Aerobic methoxydotrophy: growth on methoxylated aromatic compounds by Methylobacterium

Abstract

Microorganisms faces many barriers in the degradation of the polycyclic aromatic polymer lignin, one of which is an abundance of methoxy substituents. Demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a potent cellular toxin that organisms must eliminate in order to further degrade the aromatic ring. Here we provide the first comprehensive description of the ecology and evolution of the catabolism of methoxylated aromatics in the genus Methylobacterium, a plant-associated genus of methylotrophs capable of using formaldehyde for growth. Using comparative genomics, we found that the capacity for aromatic catabolism is ancestral to two clades, but has also been acquired horizontally by other members of the genus. Through laboratory growth assays, we demonstrated that several Methylobacterium strains can grow on p-hydroxybenzoate, protocatechuate, vanillate, and ferulate; furthermore, whereas non-methylotrophs excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. Finally, we surveyed published metagenome data to find that vanillate-degrading Methylobacterium can be found in many soil and rhizosphere ecosystems but is disproportionately prominent in the phyllosphere, and the most highly represented clade in the environment (the root-nodulating species M. nodulans) is one with few cultured representatives.

Microbial phenotypic heterogeneity in response to a metabolic toxin: Continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations

“…M . extorquens excretes formaldehyde during the first stages of the switch between multi-carbon and single-carbon metabolism [27]; in addition, formaldehyde is a metabolic intermediate in the consumption of many lignin-derived aromatic compounds [46,47], and we have observed lignin degraders to excrete formaldehyde into the growth medium at millimolar levels during growth in batch liquid culture on methoxylated aromatic compounds [48]. Thus, it is possible that, in the environment, formaldehyde concentrations in the millimolar range might accumulate transiently on the microscale, especially within cell aggregates such as those observed on plant leaves [49].…”

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community

“…Our initial experiments aimed to define the role of toxic compounds in our community, particularly formaldehyde generation and consumption, and formaldehyde-mediated growth inhibition. Previous work in our lab has shown that P. putida growing on vanillic acid can generate formaldehyde that escapes the cell to accumulate in the growth medium [23]. However, the effect of that formaldehyde on other members of the microbial community is unknown.…”

“…The Methylobacterium and Methylorubrum clade encompasses a diverse range of species in a variety of metabolic niches, including commensal relationships with plants as well as independently, in soil and leaf litter [22]. While the extent of the metabolic capabilities of the genus is not fully characterized-and recent work suggests some species may have the ability to utilize lignin-derived aromatic compounds [23]-we chose to include in our consortium, M. extorquens PA1, a model organism for which extensive metabolic and physiological data exist [21,[24][25][26]. The other bacterial members of this defined community included Pseudomonas putida, a canonical lignin degrader that has been studied extensively for its aromatic catabolism [20,[27][28][29][30], and Cellulomonas fimi, a cellulose degrader of interest for its ability to utilize diverse polysaccharides and to channel the products of their degradation to other organisms in co-culture [31][32][33].…”

Comprehensive phylogenomics of Methylobacterium reveals four evolutionary distinct groups and underappreciated phyllosphere diversity

“…For example, the evolutionary distinction between groups A and D, and their importance in Methylobacterium diversity, could not have been revealed without a thorough investigation of diversity in the phyllosphere, from which the majority of candidate species from groups A, B and D were isolated. A recent survey of Methylobacterium in metagenomes from various biomes (Lee et al, 2022) the aerial part of plants. Similarly, we recently showed that groups A and D were the dominant Methylobacterium groups in the phyllosphere of trees from temperate forests (Leducq et al, 2022).…”