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Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest

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Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
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School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, Thailand
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School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Enzyme Technology Research Team, Biorefinery and Bioproduct Technology Research Group, National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand
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Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Environmental Science Research Center (ESRC), Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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Authors to whom correspondence should be addressed.
Academic Editor: Yanbin Hao
Biology 2022, 11(4), 519; https://doi.org/10.3390/biology11040519
Received: 18 February 2022 / Revised: 17 March 2022 / Accepted: 24 March 2022 / Published: 28 March 2022
(This article belongs to the Section Microbiology)
Isoprene, 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.
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. View Full-Text
Keywords: isoprene; climate-active gas; isoprene degradation; genome; Alcaligenes isoprene; climate-active gas; isoprene degradation; genome; Alcaligenes
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MDPI and ACS Style

Uttarotai, T.; Sutheeworapong, S.; Crombie, A.T.; Murrell, J.C.; Mhuantong, W.; Noirungsee, N.; Wangkarn, S.; Bovonsombut, S.; McGenity, T.J.; Chitov, T. Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest. Biology 2022, 11, 519. https://doi.org/10.3390/biology11040519

AMA Style

Uttarotai T, Sutheeworapong S, Crombie AT, Murrell JC, Mhuantong W, Noirungsee N, Wangkarn S, Bovonsombut S, McGenity TJ, Chitov T. Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest. Biology. 2022; 11(4):519. https://doi.org/10.3390/biology11040519

Chicago/Turabian Style

Uttarotai, Toungporn, Sawannee Sutheeworapong, Andrew T. Crombie, J. C. Murrell, Wuttichai Mhuantong, Nuttapol Noirungsee, Sunanta Wangkarn, Sakunnee Bovonsombut, Terry J. McGenity, and Thararat Chitov. 2022. "Genome Characterisation of an Isoprene-Degrading Alcaligenes sp. Isolated from a Tropical Restored Forest" Biology 11, no. 4: 519. https://doi.org/10.3390/biology11040519

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