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...
Published in: | International Journal of Molecular Sciences |
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ftnerc:oai:nora.nerc.ac.uk:528542 2023-05-15T13:41:45+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 Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Futamata, Hiroyuki Zulkharnain, Azham Suzuki, Kenshi Khalil, Khalilah Abdul Shaharuddin, Noor Azmi Alias, Siti Aisyah González-Rocha, Gerardo Ahmad, Siti Aqlima 2020-12-09 text http://nora.nerc.ac.uk/id/eprint/528542/ https://nora.nerc.ac.uk/id/eprint/528542/1/ijms-21-09363.pdf https://www.mdpi.com/1422-0067/21/24/9363 en eng MDPI https://nora.nerc.ac.uk/id/eprint/528542/1/ijms-21-09363.pdf Lee, Gillian Li Yin; Zakaria, Nur Nadhirah; Convey, Peter orcid:0000-0001-8497-9903 Futamata, Hiroyuki; Zulkharnain, Azham; Suzuki, Kenshi; Khalil, Khalilah Abdul; Shaharuddin, Noor Azmi; Alias, Siti Aisyah; González-Rocha, Gerardo; 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), 9363. 20, pp. https://doi.org/10.3390/ijms21249363 <https://doi.org/10.3390/ijms21249363> cc_by_4 CC-BY Publication - Article PeerReviewed 2020 ftnerc https://doi.org/10.3390/ijms21249363 2023-02-04T19:51:07Z 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 Natural Environment Research Council: NERC Open Research Archive Antarctic King George Island South Shetland Islands International Journal of Molecular Sciences 21 24 9363 |
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Open Polar |
collection |
Natural Environment Research Council: NERC Open Research Archive |
op_collection_id |
ftnerc |
language |
English |
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 |
Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Futamata, Hiroyuki Zulkharnain, Azham Suzuki, Kenshi Khalil, Khalilah Abdul Shaharuddin, Noor Azmi Alias, Siti Aisyah González-Rocha, Gerardo Ahmad, Siti Aqlima |
spellingShingle |
Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Futamata, Hiroyuki Zulkharnain, Azham Suzuki, Kenshi Khalil, Khalilah Abdul Shaharuddin, Noor Azmi Alias, Siti Aisyah González-Rocha, Gerardo 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 |
author_facet |
Lee, Gillian Li Yin Zakaria, Nur Nadhirah Convey, Peter Futamata, Hiroyuki Zulkharnain, Azham Suzuki, Kenshi Khalil, Khalilah Abdul Shaharuddin, Noor Azmi Alias, Siti Aisyah González-Rocha, Gerardo Ahmad, Siti Aqlima |
author_sort |
Lee, Gillian Li Yin |
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 |
publishDate |
2020 |
url |
http://nora.nerc.ac.uk/id/eprint/528542/ https://nora.nerc.ac.uk/id/eprint/528542/1/ijms-21-09363.pdf https://www.mdpi.com/1422-0067/21/24/9363 |
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_relation |
https://nora.nerc.ac.uk/id/eprint/528542/1/ijms-21-09363.pdf Lee, Gillian Li Yin; Zakaria, Nur Nadhirah; Convey, Peter orcid:0000-0001-8497-9903 Futamata, Hiroyuki; Zulkharnain, Azham; Suzuki, Kenshi; Khalil, Khalilah Abdul; Shaharuddin, Noor Azmi; Alias, Siti Aisyah; González-Rocha, Gerardo; 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), 9363. 20, pp. https://doi.org/10.3390/ijms21249363 <https://doi.org/10.3390/ijms21249363> |
op_rights |
cc_by_4 |
op_rightsnorm |
CC-BY |
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 |
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1766157054646419456 |