Abstract:

Forty Spartina plants were collected from the field in September 2016. Root, leaf and soil samples were sent to Duke University for paired-end amplicon sequencing of the 16S region for bacterial DNA. This dataset includes metadata (experimental design), environmental measurements (polycyclic aromatic hydrocarbons, pH, conductivity, latitude and longitude), and links to the raw sequences and accession number from National Center for Biotechnology Information (NCBI) GenBank.

Suggested Citation:

Stephen Formel. 2020. Bacterial amplicon sequencing of Spartina alterniflora endosymbionts and rhizosphere, Bay Jimmy and Fourchon, Louisiana, 2016-09-23 to 2016-09-30. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-rk1q-y332

Purpose:

The study was conducted to determine how environmental contaminants and perturbations can impact plant microbiomes.

Data Parameters and Units:

SampleID: Sample ID corresponding to the Lumibao et. al., (2018). Read as: [Project Name].[Site][Treatment].[TissueType][PlantID]. For example: S6.FO.S9 is the S6 project, sample from the Fourchon Oiled site. Tissue is the soil from plant 9 of that transect. DukeID: Duke University sequenced the samples for the 16S metagenome and elected to use a different sample ID format than the Lumibao et. al, (2018). Read as: [TissueType][Site][Treatment][PlantID]. For example: SFO9 is the soil sample from the Fourchon Oiled site, 9th plant of that transect. collection_date: date samples were collected in mm/dd/yy Coordinates: Lat/Long coordinates were estimated with a Garmin eTrex 10 Lat: Above coordinates converted to decimal degrees Long: Above coordinates converted to decimal degrees Tissue: Tissue from which DNA was extracted. Soil, Root, or Leaf Site: Site at which sample was taken: Bay Jimmy, Louisiana (BJ) or Fourchon, Louisiana (F) Treatment: Oiled or Unoiled. Refers to whether oil reached the area in which transect was taken during the Deepwater Horizon oil spill. pH: pH of rhizospheric porewater. Value is standardized to 25C. Instrument was an Ultrameter II 6Psi by Myron L Company cond: conductivity of rhizospheric porewater. Value is standardized to 25C and unit is milliSiemens (mS) per cm. Instrument was an Ultrameter II 6Psi by Myron L Company tds: total dissolved solids of rhizospheric porewater, in parts-per-thousand. Value is standardized to 25C and unit is milliSiemens (mS) per cm. Instrument was an Ultrameter II 6Psi by Myron L Company total_relevant_PAH: unit = ug per gram. Summed abundance of C1-C4 naphthalenes, C1-C3 dibenzothiophenes, C1-C4 phenanthrenes, C1-C3 chrysenes phen_WR: weathering ratio of C1-C4 phenanthrenes/(C1-C4 phenanthrenes + C1-C3 chrysenes) dibenz_WR: weathering ratio of C1-C3 dibenzothiophenes/(C1-C3 dibenzothiophenes + C1-C3 chrysenes) BioProject: Bioproject accession number for NCBI Genbank BioSample Accession: Biosample accession number for NCBI Genbank SRR Accession: SRR accession number for NCBI Genbank Link to original R1 file: Link to the original R1 reads file that was uploaded to NCBI GenBank Link to original R2 file: Link to the original R2 reads file that was uploaded to NCBI GenBank

Methods:

For detailed field methods, please refer to Lumibao et. al., (2018) doi: https://doi.org/10.1016/j.scitotenv.2018.06.077

Instruments:

Ultrameter II 6Psi by Myron L Company.

Provenance and Historical References:

Lumibao, C. Y., Formel, S., Elango, V., Pardue, J. H., Blum, M., & Van Bael, S. A. (2018). Persisting responses of salt marsh fungal communities to the Deepwater Horizon oil spill. Science of The Total Environment, 642, 904–913. doi:10.1016/j.scitotenv.2018.06.077

Individual Files: