Abstract:

The table is the raw (non-rarified) fungal OTU (operational taxonomic unit) abundances table generated from leaves, roots and soil of 40 individual plants by sequencing the Internal Transcribed Spacer (ITS)1 region. Fungal endophyte response variables will be abundance, diversity & spp. composition in roots, leaves and soil using culture-independent sequencing for taxonomy; and high throughput sequencing for community analyses. Environmental parameters including PAH, conductivity, etc measured from individual plant as well as site/location from where the plant samples were taken and individual plant GPS coordinates are included in the metadata table. Each OTU represent a unique sequence. Taxa assignment of OTUs using BLAST alignment against UNITE reference database v7.2 can be found on the second worksheet of the excel file. Raw Illumina ITS sequences were submitted in NCBI Sequence Read Archive (SRA) under the BioProjectID PRJNA475039. This dataset supports publication- Lumibao, Candice Y., Stephen Formel, Vijaikrishnah Elango, John H. Pardue, Michael Blum, and Sunshine A. Van Bael. 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

Suggested Citation:

Van Bael, Sunshine and Candice Lumibao. 2018. Fungal amplicon sequencing of Spartina alterniflora endosymbionts and rhizosphere collected from Barataria Bay and Fourchon, September 2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7ZP44P4

Publications:

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

Purpose:

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

Data Parameters and Units:

Metadata_Spartina_FungalMicrobi: SampleID, Coordinates (Latitude degree minutes Longitude degree minutes), Latitude (decimal degrees), Longitude (decimal degrees), Tissue (root, leaf, or soil), Site (BJ-Bay Jimmy or F-Fourchon), Treatment (oiled or non-oiled represent areas within Barataria Bay and Port Fourchon that were oiled during the Deepwater Horizon spill and not oiled, respectively), pH (soil pH), Conductivity (mS, ppt), Total dissolved solids (tds, ppt), Polycyclic aromatic hydrocarbons (PAH, u/ug), Phenanthrene weathering ratio relative to chrysene (PWR), Dibenzothiopene weathering ratio relative to chrysene (DWR), "derep_" denotes each fungal OTU (operational taxonomic unit) and numbers on columns are sequence counts Taxa_Assignment_of_OTUs: OTU ID, Taxonomic assignment of OTU when available, OTU sequence counts SRA MetaData RunInfo: Bioproject accession, Biosample accession, Library ID, Title, Library strategy, Library source, Library selection, Library layout, Platform, Instrument model, Design description, Filetype, Filename

Methods:

Information of calculating values for the oil data e.g., Pwr, PAH can be found in the supplementary information of the publication: Lumibao, Candice Y., Stephen Formel, Vijaikrishnah Elango, John H. Pardue, Michael Blum, and Sunshine A. Van Bael. 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: