Abstract:

This dataset includes an inventory of taxonomically classified bacterial 16S rRNA sequence libraries from Louisiana marsh sediment collected in May 2015. Inland soil and subtidal sediment samples were collected 5 m inland from the marsh edge, 1-2m offshore from the marsh edge, and offshore at the approximate location of the marsh edge in 2010 (as noted). Complementary field data for the May 2015 collection are reported separately and is available under GRIIDC Unique Dataset Identifier (UDI) R4.x264.198:0001 (DOI: 10.7266/N7HM56JT).

Suggested Citation:

Engel, Annette Summers and Audrey T. Paterson. 2020. Bacterial diversity data supporting changes in Louisiana marsh sediment microbial communities after the Deepwater Horizon oil spill, 2015-05-12 to 2015-05-14. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-zf0n-9g65

Purpose:

This dataset is a component of a longitudinal study of marsh microbial diversity and sediment properties before, during, and after oil deposition associated with the Deepwater Horizon oil spill.

Data Parameters and Units:

Data are reported as classified sequence abundance (phylum and class). For each sample, data are reported as follows: Sample ID (user-defined identifier for each sample); Latitude (in decimal degrees N); Longitude (in decimal degrees W); Collection Date (DD-MMM-YYYY); Sample Description (descriptive details of specific sample location and core slice); Geographic Location Name (descriptive details of broad sampling area); total classified sequences.

Methods:

Total nucleic acids were extracted in triple replicate from three to six grams of marsh sediment or soil. Samples were subjected to DNA isolation methods that incorporated sucrose lysis buffer with lysozyme and a solution of proteinase K/CTAB/SDS; incubation at 55 degrees C while shaking at 40-120 rpm; nucleic acids precipitation in isopropanol at -20 degrees C; and ethanol washing. This approach was modified from Guerry et al. (1973), Somerville et al. (1989), Zhou et al. (1996), and Mitchell and Takacs-Vesbach (2008). 16S rRNA gene libraries for bacteria and archaea were sequenced by the Molecular Research LP (Shallowater, TX) using the Illumina MiSeq platform and paired-end 2 × 300 bp kit, according to the manufacturer's instructions (Illumina, San Diego, CA, USA). 16S rRNA gene libraries were processed using the microbial ecology community software Mothur (Schloss, 2009) and the MiSeq SOP (Kozich et al., 2013) as a processing guide. Paired-end reads were generated using a primer set to target bacterial genes (27F and 519R); to remove anomalously joined forward and reverse sequences, contigs that were shorter or longer than the expected size of each target region were excluded from analysis. Briefly, contigs were screened for quality, aligned using the mothur-compatible formatted SILVA reference files (version 128), re-screened and filtered; the search was used to remove chimera sequences (https://github.com/torognes/vsearch). Sequences were classified using the SILVA reference (version 128). Inventories of processed classified reads are provided for each sediment sample.

Instruments:

16S rRNA gene sequence libraries were generated using the Illumina MiSeq platform (Illumina, San Diego, CA, USA).

Provenance and Historical References:

Guerry, P., LeBlanc, D. J., & Falkow, S. (1973). General method for the isolation of plasmid deoxyribonucleic acid. Journal of Bacteriology, 116(2), 1064-1066. Kozich, J. J., Westcott, S. L., Baxter, N. T., Highlander, S. K., & Schloss, P. D. (2013). Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology, 79(17), 5112–5120. doi:10.1128/aem.01043-13 Mitchell, K. R., & Takacs-Vesbach, C. D. (2008). A comparison of methods for total community DNA preservation and extraction from various thermal environments. Journal of Industrial Microbiology & Biotechnology, 35(10), 1139–1147. doi:10.1007/s10295-008-0393-y Schloss, P. D. (2009). A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies. PLoS ONE, 4(12), e8230. doi:10.1371/journal.pone.0008230 Somerville, C. C., Knight, I. T., Straube, W. L., & Colwell, R. R. (1989). Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Applied and environmental microbiology, 55(3), 548-554. Zhou, J., Bruns, M. A., & Tiedje, J. M. (1996). DNA recovery from soils of diverse composition. Applied and environmental microbiology, 62(2), 316-322.

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