Abstract
BackgroundMethanol 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.ResultsApplication 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 13C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the 13C-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 13CO2 atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere.ConclusionIn 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.48Q8VLgPYzztrQXqtA_fDqVideo abstract
Highlights
The large amount of carbon released to the soil via the roots of growing plants (1–20% of total photosynthate [1]) has a profound impact on the microbial communities in soil [2]
Thirty-four methylotrophic genera were identified in the 16S rRNA gene profile of the unplanted soil, at a combined relative abundance of 15.4%, and 35 methylotrophic genera were distributed across pea and wheat rhizosphere soils, at 15.8% and 14.4% relative abundance respectively
Methylotrophs were shown to be abundant in the unplanted soil, pea rhizosphere soil and wheat rhizosphere soil, and their diversity was influenced by pea and wheat plants
Summary
The large amount of carbon released to the soil via the roots of growing plants (1–20% of total photosynthate [1]) has a profound impact on the microbial communities in soil [2]. Root exudates include organic acids, sugars, alcohols, mucilage, sloughed off cells and (2020) 8:31 substantial proportion of the methanol produced by plants before it can escape to the atmosphere [7]. The reasons for changes in the abundance of methylotrophs in the soil in response to plant growth are hard to identify, since many of these methylotrophs can use multi-carbon compounds, which could be supplied either directly from the plant or from the exudate-induced accelerated breakdown of recalcitrant soil organic matter (SOM) [19]. 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). 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
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