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

Abstract

AbstractThe 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 these metals. To investigate this, methylotrophs were isolated from soybean leaves by selecting for bacteria capable of methanol oxidation with lanthanide cofactors. 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 theextorquensclade ofMethylobacterium, withrpoBproviding higher resolution than 16srRNA for strain-specific identification. Despite the 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. 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 multicarbon substrates utilized by members of theextorquensclade in the phyllosphere. Whole genome sequences of eleven novel strains are reported. 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.ImportanceLanthanides are essential metals for life. The identification of lanthanide-associated processes has been well-studied in methylotrophic bacteria, which are plant symbionts that utilize reduced one-carbon compounds for growth. Yet, the importance of lanthanides in plant-microbe interactions and the effects of lanthanides on microbial physiology and colonization in plants remains poorly understood. Here, we characterize the first methylotrophic bacterial community isolated from the phyllosphere in a lanthanide-dependent manner. We have identified strains encoding identical lanthanide-dependent enzymes yet exhibiting differences in lanthanide-associated growth, and have identified strains lacking lanthanide-associated genes thought to be important for phyllosphere colonization. In addition, we have identified many strains capable of metabolisms that were thought to be rare within this clade. Overall, our isolates serve as a microcosm by which to interrogate how lanthanides influence methylotrophic physiology in plant environments and highlights how phylogenetically similar strains can diverge greatly in metabolic potential.