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...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English English English |
| Published: |
Frontiers
2018
|
| Subjects: | |
| Online Access: | 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 |
| _version_ | 1848786844359065600 |
|---|---|
| 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 |
| building | IIUM Repository |
| collection | Online Access |
| 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. |
| first_indexed | 2025-11-14T17:15:29Z |
| format | Article |
| id | iium-67881 |
| institution | International Islamic University Malaysia |
| institution_category | Local University |
| language | English English English |
| last_indexed | 2025-11-14T17:15:29Z |
| publishDate | 2018 |
| publisher | Frontiers |
| recordtype | eprints |
| repository_type | Digital Repository |
| 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 |
| 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 |
| title | 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_short | 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 |
| topic | QR Microbiology |
| 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 |