Novel isoprene-degrading proteobacteria from soil and leaves identified by cultivation and metagenomics analysis of stable isotope probing experiments

Larke-Mejía, Nasmille L., Crombie, Andrew T., Pratscher, Jennifer, McGenity, Terry J. and Murrell, J. Colin (2019) Novel isoprene-degrading proteobacteria from soil and leaves identified by cultivation and metagenomics analysis of stable isotope probing experiments. Frontiers in Microbiology, 10. ISSN 1664-302X

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Isoprene is a climate-active gas and one of the most abundant biogenic volatile organic compounds (BVOC) released into the atmosphere. In the terrestrial environment, plants are the primary producers of isoprene, releasing between 500 and 750 million tons per year to protect themselves from environmental stresses such as direct radiation, heat, and reactive oxygen species. While many studies have explored isoprene production, relatively little is known about consumption of isoprene by microbes and the most well-characterized isoprene degrader is a Rhodococcus strain isolated from freshwater sediment. In order to identify a wider range of bacterial isoprene-degraders in the environment, DNA stable isotope probing (DNA-SIP) with 13C-labeled isoprene was used to identify active isoprene degraders associated with soil in the vicinity of a willow tree. Retrieval by PCR of 16S rRNA genes from the 13C-labeled DNA revealed an active isoprene-degrading bacterial community dominated by Proteobacteria, together with a minor portion of Actinobacteria, mainly of the genus Rhodococcus. Metagenome sequencing of 13C-labeled DNA from SIP experiments enabled analysis of genes encoding key enzymes of isoprene metabolism from novel isoprene degraders. Informed by these DNA-SIP experiments and working with leaves and soil from the vicinity of tree species known to produce high amounts of isoprene, four novel isoprene-degrading strains of the genera Nocardioides, Ramlibacter, Variovorax and Sphingopyxis, along with strains of Rhodococcus and Gordonia, genera that are known to contain isoprene-degrading strains, were isolated. The use of lower concentrations of isoprene during enrichment experiments has revealed active Gram-negative isoprene-degrading bacteria associated with isoprene-emitting trees. Analysis of isoprene-degradation genes from these new isolates provided a more robust phylogenetic framework for analysis of isoA, encoding the α-subunit of the isoprene monooxygenase, a key molecular marker gene for cultivation-independent studies on isoprene degradation in the terrestrial environment.

Item Type: Article
Additional Information: Funding information: The work on this project was funded through the European Research Council (ERC) Advanced Grant (IsoMet 694578) to JCM, the Natural Environment Research Council (NERC) grants to JCM (NE/J009725/1) and TJM (NE/J009555/1), and Earth and Life Systems Alliance (ELSA) at the University of East Anglia. Colombian Government Scholarship (No. 646, Colciencias/Newton Fund, 2014) was awarded to NLL-M. We acknowledge the award of a Leverhulme Early Career Fellowship (ECF-2016-626) to ATC. JP was supported by a NERC Independent Research Fellowship (NE/L010771/2).
Uncontrolled Keywords: sdg 13 - climate action ,/dk/atira/pure/sustainabledevelopmentgoals/climate_action
Faculty \ School: Faculty of Science > School of Biological Sciences
Faculty of Science > School of Environmental Sciences
Depositing User: LivePure Connector
Date Deposited: 03 Jan 2020 04:01
Last Modified: 29 Jun 2023 12:30
DOI: 10.3389/fmicb.2019.02700

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