Abstract:
SEED annotated metagenome data from 14 benthic sediment samples. Raw, unassembled reads were annotated in MG-RAST using SEED, with a maximum e-value of 1x10-3, a minimum identity of 50%, and minimum identity cutoff of 15.
Suggested Citation:
Nicole Scott. 2015. SEED annotated Metagenome data generated from 14 benthic sediment samples taken from the Northern Gulf of Mexico, September to October 2010. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7D21VMM
Purpose:
Purpose 1: Understanding microbial community responses to oil spills is crucial for guiding and monitoring remediation procedures. Surface sediment samples were collected at 64 locations in the Gulf of Mexico along a gradient of oil contamination caused by the Deepwater Horizon (DWH) oil spill. All samples were sequenced to determine the community composition based on their 16S rRNA gene profiles, and metagenome sequences were collected for 14 of these samples. Two OTUs were more abundant in the samples with the highest hydrocarbon concentrations: these included an uncharacterized gammaproteobacterial species (97% or greater 16S rRNA gene similarity) and an OTU similar to Colwellia psychrerythraea strain 34H. The metagenomes from samples that exceeded the EPA’s polyaromatic hydrocarbon (PAH) benchmark concentrations (7/14 samples) differed significantly in many functional pathways, such as aromatic hydrocarbon degradation, from less contaminated samples. A dominant hydrocarbon degradation pathway that emerged from metagenome sequence data encoded cyclohexane degradation with butane monooxygenase. This pathway was previously reported in Brachymonas petroleovorans CHX, which can grow on many substrates, including aliphatic and aromatic hydrocarbons. The metagenome data suggested that members of the microbial community in sediments could degrade both aliphatics and aromatics; we validated this hypothesis using 14C experiments. Comparison to metagenome data from the deep-sea plume revealed that the microbial community structure and functional pathways in the surficial sediment samples differed substantially, suggesting that the catabolic potential of microorganisms in these two environments differs. Our results suggest that, as in the deep-sea plume, there was a shift in the sediment microbial community structure, but that the dominant microbial players and metabolic processes in sediments impacted by the DWH oil spill differ from those reported in the water column. Consequently, monitoring of both the water column and the sediment may be necessary to understand the consequences of oil spills. Purpose 2: During hydrocarbon exposure, the composition and functional dynamics of marine microbial communities are altered, favoring bacteria that can utilize this rich carbon source. Initial exposure of high levels of hydrocarbons in aerobic surface sediments can enrich growth of heterotrophic microorganisms having hydrocarbon degradation capacity. As a result, there can be a localized reduction in oxygen potential within the surface layer of marine sediments causing anaerobic zones. We hypothesized that increasing exposure to elevated hydrocarbon concentrations would positively correlate with an increase in denitrification processes and the net accumulation of dinitrogen. This hypothesis was tested by comparing the relative abundance of genes associated with nitrogen metabolism and nitrogen cycling identified in 8 metagenomes from sediments contaminated by polyaromatic hydrocarbons from the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico, and 6 without PAHs.
Data Parameters and Units:
MG-RAST files SEED.tsv -- Metagenome (sample name), source (treatment), function number of times a particular functional role is detected (count), abundance of gene (count), average eValue for all the hits (%), average % identified average match of your reads to database hits (%), average sequence alignment length (numeric), # hits to the database (count). Env_data.MasonBP.full.Untransformed.VER3.txt -- Cruise (ID), Sample (ID), MGRAST (ID), Latitude (decimal degrees), Longitude (decimal degrees), Distance from wellhead (kilometers), [Dissolved phosphate, Dissolved Inorganic nitrogen, Total Ammonium, Dissolved Nitrate] (micrograms/Liter - µg/L), [Total Nitrogen, Total Carbon ,Total Sulfur] (% dry weight), [total petroleum hydrocarbons, sum of aromatic, sum of alkanes, sum of branched alkanes, sum of cyclic alkanes, sum of other, sum of polycyclic aromatic hydrocarbons PAH] (micrograms/kilograms-µg/kg), Designations Exceeds EPA-BM (0-no, 1-yes), water depth (meters).
View Metadata