Abstract
These data are identified ciliates from deepwater and sediment-water interface samples from the northern Gulf of Mexico based on sequences of cloned 17S rRNA genes.
Purpose
The goal was to examine the diversity and stability of ciliate community structure in deepwater and sediment water interface (immediately above sediments) in deep Gulf of Mexico samples that may have been impacted by the Deepwater Horizon Oil Spill.
Keywords
ciliate community structure
UDI
R1.x135.120:0001
Date
July 2014
Point of Contact
Name
Wade H. Jeffrey
Organization
University of West Florida / Center for Environmental Diagnostics and Bioremediation
Funding Source
RFP-1
DOI
10.7266/N7RB72KS
Rights Information
This work is licensed under a
Creative Commons Public Domain Dedication 1.0 License.
Scholar Commons Citation
Wade Jeffrey. 2014. Gulf of Mexico Deepwater Ciliate communities, August 16-28, 2013.. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7RB72KS
Comments
Supplemental Information
Computative identification of individual clones. Samples are identified by the station location from which they were collected and by the depth (either water column depth in meters (m) or Water over Core (WOC)). Ciliate_sequencing_summary.xlsx-- excel spreadsheet tab named Header: Station (1.DSH07, 2.DWH, 3.SE02, 4.SL1040, 5.SL5100, 6.SL7150, 7.SL9150, 8.SL11150, 9.SL14100, 10.SL16150), Date (MM/DD/YYYY), Latitude (decimal degrees), Longitude (decimal degrees), site map (Note: the map contains an additional 11.SW01 site without data in the excel file), sample photo of the WOC "Water over Core" (or water column at specified meter depths) collected on Sterivex filters. DATA PARAMETERS Clone ID, Organism, Accession #, Max Identity % were collected for the excel spreadsheet tabs 1.DSH07, 2.a.DWH1570m, 2.b.DWH_WOC, 3.SE02_WOC, 4.a.SL1040_55m, 4.b.SL1040_surface, 4.c.SL1040_WOC, 5.a.SL5100_167m, 5.b.SL5100_WOC, 6.a.SL7150_340m, 6.b.SL7150_WOC, 7.SL9150_WOC, 8.SL11150_WOC, 9.a.SL14100_204m, 9.b.SL14100_WOC, 10.SL16150_WOC.||Samples collected during a research cruise aboard the RV WEATHERBIRD II during August 2013 in the northern Gulf of Mexico. |All samples were collected on Sterivex® filters and immediately frozen. DNA was extracted by removing the filter from its housing and extracting using the PowerSoil DNA extraction kit (MoBio® Laboratories, Inc., Carlsbad, CA, USA). PCR amplification of ciliate 17S rRNA was performed using primers as described by Dopheide et al. 2008. PCR products were gel purified, cloned into pCR 2.1 TOPO vector (Life Technologies, Carlsbad, CA, USA) and transformed into elctrocompetent E. coli. Transformants were shipped to Beckman-Coulter Genomics (Danvers, MA, USA) for Sanger Sequencing. Sequence data were then trimmed and evaluated for quality using CodonCode Aligner version 4.14 (CodonCode Corporation, Centerville, MA, USA). Sequence data was analyzed for infractions using software prior to evaluation using the NCBI database via Basic Local Alignment Search Tool (BLAST).|Identify percentage match to existing data bases|Dopheide A, G. Lear, R. Stott and G Lewis. 2008. Molecular Characterization of Ciliate Diversity in Stream Biofilms. Appl. Environ. Microbiol. 2008, 74(6):1740. DOI: 10.1128/AEM.01438-07.