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.

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 Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons

2015 ◽  
Vol 81 (11) ◽  
pp. 3775-3781 ◽  
Author(s):  
Elyse A. Rodgers-Vieira ◽  
Zhenfa Zhang ◽  
Alden C. Adrion ◽  
Avram Gold ◽  
Michael D. Aitken
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Contaminated Soils ◽  
Stable Isotope Probing ◽  
Content Type ◽  
Manufactured Gas Plant ◽  
Degrading Bacteria ◽  
Before And After ◽  
Polycyclic Aromatic ◽  
Genotoxic Compounds

ABSTRACTQuinones and other oxygenated polycyclic aromatic hydrocarbons (oxy-PAHs) are toxic and/or genotoxic compounds observed to be cocontaminants at PAH-contaminated sites, but their formation and fate in contaminated environmental systems have not been well studied. Anthracene-9,10-dione (anthraquinone) has been found in most PAH-contaminated soils and sediments that have been analyzed for oxy-PAHs. However, little is known about the biodegradation of oxy-PAHs, and no bacterial isolates have been described that are capable of growing on or degrading anthraquinone. PAH-degradingMycobacteriumspp. are the only organisms that have been investigated to date for metabolism of a PAH quinone, 4,5-pyrenequinone. We utilized DNA-based stable-isotope probing (SIP) with [U-13C]anthraquinone to identify bacteria associated with anthraquinone degradation in PAH-contaminated soil from a former manufactured-gas plant site both before and after treatment in a laboratory-scale bioreactor. SIP with [U-13C]anthracene was also performed to assess whether bacteria capable of growing on anthracene are the same as those identified to grow on anthraquinone. Organisms closely related toSphingomonaswere the most predominant among the organisms associated with anthraquinone degradation in bioreactor-treated soil, while organisms in the genusPhenylobacteriumcomprised the majority of anthraquinone degraders in the untreated soil. Bacteria associated with anthracene degradation differed from those responsible for anthraquinone degradation. These results suggest thatSphingomonasandPhenylobacteriumspecies are associated with anthraquinone degradation and that anthracene-degrading organisms may not possess mechanisms to grow on anthraquinone.

scholarly journals Characterization of Polycyclic Aromatic Hydrocarbons and Bioaugmentation Potential of Locally Isolated Beneficial Microorganisms Consortium for Treatment of Tar-Balls

2021 ◽  
Vol 19 (3) ◽  
pp. 246-254
Author(s):  
Nur Zaida Zahari ◽  
◽  
Erma Hani Baharudzaman ◽  
Piakong Mohd Tuah ◽  
Fera Nony Cleophas ◽  
...  
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Aromatic Hydrocarbons ◽  
Microbial Population ◽  
Oil Spills ◽  
Beneficial Microorganisms ◽  
Tar Balls ◽  
Polycyclic Aromatic ◽  
Biodegradation Study ◽  
Bioreactor System

Oil spills are one of the environmental pollutions that commonly occur along coastal areas. Tar-balls are one of the products that come from the oil spill pollution. In this study, tar-ball pollution was monitored at 10 points along the coastline of Marintaman Beach in Sipitang, Sabah, Malaysia. This research determined the physical characteristics, composition, and concentration of Polycyclic Aromatic Hydrocarbons (PAHs) in tar-balls. The total number of tar-balls collected was 227 (n=227). The tar-balls were observed in various shapes and the sizes were recorded in the range of 0.1 cm to 6.9 cm. The composition and concentration of Polycyclic Aromatic Hydrocarbons (PAHs) in the outer and inner layer of tar-balls were determined. The results showed that the main Polycyclic Aromatic Hydrocarbons (PAHs) compounds were found in inner layers of the tar-balls with benzo (g,h,i) perylene (72.26 mg/kg), flourene (59.87 mg/kg), dibenzo (a,h) anthracene (44.48 mg/kg), indeno (1,2,3-c,d) pyrene (78.18 mg/kg), and benzo (e) fluoranthene (45.70 mg/kg), respectively. Further research was done with the bioaugmentation study of locally isolated beneficial microorganisms (LIBeM) consortium for treatment of tar-balls in an Aerated Static Pile (ASP) bioreactor system. The results showed that, after 84 days of treatment, this consortium, consisting of C. tropicalis-RETL-Cr1, C. violaceum-MAB-Cr1, and P. aeruginosa-BAS-Cr1, was able to degrade total petroleum hydrocarbon (TPH) by 84% as compared to natural attenuation (19%). The microbial population of this consortium during the biodegradation study is also discussed in this paper.

scholarly journals Assessment of the biodegradation capacity of Azolla on polycyclic aromatic hydrocarbons in crude oil

2018 ◽  
Vol 20 (3) ◽  
pp. 465-470
Keyword(s):  
Polycyclic Aromatic Hydrocarbons ◽  
Crude Oil ◽  
Aromatic Hydrocarbons ◽  
Oil Spills ◽  
Dependent Manner ◽  
Measured Intensity ◽  
Azolla Filiculoides ◽  
Concentration Dependent Manner ◽  
Plant Samples ◽  
Polycyclic Aromatic

<p>In this study, the potential use of Azolla filiculoides Lam. for the bioremediative solution to polycyclic aromatic hydrocarbon (PAH) pollution due to crude oil spills in freshwater was investigated. The plants were grown in nitrogen-free Hoagland nutrient solution media containing 0.05%, 0.1%, 0.2%, 0.3%, 0.4% and 0.5% crude oil by volume for 15 days under greenhouse conditions. Relative growth rates of A. filiculoides decreased in the presence of crude oil in a concentration-dependent manner. The probable influence of A. filiculoides on the biodegradation of polycyclic aromatic hydrocarbons was measured by using synchronous UV fluorescence spectroscopy. GC-MS analysis were also carried out to elucidate the behavior of the oil in experimental and control samples. Although 1-2 rings PAHs have not been encountered in control or plant samples, the measured intensity for 3-4 ring PAHs in plant samples was remarkably lower in comparison to the control. Furthermore, these results demonstrated that the predominant efficacy of the A. filiculoides was for 3-4 ring PAHs at the range 0.05 to 0.2% crude oil concentrations. It could be concluded that the bioremediative potential of A. filiculoides for the removal of polycyclic aromatic hydrocarbons strongly depends on the amount of oil in the contaminated water resource. In other words, A. filiculoides could be used more effectively after the removal of excess crude oil in the spilled freshwater areas.</p>

scholarly journals Isolation and characterization of bacteria with multiple traits: Hydrocarbon degradation, antibiotic-resistant and metal tolerant

2019 ◽  
Vol 10 (4) ◽  
pp. 3789-3795 ◽  
Author(s):  
Neeta Bhagat ◽  
Pranita Roy ◽  
Sohini Singh ◽  
Tanu Allen
Keyword(s):  
Heavy Metals ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Soil Pollution ◽  
Aromatic Hydrocarbons ◽  
Well Being ◽  
Antibiotic Resistant ◽  
Morphological Studies ◽  
Isolation And Characterization ◽  
Degrading Bacteria ◽  
Polycyclic Aromatic

Increasing soil pollution all over the world has instigated global concerns as enormous quantities of toxic chemicals and heavy metals like cadmium, lead, mercury, petrochemicals, insecticides, polycyclic aromatic hydrocarbons (PAHs) and chlorophenols are finding their way into the environment, affecting the land and soil, causing soil pollution and thus posing a threat and menace to health and well- being of people and ecosystem. The ubiquitous dissemination, low bioavailability, high perseverance of contaminants like poly-hydrocarbon and metals in soil have the potentially destructive effects to human health, envisages to study the biodegradation of PAHs (polycyclic aromatic hydrocarbons) and PACs (polycyclic aromatic compounds). The diversity of micro-organisms that diminish the PAHs/PACs can be utilized in the advancement of bioremediation techniques. The role of metal-tolerant, (PAH)-degrading bacteria helps in the biodegradation of organic compounds at miscellaneous polluted sites. The isolation of (PAHs)-degrading bacteria from contaminated soil samples collected from garages and petrol pumps of Delhi and NCR region was carried out in the present study.  Also, the bacterial samples were tested for the tolerance towards 4 heavy metals- arsenic (As), lead (Pb), cadmium (Cd), and mercury (Hg). Morphological studies and biochemical tests were conducted to find the genera of the bacterial samples. The study indicates that hydrocarbons were degraded by the isolates P1, P2, P4, P5, P5*, G1, G3. These isolates were also found to be tolerant at a high concentration of metals (Arsenic, Cadmium, Mercury, and Lead) as minimum inhibitory concentration (MIC) was also calculated. Antibiotic susceptibility of the isolates was tested against various antibiotics. Thus the study suggests that the isolates identified as Pseudomonas aeruginosa, Acinetobacter baumanii, and Klebsiella pneumoniae are not only PAH-degrading but metal-tolerant and antibiotic-resistant too and are of immense potential for bioremediation of contaminated soils.

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