Stenotrophomonas sp. Pemsol isolated from crude oil contaminated soil in Mexico that can degrade polycyclic aromatic hydrocarbons and its whole genome sequence analyzed

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1 Laboratorio de Biotecnologia Genomica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
2 Science policy and Innovation studies, National Center for Technology Management Obafemi Awolowo University campus Ile-ife, Ile-Ife, Osun, Nigeria
3 Microbiology Department, Osun state University, Oshogbo, Osun, Nigeria
4 Centro de Investigación en Dinámica Celular,, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos (UAEM), 62209,, Cuernavaca,, Morelos, Mexico
5 Laboratorio de Estudios Ecogenómicos, Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
6 Laboratorio de Biotecnologia Famaceutica, Centro de Biotecnologia Genomica, Instituto Politecnico Nacional, Mexico, Reynosa, Tamaulipas, Mexico
7 Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Tepetitla, Tlaxcala, Mexico
DOI
10.7287/peerj.preprints.27617v1
Published
Accepted
Subject Areas
Genomics, Microbiology, Molecular Biology
Keywords
Stenotrophomonas, Sequencing., Biphenyl, Polycyclic Aromatic Hydrocarbon (PAH), Naphthalene, degradation
Copyright
© 2019 Elufisan et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, 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 Preprints) and either DOI or URL of the article must be cited.
Cite this article
Elufisan TO, Rodríguez-Luna IC, Oyedara OO, Sánchez-Varela A, Hernandez Mendoza A, Dantan Gonzalez E, Paz-González AD, Muhammad K, Rivera G, Villalobos-Lopez MÁ, Guo X. 2019. Stenotrophomonas sp. Pemsol isolated from crude oil contaminated soil in Mexico that can degrade polycyclic aromatic hydrocarbons and its whole genome sequence analyzed. PeerJ Preprints 7:e27617v1

Abstract

Background: Stenotrophomonas are ubiquitous gram-negative bacteria which 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 antimicrobial agents because of their recalcitrant nature to many toxic compounds. Method. Stenotrophomonas sp. Pemsol was isolated from a crude oil contaminated soil. The capability of this isolate to tolerate and degrade polycyclic aromatic hydrocarbons (PAHs) (anthracene, anthraquinone, biphenyl, naphthalene, phenanthrene, phenanthridine and xylene) was evaluated on Bush Nell Hass medium containing PAHs as the unique 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). Results. Complete degradation of naphthalene at a concentration of 1 mg/mL was obtained and a newly formed catechol peak obtained from the UPLC-MS and GC-MS confirmed the degradation. The strain Pemsol lacked the ability to produce biosurfactant so that it cannot bio-emulsify PAHs. The whole genome analysis of Stenotrophomonas sp. Pemsol revealed a wealth of genes for hydrocarbon utilization and interaction with the environment and the presence of 147 genes associated with the degradation of PAHs, some of which are strain-specific on the genomic islands. Few genes are associated with bio-emulsification indicated that Pemsol without biosurfactant production has a genetic basis. This is the first report of the complete genome analysis sequence of a PAH-degrading Stenotrophomonas. Stenotrophomonas sp. Pemsol possesses features that makes it a good bacterium for genetic engineering and will therefore be a good tool for the remediation of crude oil or PAH-contaminated soil.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Supplementary file 2aTable of COGs comparison statistic between Stenotrophomonas sp. Pemsol and five other PAH degrading bacteria

COGs category comparison betwen Pemsol and and five other PAH degrading bacteria

DOI: 10.7287/peerj.preprints.27617v1/supp-1

Supplementary file 2b: Table for the COGs category comparison betwen Pemsol and selected member of other Stenotrophomonas species

COGs category comparison betwen Pemsol and selected member of other Stenotrophomonas species.

DOI: 10.7287/peerj.preprints.27617v1/supp-2

Tables for the genes involved in the degradation and survival of Pemsol

The tables contain the genes associated with PAH degradation by pemsol and their function, the genes that are on the genomic island, and the genes that are unique to Pemsol

DOI: 10.7287/peerj.preprints.27617v1/supp-3

raw table for figure 2

The table contains the growth of Stenotrophomonas sp. Pemsol in different PAH studies in the 8 days of tolerance studies

DOI: 10.7287/peerj.preprints.27617v1/supp-4

This table contains the growth of Pemsol and other hydrocarbon degrading bacteria tested for their tolerance and growth in PAH in a 20 day tolerance study prior to degradation analysis. It also contain the table for the emulsion test of Pemsol as compared

EACH TABLE represents Stenotrophomonas species' growth in different PAH

DOI: 10.7287/peerj.preprints.27617v1/supp-5

Figures showing the spectra from FTIR,and UPLC MS analysis for the product formed from the degradation of naphthalene by Pemsol

Figure 1 contains FTIR spectrum while figure 2 and 3 contain UPLC MS spectra

DOI: 10.7287/peerj.preprints.27617v1/supp-6