Abstract:

This dataset contains an inventory of taxonomically classified bacterial amplicons (454 pyrosequencing) from marsh water collected biannually (Spring and Fall) in 2013 and 2014, a component of a longitudinal study of marsh microbial diversity before, during and after the Deepwater Horizon oil spill. Complementary field data are reported separately and are available under GRIIDC UDIs R1.x139.143:0013, R1.x139.143:0015, R1.x139.143:0035, and R1.x139.143:0043.

Suggested Citation:

Engel, Annette Summers. 2019. Water column bacterial communities in Louisiana marshes, 2013-05-21 to 2014-10-29. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-yk9p-vz90

Purpose:

The goal of this dataset is to assess and track bacterial community composition in Louisiana marshes over time.

Data Parameters and Units:

Data are reported as classified 454 amplicon abundance at the bacterial phylum (Worksheet: Phylum) and class levels (Worksheet: Class). For each sample, data are reported as follows: MIMS ID (User defined identifier for each sample); Latitude, Longitude (decimal degrees N, decimal degrees W); Collection date (DD-Mon-YYYY); Sample Description (description of the type of sample collected); Geographic Location Name (general text description of the sampling area); total classified amplicons.

Methods:

Total nucleic acids were extracted from duplicate 0.22 micron PVDF Sterivex filters (EMD Millipore, Billerica, MA, USA) using the MoBio PowerWater Sterivex DNA Isolation Kit according to the manufacturer protocol (MoBio Laboratories Inc., Carlsbad, CA, USA). Amplification and pyrosequencing of the V1-V3 region of 16S rRNA genes were done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Shallowater, TX). Raw 16S rRNA gene sequences were processed using the microbial ecology community software Mothur (http://www.mothur.org/wiki/Download_mothur) (Schloss et al., 2011). Amplicons were trimmed for length (200-500bp) and quality (average quality score of 20 over a sliding window of 50bp), aligned and classified using the SILVA reference database, Release 102 (https://www.arb-silva.de/silva-license-information), screened and filtered, and removed of chimera detected by UCHIME (http://drive5.com/uchime) (Schloss et al., 2011). Inventories of processed reads classified at the phylum and class levels are provided for each sample.

Instruments:

Pyrosequencing of the V1-V3 region of 16S rRNA genes was done using a 454 GS FLX Titanium (Roche, 454 Life Sciences, Branford, CT, USA) by the Molecular Research LP (Shallowater, TX).

Provenance and Historical References:

Schloss, P. D., Gevers, D., & Westcott, S. L. (2011). Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies. PLoS ONE, 6(12), e27310. doi:10.1371/journal.pone.0027310

Individual Files: