Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere
            <i>Methylobacterium</i>
            Diversity

Leducq, Jean-Baptiste; Seyer-Lamontagne, Émilie; Condrain-Morel, Domitille; Bourret, Geneviève; Sneddon, David; Foster, James A.; Marx, Christopher J.; Sullivan, Jack; Shapiro, B. Jesse; Kembel, Steven W.

doi:10.1128/mbio.03175-21

Cited by 9 publications

(7 citation statements)

References 65 publications

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“…Locus tags are given in Supplementary Table 1 . The clade structure generally agrees with previous Methylobacterium phylogenies based on 16S rRNA, rpoB , or core genes, though some analyses find clade A not to be monophyletic ( Green and Ardley, 2018 ; Alessa et al, 2021 ; Leducq et al, 2022 ).…”

Section: Methodssupporting

confidence: 85%

“…Two additional phylogenies were constructed as Supplementary Information : one containing all the Methylobacterium strains surveyed for this study, using the rpoB gene ( Leducq et al, 2022 ) with B. diazoefficiens USDA 110 as an outgroup; and one showing the relationships of the Rieske [2Fe-2S] oxygenase homologs. The rpoB tree includes five of the Methylobacterium strains carrying aromatic catabolism genes (sp.…”

Section: Methodsmentioning

confidence: 99%

“…The phylogeny was composed using a concatenated alignment of four housekeeping genes ( atpD, recA, rpob , and 16S rRNA), with Prochlorococcus marinus as an outgroup (not shown). Clade A/B/C designations are in accordance with ( Green and Ardley, 2018 ; Alessa et al, 2021 ; Leducq et al, 2022 ). Branch labels indicate bootstrap percent; values < 50 are not shown.…”

Section: Introductionmentioning

confidence: 99%

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Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae

2022

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Pink-pigmented facultative methylotrophs have long been studied for their ability to grow on reduced single-carbon (C1) compounds. The C1 groups that support methylotrophic growth may come from a variety of sources. Here, we describe a group of Methylobacterium strains that can engage in methoxydotrophy: they can metabolize the methoxy groups from several aromatic compounds that are commonly the product of lignin depolymerization. Furthermore, these organisms can utilize the full aromatic ring as a growth substrate, a phenotype that has rarely been described in Methylobacterium. We demonstrated growth on p-hydroxybenzoate, protocatechuate, vanillate, and ferulate in laboratory culture conditions. We also used comparative genomics to explore the evolutionary history of this trait, finding that the capacity for aromatic catabolism is likely ancestral to two clades of Methylobacterium, but has also been acquired horizontally by closely related organisms. In addition, we surveyed the published metagenome data to find that the most abundant group of aromatic-degrading Methylobacterium in the environment is likely the group related to Methylobacterium nodulans, and they are especially common in soil and root environments. The demethoxylation of lignin-derived aromatic monomers in aerobic environments releases formaldehyde, a metabolite that is a potent cellular toxin but that is also a growth substrate for methylotrophs. We found that, whereas some known lignin-degrading organisms excrete formaldehyde as a byproduct during growth on vanillate, Methylobacterium do not. This observation is especially relevant to our understanding of the ecology and the bioengineering of lignin degradation.

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Section: Methodssupporting

confidence: 85%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae

2022

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“…Many of the published metagenomic studies which have used phylogeny have done so by using phylogenies inferred from partial or full-length single gene sequences (e.g., the 16S rRNA gene) recovered from amplicon-based sequencing data ( 12 , 20 , 32 – 36 ). These phylogenies may be poorly resolved given the limited genetic data used and are constrained to only the set of taxa found in the samples, which limits the power of simulation modeling to describe community structure.…”

Section: Introductionmentioning

confidence: 99%

PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities

Huang

Erickson

Meng

2023

mBio

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“…While stochastic dispersal is expected to homogenize local communities, the existence of dispersal limitation and priority effects (i.e. the arrival order of bacterial taxa) can lead to remarkable variation in the composition of phyllosphere bacteria among different neighborhood plant communities and along spatial distance gradients (Finkel et al ., 2012; Lajoie & Kembel, 2021b; Leducq et al ., 2022; Meyer et al ., 2022). However, the relative importance of stochastic vs deterministic process in shaping phyllosphere bacteria community assembly remains unclear (Cordovez et al ., 2019; Fitzpatrick et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude‐dependent mechanisms

Wang,

Jiang,

Zhang

et al. 2023

New Phytologist

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Summary Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors. We found that host‐related factors were increasingly important in explaining bacterial assembly at higher latitudes while nonhost factors including abiotic environments, spatial proximity and plant neighbors were more important at lower latitudes. We further showed that local plant–bacteria associations were interconnected by hub bacteria taxa to form metacommunity‐level networks, and the spatial distribution of these hub taxa was controlled by hosts and spatial factors with varying importance across latitudes. For the first time, we documented a latitude‐dependent importance in the driving factors of phyllosphere bacteria assembly and distribution, serving as a baseline for predicting future changes in plant phyllosphere microbiomes under global change and human activities.

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Fine-Scale Adaptations to Environmental Variation and Growth Strategies Drive Phyllosphere Methylobacterium Diversity

Abstract: Methylobacterium is a bacterial group tied to plants. Despite the ubiquity of methylobacteria and the importance to their hosts, little is known about the processes driving Methylobacterium community dynamics.

Cited by 9 publications

References 65 publications

Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae

Aerobic Methoxydotrophy: Growth on Methoxylated Aromatic Compounds by Methylobacteriaceae

PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities

Diversity and biogeography of plant phyllosphere bacteria are governed by latitude‐dependent mechanisms

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