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

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

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Abstract

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.

Item Type:	Article (Journal)
Additional Information:	5512/67881
Uncontrolled Keywords:	polycyclic aromatic hydrocarbons, microbiome, bioremediation, soil, phenanthrene
Subjects:	Q Science > QR Microbiology
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Science Kulliyyah of Science > Department of Biotechnology
Depositing User:	Dr. Mardiana Mohd. Ashaari
Date Deposited:	30 Nov 2018 16:42
Last Modified:	27 Jan 2019 17:03
URI:	http://irep.iium.edu.my/id/eprint/67881

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