Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest
Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. S...
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Published in | Biology (Basel, Switzerland) Vol. 11; no. 4; p. 519 |
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Abstract | Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism. |
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AbstractList | Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism. Simple SummaryIsoprene, a volatile hydrocarbon, is the second most abundantly produced climate-active gas, with largely indirect detrimental impacts, such as extending the residence time of the greenhouse gas methane. Isoprene is mainly emitted by plants and can be consumed by a range of microbes inhabiting diverse environments, including soil. Here, the ability of soil bacteria to degrade isoprene was investigated. Soil samples were taken from beneath wild Himalayan cherry trees in a tropical restored forest area, and an Alcaligenes sp. (strain 13f) was isolated. This isolate used isoprene as a sole source of carbon and energy (32.6% of isoprene was consumed in 18 days). A surprising finding from the genome analysis of Alcaligenes sp. strain 13f was that the well-characterised genes and genetic organisation typical of other isoprene-degrading bacteria were not observed. Thus, we propose that this strain uses a different metabolic pathway for isoprene degradation.AbstractIsoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism. Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism.Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an important sink for isoprene due to its consumption by microbes. In this study, we report the ability of a soil bacterium to degrade isoprene. Strain 13f was isolated from soil beneath wild Himalayan cherry trees in a tropical restored forest. Based on phylogenomic analysis and an Average Nucleotide Identity score of >95%, it most probably belongs to the species Alcaligenes faecalis. Isoprene degradation by Alcaligenes sp. strain 13f was measured by using gas chromatography. When isoprene was supplied as the sole carbon and energy source at the concentration of 7.2 × 105 ppbv and 7.2 × 106 ppbv, 32.6% and 19.6% of isoprene was consumed after 18 days, respectively. Genome analysis of Alcaligenes sp. strain 13f revealed that the genes that are typically found as part of the isoprene monooxygenase gene cluster in other isoprene-degrading bacteria were absent. This discovery suggests that there may be alternative pathways for isoprene metabolism. |
Author | Sutheeworapong, Sawannee Wangkarn, Sunanta McGenity, Terry J. Uttarotai, Toungporn Mhuantong, Wuttichai Murrell, J. Colin Crombie, Andrew T. Chitov, Thararat Noirungsee, Nuttapol Bovonsombut, Sakunnee |
AuthorAffiliation | 4 School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK; a.crombie@uea.ac.uk (A.T.C.); j.c.murrell@uea.ac.uk (J.C.M.) 5 Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand; wuttichai.mhu@biotec.or.th 1 Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; toungporn_u@cmu.ac.th (T.U.); nuttapol.n@cmu.ac.th (N.N.); sakunnee.b@cmu.ac.th (S.B.) 3 School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; sawannee.sut@kmutt.ac.th 7 Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand 6 Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; sunanta@chiangmai.ac.th 2 School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK |
AuthorAffiliation_xml | – name: 5 Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand; wuttichai.mhu@biotec.or.th – name: 6 Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; sunanta@chiangmai.ac.th – name: 3 School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand; sawannee.sut@kmutt.ac.th – name: 4 School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK; a.crombie@uea.ac.uk (A.T.C.); j.c.murrell@uea.ac.uk (J.C.M.) – name: 7 Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand – name: 1 Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand; toungporn_u@cmu.ac.th (T.U.); nuttapol.n@cmu.ac.th (N.N.); sakunnee.b@cmu.ac.th (S.B.) – name: 2 School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK |
Author_xml | – sequence: 1 givenname: Toungporn surname: Uttarotai fullname: Uttarotai, Toungporn – sequence: 2 givenname: Sawannee surname: Sutheeworapong fullname: Sutheeworapong, Sawannee – sequence: 3 givenname: Andrew T. surname: Crombie fullname: Crombie, Andrew T. – sequence: 4 givenname: J. Colin surname: Murrell fullname: Murrell, J. Colin – sequence: 5 givenname: Wuttichai orcidid: 0000-0002-3355-0071 surname: Mhuantong fullname: Mhuantong, Wuttichai – sequence: 6 givenname: Nuttapol surname: Noirungsee fullname: Noirungsee, Nuttapol – sequence: 7 givenname: Sunanta surname: Wangkarn fullname: Wangkarn, Sunanta – sequence: 8 givenname: Sakunnee surname: Bovonsombut fullname: Bovonsombut, Sakunnee – sequence: 9 givenname: Terry J. orcidid: 0000-0002-1497-8822 surname: McGenity fullname: McGenity, Terry J. – sequence: 10 givenname: Thararat surname: Chitov fullname: Chitov, Thararat |
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Snippet | Isoprene is a climate-active biogenic volatile organic compound (BVOC), emitted into the atmosphere in abundance, mainly from terrestrial plants. Soil is an... Simple SummaryIsoprene, a volatile hydrocarbon, is the second most abundantly produced climate-active gas, with largely indirect detrimental impacts, such as... |
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SubjectTerms | Alcaligenes Bacteria Biodegradation Carbon climate-active gas Enzymes Gas chromatography genome Genomes Genomic analysis Gram-positive bacteria Greenhouse gases Isoprene isoprene degradation Metabolic pathways Metabolism Monooxygenase National parks Organic compounds Prunus cerasoides Soil microorganisms VOCs Volatile organic compounds |
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Title | Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest |
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