Abstract
ABSTRACTMethylobacterium is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. In two temperate forests, we investigated how phylogenetic diversity within Methylobacterium is structured by biogeography, seasonality, and growth strategies. Using deep, culture-independent barcoded marker gene sequencing coupled with culture-based approaches, we uncovered a considerable diversity of Methylobacterium in the phyllosphere. We cultured different subsets of Methylobacterium lineages depending upon the temperature of isolation and growth (20°C or 30°C), suggesting long-term adaptation to temperature. To a lesser extent than temperature adaptation, Methylobacterium diversity was also structured across large (>100 km; between forests) and small (<1.2 km; within forests) geographical scales, among host tree species, and was dynamic over seasons. By measuring the growth of 79 isolates during different temperature treatments, we observed contrasting growth performances, with strong lineage- and season-dependent variations in growth strategies. Finally, we documented a progressive replacement of lineages with a high-yield growth strategy typical of cooperative, structured communities in favor of those characterized by rapid growth, resulting in convergence and homogenization of community structure at the end of the growing season. 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 work paves the way for further investigation of adaptive strategies and traits within a ubiquitous phyllosphere genus.
Highlights
Methylobacterium is a prevalent bacterial genus of the phyllosphere
153 Methylobacterium isolates built from available genomic databases showed that plants (65% of isolates) and especially the phyllosphere compartment (41% of isolates) were the most prevalent source of Methylobacterium sampled to date (Fig. 1; see Data Set S1a in the supplemental material)
Methylobacterium diversity was heterogeneously distributed at local spatial scale, as we observed a significant increase of community dissimilarity (Bray-Curtis index [BC]) with geographical distance separating two samples within Mont Saint Hilaire (MSH) but not Station Biologique des Laurentides (SBL) (P . 0.05) (Table 2; Fig. 4b)
Summary
Methylobacterium is a prevalent bacterial genus of the phyllosphere. Despite its ubiquity, little is known about the extent to which its diversity reflects neutral processes like migration and drift, versus environmental filtering of life history strategies and adaptations. To date, the majority of studies of the diversity of plant-associated microbes have been based on the use of universal marker genes such as the bacterial 16S rRNA gene, providing a global picture of long-term bacterial adaptation to different biomes and host plants at broad phylogenetic scales [17] These studies lack sufficient resolution to assess the evolutionary processes at finer spatial and temporal scales that lead to the origin of adaptations within microbial genera and species [18, 19]. Methylobacterium was mostly isolated assuming that its optimal growth was in the range of 25 to 30°C [45], an approach
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