Identification and characterisation of isoprene-degrading bacteria in an estuarine environment.

Antonia Johnston,Gregg M. Whited,Andrew T. Crombie,Terry J. McGenity,Leanne Sims,J. Colin Murrell,Myriam El Khawand

doi:10.1111/1462-2920.13842

Antonia Johnston, Gregg M. Whited + Show 5 more

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https://doi.org/10.1111/1462-2920.13842

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Abstract

SummaryApproximately one‐third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA‐Stable Isotope Probing (DNA‐SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene‐degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four‐component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA‐SIP and to characterise marine isoprene‐degrading bacteria at the physiological and molecular level.

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This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record
Water and sediment samples were taken from the Colne Estuary, (Wivenhoe, Essex, UK) and the bacterial community characterised by sequencing of 16S rRNA gene amplicons
We identified Actinobacteria of the genera Mycobacterium and Microbacterium as the predominant isoprene degraders in DNA-Stable Isotope Probing (DNA-SIP) enrichments

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Introduction

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. El Khawand et al, (2016) showed that isoprene-degrading Rhodococcus spp. were abundant in isoprene-enriched soil microcosms, and that members of the Comamonadaceae were active in isoprene degradation These authors developed PCR primers targeting isoA, encoding the alpha-subunit of the hydroxylase component of isoprene monooxygenase (IsoMO), which were used to retrieve isoA sequences from diverse environmental samples and provided a snapshot of the active terrestrial isoprene-degrading community. The enriched samples were dominated by Actinobacteria, and several isoprene-degrading strains were isolated (Acuña Alvarez et al, 2009) Mixtures of these bacteria consumed isoprene produced in microcosms by algal cultures, suggesting that isoprene degradation by bacteria could occur in these environments. No studies have directly identified the metabolically active isoprene degraders in marine or estuarine environments or searched for the genes involved

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