Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07
Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bact...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
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MDPI
2020
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| Online Access: | http://psasir.upm.edu.my/id/eprint/85909/ |
| _version_ | 1848860209530798080 |
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| author | Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Convey, Hiroyuki Futamata Zulkharnain, Azham Suzuki, Kenshi Abdul Khalil, Khalilah Shaharuddin, Noor Azmi Alias, Siti Aisyah Gerardo, González-Rocha Ahmad, Siti Aqlima |
| author_facet | Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Convey, Hiroyuki Futamata Zulkharnain, Azham Suzuki, Kenshi Abdul Khalil, Khalilah Shaharuddin, Noor Azmi Alias, Siti Aisyah Gerardo, González-Rocha Ahmad, Siti Aqlima |
| author_sort | Lee, Gillian Li Yin |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica. |
| first_indexed | 2025-11-15T12:41:36Z |
| format | Article |
| id | upm-85909 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T12:41:36Z |
| publishDate | 2020 |
| publisher | MDPI |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-859092023-10-19T21:14:57Z http://psasir.upm.edu.my/id/eprint/85909/ Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Convey, Hiroyuki Futamata Zulkharnain, Azham Suzuki, Kenshi Abdul Khalil, Khalilah Shaharuddin, Noor Azmi Alias, Siti Aisyah Gerardo, González-Rocha Ahmad, Siti Aqlima Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica. MDPI 2020 Article PeerReviewed Lee, Gillian Li Yin and Zakaria, Nur Nadhirah and Convey, Peter and Convey, Hiroyuki Futamata and Zulkharnain, Azham and Suzuki, Kenshi and Abdul Khalil, Khalilah and Shaharuddin, Noor Azmi and Alias, Siti Aisyah and Gerardo, González-Rocha and Ahmad, Siti Aqlima (2020) Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07. International Journal of Molecular Sciences, 21 (24). pp. 1-20. ISSN 1661-6596; ESSN: 1422-0067 https://www.mdpi.com/1422-0067/21/24/9363 10.3390/ijms21249363 |
| spellingShingle | Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Convey, Hiroyuki Futamata Zulkharnain, Azham Suzuki, Kenshi Abdul Khalil, Khalilah Shaharuddin, Noor Azmi Alias, Siti Aisyah Gerardo, González-Rocha Ahmad, Siti Aqlima Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 |
| title | Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 |
| title_full | Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 |
| title_fullStr | Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 |
| title_full_unstemmed | Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 |
| title_short | Statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, Rhodococcus sp. strain AQ5-07 |
| title_sort | statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, rhodococcus sp. strain aq5-07 |
| url | http://psasir.upm.edu.my/id/eprint/85909/ http://psasir.upm.edu.my/id/eprint/85909/ http://psasir.upm.edu.my/id/eprint/85909/ |