Molecular ecology of isoprene degraders in the terrestrial environment

Isoprene (2-methyl 1, 3-butadiene) is the most abundant non-methane BVOC (biogenic volatile organic compound) released into the atmosphere. Terrestrial plants are the primary producers of isoprene and release 500-750 million tonnes of isoprene per year, to protect themselves from abiotic environmental stresses such as heat and reactive oxygen species. Many studies have explored isoprene production but very little is known about consumption of isoprene by microbes. Cleveland and Yavitt in 1998 (Cleveland and Yavitt 1998), and more recently Khawand et al. 2016 (Khawand et al. 2016), demonstrated that microbes isolated from terrestrial environments are capable of using isoprene as sole carbon and energy source. By applying cultivation-dependent and cultivation-independent techniques, such as DNA Stable Isotope Probing (Dumont and Murrell 2005), my objective was to determine the distribution, diversity and activity of isoprene-degrading bacteria in the terrestrial environment. Isoprene-degrading microbes were enriched by adding 13 to 50 ppm isoprene to microcosms using topsoil from a willow tree and topsoil/leaves from an oil palm tree. DNA stable isotope probing, using 13C-labelled isoprene, assisted in revealing the diversity of active isoprene degraders by labelling organisms that incorporated the isoprene, directly or indirectly. PCR retrieval of partial 16S rRNA genes from this DNA revealed labelled members of the genera Ramlibacter, Variovorax, Rhodococcus and Methylibium, for willow soil, and Rhodococcus, Gordonia, Aquabacterium, Aquincola, Methylobacterium and members from the Sphingomonadaceae family, for the oil palm tree. Using cultivation-dependent methods I isolated seven phylogenetically different isoprene-utilizing bacteria of the genera Rhodococcus, Nocardioides and Variovorax from willow soil environment; another four phylogenetically different bacteria belonging to the genera Gordonia, Sphingopyxis and Sphingobacterium from the oil palm tree. Results suggest Rhodococcus is a cosmopolitan isoprene-degrader, present in a variety of environments, and different isoprene-degrading bacteria were found associated to willow and oil palm trees.