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 inBiology (Basel, Switzerland) Vol. 11; no. 4; p. 519
Main Authors Uttarotai, Toungporn, Sutheeworapong, Sawannee, Crombie, Andrew T., Murrell, J. Colin, Mhuantong, Wuttichai, Noirungsee, Nuttapol, Wangkarn, Sunanta, Bovonsombut, Sakunnee, McGenity, Terry J., Chitov, Thararat
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Published Switzerland MDPI AG 28.03.2022
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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.
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
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Keywords genome
isoprene degradation
climate-active gas
isoprene
Alcaligenes
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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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StartPage 519
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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Volume 11
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