Sphingopyxis sp. Strain OPL5, an Isoprene-Degrading Bacterium from the Sphingomonadaceae Family Isolated from Oil Palm Leaves

Abstract

The volatile secondary metabolite, isoprene, is released by trees to the atmosphere in enormous quantities, where it has important effects on air quality and climate. Oil palm trees, one of the highest isoprene emitters, are increasingly dominating agroforestry over large areas of Asia, with associated uncertainties over their effects on climate. Microbes capable of using isoprene as a source of carbon for growth have been identified in soils and in the tree phyllosphere, and most are members of the Actinobacteria. Here, we used DNA stable isotope probing to identify the isoprene-degrading bacteria associated with oil palm leaves and inhabiting the surrounding soil. Among the most abundant isoprene degraders of the leaf-associated community were members of the Sphingomonadales, although no representatives of this order were previously known to degrade isoprene. Informed by these data, we obtained representatives of the most abundant isoprene degraders in enrichments, including Sphingopyxis strain OPL5 (Sphingomonadales), able to grow on isoprene as the sole source of carbon and energy. Sequencing of the genome of strain OPL5, as well as a novel Gordonia strain, confirmed their pathways of isoprene degradation and broadened our knowledge of the genetic and taxonomic diversity of this important bacterial trait.

‘Omics‐guided prediction of the pathway for metabolism of isoprene by Variovorax sp. WS11

“…All isoprene‐degrading bacteria characterized thus far employ the first steps of isoprene oxidation identified in Rhodococcus sp. AD45 (Crombie et al, 2015 ; Dawson et al, 2020 ; Gibson et al, 2020 ; Larke‐Mejía et al, 2020 ; van Hylckama Vlieg et al, 2000 ). Isoprene monooxygenase (IsoMO, encoded by isoABCDEF ) catalyses the initial oxidation of isoprene to epoxyisoprene (Crombie et al, 2015 ; Dawson et al, 2020 ; Sims et al, 2022 ; van Hylckama Vlieg et al, 2000 ).…”

Isoprene-Degrading Bacteria from Soils Associated with Tropical Economic Crops and Framework Forest Trees

“…Prior to this study, little was known about isoprene-degrading microorganisms in tropical soils, with just a few studies analysing isoprene degraders in soil associated with oil palm trees, but growing in temperate environments [ 52 , 53 ], or in soil transported to the UK [ 20 ]. Oil-palm soil was found to have the highest abundance of isoprene monooxygenase genes ( isoA ), determined by quantitative PCR [ 20 , 54 ].…”

“…Oil-palm soil was found to have the highest abundance of isoprene monooxygenase genes ( isoA ), determined by quantitative PCR [ 20 , 54 ]. In these studies, genera such as Rhodococcus, Gordonia, Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea were identified as isoprene-degrading bacteria by DNA stable isotope probing [ 20 , 52 , 53 , 55 ]. A wider variety of genera has also been implicated in isoprene degradation in temperate soils [ 17 , 19 , 20 , 54 , 55 ].…”

“…Given that seasonal differences in the microbiota are commonly observed in soils [50], including tropical rubber-plantation soils [51], it is probable that any seasonal difference was masked by the overriding selective pressure of enrichment with isoprene. Prior to this study, little was known about isoprene-degrading microorganisms in tropical soils, with just a few studies analysing isoprene degraders in soil associated with oil palm trees, but growing in temperate environments [52,53], or in soil transported to the UK [20]. Oil-palm soil was found to have the highest abundance of isoprene monooxygenase genes (isoA), determined by quantitative PCR [20,54].…”

Peering down the sink: A review of isoprene metabolism by bacteria

“…AD45 was incubated with isoprene or epoxyisoprene, the first metabolic intermediate in the iso metabolic pathway. This iso gene cluster contains a core set of 11 genes which were subsequently identified in the genomes of extant isoprene degraders and as partially complete gene clusters in metagenome‐assembled genomes (MAGs) from isoprene‐enriched environmental samples (Carrión, McGenity, & Murrell, 2020; Crombie et al, 2018; Dawson et al, 2020; Johnston et al, 2017; Larke‐Mejía et al, 2020). These 11 core genes comprise isoABCDEF (encoding IsoMO), isoG (putative CoA‐transferase), isoI (glutathione S‐ transferase—GST), isoH (NAD + ‐dependent dehydrogenase), isoJ (GST), and aldH (putative aldehyde dehydrogenase).…”