title: Systems-level Proteomics of Two Ubiquitous Leaf Commensals Reveals Complementary Adaptive Traits for Phyllosphere Colonization.
abstract: Plants are colonized by a diverse community of microorganisms, the plant microbiota, exhibiting a defined and conserved taxonomic structure. Niche separation based on spatial segregation and complementary adaptation strategies likely forms the basis for coexistence of the various microorganisms in the plant environment. To gain insights into organism-specific adaptations on a molecular level, we selected two exemplary community members of the core leaf microbiota and profiled their proteomes upon Arabidopsis phyllosphere colonization. The highly quantitative mass spectrometric technique SWATH MS was used and allowed for the analysis of over two thousand proteins spanning more than three orders of magnitude in abundance for each of the model strains. The data suggest that Sphingomonas melonis utilizes amino acids and hydrocarbon compounds during colonization of leaves whereas Methylobacterium extorquens relies on methanol metabolism in addition to oxalate metabolism, aerobic anoxygenic photosynthesis and alkanesulfonate utilization. Comparative genomic analyses indicates that utilization of oxalate and alkanesulfonates is widespread among leaf microbiota members whereas, aerobic anoxygenic photosynthesis is almost exclusively found in Methylobacteria. Despite the apparent niche separation between these two strains we also found a relatively small subset of proteins to be coregulated, indicating common mechanisms, underlying successful leaf colonization. Overall, our results reveal for two ubiquitous phyllosphere commensals species-specific adaptations to the host environment and provide evidence for niche separation within the plant microbiota.
authors.affiliation: From the ‡Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Müller
authors.affiliation: §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland.
authors.forename: Olga T
authors.initials: OT
authors.lastname: Schubert
authors.affiliation: §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland.
authors.forename: Hannes
authors.initials: H
authors.lastname: Röst
authors.affiliation: §Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; ¶Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: From the ‡Department of Biology, Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; jvorholt@ethz.ch.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Vorholt
mesh_terms: D000222:Adaptation, Physiological; D000596:Amino Acids / Q000378:metabolism; D017360:Arabidopsis / Q000382:microbiology*; D001426:Bacterial Proteins / Q000032:analysis*; D006838:Hydrocarbons / Q000378:metabolism; D013058:Mass Spectrometry; D020580:Methylobacterium / Q000254:growth & development* / Q000378:metabolism; D010788:Photosynthesis; D018515:Plant Leaves / Q000382:microbiology; D040901:Proteomics / Q000379:methods*; D013045:Species Specificity; D020578:Sphingomonas / Q000254:growth & development* / Q000378:metabolism; D013559:Symbiosis
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D006838:Hydrocarbons