In this work, we present peak-cognizant quantification of environmental weathering of crude oil from the from the Deepwater Horizon oil spill. The key idea is to autonomously extract peak information from raw gas chromatography-mass spectrometry (GC-MS) signals from crude oil samples, and represent the relative weathering of different peaks in a graph-based quantitative computational framework. We also present results from pre-processing the raw signals with baseline correction and signal normalization. Retention time alignment is performed by first aligning the source oil by determining the retention time drift between prominent peaks within the signals and applying the calculated drift to the weathered oil samples. Peak finding, validation, and grouping of the five weathered oil samples to a source oil sample allows compound associations to be discovered. We present preliminary results as graphical visualizations allowing for rapid and precise interpretation of weathering compounds within polycyclic aromatic hydrocarbons (PAH). Results presented were generated with oil samples showing different degrees of weathering collected from the Deepwater Horizon spill.
Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater
ABSTRACT Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)—toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus . We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared more »
- Editors:
- Rappe, Michael S.
- Award ID(s):
- 1737409
- Publication Date:
- NSF-PAR ID:
- 10277550
- Journal Name:
- mSystems
- Volume:
- 6
- Issue:
- 3
- ISSN:
- 2379-5077
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
- Publisher's Version of Record
- https://doi.org/10.1128/mSystems.00245-21
