scholarly journals Metagenomics and stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

2019 ◽  
Author(s):  
Ella T. Sieradzki ◽  
Michael Morando ◽  
Jed A. Fuhrman
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Los Angeles ◽  
Stable Isotope ◽  
Aromatic Hydrocarbons ◽  
Degradation Pathway ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
Port Of Los Angeles ◽  
Polycyclic Aromatic ◽  
Bacterial Biodegradation

AbstractBacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts 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 low chronic inputs can respond to an acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We show a switch in the composition of the PAH degrading community from diverse early-responding generalists to late-blooming specialized degraders. This switch demonstrates the ability of the local seed community of degraders at the Port of LA to incorporate carbon from PAHs independently of a labile-hydrocarbon degrading succession. We were able to directly show that assembled genomes belonged to 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 any of those genomes and even when combining genes from the entire microbial community. We use metabolic pathways identified in those genomes to generate metagenomic-based recommendations for future optimization of PAHs bioremediation.

scholarly journals Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater

mSystems ◽  
2021 ◽  
Vol 6 (3) ◽  
Author(s):  
Ella T. Sieradzki ◽  
Michael Morando ◽  
Jed A. Fuhrman
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Microbial Community ◽  
Los Angeles ◽  
Stable Isotope ◽  
Aromatic Hydrocarbons ◽  
Oil Spills ◽  
Stable Isotope Probing ◽  
Degrading Bacteria ◽  
Port Of Los Angeles ◽  
Polycyclic Aromatic

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 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.

scholarly journals Metagenomics and quantitative stable isotope probing offer insights into metabolism of polycyclic aromatic hydrocarbons degraders in chronically polluted seawater

2020 ◽  
Author(s):  
Ella T. Sieradzki ◽  
Michael Morando ◽  
Jed A. Fuhrman
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Microbial Community ◽  
Los Angeles ◽  
Stable Isotope ◽  
Oil Spill ◽  
Aromatic Hydrocarbons ◽  
Oil Spills ◽  
Stable Isotope Probing ◽  
Port Of Los Angeles ◽  
Polycyclic Aromatic

AbstractBacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs): toxic and recalcitrant components of crude oil as well as byproducts 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 low chronic inputs can respond to acute pollution. We investigated the diversity and functional potential of a similar seed community in the Port of Los Angeles, a chronically polluted site, using stable isotope probing with naphthalene, deep-sequenced metagenomes and carbon incorporation rate measurements at the port and in two sites further into the San Pedro Channel. We demonstrate the ability of a local seed community of degraders at the Port of LA to incorporate carbon from naphthalene, leading to a quick shift in the microbial community composition to be dominated by these normally rare taxa. We were able to directly show that assembled genomes belonged to 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 and even when combining genes from the entire microbial community. We analyze metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate metagenomic-based recommendations for future optimization of PAHs bioremediation.ImportanceOil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil, and have a significant role in degradation of oil spills. The most recalcitrant and toxic component of oil is polycyclic aromatic hydrocarbons. Therefore, the bacteria who can break those molecules down are of particular importance. We identified such bacteria at the port of Los Angeles, one of the busiest ports worldwide, and characterized their metabolic capabilities. Based on those analyses we proposed chemical targets to stimulate the activity of these bacteria in case of an oil spill in the port of LA.

Characteristics of Highway Stormwater Runoff in Los Angeles: Metals and Polycyclic Aromatic Hydrocarbons

2009 ◽  
Vol 81 (3) ◽  
pp. 308-318 ◽  
Author(s):  
Sim-Lin Lau ◽  
Younghan Han ◽  
Joo-Hyon Kang ◽  
Masoud Kayhanian ◽  
Michael K. Stenstrom
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Los Angeles ◽  
Aromatic Hydrocarbons ◽  
Stormwater Runoff ◽  
Polycyclic Aromatic

scholarly journals Occurrence and Phylogenetic Diversity of Sphingomonas Strains in Soils Contaminated with Polycyclic Aromatic Hydrocarbons

2004 ◽  
Vol 70 (4) ◽  
pp. 1944-1955 ◽  
Author(s):  
Natalie M. E. J. Leys ◽  
Annemie Ryngaert ◽  
Leen Bastiaens ◽  
Willy Verstraete ◽  
Eva M. Top ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Rrna Gene ◽  
Soil Dna ◽  
Detection Techniques ◽  
Polycyclic Aromatic

ABSTRACT Bacterial strains of the genus Sphingomonas are often isolated from contaminated soils for their ability to use polycyclic aromatic hydrocarbons (PAH) as the sole source of carbon and energy. The direct detection of Sphingomonas strains in contaminated soils, either indigenous or inoculated, is, as such, of interest for bioremediation purposes. In this study, a culture-independent PCR-based detection method using specific primers targeting the Sphingomonas 16S rRNA gene combined with denaturing gradient gel electrophoresis (DGGE) was developed to assess Sphingomonas diversity in PAH-contaminated soils. PCR using the new primer pair on a set of template DNAs of different bacterial genera showed that the method was selective for bacteria belonging to the family Sphingomonadaceae. Single-band DGGE profiles were obtained for most Sphingomonas strains tested. Strains belonging to the same species had identical DGGE fingerprints, and in most cases, these fingerprints were typical for one species. Inoculated strains could be detected at a cell concentration of 104 CFU g of soil−1. The analysis of Sphingomonas population structures of several PAH-contaminated soils by the new PCR-DGGE method revealed that soils containing the highest phenanthrene concentrations showed the lowest Sphingomonas diversity. Sequence analysis of cloned PCR products amplified from soil DNA revealed new 16S rRNA gene Sphingomonas sequences significantly different from sequences from known cultivated isolates (i.e., sequences from environmental clones grouped phylogenetically with other environmental clone sequences available on the web and that possibly originated from several potential new species). In conclusion, the newly designed Sphingomonas-specific PCR-DGGE detection technique successfully analyzed the Sphingomonas communities from polluted soils at the species level and revealed different Sphingomonas members not previously detected by culture-dependent detection techniques.

scholarly journals Gallaecimonas pentaromativorans gen. nov., sp. nov., a bacterium carrying 16S rRNA gene heterogeneity and able to degrade high-molecular-mass polycyclic aromatic hydrocarbons

2010 ◽  
Vol 60 (3) ◽  
pp. 504-509 ◽  
Author(s):  
Arturo Rodríguez-Blanco ◽  
Gilles Vetion ◽  
Marie-Line Escande ◽  
Daniel Delille ◽  
Jean-François Ghiglione
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Mass ◽  
Aromatic Hydrocarbons ◽  
Direct Sequencing ◽  
High Molecular Mass ◽  
Intertidal Sediment ◽  
Rrna Gene ◽  
Polycyclic Aromatic

A Gram-negative, rod-shaped, halotolerant bacterium, designated strain CEE_131T, which degraded high-molecular-mass polycyclic aromatic hydrocarbons of four and five rings, was isolated from intertidal sediment of Corcubion Ria in Cee, A Coruña, Spain. Direct sequencing showed ambiguities and suggested heterogeneity. Cloned 16S rRNA gene sequence PCR products yielded five different sequences varying at five positions. Strain CEE_131T showed rather distant relationships to its phylogenetically closest neighbours, including the genera Rheinheimera and Serratia, exhibiting 91 % sequence similarity with Rheinheimera perlucida BA131T and Serratia proteamaculans subsp. quinovora DSM 4597T. The major fatty acids were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. The DNA G+C content was 41.7 mol%. On the basis of these distinct phenotypic and genotypic characteristics, strain CEE_131T is considered to represent a novel species in a new genus in the class Gammaproteobacteria, for which the name Gallaecimonas pentaromativorans gen. nov., sp. nov. is proposed. The type strain is CEE_131T (=DSM 21945T=CECT 7479T).

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