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Background  Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils.    Results  Application of probes for methanol dehydrogenase genes ( mxaF ,  xoxF ,  mdh2 ) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including  Hyphomicrobium ,  Methylobacterium  and members of the  Comamonadaceae . The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using  13 C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the  13 C-labelled DNA revealed members of the  Methylophilaceae  as highly abundant and active in all soils examined. There was greater diversity of active members of the  Methylophilaceae  and  Comamonadaceae  and of the genus  Methylobacterium  in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a  13 CO 2  atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the  Actinomycetales , assimilated plant exudates in the pea rhizosphere.    Conclusion  In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle.Video abstract

Impact of plants on the diversity and activity of methylotrophs in soil