Skip to main content
Book cover

Aerobic Utilization of Hydrocarbons, Oils and Lipids pp 1–15Cite as

Genetics and Ecology of Isoprene Degradation

Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

Approximately 550 million tonnes of the monoterpene, isoprene, are emitted to the atmosphere annually, principally from terrestrial plants. In contrast to methane, which is emitted in similar quantities, little is known about the biodegradation of isoprene. However, 30 years ago, bacteria capable of living on isoprene as a sole source of carbon and energy were described, although they were not investigated in detail. Recently there has been renewed interest in the potential of bacteria living in soils, marine sediments, and on the leaves of plants to degrade isoprene. Isolates capable of isoprene metabolism use a multicomponent soluble monooxygenase, which contains a diiron center at the active site, to oxidize isoprene to the epoxide, and all isolates described to date depend on glutathione for subsequent metabolic steps. The diversity of isoprene degraders has been investigated in terrestrial and marine environments using DNA-stable isotope probing (DNA-SIP), together with the use of gene probes targeting the monooxygenase active-site subunit. Gaps in our knowledge and future research directions are described.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  • Acuña Alvarez L, Exton DA, Timmis KN, Suggett DJ, McGenity TJ (2009) Characterization of marine isoprene-degrading communities. Environ Microbiol 11:3280–3291

    CrossRef  Google Scholar 

  • Bäck J, Aaltonen H, Hellén H, Kajos MK, Patokoski J, Taipale R et al (2010) Variable emissions of microbial volatile organic compounds (MVOCs) from root-associated fungi isolated from Scots pine. Atmos Environ 44:3651–3659

    CrossRef  Google Scholar 

  • Carlton AG, Wiedinmyer C, Kroll JH (2009) A review of Secondary Organic Aerosol (SOA) formation from isoprene. Atmos Chem Phys 9:4987–5005

    CrossRef  CAS  Google Scholar 

  • Chen Y, Ding Y, Yang L, Yu J, Liu G, Wang X et al (2014) Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Res 42:1052–1064

    CrossRef  CAS  PubMed  Google Scholar 

  • Cleveland CC, Yavitt JB (1997) Consumption of atmospheric isoprene in soil. Geophys Res Lett 24:2379–2382

    CrossRef  CAS  Google Scholar 

  • Cleveland CC, Yavitt JB (1998) Microbial consumption of atmospheric isoprene in a temperate forest soil. Appl Environ Microbiol 64:172–177

    CAS  PubMed  PubMed Central  Google Scholar 

  • Crombie AT, Khawand ME, Rhodius VA, Fengler KA, Miller MC, Whited GM et al (2015) Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle. Environ Microbiol 17:3314–3329

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  • Dumont MG, Murrell JC (2005a) Stable isotope probing – linking microbial identity to function. Nat Rev Microbiol 3:499–504

    CrossRef  CAS  PubMed  Google Scholar 

  • Dumont MG, Murrell JC (2005b) Community-level analysis: key genes of aerobic methane oxidation. Methods Enzymol 397:413–427

    CrossRef  CAS  PubMed  Google Scholar 

  • El Khawand M, Crombie AT, Johnston A, Vavlline DV, McAuliffe JC, Latone JA et al (2016) Isolation of isoprene degrading bacteria from soils, development of isoA gene probes and identification of the active isoprene-degrading soil community using DNA-stable isotope probing. Environ Microbiol 18:2743–2753

    CrossRef  PubMed  Google Scholar 

  • Ewers J, Freier-Schroder D, Knackmuss HJ (1990) Selection of trichloroethene (TCE) degrading bacteria that resist inactivation by TCE. Arch Microbiol 154:410–413

    CrossRef  CAS  PubMed  Google Scholar 

  • Exton DA, Suggett DJ, McGenity TJ, Steinke M (2013) Chlorophyll-normalized isoprene production in laboratory cultures of marine microalgae and implications for global models. Limnol Oceanogr 58:1301–1311

    CrossRef  Google Scholar 

  • Exton DA, McGenity TJ, Steinke M, Smith DJ, Suggett DJ (2015) Uncovering the volatile nature of tropical coastal marine ecosystems in a changing world. Glob Chang Biol 21:1383–1394

    CrossRef  PubMed  Google Scholar 

  • Fall R, Copley SD (2000) Bacterial sources and sinks of isoprene, a reactive atmospheric hydrocarbon. Environ Microbiol 2:123–130

    CrossRef  CAS  PubMed  Google Scholar 

  • Fares S, Brilli F, Noguès I, Velikova V, Tsonev T, Dagli S, Loreto F (2008) Isoprene emission and primary metabolism in Phragmites australis grown under different phosphorus levels. Plant Biol 10:38–43

    CrossRef  CAS  PubMed  Google Scholar 

  • Fini A, Brunetti C, Loreto F, Centritto M, Ferrini F, Tattini M (2017) Isoprene responses and functions in plants challenged by environmental pressures associated to climate change. Front Plant Sci 8:1281

    Google Scholar 

  • Gelmont D, Stein RA, Mead JF (1981) Isoprene – the main hydrocarbon in human breath. Biochem Biophys Res Commun 99:1456–1460

    CrossRef  CAS  PubMed  Google Scholar 

  • Gray CM, Helmig D, Fierer N (2015) Bacteria and fungi associated with isoprene consumption in soil. Elem Sci Anth 3:000053

    CrossRef  Google Scholar 

  • Guenther A, Karl T, Harley P, Wiedinmyer C, Palmer PI, Geron C (2006) Estimates of global terrestrial isoprene emissions using MEGAN (Model of Emissions of Gases and Aerosols from Nature). Atmos Chem Phys 6:3181–3210

    CrossRef  CAS  Google Scholar 

  • Guenther AB, Jiang X, Heald CL, Sakulyanontvittaya T, Duhl T, Emmons LK, Wang X (2012) The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions. Geosci Model Dev 5:1471–1492

    CrossRef  CAS  Google Scholar 

  • Hewitt CN, MacKenzie AR, Di Carlo P, Di Marco CF, Dorsey JR, Evans M et al (2009) Nitrogen management is essential to prevent tropical oil palm plantations from causing ground-level ozone pollution. Proc Natl Acad Sci 106:18447–18451

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  • Holmes AJ, Coleman NV (2008) Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts. Antonie Van Leeuwenhoek 94:75–84

    CrossRef  CAS  PubMed  Google Scholar 

  • Johnston A, Crombie AT, El Khawand M, Sims L, Whited G, McGenity TJ, Murrell JC (2017) Identification and characterisation of isoprene-degrading bacteria in an estuarine environment. Environ Microbiol 19:3526–3537

    CrossRef  CAS  PubMed  Google Scholar 

  • Kotani T, Yamamoto T, Yurimoto H, Sakai Y, Kato N (2003) Propane monooxygenase and NAD+-dependent secondary alcohol dehydrogenase in propane metabolism by Gordonia sp. strain TY-5. J Bacteriol 185:7120–7128

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  • Krishnakumar AM, Sliwa D, Endrizzi JA, Boyd ES, Ensign SA, Peters JW (2008) Getting a handle on the role of coenzyme M in alkene metabolism. Microbiol Mol Biol Rev 72:445–456

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  • Kuzma J, Nemecek-Marshall M, Pollock W, Fall R (1995) Bacteria produce the volatile hydrocarbon isoprene. Curr Microbiol 30:97–103

    CrossRef  CAS  PubMed  Google Scholar 

  • Leahy JG, Batchelor PJ, Morcomb SM (2003) Evolution of the soluble diiron monooxygenases. FEMS Microbiol Rev 27:449–479

    CrossRef  CAS  PubMed  Google Scholar 

  • Loivamäki M, Mumm R, Dicke M, Schnitzler J-P (2008) Isoprene interferes with the attraction of bodyguards by herbaceous plants. Proc Natl Acad Sci 105:17430–17435

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Loreto F, Ciccioli P, Brancaleoni E, Valentini R, De Lillis M, Csiky O, Seufert G (1998) A hypothesis on the evolution of isoprenoid emission by oaks based on the correlation between emission type and Quercus taxonomy. Oecologia 115:302–305

    CrossRef  PubMed  Google Scholar 

  • Luo G, Yu F (2010) A numerical evaluation of global oceanic emissions of α-pinene and isoprene. Atmos Chem Phys 10:2007–2015

    CrossRef  CAS  Google Scholar 

  • Lv X, Xie W, Lu W, Guo F, Gu J, Yu H, Ye L (2014) Enhanced isoprene biosynthesis in Saccharomyces cerevisiae by engineering of the native acetyl-CoA and mevalonic acid pathways with a push-pull-restrain strategy. J Biotechnol 186:128–136

    CrossRef  CAS  PubMed  Google Scholar 

  • MacEachran DP, Sinskey AJ (2013) The Rhodococcus opacus TadD protein mediates triacylglycerol metabolism by regulating intracellular NAD(P)H pools. Microb Cell Factories 12:104

    CrossRef  Google Scholar 

  • Magel E, Mayrhofer S, Müller A, Zimmer I, Hampp R, Schnitzler JP (2006) Photosynthesis and substrate supply for isoprene biosynthesis in poplar leaves. Atmos Environ 40:138–151

    CrossRef  Google Scholar 

  • Marienhagen J, Bott M (2013) Metabolic engineering of microorganisms for the synthesis of plant natural products. J Biotechnol 163:166–178

    CrossRef  CAS  PubMed  Google Scholar 

  • McDonald IR, Bodrossy L, Chen Y, Murrell JC (2008) Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 74:1305–1315

    CrossRef  CAS  PubMed  Google Scholar 

  • McGenity TJ, Crombie AT, Murrell JC (2017) Microbial cycling of isoprene, the most abundantly produced biological volatile organic compound on earth. ISME J (in press)

    Google Scholar 

  • Morais ARC, Dworakowska S, Reis A, Gouveia L, Matos CT, Bogdał D, Bogel-Łukasik R (2015) Chemical and biological-based isoprene production: green metrics. Catal Today 239:38–43

    CrossRef  CAS  Google Scholar 

  • Murphy G (2017) Isoprene degradation in the terrestrial environment. PhD thesis, Department of Biological Sciences, University of Essex, Colchester

    Google Scholar 

  • Murrell JC, Whiteley AS (2011) Stable isotope probing and related technologies. American Society of Microbiology, Washington, DC

    CrossRef  Google Scholar 

  • Pacifico F, Harrison SP, Jones CD, Sitch S (2009) Isoprene emissions and climate. Atmos Environ 43:6121–6135

    CrossRef  CAS  Google Scholar 

  • Palmer PI, Shaw SL (2005) Quantifying global marine isoprene fluxes using MODIS chlorophyll observations. Geophys Res Lett 32:L09805

    Google Scholar 

  • Pegoraro E, Abrell L, Van Haren J, Barron-Gafford G, Grieve KA, Malhi Y et al (2005) The effect of elevated atmospheric CO2 and drought on sources and sinks of isoprene in a temperate and tropical rainforest mesocosm. Glob Chang Biol 11:1234–1246

    CrossRef  Google Scholar 

  • Pegoraro E, Rey ANA, Abrell L, Van Haren J, Lin G (2006) Drought effect on isoprene production and consumption in Biosphere 2 tropical rainforest. Glob Chang Biol 12:456–469

    CrossRef  Google Scholar 

  • Rohmer M. 1999. The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. Nat Prod Rep 16:565–74

    CrossRef  CAS  PubMed  Google Scholar 

  • Sanderson MG, Jones CD, Collins WJ, Johnson CE, Derwent RG (2003) Effect of climate change on isoprene emissions and surface ozone levels. Geophys Res Lett 30:1936. https://doi.org/10.1029/2003GL017642

    Google Scholar 

  • Sharkey TD, Singsaas EL, Vanderveer PJ, Geron C (1996) Field measurements of isoprene emission from trees in response to temperature and light. Tree Physiol 16:649–654

    CrossRef  CAS  PubMed  Google Scholar 

  • Sharkey TD, Wiberley AE, Donohue AR (2008) Isoprene emission from plants: why and how. Ann Bot 101:5–18

    CrossRef  CAS  PubMed  Google Scholar 

  • Shaw SL, Gantt B, Meskhidze N (2010) Production and emissions of marine isoprene and monoterpenes: a review. Adv Meteorol 2010:art. ID 408696

    CrossRef  Google Scholar 

  • Shennan JL (2006) Utilisation of C2–C4 gaseous hydrocarbons and isoprene by microorganisms. J Chem Technol Biotechnol 81:237–256

    CrossRef  CAS  Google Scholar 

  • Srikanta Dani KG, Silva Benavides AM, Michelozzi M, Peluso G, Torzillo G, Loreto F (2017) Relationship between isoprene emission and photosynthesis in diatoms, and its implications for global marine isoprene estimates. Mar Chem 189:17–24

    CrossRef  CAS  Google Scholar 

  • Srivastva N, Shukla AK, Singh RS, Upadhyay SN, Dubey SK (2015) Characterization of bacterial isolates from rubber dump site and their use in biodegradation of isoprene in batch and continuous bioreactors. Bioresour Technol 188:84–91

    CrossRef  CAS  PubMed  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30:2725–2729

    CrossRef  CAS  PubMed  PubMed Central  Google Scholar 

  • van Ginkel CG, Welten HGJ, de Bont JAM (1987a) Oxidation of gaseous and volatile hydrocarbons by selected alkene-utilizing bacteria. Appl Environ Microbiol 53:2903–2907

    PubMed  PubMed Central  Google Scholar 

  • van Ginkel CG, de Jong E, Tilanus JWR, de Bont JAM (1987b) Microbial oxidation of isoprene, a biogenic foliage volatile and of 1,3-butadiene, an anthropogenic gas. FEMS Microbiol Lett 45:275–279

    CrossRef  Google Scholar 

  • van Hylckama Vlieg JET, Kingma J, van den Wijngaard AJ, Janssen DB (1998) A glutathione S-transferase with activity towards cis-1,2-dichloroepoxyethane is involved in isoprene utilization by Rhodococcus sp. strain AD45. Appl Environ Microbiol 64:2800–2805

    PubMed  PubMed Central  Google Scholar 

  • van Hylckama Vlieg JET, Kingma J, Kruizinga W, Janssen DB (1999) Purification of a glutathione S-transferase and a glutathione conjugate-specific dehydrogenase involved in isoprene metabolism in Rhodococcus sp. strain AD45. J Bacteriol 181:2094–2101

    PubMed  PubMed Central  Google Scholar 

  • van Hylckama Vlieg JET, Leemhuis H, Spelberg JHL, Janssen DB (2000) Characterization of the gene cluster involved in isoprene metabolism in Rhodococcus sp. strain AD45. J Bacteriol 182:1956–1963

    CrossRef  PubMed  PubMed Central  Google Scholar 

  • Wang Y, Huang WE, Cui L, Wagner M (2016) Single cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol 41:34–42

    CrossRef  CAS  PubMed  Google Scholar 

  • Zeinali N, Altarawneh M, Li D, Al-Nu’airat J, Dlugogorski BZ (2016) New mechanistic insights: why do plants produce isoprene? ACS Omega 1:220–225

    CrossRef  CAS  Google Scholar 

Download references

Acknowledgments

The authors acknowledge funding from the Earth and Life Systems Alliance (ELSA) at the Norwich Research Park, a Natural Environment Research Council (NERC) grant to JCM (NE/J009725/1) and TJM (NE/J009555/1), an ERC Advanced Grant to JCM (694578 – IsoMet), and Colciencias (Government of Colombia) and Newton Fund support for a studentship to NLMF.

Author information

Authors and Affiliations

  1. School of Biological Sciences, University of East Anglia, Norwich, UK

    Andrew T. Crombie

  2. School of Environmental Sciences, University of East Anglia, Norwich, UK

    Nasmille L. Mejia-Florez & J. Colin Murrell

  3. School of Biological Sciences, University of Essex, Colchester, UK

    Terry J. McGenity

Authors
  1. Andrew T. Crombie
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nasmille L. Mejia-Florez
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Terry J. McGenity
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. Colin Murrell
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andrew T. Crombie .

Editor information

Editors and Affiliations

  1. CSIC Campus de Cantoblanco, Centro Nacional de Biotecnología CSIC Campus de Cantoblanco, Madrid, Spain

    Prof. Dr. Fernando Rojo

Rights and permissions

Reprints and Permissions

Copyright information

© 2018 Crown Copyright

About this entry

Verify currency and authenticity via CrossMark

Cite this entry

Crombie, A.T., Mejia-Florez, N.L., McGenity, T.J., Murrell, J.C. (2018). Genetics and Ecology of Isoprene Degradation. In: Rojo, F. (eds) Aerobic Utilization of Hydrocarbons, Oils and Lipids. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-39782-5_27-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-39782-5_27-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-39782-5

  • Online ISBN: 978-3-319-39782-5

  • eBook Packages: Springer Reference Biomedicine & Life SciencesReference Module Biomedical and Life Sciences