 North bounding coordinate: 25.22 South bounding coordinate: 25.22 Temporal Coverage Start Date: 2018 End Date: 2018 Data Table 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 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 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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: 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 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. Dataset Keywords 16S rRNA amplicon sequencing Saltwater intrusion simulation GenBank data inventory FCE LTER Florida Coastal Everglades LTER LTER genomics microbes disturbance Maintenance 1264.1: 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