Abstract:

DNA extracted from sediments of oiled sheared and intact salt marsh margins from coastal Louisiana, 2017 and was subjected to 18SrRNA gene amplification and high-throughput Illumina sequencing. Sequence data was submitted to GenBank.

Suggested Citation:

Rayle, Patrick M.. 2022. 18S metagenomic sequencing of DNA isolated from sediments from formerly oiled sheared and intact salt marsh margins from coastal Louisiana, 2017. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/PM77XYBH

Purpose:

This dataset was generated in order to compare the organisms present in sheared and intact marsh margins following oiling from the BP spill. These oiled marsh sites were impacted by Hurricane Isaac in 2012, leading to the shearing. In addition, a number of chemical variables from the soil samples were analyzed to determine if diversity was impacted by those variables.

Data Parameters and Units:

Sequences of the 18SrRNA genes were submitted to GenBank and links to the submissions are provided along with the date, geospatial location of collections and chemical analysis data.

Methods:

DNA was extracted from soil samples collected from sheared and intact marsh margins in coastal Louisiana. This DNA was then amplified using the forward primer Illumina_Euk_1391f (Amaral-Zettler et al. 2009) and reverse primer Illumina_EukBr (Stoeck et al. 2010). In addition, DNA was extracted again from the same samples following an additional processing step to separate the organic matter from the sediment. For this process, sediment was flushed through a 500 μm sieve onto a 45 μm sieve. The material retained on the 45 μm sieve was then mixed with Ludox (a coloidal silica solution) and centrifuged at 15 minutes at 4500 rpm. The supernatant (organic material) was rinsed of the Ludox and then subjected to the same DNA extraction and amplification process. Samples which were processed in this manner have an F at the end of the sample designation.

Provenance and Historical References:

Amaral-Zettler Linda A., Elizabeth A. McCliment, Hugh W. Ducklow, and Susan M. Huse. 2009. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS One. 2009 Jul 27;4(7):e6372. doi: 10.1371/journal.pone.0006372. Erratum in: PLoS One 4(12). DOI: 10.1371/journal.pone.0006372 PMID: 19633714; PMCID: PMC2711349. Stoeck Thorsten, David Bass, Markus Nebel, Richard Christen, Meredith D. Jones, Hand-Werner Breiner, Thomas A. Richards. 2010. Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol. 19 Suppl 1:21-31. DOI: 10.1111/j.1365-294X.2009.04480.x. PMID: 20331767.

Individual Files: