Abstract:

Soil samples were collected from 21 sites in northern Barataria Bay in spring and fall, along with other ecosystem parameters. Sample sites were classified as reference, moderately oiled, and heavily oiled. To study the soil microbial community, DNA was extracted from soil samples, sequenced with Illumina MiSeq, and processed with QIIME.

Suggested Citation:

A Hou, G Cagle. 2017. Soil microbial community in reference and oiled sites, northern Barataria Bay, 2015-2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7FX77T2

Purpose:

The purpose of this study is to examine responses of soil microbial community structure and function to the various oiling intensities. Multi-year sampling is intended to evaluate the recovery of the soil microbial community.

Data Parameters and Units:

File: 21sites-2015-otu-w-tax.xlsx: sample ID (internal sample ID), treatment (RF= reference, MD = moderate oiling, HV = heavy oiling), Year (2015), Month (October, June), Season (Spring, fall), operational taxonomic units - counts (Kingdom, Phylum, Class, Order, Family, Genus, Species). R2.x211.000-0009-SraRunTable.txt - Biosample (NCBI biosample accession), Experiment (NCBI experiment accession), Library name (NCBI library name), MBases (megabases), MBytes (megabytes), oiling category (reference, moderate, heavy), Run (NCBI run accession), SRA sample (NCBI SRA accession), sample name (internal sample name), station (sample site), collection date (YYYY-MM), Assay type (assay method used), AvgSpotLen, Bioproject (NCBI project accession), BioSampleModel (NCBI model used), consent, insert size, Instrument (instrument used), librarylayout, libraryselection, librarysource, loaddate (MM/DD/YYYY) (date data submitted to NCBI), organism, platform, releasedate (MM/DD/YYYY) (date data released to public), SRA Study (NCBI SRA study accession), depth (depth of sediment sampled), elev (elevation), env_biome (biome sampled), env_feature (environmental feature sampled), env_material (environmental material sampled), geo_loc_name (geographic location name), lat_long (latitude decimal degrees N longitude decimal degrees W). GPS Coordinates for Sampling Sites.xls - site (sample site code), GPS coordinates (latitude decimal degrees N longitude decimal degrees W)

Methods:

The top two cm of soil was collected at each site, proximal to the site of collection of the other types samples from this study. The soil was transported to the lab on ice and stored at -80°C. DNA was extracted from each soil sample, checked for purity, and amplified by PCR of the V4 barcode region, 16S rDNA for prokaryotes. Sequencing of PCR amplicons was conducted with Illumina MiSeq. DNA processing was done in QIIME v. 1.9.1 with default settings except for a Phred score of 25. The data are observations of OTUs (operational taxonomic units) in each sample. The data are count data of each OTU recorded in each sample. The sample description information is in the excel file on a separate sheet.

Individual Files: