Dataset title: 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 Dataset ID: doi:10.6073/pasta/5b35f07c8f4c77dd05897907c6f77765 Dataset Creator Name: Ulrich Stingl Email: ustingl@ufl.edu Name: Chang Jae Choi Email: changjae.choi@ufl.edu Metadata Provider Organization: Florida Coastal Everglades LTER Email: fcelter@fiu.edu URL: http://fcelter.fiu.edu 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 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/Ph1a West bounding coordinate: -80.59029790000001 East bounding coordinate: -80.59029790000001 North bounding coordinate: 25.42388762 South bounding coordinate: 25.42388762 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/Ph8 West bounding coordinate: -80.52455665 East bounding coordinate: -80.52455665 North bounding coordinate: 25.23269749 South bounding coordinate: 25.23269749 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: 2017 End Date: 2022 Data Table 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 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: 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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 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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 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 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. Dataset Keywords 16S rRNA 18S rRNA amplicon sequencing data inventory LTER FCE LTER Florida Coastal Everglades LTER microbes genomics disturbance Maintenance 1247.3: Data inventory package created. Dataset Contact Name: Ulrich Stingl Email: ustingl@ufl.edu Name: Chang Jae Choi Email: changjae.choi@ufl.edu Position: Information Manager Organization: Florida Coastal Everglades LTER Address: Florida International University, 11200 SW 8th Street, OE 148 Miami, FL 33199 Email: fcelter@fiu.edu URL: http://fcelter.fiu.edu