Abstract:

Demultiplexed forward reads and mapping file for 709 16S amplicon GoM samples. Bacterial communities associated with sediment and water column samples collected as described above were analyzed by first extracting DNA as per standard protocols http://www.earthmicrobiome.org/emp-standard-protocols/dna-extraction-protocol/). This protocol uses a modified PowerSoil-htp 96 well DNA Isolation Kit (MoBio) with an epMotion 5075 Vac robotic platform (Eppendorf, Hauppauge, NY). DNA was amplified in triplicate using bacterial and archaeal primers 515F and 806R that target the V4-V5 hypervariable region of the 16S rRNA gene in E. coli. Specific methods are outlined by the Earth Microbiome Project (http://www.earthmicrobiome.org/emp-standard-protocols/16s/) and also described in (Caporaso et al., 2012).Amplified samples were barcoded and run on a single MiSeq run generating between 500-200,000 reads per sample..

Suggested Citation:

Scott, Nicole and Gilbert, Jack. 2015. 16S microbial data generated from sediment and water column samples collected from May 2010 to June 2012. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7HT2M9K

Publications:

Mason, O. U., Scott, N. M., Gonzalez, A., Robbins-Pianka, A., Bælum, J., Kimbrel, J., … Jansson, J. K. (2014). Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J, 8(7), 1464–1475. doi:10.1038/ismej.2013.254

Scott, N. M., Hess, M., Bouskill, N. J., Mason, O. U., Jansson, J. K., & Gilbert, J. A. (2014). The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00108

Purpose:

The Deepwater Horizon oil spill released several millions of barrels of hydrocarbons into the GoM over 3 months in 2010. Though shifts in microbial assemblages have been well documented during the spill, the impact on nutrient and metabolic cycling has yet to be unraveled. Oil contamination causes shifts in the availability of inorganic and organic nutrients and in turn can change the metabolic dynamics of the microbial communities that utilize these as energy sources. These shifts can therefore impact the functioning of nutrient and biogeochemical cycling in marine environments. We hypothesize that since microbiota are sensitive indicators of environmental change, we can use the dynamic responses of microbial assemblages to monitor shifts in nutrient and metabolic cycling, specifically those related to: nitrogen, iron, and sulfate and methane metabolism. We can predict these changes in metabolism using Predicted Relative Metabolic Turnover (PRMT) in sediment and water column samples collected during and after the Macondo well spill. PRMT translates the relative abundance of annotated enzymes in a metagenome into a predicted turnover of the metabolites transformed by those functions. PRMT was applied to 14 sequenced metagenomes and to over 700 simulated metagenomes (predicted from 16S rRNA amplicon data using PICRUSt) from contaminated and uncontaminated marine sediments in the GoM.

Data Parameters and Units:

.fna -- FASTA sequence data, MappingFile.v1.txt -- #SampleID, Oiled (yes, no, or N/A), Cruise (research vessel name and number/date) [WaltonSmith, CapeHatteras, Endeavor Cruise 496/509, Pelican Sept 2010, Atlantis, Oceanus 2010], env_feature (marine_sediment/seawater], sample_name_Teske ["E002.06,0-3cm", "Event019.02-B3", "OS2-C59-B6", 9999], altitude (meters), collection_date (MM.DD.YYYY), country [Gulf of Mexico], WaterDepth (meters), emp_status [ENV], env_biome [marine_biome], env_matter [marine_sediment/seawater], sample_location [UNC/UGA], collection_date2 (MM/DD/YYYY), latitude (degrees.arc minutes.arc seconds), longitude (degrees.arc minutes.arc seconds), Description [marine sediment metagenome/seawater metagenome]

Individual Files: