Abstract
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.
Highlights
Out of the many non-methane biogenic volatile organic compounds (BVOC), isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in the greatest amount (Guenther et al, 2012)
The 16S rRNA gene sequencing data showed that the bacterial communities in light and heavy DNA fractions in 12C-isoprene enrichments were similar to each other, but distinct from the labeled isoprene degraders represented by the heavy DNA retrieved from incubations with 13C-labeled isoprene
Since the 13C-labeled DNA from DNA stable isotope probing (DNA-SIP) soil incubations was enriched in active isoprene-degraders, we examined the diversity of isoA genes in this DNA using shotgun metagenomics
Summary
Out of the many non-methane biogenic volatile organic compounds (BVOC), isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in the greatest amount (approximately 535 Tg y−1) (Guenther et al, 2012). With high nitrogen oxide levels, the result is formation of tropospheric ozone, with consequences for human health and crop yield (Ashworth et al, 2013). These reactions result in a global warming effect, both directly and due to an increased lifetime of methane, for which oxidation by hydroxyl radicals is the primary sink (Folberth et al, 2006). Isoprene secondary oxidation products form particulates, giving rise to haze, smog and cloud condensation nuclei, affecting the planetary albedo (Carlton et al, 2009)
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