Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) enc...

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Main Authors:	Storey, Sean, Mohd Ashaari, Mardiana, Clipson, Nicholas, Doyle, Evelyn, de Menezes, Alexandre
Format:	Article
Language:	English English English
Published:	Frontiers 2018
Subjects:	QR Microbiology
Online Access:	http://irep.iium.edu.my/67881/ http://irep.iium.edu.my/67881/ http://irep.iium.edu.my/67881/ http://irep.iium.edu.my/67881/1/Mardiana_2018.pdf http://irep.iium.edu.my/67881/7/67881_Opportunistic%20bacteria%20dominate%20the%20soil%20microbiome_SCOPUS.pdf http://irep.iium.edu.my/67881/13/67881%20Opportunistic%20Bacteria%20Dominate%20the%20Soil%20Microbiome%20WOS.pdf

id	iium-67881
recordtype	eprints
spelling	iium-678812019-01-27T09:03:43Z http://irep.iium.edu.my/67881/ Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study Storey, Sean Mohd Ashaari, Mardiana Clipson, Nicholas Doyle, Evelyn de Menezes, Alexandre QR Microbiology Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ∼20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols. Frontiers 2018-11-21 Article PeerReviewed application/pdf en http://irep.iium.edu.my/67881/1/Mardiana_2018.pdf application/pdf en http://irep.iium.edu.my/67881/7/67881_Opportunistic%20bacteria%20dominate%20the%20soil%20microbiome_SCOPUS.pdf application/pdf en http://irep.iium.edu.my/67881/13/67881%20Opportunistic%20Bacteria%20Dominate%20the%20Soil%20Microbiome%20WOS.pdf Storey, Sean and Mohd Ashaari, Mardiana and Clipson, Nicholas and Doyle, Evelyn and de Menezes, Alexandre (2018) Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study. Frontiers in Microbiology, 9. pp. 1-13. E-ISSN 1664-302X https://www.frontiersin.org/articles/10.3389/fmicb.2018.02815/full 10.3389/fmicb.2018.02815
repository_type	Digital Repository
institution_category	Local University
institution	International Islamic University Malaysia
building	IIUM Repository
collection	Online Access
language	English English English
topic	QR Microbiology
spellingShingle	QR Microbiology Storey, Sean Mohd Ashaari, Mardiana Clipson, Nicholas Doyle, Evelyn de Menezes, Alexandre Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
description	Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ∼20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.
format	Article
author	Storey, Sean Mohd Ashaari, Mardiana Clipson, Nicholas Doyle, Evelyn de Menezes, Alexandre
author_facet	Storey, Sean Mohd Ashaari, Mardiana Clipson, Nicholas Doyle, Evelyn de Menezes, Alexandre
author_sort	Storey, Sean
title	Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
title_short	Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
title_full	Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
title_fullStr	Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
title_full_unstemmed	Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
title_sort	opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study
publisher	Frontiers
publishDate	2018
url	http://irep.iium.edu.my/67881/ http://irep.iium.edu.my/67881/ http://irep.iium.edu.my/67881/ http://irep.iium.edu.my/67881/1/Mardiana_2018.pdf http://irep.iium.edu.my/67881/7/67881_Opportunistic%20bacteria%20dominate%20the%20soil%20microbiome_SCOPUS.pdf http://irep.iium.edu.my/67881/13/67881%20Opportunistic%20Bacteria%20Dominate%20the%20Soil%20Microbiome%20WOS.pdf
first_indexed	2023-09-18T21:36:23Z
last_indexed	2023-09-18T21:36:23Z
_version_	1777412848287219712

Opportunistic bacteria dominate the soil microbiome response to phenanthrene in a microcosm-based study

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