Phyllosphere microbiome


Plants do not exist as sterile organisms but are populated by microorganisms both below (rhizosphere) and above the ground (phyllosphere). We are interested in a systems-level understanding of the phyllosphere with the aim to identify organizing principles of bacterial community members. We developed a cultivation-independent metaproteogenomic approach and applied it to phyllosphere communities of different host plants in planta in order to get an unbiased view on the overall bacterial community composition and in particular to identify abundant proteins as a proxy for important protein function of community members in the habitat.

Such analyses are paralleled by work using synthetic microbial communities colonizing Arabidopsis thaliana. We are testing indigenous commensal bacteria and their interaction with the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on the model plant and investigate underlying mechanisms of plant protection.


Recent Publications

  • Molecular Basis of Growth Inhibition by Acetate of an Adenylate Cyclase-Deficient Mutant of Corynebacterium glutamicum
    Wolf, Natalie; Bussmann, Michael; Koch-Koerfges, Abigail; Katcharava, Nino; Schulte, Julia; et al.
    Frontiers In Microbiology 11 Article Number: 87 DOI: 10.3389/fmicb.2020.00087    FEB 11 2020
  • Consistent host and organ occupancy of phyllosphere bacteria in a community of wild herbaceous plant species
    Massoni, Julien; Bortfeld-Miller, Miriam; Jardillier, Ludwig; Salazar, Guillem; Sunagawa, Shinichi; Vorholt JA
    Isme Journal,  DOI: 10.1038/s41396-019-0531-8
  • Escherichia coli in Auto(trophic) Mode
    Erb, Tobias J.; Keller, Philipp; Vorholt, Julia A.
    Cell,  DOI: 10.1016/j.cell.2019.10.040
  • Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Brown, Peter; Tan, Aik-Choon; El-Esawi, Mohamed A.; Liehr, Thomas; Blanck, Oliver; et al.
    Database-the Journal Of Biological Databases And Curation DOI: 10.1093/database/baz085 
  • Fluidic Force Microscopy Captures Amyloid Bonds between Microbial Cells
    Dehullu, J; Vorholt, JA; Lipke, PN; Dufrene, YF
    TRENDS IN MICROBIOLOGY, 27 (9):728-730; 10.1016/j.tim.2019.06.001 SEP 2019
  • A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota
    Mittelviefhaus, M; Muller, DB; Zambelli, T; Vorholt, JA
    ISME JOURNAL, 13 (7):1878-1882; 10.1038/s41396-019-0404-1 JUL 2019
  • Complex general stress response regulation in Sphingomonas melonis Fr1 revealed by transcriptional analyses
    Gottschlich, L; Geiser, P; Bortfeld-Miller, M; Field, CM; Vorholt, JA
    SCIENTIFIC REPORTS, 9 10.1038/s41598-019-45788-7 JUN 28 2019
  • Fluidic Force Microscopy Demonstrates That Homophilic Adhesion by Candida albicans Als Proteins Is Mediated by Amyloid Bonds between Cells
    Dehullu, J; Valotteau, C; Herman-Bausier, P; Garcia-Sherman, M; Mittelviefhaus, M; Vorholt, JA; Lipke, PN; Dufrene, YF
    NANO LETTERS, 19 (6):3846-3853; 10.1021/acs.nanolett.9b01010 JUN 2019
  • Use of rare-earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1
    Ochsner, AM; Hemmerle, L; Vonderach, T; Nussli, R; Bortfeld-Miller, M; Hattendorf, B; Vorholt, JA
    MOLECULAR MICROBIOLOGY, 111 (5):1152-1166; 10.1111/mmi.14208 MAY 2019
Julia Vorholt

Prof. Dr. Julia Vorholt
ETH Zurich
Institute of Microbiology
8093 Zurich

Tel: +41 (0)44 632 55 24

Research topics

  • Metaproteome/-genome analysis of microbial communities
  • Synthetic bacterial communities
  • Plant probiotics
  • Identification of traits important for phyllosphere colonization
  • General stress response in Alphaproteobacteria
  • One carbon metabolism



  • Microbial community analyses
  • Proteomics
  • Metabolomics
  • Microscopy (FISH)
  • Single cell manipulation using FluidFM technology