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

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, bior...

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Autores principales: Elufisan, Temidayo O., Rodríguez-Luna, Isabel C., Oyedara, Omotayo Opemipo, Sánchez-Varela, Alejandro, Hernández-Mendoza, Armando, Dantán Gonzalez, Edgar, Paz-González, Alma D., Muhammad, Kashif, Rivera, Gildardo, Villalobos-Lopez, Miguel Angel, Guo, Xianwu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6951288/
https://www.ncbi.nlm.nih.gov/pubmed/31934497
http://dx.doi.org/10.7717/peerj.8102
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author Elufisan, Temidayo O.
Rodríguez-Luna, Isabel C.
Oyedara, Omotayo Opemipo
Sánchez-Varela, Alejandro
Hernández-Mendoza, Armando
Dantán Gonzalez, Edgar
Paz-González, Alma D.
Muhammad, Kashif
Rivera, Gildardo
Villalobos-Lopez, Miguel Angel
Guo, Xianwu
author_facet Elufisan, Temidayo O.
Rodríguez-Luna, Isabel C.
Oyedara, Omotayo Opemipo
Sánchez-Varela, Alejandro
Hernández-Mendoza, Armando
Dantán Gonzalez, Edgar
Paz-González, Alma D.
Muhammad, Kashif
Rivera, Gildardo
Villalobos-Lopez, Miguel Angel
Guo, Xianwu
author_sort Elufisan, Temidayo O.
collection PubMed
description 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.
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spelling pubmed-69512882020-01-13 The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico Elufisan, Temidayo O. Rodríguez-Luna, Isabel C. Oyedara, Omotayo Opemipo Sánchez-Varela, Alejandro Hernández-Mendoza, Armando Dantán Gonzalez, Edgar Paz-González, Alma D. Muhammad, Kashif Rivera, Gildardo Villalobos-Lopez, Miguel Angel Guo, Xianwu PeerJ Genomics 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. PeerJ Inc. 2020-01-06 /pmc/articles/PMC6951288/ /pubmed/31934497 http://dx.doi.org/10.7717/peerj.8102 Text en ©2020 Elufisan et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Genomics
Elufisan, Temidayo O.
Rodríguez-Luna, Isabel C.
Oyedara, Omotayo Opemipo
Sánchez-Varela, Alejandro
Hernández-Mendoza, Armando
Dantán Gonzalez, Edgar
Paz-González, Alma D.
Muhammad, Kashif
Rivera, Gildardo
Villalobos-Lopez, Miguel Angel
Guo, Xianwu
The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
title The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
title_full The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
title_fullStr The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
title_full_unstemmed The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
title_short The Polycyclic Aromatic Hydrocarbon (PAH) degradation activities and genome analysis of a novel strain Stenotrophomonas sp. Pemsol isolated from Mexico
title_sort polycyclic aromatic hydrocarbon (pah) degradation activities and genome analysis of a novel strain stenotrophomonas sp. pemsol isolated from mexico
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6951288/
https://www.ncbi.nlm.nih.gov/pubmed/31934497
http://dx.doi.org/10.7717/peerj.8102
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