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

Abstract

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.

Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome

“…Pseudomonadaceae were identified as potential root exudate utilisers within the rhizosphere, in agreement with previous studies [42,66]. These bacterial groups were also consistently enriched in the rhizosphere or endosphere, regardless of soil type.…”

Elevated Atmospheric CO2 and Nitrogen Fertilization Affect the Abundance and Community Structure of Rice Root-Associated Nitrogen-Fixing Bacteria

“…The N 2 -fixing activity of diazotrophic methanotrophs under N-rich conditions needs to be studied in more detail in the future. Moreover, methanotrophic N 2 -fixing bacteria (Methylosinus and Methylocystis) in the roots, and other N 2 -fixing bacteria, such as Bradyrhizobium, Rhizobium, and Methyloceanibacter, which are frequently detected as methanol-oxidizing bacteria using metaproteomics or functional gene mxaF/xoxF sequencing analysis (Bao et al, 2014a;Macey et al, 2020), may utilize the methanol produced via the methane oxidation process to perform N 2 fixation. However, this relationship changes with nitrogen supplementation because the N 2 -fixing capacity of Bradyrhizobium and Rhizobium is inhibited by nitrogen (Kumar et al, 2018), while that of diazotrophic methanotrophs is more stable.…”

“…In addition, eCO 2 significantly increases the total organic carbon content of rice root exudates (Bhattacharyya et al, 2013), which may influence the diversity and activity of rhizospheric and root-associated C1 bacteria. Macey et al (2020) reported that methanol-utilizing methylotrophs were widely distributed in land plant-associated soil because they use the methanol produced as a metabolic byproduct during plant growth. Thus, C1-cycling bacteria in the root zones of both terrestrial plants and aquatic plants are important for the balance of carbon and nitrogen cycling and can increase benefits for plant growth.…”

Invasive grass dominance over native forbs is linked to shifts in the bacterial rhizosphere microbiome

“…Bacteria in this family have been found in soils with high heavy metal content and include microbes critical for heavy metal attenuation and immobilization [73,74]. Members of Methylophilaceae also form tight symbioses with plants [75][76][77] and are even known to promote seed germination and plant growth [76]. This family may include important taxa for serpentine-adapted species, with a decrease in relative abundance driving negative effects through reduced heavy metal attenuation and plant growth.…”