Abstract:

DNA was extracted from soil marsh samples collected from different salinity zones in coastal Louisiana between 2018-07-13 to 2018-07-27, following a 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 DNA extraction and amplification process using the forward primer Illumina_Euk_1391f (Amaral-Zettler et al. 2009) and reverse primer Illumina_EukBr (Stoeck et al. 2010). Following amplification the DNA was sequenced on an Illumina Hiseq 2500 platform. Sequences of the 18SrRNA genes were submitted to GenBank and links to the submissions will be provided along with the date, geospatial location of collections and chemical analysis data.

Suggested Citation:

Rayle, Patrick M.. 2022. 18S metagenomic sequencing of DNA isolated from salt marsh sediments of varying salinities from coastal Louisiana, 2018-07-13 to 2018-07-27. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/8D8CSMAP

Purpose:

This dataset was generated in order to compare the meiofaunal organisms present in marsh margins in different salinity zones across coastal Louisiana to determine potential impacts on marshes due to changes in salinity regime due to planned freshwater diversions. 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. The headers are Sampleid, Genbank Acession Number, GenBank BioProject Number, Original sample designation, Year, Month, Day, Site, Area, Sheared, Tidal Position, Longitude, Latitude, HAE (Height Above Ellipsoid), DO%, AnoxicDepth (cm) , SalinityConductivity (ppt), Air Temperature (C ), day extracted, Sample.name, Site, dfe, Region, salinitycat, salinitycat.org, percent.Organic.Matter, Boron.ppm, Carbon.percent, Nitrogen.percent, Aluminum.ppm, Copper.ppm, Iron.ppm, Manganese.ppm, Zinc.ppm, Calcium.ppm, Magnesium.ppm, pH.1.1.Water, Phosphorus.ppm, Potassium.ppm, Sodium.ppm, Sulfur.ppm, Chloride.ppm, Conductivity.dS.m, Salts.ppm, SAR, and CN.ratio.

Methods:

DNA was extracted again from soil samples samples collected from different salinity zones following a 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 DNA extraction and amplification process using the forward primer Illumina_Euk_1391f (Amaral-Zettler et al. 2009) and reverse primer Illumina_EukBr (Stoeck et al. 2010). Following amplification the DNA was sequenced on an Illumina Hiseq 2500 platform.

Provenance and Historical References:

Amaral-Zettler Linda A., Elizabeth A. McCliment, High W. Ducklow, 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 4(7): e6372. DOI: 10.1371/journal.pone.0006372 Stoeck Thorsten, David Bass, Markus Nebel, Richard Christen, Meredith M. Jones, Hans-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. 2010 Mar;19 Suppl 1:21-31. DOI: 10.1111/j.1365-294X.2009.04480.x. PMID: 20331767

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