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...
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ftdoajarticles:oai:doaj.org/article:9855f4d746674761ba79f28da2709a5f 2023-05-15T13:47:42+02:00 Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad 2020-12-01T00:00:00Z https://doi.org/10.3390/ijms21249363 https://doaj.org/article/9855f4d746674761ba79f28da2709a5f EN eng MDPI AG https://www.mdpi.com/1422-0067/21/24/9363 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067 doi:10.3390/ijms21249363 1422-0067 1661-6596 https://doaj.org/article/9855f4d746674761ba79f28da2709a5f International Journal of Molecular Sciences, Vol 21, Iss 9363, p 9363 (2020) Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway Biology (General) QH301-705.5 Chemistry QD1-999 article 2020 ftdoajarticles https://doi.org/10.3390/ijms21249363 2022-12-31T06:38:17Z 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. Article in Journal/Newspaper Antarc* Antarctic Antarctica King George Island South Shetland Islands Directory of Open Access Journals: DOAJ Articles Antarctic King George Island South Shetland Islands International Journal of Molecular Sciences 21 24 9363 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway Biology (General) QH301-705.5 Chemistry QD1-999 |
spellingShingle |
Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway Biology (General) QH301-705.5 Chemistry QD1-999 Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07 |
topic_facet |
Antarctica Rhodococcus next-generation sequencing de novo assembly β-keto-adipate pathway Biology (General) QH301-705.5 Chemistry QD1-999 |
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. |
format |
Article in Journal/Newspaper |
author |
Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad |
author_facet |
Gillian Li Yin Lee Nur Nadhirah Zakaria Peter Convey Hiroyuki Futamata Azham Zulkharnain Kenshi Suzuki Khalilah Abdul Khalil Noor Azmi Shaharuddin Siti Aisyah Alias Gerardo González-Rocha Siti Aqlima Ahmad |
author_sort |
Gillian Li Yin Lee |
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_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_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_sort |
statistical optimisation of phenol degradation and pathway identification through whole genome sequencing of the cold-adapted antarctic bacterium, rhodococcus sp. strain aq5-07 |
publisher |
MDPI AG |
publishDate |
2020 |
url |
https://doi.org/10.3390/ijms21249363 https://doaj.org/article/9855f4d746674761ba79f28da2709a5f |
geographic |
Antarctic King George Island South Shetland Islands |
geographic_facet |
Antarctic King George Island South Shetland Islands |
genre |
Antarc* Antarctic Antarctica King George Island South Shetland Islands |
genre_facet |
Antarc* Antarctic Antarctica King George Island South Shetland Islands |
op_source |
International Journal of Molecular Sciences, Vol 21, Iss 9363, p 9363 (2020) |
op_relation |
https://www.mdpi.com/1422-0067/21/24/9363 https://doaj.org/toc/1661-6596 https://doaj.org/toc/1422-0067 doi:10.3390/ijms21249363 1422-0067 1661-6596 https://doaj.org/article/9855f4d746674761ba79f28da2709a5f |
op_doi |
https://doi.org/10.3390/ijms21249363 |
container_title |
International Journal of Molecular Sciences |
container_volume |
21 |
container_issue |
24 |
container_start_page |
9363 |
_version_ |
1766247742167842816 |