Abstract:
This collection of datasets is generated from high-throughput rRNA gene sequencing of dissimilatory (bi)sulfite reductase (dsrB) gene of sulfate-reducing bacteria (SRB) and 16S rRNA gene of the total microbial community. A sediment microcosm was prepared to study how the addition of water-accommodated fractions (WAF) of crude oil affect the sediment microbial community. We hypothesize that the addition of hydrocarbons will decrease oxygen concentrations in favor of anaerobic degradation, and sulfate-reducing bacteria (SRB) group may increase its abundance. Research background and DNA sequence data can be accessed at the National Center for Biotechnology Information (NCBI) under accession number PRJNA631345.
Suggested Citation:
Megan E. Feeney, Hidetoshi Urakawa. 2020. Oiling effects on sulfate-reducing bacterial communities in coastal marine sediment microcosms, based on samples collected at Chandeleur Island, Louisiana (2016) and Estero Bay, Florida (2013, 2015). Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/AD6DKMAF
Data Parameters and Units:
Sequence data have been submitted to NCBI. The accession is: PRJNA631345
To access summary: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA631345
To browse a list of datasets: https://www.ncbi.nlm.nih.gov/sra?linkname=bioproject_sra_all&from_uid=631345
The PRJNA631345_Oiling_effects_on_ sulfate_reducing_bacterial.txt file contains detail information regarding the submission at NCBI and includes: Run (SRR11743447-SRR11743462), Assay Type (AMPLICON), AvgSpotLen (501), Bases, BioProject (PRJNA631345), BioSample (SAMN14839057-SAMN14839064), BioSampleModel (Metagenome or environmental), Bytes, Center Name (FLORIDA GULF COAST UNIVERSITY), Collection_Date (MM/DD/YYYY), Consent (public), DATASTORE filetype (fastq, sra), DATASTORE provider, DATASTORE region, depth_(cm), Experiment, geo_loc_name_country (USA), geo_loc_name_country_continent (North America), geo_loc_name (Chandeleur Island, Louisiana and Estero Bay, Florida), Instrument (Illumina MiSeq), isolation_source (marine sediment), lat_lon (26.332389 N 81.838 W; 29.89545 N 88.82778 W; 29.86375 N 88.84147 W), Library Name, LibraryLayout (PAIRED), LibrarySelection (PCR), LibrarySource (METAGENOMIC), Organism (sediment metagenome), Platform (ILLUMINA), ReleaseDate (YYYY-MM-DD), Sample Name, source_material_id, SRA Study (SRP260884).
Methods:
A sediment microcosm was prepared to study how the addition of water-accommodated fractions (WAF) of crude oil affect the sediment microbial community.
The water-accommodated fraction (WAF) was mixed using a stir-plate with a speed of 240 RPM and octagonal stir bars for at least 72 hours in direct sunlight. In order to avoid gas expansion problems, 20% of headspace was left in each bottle. The containers were cleaned and capped, then wrapped with electrical tape to prevent the cap from dislodging due to pressure. After mixing was complete, the WAF was floating on the top of a slightly yellow aqueous solution. The WAF was then drained into two 24.6 L glass containers and stored at -20 °C to avoid breakdown. The mixing containers were cleaned thoroughly using dichloromethane, followed by methanol to remove residual crude oil and related contamination. The containers were then washed with methanol and a series of methanol/water rinses. The waste crude oil was then placed in a 50-gallon (189.271 L) plastic waste container for disposal.
Sediment samples were used to determine the 16S rRNA gene and dissimilatory (bi)sulfite reductase (dsrB) gene of microbial communities. DNA extraction was performed with a PowerMag DNA Isolation kit by using KingFisher Nucleic Acid and Protein Purification System. DNA samples were sequenced using the Illumina MiSeq platform. Samples were sequenced using the 16S rRNA gene primers 515F and 926pfR, and the dsrB gene primers (dsrLF and dsrLR).
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