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 V4 hypervariable region of the 16S rRNA gene and are reported in the context of associated standing vegetation. Data represent samples from two collection strategies: 1) inland soil cores collected 5 m from the marsh edge at two long term study sites, sampled biannually from 2010-2016, and 2) marsh soil from plots that represent four types of dominant marsh vegetation, Spartina alterniflora, Spartina patens, Juncus roemerianus, and Distichlis spicata, collected in 2015 and 2016. Supplemental field data are available under GRIIDC Unique Dataset Identifiers (UDIs): R4.x264.198:0001 (DOI: 10.7266/N7HM56JT), R4.x264.198:0004 (DOI: 10.7266/N7FB5197), R4.x264.000:0063 (DOI: 10.7266/N7NG4P4Q) and R4.x264.000:0064 (DOI: 10.7266/N7HQ3XD0). Additional classified 16S rRNA sequence libraries for the V1-V3 hypervariable regions are available separately under UDI R6.x808.000.0049 (DOI: 10.7266/n7-bzrv-0n54).

Suggested Citation:

Engel, Annette Summers and Audrey T. Paterson. 2020. Bacterial and archaeal communities in marsh soil associated with Spartina alterniflora, Spartina patens, Juncus roemerianus, and Distichlis spicata in Bay Sansbois and Bay Batiste, Louisiana, 2013-2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-dt8z-jb50

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. The data are used to identify ecosystem variables that impact the efficacy and interpretation of soil microbiomes as indicators of marsh ecosystem processes and health.

Data Parameters and Units:

Data are reported as classified sequence abundance (using SILVA version 132 as the classification reference). Bacterial phylotypes are reported at the phylum and class levels. Archaeal phylotypes are reported at the phylum, class and order 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); Sample Method Description (descriptive details of specific sample location and type); % Vegetation Cover for five vegetation types (Spartina alterniflora, Juncus roemerianus, Distichlis spicata, Spartina patens, Blutaparon vermiculare); total classified 16S rRNA gene (V4 hypervariable region) sequences.

Methods:

Total nucleic acids were extracted from three to six grams of marsh 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 libraries for bacteria and archaea were sequenced by the Molecular Research LP (Shallowater, TX) using the MiSeq platform, 515FB and 806RB primers, and the paired-end 2 × 300 bp kit according to the manufacturer's instructions (Illumina, San Diego, CA, USA). 16S rRNA libraries were processed using the microbial ecology community software Mothur (Schloss, 2009) and the MiSeq SOP (Kozich et al., 2013). 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.

Individual Files: