Abstract:

Shotgun metagenomes were sequenced from marsh subtidal sediment samples collected near Bay Sansbois, Port Sulphur, Louisiana, in May 2010, September 2011, May 2014 and May 2015. Samples were collected 1-2 m offshore from the marsh vegetation edge. For each sample, libraries were sequenced using Illumina HiSeq 2X150 bp and 2X250 bp paired-end technology. Raw, unassembled reads are available for download at metagenomics analysis server: https://www.mg-rast.org/linkin.cgi?project=mgp19524 (MG-RAST Project ID mgp19524).

Suggested Citation:

Engel, Annette Summers, Paterson, Audrey. 2019. Shotgun metagenomic data from marsh sediment from Bay Sansbois, Louisiana from 2010-05-25 to 2015-05-14. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-rf4s-vq73

Purpose:

This dataset explores the metagenomic diversity of microorganisms from coastal marsh sediments that were affected by the Deepwater Horizon oil spill in 2010.

Data Parameters and Units:

sample_name: Unique name or id of the sample; mgrast_id: MG-RAST Sample ID; biome: Description of the major class of ecologically similar communities or plants, animals, and other organisms; collection_date: The date of sampling (YYYY-MM-DD); country: The geographical origin of the sample as defined by the country; env_package: MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained; feature: Description of geographic environmental features; latitude: The geographical origin of the sample as defined by latitude in decimal degrees; location: The geographical origin of the sample as defined by the specific local region name; longitude: The geographical origin of the sample as defined by longitude in decimal degrees; material: The environmental matter that was displaced by the sample, prior to the sampling event; collection_time: The local time of sampling (HH:MM:SS); collection_timezone: The time zone of sampling (coordinated universal time zone); elevation: The elevation of the sampling site in meters as measured by the vertical distance from mean sea level; samp_collect_device: The method or device employed for isolating/collecting the sample; samp_mat_process: Description of the processing applied to the sample during or after retrieval from the environment; temperature: Temperature of the sample in Celsius at time of sampling; continent: The geographical origin of the sample as defined by continent (Africa, Antarctica, Asia, Australia, Europe, North America, South America).

Methods:

Total nucleic acids were extracted in triplicate. Three to six grams of marsh sediment 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). Shotgun metagenome libraries were sequenced using the Illumina HiSeq 2500 platform (Illumina, Inc., San Diego, CA, USA) by the Molecular Research LP (Shallowater, TX). Raw reads were uploaded to the Metagenome Rapid Annotation using Subsystem Technology Server for public access and analysis.

Instruments:

Shotgun metagenome libraries were sequenced using the Illumina HiSeq 2500 platform (Illumina, Inc., 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. 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 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. Appl. Environ. Microbiol., 55(3), 548-554. Zhou, J., Bruns, M. A., & Tiedje, J. M. (1996). DNA recovery from soils of diverse composition. Appl. Environ. Microbiol., 62(2), 316-322.

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