Methylobacterium symbioticum sp. nov., a new species isolated from spores of Glomus iranicum var. tenuihypharum

Seyer-Lamontagne

Condrain-Morel

et al. 2021

Preprint

Methylobacterium is one of the most prevalent bacterial genera of the phyllosphere, present on the leaves of nearly every plant. Despite its ubiquity and its importance for host plant function, little is known about whether diversity over space and time within the genus reflects neutral processes like migration and drift, or environmental filtering of life history strategies and adaptations to temperature and host tree species. Here, we investigated how phylogenetic diversity within the genus Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we quantified seasonal shifts in Methylobacterium diversity over a year from early summer to fall in two temperate forests in Quebec, Canada. As an alternative to the 16S rRNA gene, we used rpoB, a highly polymorphic marker gene, which has not experienced detectable horizontal gene transfer nor copy number variation in Methylobacterium genomes. We cultured very different subsets of Methylobacterium diversity from the same leaf, depending upon the temperature of isolation and growth (20 C or 30 C). For instance, one the most abundant Methylobacterium lineages was almost exclusively isolated at 20 C, suggesting long-term adaptation to temperature. Both culture and barcoding approaches revealed that a considerable and previously underestimated diversity of Methylobacterium colonize the surface of leaves in temperate forests. This diversity was strongly structured according to both large (>100km; between forests) and small geographical scales (<1.2km within forests), and among host tree species, and was dynamic over seasonal time scales. To determine if these seasonal effects were driven by temperature, we measured growth of 79 isolates at different temperature treatments. Different lineages showed subtle and significant differences in growth performance when subject to temperature increase or decrease, but most have higher yield and slower growth rate at 20 than 30C, with strong lineage- and season-dependant variation in their overall growth strategies. We proposed that the homogenization of Methylobacterium community structure observed over a growing season resulted from the progressive replacement of isolates with high yield strategy typical of cooperative, structured communities, by isolates with rapid growth. Together our results show how Methylobacterium is phylogenetically structured into lineages with distinct growth strategies, which helps explain their differential abundance across regions, host tree species, and time. This works paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus.

Section: Thementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Seyer-Lamontagne

Condrain-Morel

et al. 2021

Preprint

“…Experimental studies have shown the important roles of Methylobacterium in plant physiology, including growth stimulation through hormone secretion ( 25 – 27 ), heavy metal sequestration ( 27 ), antiphytopathogenic compound secretion, and nitrogen fixation in plant nodules ( 28 ), sparking increasing interest in the use of Methylobacterium in plant biotechnology applications ( 27 , 29 , 30 ). Although up to 64 Methylobacterium species have been described ( 31 – 39 ), genomic and phenotypic information was until recently limited to a small number of model species: M. extorquens , M. populi , M. nodulans , M. aquaticum , and M. radiotolerans , mostly isolated from anthropogenic environments and only rarely from plants ( 40 – 44 ). Additionally, Methylobacterium was mostly isolated assuming that its optimal growth was in the range of 25 to 30°C ( 45 ), an approach that could bias strain collections toward mesophyllic isolates to the exclusion of isolates from temperate forests, where temperatures typically range from 10 to 20°C during the growing season ( 46 ).…”

Section: Introductionmentioning

confidence: 99%

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

Seyer-Lamontagne

Condrain-Morel

et al. 2022

mBio

“…Although more than 60 Methylobacterium species have been described so far ( Green and Ardley 2018 ; Chen et al 2019 ; Feng et al 2020 ; Jia et al 2020 ; Kim, Chhetri, Kim, Lee et al 2020 ; Kim, Chhetri, Kim, Kim et al 2020 ; Ten et al 2020 ; Jiang et al 2020 ; Pascual et al 2020 ; Alessa et al 2021 ), available genomic and phenotypic information was until recently limited to a few model species, mostly from groups B and C, and mostly isolated from anthropogenically impacted environments, and in rare cases from plants ( Marx et al 2012 ; Tani et al 2015 ; Minami et al 2016 ; Morohoshi and Ikeda 2016 ; Belkhelfa et al 2018 ). Surveys of Methylobacterium diversity associated with plants have mainly focused on the rhizosphere, especially in crop species ( Sy et al 2001 ; Jourand et al 2004 ; Grossi et al 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Phylogenomics of Methylobacterium Reveals Four Evolutionary Distinct Groups and Underappreciated Phyllosphere Diversity

Genome Biology and Evolution

Sneddon

Santos

et al. 2022

Methylobacterium is a group of methylotrophic microbes associated with soil, fresh water, and particularly the phyllosphere, the aerial part of plants that has been well-studied in terms of physiology but whose evolutionary history and taxonomy are unclear. Recent work has suggested that Methylobacterium is much more diverse than thought previously, questioning its status as an ecologically and phylogenetically coherent taxonomic genus. However, taxonomic and evolutionary studies of Methylobacterium have mostly been restricted to model species, often isolated from habitats other than the phyllosphere, and have yet to utilize comprehensive phylogenomic methods to examine gene trees, gene content, or synteny. By analyzing 189 Methylobacterium genomes from a wide range of habitats, including the phyllosphere, we inferred a robust phylogenetic tree while explicitly accounting for the impact of horizontal gene transfer. We showed that Methylobacterium contains four evolutionarily distinct groups of bacteria (namely A, B, C, D), characterized by different genome size, GC content, gene content and genome architecture, revealing the dynamic nature of Methylobacterium genomes. In addition to recovering 59 described species, we identified 45 candidate species, mostly phyllosphere-associated, stressing the significance of plants as a reservoir of Methylobacterium diversity. We inferred an ancient transition from a free-living lifestyle to association with plant roots in Methylobacteriaceae ancestor, followed by phyllosphere association of three of the major groups (A, B, D), whose early branching in Methylobacterium history has been heavily obscured by HGT. Together, our work lays the foundations for a thorough redefinition of Methylobacterium taxonomy, beginning with the abandonment of Methylorubrum.