The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strainStenotrophomonas sp. Pemsol isolated from Mexico

Abstract

Background Stenotrophomonas are ubiquitous gram-negative bacteria, which can survive in a wide range of environments. They can use many substances for their growth and are known to be intrinsically resistant to many antimicrobial agents. They have been tested for biotechnological applications, bioremediation, and production of antimicrobial agents. Method Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAH) such as anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine, and xylene was evaluated in Bushnell Hass medium containing PAHs as the sole carbon sources. The metabolites formed after 30-day degradation of naphthalene by Pemsol were analyzed using Fourier Transform Infra-red Spectroscopic (FTIR), Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and Gas Chromatography-Mass Spectrometry (GC-MS). The genome of Pemsol was also sequenced and analyzed. Results Anthraquinone, biphenyl, naphthalene, phenanthrene, and phenanthridine except xylene can be used as sole carbon sources for Pemsol’s growth in Bushnell Hass medium. The degradation of naphthalene at a concentration of 1 mg/mL within 30 days was tested. A newly formed catechol peak and the disappearance of naphthalene peak detected on the UPLC-MS, and GC-MS analyses spectra respectively confirmed the complete degradation of naphthalene. Pemsol does not produce biosurfactant and neither bio-emulsify PAHs. The whole genome was sequenced and assembled into one scaffold with a length of 4,373,402 bp. A total of 145 genes involved in the degradation of PAHs were found in its genome, some of which are Pemsol-specific as compared with other 11 Stenotrophomonas genomes. Most specific genes are located on the genomic islands. Stenotrophomonas sp. Pemsol’s possession of few genes that are associated with bio-emulsification gives the genetic basis for its inability to bio-emulsify PAH. A possible degradation pathway for naphthalene in Pemsol was proposed following the analysis of Pemsol’s genome. ANI and GGDH analysis indicated that Pemsol is likely a new species of Stenotrophomonas. It is the first report on a complete genome sequence analysis of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that make it a good bacterium for genetic engineering and will be an excellent tool for the remediation of crude oil or PAH-contaminated soil.

Complete Genome Report of a Hydrocarbon-Degrading Sphingobium yanoikuyae S72

“…Others include S-(hydroxymethyl) glutathione dehydrogenase/alcohol dehydrogenase (A6768_05785, COG R) that is associated with the degradation of naphthalene and chloroalkane). Alcohol dehydrogenase (cytochrome c) (A6768_00755, COG G), aldehyde dehydrogenase (NAD+) (A6768_10925, COG E), aldo/keto oxidoreductase (A6768_11370, COG R), phenylacetaldehyde dehydrogenase (A6768_11850, COG C) known to participate in the degradation of fluorobenzoate toluene and naphthalene are also present in S72 [3,8]. Other hydrocarbon degrading genes identified in S72 include propanolpreferring alcohol dehydrogenase (A6768_17370, EC:1.1.1.1), carboxymethylenebutenolidase (A6768_23915), catechol 1,2-dioxygenase (A6768_16795), muconate cycloisomerase (A6768_16805), aryl-alcohol dehydrogenase (A6768_11850), 2-keto-4-pentenoate hydratase (A6768_14055), oxalocrotonate tautomerase (A6768_04785) benzoate 1,2-dioxygenase alpha subunit (A6768_16790), benzoate/toluate 1,2-dioxygenase beta subunit (Ben B), dihydroxy cyclohexadiene carboxylate dehydrogenase (Ben D).…”

“…These compounds are said to be the most common contaminant of soils and ground water owing to frequent leakage and accidental spillage [2]. On the other hand, polycyclic aromatic hydrocarbons (PAHs) are important pollutants which always find their way into the environment through various human activities such as the burning of fossil fuels, oil spillages, and sometimes during vehicle repairs [3]. The release of PAH and BTEX to surrounding air is worrisome because of the associated hazards on people, animal, and plants [2].…”

Antimicrobial susceptibility pattern of Stenotrophomonas species isolated from Mexico

“…These features could be a form of biological fitness for continuous adaptation in their environment 24 , 41 . Likewise, an isolate ( S. maltophilia strain Pemsol 49 ) from contaminated regions showed features that could enhance the degradation of different pollutants. Thus, it may possess attribute which could be employed for bioremediation.…”

Assessment of the Degradation Potential and Genomic Insights towards Phenanthrene by Dietzia psychralcaliphila JI1D

“…Whole genome sequencing allows a comprehensive methodology into the genomic features of bacteria. The genome annotation gives a complete understanding of the dedicated aromatic degrading genes coding for the enzyme, dioxygenase, monooxygenase, dehydrogenase, and decarboxylases [ 12 , 13 ]. Various catabolic pathways have been described for phenanthrene degradation [ 12 , 14 ], where the parent hydrocarbon is shredded into its corresponding catechol-derived daughter products.…”

“…The genome annotation gives a complete understanding of the dedicated aromatic degrading genes coding for the enzyme, dioxygenase, monooxygenase, dehydrogenase, and decarboxylases [ 12 , 13 ]. Various catabolic pathways have been described for phenanthrene degradation [ 12 , 14 ], where the parent hydrocarbon is shredded into its corresponding catechol-derived daughter products. This combined approach is a powerful tool in identifying suitable candidates to construct a bacterial consortium for in situ bioremediation techniques [ 15 ].…”