Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater
| Autor: | Jed A. Fuhrman, Ella T. Sieradzki, Michael Morando |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Pollution
Biogeochemical cycle Physiology media_common.quotation_subject aromatic hydrocarbons Stable-isotope probing Polycyclic aromatic hydrocarbon marine microbiology microbial ecology Biochemistry Microbiology 03 medical and health sciences chemistry.chemical_compound Bioremediation Microbial ecology bioremediation Genetics 14. Life underwater Molecular Biology stable isotope probing Ecology Evolution Behavior and Systematics 030304 developmental biology Naphthalene media_common chemistry.chemical_classification 0303 health sciences metagenomics biology 030306 microbiology Cycloclasticus Biodegradation biology.organism_classification QR1-502 6. Clean water Computer Science Applications chemistry Microbial population biology 13. Climate action Metagenomics Modeling and Simulation Environmental chemistry Environmental science Bacteria Research Article |
| Zdroj: | mSystems mSystems, Vol 6, Iss 3 (2021) |
| ISSN: | 2379-5077 |
| Popis: | Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. 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 metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids. IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA. |
| Databáze: | OpenAIRE |
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