Abstract:

To determine the effects of oil and dispersant on eukaryotic microbial communities, mesocosm experiments were run with natural microbial communities from both an open ocean and coastal site. Samples were taken every 12 hours and filtered onto 0.2 um pore size filters to determine the large size fraction of the microbial community. Samples were then extracted for DNA, amplified using Bradley et al., 2016 primers for the 18S rRNA V8/V9 region and submitted for sequencing. Data include the raw paired end reads from this analysis and was later processed using the bioinformatics tool, mothur. Data were combined with the 10um size fraction for whole community analysis throughout the experiment.

Suggested Citation:

Jason Sylvan, Shawn Doyle, Samantha Setta, Genmei Lin. 2019. ADDOMEx Tier 3 Experiments: Mesocosm #3 Gulf of Mexico open ocean waters (GOMOO) and Mesocosm #4 Gulf of Mexico coastal waters (GOMCOAST) 0.2 um filter size. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/8B8S9NTW

Purpose:

Mesocosm experiments were conducted to simulate conditions during the Deepwater Horizon oil spill, using a natural microbial community collected from the Gulf of Mexico and varying concentrations of oil and/or dispersant.

Data Parameters and Units:

Run, Assay Type, AvgSpotLen, BioProject, BioSample, BioSampleModel, Center Name, collection_date (Mon-YY), Consent, DATASTORE filetype, DATASTORE provider, DATASTORE region, Depth (meters), Description, env_biome, env_feature, env_material, Experiment, geo_loc_name_country, geo_loc_name_country_continent, geo_loc_name, Instrument (Illumina MiSeq), lat_lon (decimal degrees), Library Name, LibraryLayout, LibrarySelection, LibrarySource (Metagenomic), MBases, MBytes, Organism (marine metagenome), Platform (Illumina), ReleaseDate, sample_acc, Sample Name, sample_title, seq_methods, SRA Study, elev (elevation).

Methods:

Water was collected every 12 hours during this sampling to determine the changing community composition for the duration of the experiment. Samples were sequentially filtered from 0.2-10 um to analyze changes in the eukaryotic community compared and combined with the larger eukaryotes analyzed in a separate dataset (10um).

Instruments:

Illumina MiSeq

Provenance and Historical References:

Bradley, I. M., Pinto, A. J., & Guest, J. S. (2016). Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities. Applied and Environmental Microbiology, 82(19), 5878–5891. doi:10.1128/aem.01630-16

Individual Files: