Lanthanide-dependent isolation of phyllosphere methylotrophs selects for a phylogenetically conserved but metabolically diverse community

Abstract

The influence of lanthanide biochemistry during methylotrophy demands a reassessment of how the composition and metabolic potential of methylotrophic phyllosphere communities are affected by the presence of lanthanides. To investigate this, methylotrophs - predominant members of the phyllosphere - were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors. Strikingly, of the 344 pink-pigmented facultative methylotroph isolates, none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and to model strains from the extorquens clade of Methylobacterium, with rpoB providing higher resolution than 16s rRNA for strain-specific identification. Despite low species diversity, the metabolic capabilities of the community diverged greatly. Strains encoding identical PQQ-dependent alcohol dehydrogenases displayed significantly different growth from each other on alcohols in the presence and absence of lanthanides. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, expanding the range of multicarbon substrates utilized by extorquens clade members. Whole-genome sequences of eleven novel strains are reported. We hypothesize that the expansion of metabolic capabilities and differential lanthanide metabolisms among closely related strains point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.