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 10um 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 0.2um size fraction for whole community analysis.
Suggested Citation:
Jason Sylvan, Shawn Doyle, Samantha Setta, Genmei Lin. 2020. ADDOMEx Tier 3 Experiments: Mesocosm #3 Gulf of Mexico open ocean waters (GOMOO) and Mesocosm #4 Gulf of Mexico coastal waters (GOMCOAST) 10 um filter size. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/AM04VH3H
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:
AvgSpotLen, BioSample, DATASTORE_filetype, DATASTORE_provider, DATASTORE_region, Experiment, Library_Name, MBases, MBytes, Run, SRA_Sample, Sample_Name, description, geo_loc_name, lat_lon (decimal degrees), sample_title, Assay_Type, BioProject, BioSampleModel, Center_Name, Consent, InsertSize, Instrument (Illumina MiSeq), LibraryLayout, LibrarySelection, LibrarySource (METAGENOMIC), LoadDate (MM/DD/YYYY), Organism (marine metagenome), Platform (ILLUMINA), ReleaseDate (MM/DD/YYYY), SRA_Study, collection_date (Mon-YY), depth (meters), elev (elevation), env_biome, env_feature (seawater), env_material (water), organism (marine metagenome), seq_methods.
Methods:
Water was collected every 12 hours during this sampling to determine the changing community composition for the duration of the experiment. Samples were filtered using a 10 um pore size and combined with smaller community members (<10um). These data were used to analyze total eukaryotic microbial community members. Data on the samples filtered using 0.2 um filter size is available under GRIIDC Unique Dataset Identifier (UDI) R6.x807.000:0050 (DOI: 10.7266/8B8S9NTW).
Water accommodated fraction (WAF) was made according to Knap et al. 1986. After filling control tanks with the sweater, WAF of oil was made by adding 25 mL (5 ml ~ every 30 min for 2.5 hrs) of Macondo surrogate oil into 130 L of seawater followed by mixing for about 24 hours. The WAF was then added with mixing into the WAF mesocosm tanks and filled to 87 L. 6 L of WAF was removed for other experiments and analyses (2 L light /dark bottles, 4 L hydrocarbon analyses).
Corexit was mixed with oil in a ratio of 1:20 and 25 mL of this mixture (5 ml every 30 min for 2.5 hrs) of surrogate oil plus Corexit was added to 130 L of seawater to make chemically enhanced water accommodated fraction (CEWAF). This CEWAF was added into the CEWAF mesocosm tanks and filled to 96 L with mixing. 13 L of CEWAF was removed for other experiments and analyses (7 L for the Diluted CEWAF (DCEWAF) mesocosms, 2 L light/dark, 4 L hydrocarbon analyses). DCEWAF was prepared by mixing 9 L of CEWAF with 78 L of the original seawater for a total volume of 87 L.
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
Knap, A. H., Burns, K. A., Dawson, R., Ehrhardt, M., & Palmork, K. H. (1986). Dissolved/dispersed hydrocarbons, tarballs and the surface microlayer: Experiences from an IOC/UNEP Workshop in Bermuda, December, 1984. Marine Pollution Bulletin, 17(7), 313–319. doi:10.1016/0025-326x(86)90217-1
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