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

Abstract

Lanthanides have emerged as important metal cofactors for biological processes. Lanthanide-associated metabolisms are well-studied in leaf symbiont methylotrophic bacteria, which utilize reduced one-carbon compounds such as methanol for growth. Yet, the importance of lanthanides in plant-microbe interactions and on microbial physiology and colonization in plants remains poorly understood. To investigate this, 344 pink-pigmented facultative methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors, but none were obligately lanthanide-dependent. Phylogenetic analyses revealed that all strains were nearly identical to each other and are part of the extorquens clade of Methylobacterium , despite variability in genome and plasmid sizes. Strain-specific identification was enabled by the higher resolution provided with rpoB compared to 16S rRNA as marker genes. Despite the low strain-level diversity, the metabolic capabilities of the collection diverged greatly. Strains encoding identical lanthanide-dependent alcohol dehydrogenases displayed significantly different growth rates and/or final ODs from each other on alcohols in the presence and absence of lanthanides. Several strains also lacked well-characterized lanthanide-associated genes thought to be important for phyllosphere colonization. Additionally, 3% of our isolates were capable of growth on sugars and 23% were capable of growth on aromatic acids, substantially expanding the range of substrates utilized by Methylobacterium extorquens in the phyllosphere. Our findings suggest that the expansion of metabolic capabilities, as well as differential usage of lanthanides and their influence on metabolism, among closely related strains point to evolution of niche partitioning strategies to promote colonization of the phyllosphere.

Importance: Lanthanide metals have long been appreciated for their role in technology, but the recent identification of lanthanides as cofactors in methylotrophic metabolism has expanded the role of lanthanides into biology. In the phyllosphere, methylotrophs are some of the most abundant bacteria found on leaf surfaces, where lanthanide concentrations are sufficiently high to support their growth. Yet, the extent to which lanthanides influence methylotrophic metabolism in the phyllosphere remains unknown. Here, we characterize a methylotrophic enrichment isolated from the phyllosphere in a lanthanide-dependent manner. We have identified (1) closely related strains with identical lanthanide-dependent enzymes that exhibit different growth on alcohols in the presence of lanthanides, (2) resilient strains lacking lanthanide-associated genes thought to be important for phyllosphere colonization, and (3) many strains capable of metabolisms that were thought to be rare within this clade. Overall, our isolates serve as a model community to interrogate how lanthanides differentially influence methylotrophic physiology.