Abstract:

This dataset contains the bacterial and archaeal 16S rRNA sequence information from the Methane Microbial Observatory for Seafloor Analysis (MIMOSA) deployment at GC600 from October 2013 (PE14-09) to March 2014 (PE14-14). The purpose of the deployment was to examine the in situ degradation of oil. The deployment contained flow-through chambers of sediment, one amended with oil and one unamended. Samples were collected from the beginning and end of the experiment. The dataset contains three types of files for both bacterial and archaeal sequences, generated from QIIME-pipeline analysis of Illumina MiSeq sequencing data: (1) FASTA formatted files of sequences of representative operational taxonomic units (OTUs), (2) a list of the abundance of each OTU in each sample, and (3) a list mapping individual sequences to each OTU.

Suggested Citation:

Beth Orcutt. 2016. MIMOSA sediment chamber 16S rRNA gene sequence data, Gulf of Mexico, October 1, 2013 to March 30, 2014. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7BK19DV

Publications:

Orcutt, B. N., Lapham, L. L., Delaney, J., Sarode, N., Marshall, K. S., Whaley-Martin, K. J., … Girguis, P. R. (2017). Microbial response to oil enrichment in Gulf of Mexico sediment measured using a novel long-term benthic lander system. Elem Sci Anth, 5(0), 18. doi:10.1525/elementa.129

Purpose:

This dataset was generated to describe bacterial and archael diversity in sediments contaminated with oil.

Data Parameters and Units:

Metadata for Sediment 16S rRNA gene sequence files Sample description: SampleID, Primer set, Description (chamber/time) Bact1, bacteria, oil chamber top/end Bact2, bacteria, oil chamber bottom/end Bact3, bacteria, control chamber top/end Bact4, bacteria, control chamber bottom/end Bact5, bacteria, background sediment/end Bact6, bacteria, control chamber/begin Bact7, bacteria, oil chamber/begin Bact8, bacteria, background sediment/begin Arc1, archaea, oil chamber top/end Arc2, archaea, oil chamber bottom/end Arc3, archaea, control chamber top/end Arc4, archaea, control chamber bottom/end Arc5, archaea, background sediment/end Arc6, archaea, control chamber/begin Arc7, archaea, oil chamber/begin Arc8, archaea, background sediment/begin File: Sediment_archaea_OTU_abundance.txt Description: CSV-formatted file of relative abundance of archaeal operational taxonomic units (OTU) in each of the samples. Column header info: OTU ID, Number of OTU Arc1, relative abundance of OTU in sample oil chamber top/end Arc2, relative abundance of OTU in sample oil chamber bottom/end Arc3, relative abundance of OTU in sample control chamber top/end Arc4, relative abundance of OTU in sample control chamber bottom/end Arc5, relative abundance of OTU in sample background sediment/end Arc6, relative abundance of OTU in sample control chamber/begin Arc7, relative abundance of OTU in sample oil chamber/begin Arc8, relative abundance of OTU in sample background sediment/begin Consensus Lineage: Taxonomic assignment of OTU File: Sediment_archaea_OTUmap.txt Description: CSV-formatted file with list of archaeal sequences belonging to each OTU, where each row lists a unique OTU in the first column, and then the names of sequences populate the following columns File: Sediment_archaea_sequences_repset.fna Description: FASTA formatted file of quality controlled representative archaeal sequences for each OTU File: Sediment_bacteria_OTU_abundance.txt Description: Relative abundance of bacterial operational taxonomic units (OTU) in each of the samples. Column header info: OTU ID, Number of OTU Bact1, relative abundance of OTU in sample oil chamber top/end Bact2, relative abundance of OTU in sample oil chamber bottom/end Bact3, relative abundance of OTU in sample control chamber top/end Bact4, relative abundance of OTU in sample control chamber bottom/end Bact5, relative abundance of OTU in sample background sediment/end Bact6, relative abundance of OTU in sample control chamber/begin Bact7, relative abundance of OTU in sample oil chamber/begin Bact8, relative abundance of OTU in sample background sediment/begin Consensus Lineage: Taxonomic assignment of OTU File: Sediment_bacteria_OTUmap.txt Description: CSV-formatted file with list of bacterial sequences belonging to each OTU, where each row lists a unique OTU in the first column, and then the names of sequences populate the following columns File: Sediment_bacteria_sequences_repset.fna Description: FASTA formatted file of quality controlled representative bacterial sequences for each OTU

Individual Files: