pubmed.ncbi.nlm.nih.gov

Molecular Ecology of Isoprene-Degrading Bacteria - PubMed

  • ️Wed Jan 01 2020

Review

Molecular Ecology of Isoprene-Degrading Bacteria

Ornella Carrión et al. Microorganisms. 2020.

Abstract

Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth's climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle.

Keywords: BVOC; DNA stable-isotope probing; climate; isoA; isoprene; isoprene monooxygenase.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1

Isoprene degradation pathway in the model isoprene-utilising bacterium Rhodococcus sp. AD45. Enzymes: IsoMO, isoprene monooxygenase; IsoI, glutathione-S-transferase; IsoH, dehydrogenase; HGMB, 1-hydroxy-2-glutathionyl-2-methyl-3-butene; GMB, 2-glutathionyl-2-methyl-3-butenal; GMBA, 2-glutathionyl-2-methyl-3-butenoic acid; GSH, reduced glutathione. The question mark indicates uncertainty in the details of the catabolic pathway from GMBA.

Figure 2
Figure 2

Isoprene degradation gene clusters from representative Gram-positive and Gram-negative isoprene-degrading bacteria. Genes encoding IsoMO (isoABCDEF) are coloured in red. Regulatory genes are shown in black. Adjacent genes not suspected to be involved in isoprene degradation are coloured in white.

Figure 3
Figure 3

Relative abundance and diversity of isoA genes in environmental samples enriched with isoprene analysed by amplicon sequencing. Amplicon sequence variants (ASVs) closely related to IsoA from Gordonia are shown in orange; ASVs with the highest homology to IsoA from Mycobacterium are represented in light blue; ASVs encoding proteins homologous to Rhodococcus IsoA are shown in dark blue; ASVs with the highest homology to Sphingopyxis IsoA are coloured in yellow; ASVs closely related to IsoA from Variovorax are represented in purple. Data from [69].

Figure 4
Figure 4

Relative abundance of isoprene degraders in natural (non-enriched) environmental samples determined by qPCR. Copies of isoA are normalised to the 16S rRNA gene copy number in each sample. Phyllosphere samples are coloured in green, soils in brown, and aquatic environments in blue. Data from [69].

Similar articles

Cited by

References

    1. Atkinson R., Arey J. Gas-phase tropospheric chemistry of biogenic volatile organic compounds: A review. Atmos. Environ. 2003;37:197–219. doi: 10.1016/S1352-2310(03)00391-1. - DOI
    1. Guenther A.B., Jiang X., Heald C.L., Sakulyanontvittaya T., Duhl T., Emmons L.K., Wang X. The model of emissions of gases and aerosols from nature version 2.1 (MEGAN2.1): An extended and updated framework for modelling biogenic emissions. Geosci. Model Dev. 2012;5:1471–1492. doi: 10.5194/gmd-5-1471-2012. - DOI
    1. Pacifico F., Harrison S.P., Jones C.D., Sitch S. Isoprene emissions and climate. Atmos. Environ. 2009;43:6121–6135. doi: 10.1016/j.atmosenv.2009.09.002. - DOI
    1. Collins W.J., Derwent R.G., Johnson C.E., Stevenson D.S. The oxidation of organic compounds in the troposphere and their global warming potentials. Clim. Chang. 2002;52:453–479. doi: 10.1023/A:1014221225434. - DOI
    1. Folberth G.A., Hauglustaine D.A., Lathière J., Brocheton F. Interactive chemistry in the Laboratoire de Météorologie Dynamique general circulation model: Model description and impact analysis of biogenic hydrocarbons on tropospheric chemistry. Atmos. Chem. Phys. 2006;6:2273–2319. doi: 10.5194/acp-6-2273-2006. - DOI

Publication types

LinkOut - more resources