Abstract:

This dataset contains an inventory of bacteria and archaea classified sequence libraries for marsh soil samples collected from Bay Sansbois and Bay Batiste, Louisiana. These taxonomic summaries are based on classification of sequences from the V1-V3 hypervariable region of the 16S rRNA gene using domain-specific primers. Replicate soil cores were collected from plots of Spartina alterniflora, Spartina patens, Juncus roemerianus, and Distichlis spicata. Samples were collected in October 2015, May 2016 and October 2016, in conjunction with the Coastal Waters Consortium’s broader studies of (1) marsh food web dynamics and (2) marsh processes and health in the aftermath of the Deepwater Horizon oil spill. Additional classified 16S rRNA sequence libraries for the V4 hypervariable region are available separately under GRIIDC Unique Dataset Identifier (UDI) R6.x808.000.0048 (DOI: 10.7266/n7-dt8z-jb50).

Suggested Citation:

Engel, Annette Summers and Audrey T. Paterson. 2020. Bacterial and archaeal communities from marsh soil associated with Spartina alterniflora, Spartina patens, Juncus roemerianus, and Distichlis spicata in Bay Sansbois and Bay Batiste, Louisiana, 2015-2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-bzrv-0n54

Purpose:

These data were generated to provide insight into the microbial communities associated with four dominant types of vegetation prevalent in Louisiana saltmarshes, Spartina alterniflora, Spartina patens, Juncus roemerianus, and Distichlis spicata.

Data Parameters and Units:

This dataset reports the abundance of classified microbial 16S rRNA gene sequences amplified with domain-specific primers targeting the V1-V3 hypervariable region. Bacterial and archaeal phylotypes are reported at the phylum and class levels. 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); Geographic Location Name (descriptive details of broad sampling area); Collection Date (Mon-YYYY); Vegetation Type (scientific name of the dominant vegetation in the sample plot); classified sequence abundance.

Methods:

Total nucleic acids were extracted 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 domain specific primers on the MiSeq platform using the 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 the primer sets 27F and 519R (bacteria) and 349F and 808R (archaea). Paired ends produced with these primer sets do not overlap fully along target regions; to make contigs, a minimum quality score threshold of 25 was applied, and in the overlapping region of paired ends a deltaq score of 5 was applied to mismatched bases. 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 assigned to phylotypes using the SILVA reference files (version 128). Inventories of processed classified reads are provided for each sediment sample.

Instruments:

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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