Abstract:

This dataset is a raw sequence reads from samples collected from Chandeleur Islands, Louisiana from 2015-06-29 to 2015-09-23. Marine sediment microbial communities play a critical role in primary production, sediment oxygenation, key biogeochemical cycles, and provide a nutrient-rich food source for benthic invertebrates. While the photosynthetic organisms drive productivity at the surface, protists and other non-photosynthetic organisms dominate metabolic processes including hydrocarbon degradation in deeper sediments. In an effort to understand the response and recovery of benthic microbial assemblages in sediments we embarked on an intensive field survey in the Chandeleur Islands, an area impacted by the Deepwater Horizon (DWH) spill. Field sites were selected representing an oiling gradient based on NOAA Shoreline Cleanup and Assessment Technique (SCAT) surveys over a range of habitats, including salt marsh, un-vegetated sand, and seagrass meadows. Triplicate sediment cores (0-30cm) were collected from each habitat across the four field sites in June and September of 2015. Cores were sectioned and sub-samples were taken for genomic DNA isolation. Microbenthic community abundance and biodiversity were investigated with Illumina MiSeq 2 x 250 bp technology for 108 sediment samples. Research background and DNA sequence data can be accessed at the National Center for Biotechnology Information (NCBI) under accession number PRJNA630066.

Suggested Citation:

Alison Robertson, Michael Parsons, Hidetoshi Urakawa. 2020. Assessment of protist biodiversity and resilience of the benthic microbial assemblages in sub-tidal and intertidal from the Chandeleur Islands, Louisiana, 2015-06-29 to 2015-09-23. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-vh1r-dy20

Purpose:

Shared research information and DNA sequences can be used as a reference by other researchers who study oiling effects on microbial communities.

Data Parameters and Units:

Sequence data have been submitted to NCBI. The accession is: PRJNA630066 To access summary: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA630066 To browse a list of datasets: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=630066 The PRJNA630066_Assessment_protist_biodiversity_resilience.txt file contains detail information regarding the submission at NCBI and includes: Run, Assay Type, AvgSpotLen, Bases, BioProject, BioSample, BioSampleModel, Bytes, Center Name, Collection_Date, Consent,DATASTORE filetype, DATASTORE provider, DATASTORE region, depth_(cm), Experiment, geo_loc_name_country, geo_loc_name_country_continent, geo_loc_name, Instrument, isolation_source, lat_lon, Library Name, LibraryLayout, LibrarySelection, LibrarySource, Organism, Platform, ReleaseDate, Sample Name, source_material_ID, SRA Study.

Methods:

Sediment cores were collected in triplicate from each site and habitat type. Cores were sectioned and horizons homogenized before subsampling for DNA extraction. DNA samples were sequenced using the Illumina MiSeq platform. Samples were sequenced using three different primer sets the 16S rRNA gene primers for Bacteria (28F and 388R), Archaea (517F and 909R), and the 18S rRNA gene primers (TAReuk454FWD1 and TAReukREV3) for Eukaryotes.

Individual Files: