Abstract:

This dataset includes an inventory of taxonomically classified bacterial 16S rRNA sequence libraries from Louisiana marsh water collected on 2015-05-12 to 2015-05-14. Complementary May 2015 field data (R4.x264.198:0001; DOI: 10.7266/N7HM56JT) and bacterial sequence libraries from sediment (R6.x808.000:0050; DOI: 10.7266/n7-zf0n-9g65) are reported separately.

Suggested Citation:

Engel, Annette Summers, Audrey T. Paterson, and Abigail Harmon. 2021. Water column bacterial communities in Louisiana marshes, 2015-05-12 to 2015-05-14. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-b2we-hb35

Purpose:

This dataset reports the 2015-05-12 to 2015-05-14 bacterial communities in marsh water. The dataset is a component of a longitudinal study of marsh microbial diversity 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); Geographic Location Name (descriptive details of broad sampling area); total classified sequences.

Methods:

Total nucleic acids were extracted from duplicate 0.22 μm PES Sterivex filters (MilliporeSigma™, Cat. No.: SVGP01050) using the MO BIO PowerWater Sterivex DNA Isolation Kit according to the manufacturer protocol (MO BIO Laboratories Inc., Carlsbad, CA, USA). Bacterial 16S rRNA libraries 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; vsearch 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 water sample.

Instruments:

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

Provenance and Historical References:

Guerry, Patricia, D.J. LeBlanc, and Stanley Falkow. 1973. General method for the isolation of plasmid deoxyribonucleic acid. Journal of Bacteriology 116(2): 1064-1066. DOI: 10.1128/JB.116.2.1064-1066.1973 Kozich, James J., Sarah L. Westcott, Nielson T. Baxter, Sarah K. Highlander, and Patrick D. Schloss. 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, Kendra R., and Cristina D. Takacs-Vesbach. 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, Patrick 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., I.T. Knight, W. L. Straube, and R. R. Colwell. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Applied and Environmental Microbiology 55(3): 548-554. DOI: 10.1128/AEM.55.3.548-554.1989 Zhou, Jizhong, Maryann V. Bruns, and James M. Tiedje. 1996. DNA recovery from soils of diverse composition. Applied and Environmental Microbiology 62(2): 316-322. DOI: 10.1128/AEM.62.2.316-322.1996

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