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Background  Approximately 500 Tg of isoprene are emitted to the atmosphere annually, an amount similar to that of methane, and despite its significant effects on the climate, very little is known about the biological degradation of isoprene in the environment. Isolation and characterisation of isoprene degraders at the molecular level has allowed the development of probes targeting  isoA  encoding the α-subunit of the isoprene monooxygenase. This enzyme belongs to the soluble diiron centre monooxygenase family and catalyses the first step in the isoprene degradation pathway. The use of probes targeting key metabolic genes is a successful approach in molecular ecology to study specific groups of bacteria in complex environments. Here, we developed and tested a novel  isoA  PCR primer set to study the distribution, abundance, and diversity of isoprene degraders in a wide range of environments.    Results  The new  isoA  probes specifically amplified  isoA  genes from taxonomically diverse isoprene-degrading bacteria including members of the genera  Rhodococcus ,  Variovorax , and  Sphingopyxis . There was no cross-reactivity with genes encoding related oxygenases from non-isoprene degraders. Sequencing of  isoA  amplicons from DNA extracted from environmental samples enriched with isoprene revealed that most environments tested harboured a considerable variety of  isoA  sequences, with poplar leaf enrichments containing more phylogenetically diverse  isoA  genes. Quantification by qPCR using these  isoA  probes revealed that isoprene degraders are widespread in the phyllosphere, terrestrial, freshwater and marine environments. Specifically, soils in the vicinity of high isoprene-emitting trees contained the highest number of isoprene-degrading bacteria.    Conclusion  This study provides the molecular ecology tools to broaden our knowledge of the distribution, abundance and diversity of isoprene degraders in the environment, which is a fundamental step necessary to assess the impact that microbes have in mitigating the effects of this important climate-active gas.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0607-0) contains supplementary material, which is available to authorized users.

Gene probing reveals the widespread distribution, diversity and abundance of isoprene-degrading bacteria in the environment