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

  • 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
  • Genome Mining-guided and MALDI Imaging-assisted Discovery of New Antibiotics
    Probst, SI; Vogel, C; Vorholt, JA; Piel, J
    CHIMIA, 72 (11):816-816; 10.2533/chimia.2018.816 NOV 2018
  • Bipartite interactions, antibiotic production and biosynthetic potential of the Arabidopsis leaf microbiome
    Helfrich, EJN; Vogel, CM; Ueoka, R; Schafer, M; Ryffel, F; Muller, DB; Probst, S; Kreuzer, M; Piel, J; Vorholt, JA
    NATURE MICROBIOLOGY, 3 (8):909-919; 10.1038/s41564-018-0200-0 AUG 2018
  • Editorial overview: Environmental microbiology: Environmental and engineered microbiomes
    Scoma, Alberto; Vorholt, Julia A.
    CURRENT OPINION IN MICROBIOLOGY   Volume: 43   Pages: V-VII   Published: JUN 2018
  • Methanol-essential growth of Escherichia coli
    Meyer, F; Keller, P; Hartl, J; Groninger, OG; Kiefer, P; Vorholt, JA
    NATURE COMMUNICATIONS, 9 10.1038/s41467-018-03937-y APR 17 2018
  • Phosphorelay through the bifunctional phosphotransferase PhyT controls the general stress response in an alphaproteobacterium
    Gottschlich, Lisa; Bortfeld-Miller, Miriam; Gabelein, Christoph; Dintner, Sebastian; Vorholt, Julia A.
    PLOS GENETICS, 14 (4):10.1371/journal.pgen.1007294 APR 2018
  • Toblerols: Cyclopropanol-Containing Polyketide Modulators of Antibiosis in Methylobacteria
    Ueoka, Reiko; Bortfeld-Miller, Miriam; Morinaka, Brandon I.; Vorholt, Julia A.; Piel, Jorn
    ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 57 (4):977-981; 10.1002/anie.201709056 JAN 22 2018
  • Replacing the Ethylmalonyl-CoA Pathway with the Glyoxylate Shunt Provides Metabolic Flexibility in the Central Carbon Metabolism of Methylobacterium extorquens AM1 
    von Borzyskowski, Lennart Schada; Sonntag, Frank; Poeschel, Laura; et al. 
    ACS SYNTHETIC BIOLOGY, 7 (1): 86-97 JAN 2018
  • Genomic features of bacterial adaptation to plants 
    Levy, Asaf; Gonzalez, Isai Salas; Mittelviefhaus, Maximilian; et al. 
    NATURE GENETICS, 50 (1): 138-+ JAN 2018
  • Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software 
    Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter; et al. 
    NATURE METHODS, 14 (11): 1063-+ NOV 2017
  • Transposon Sequencing Uncovers an Essential Regulatory Function of Phosphoribulokinase for Methylotrophy 
    Ochsner, Andrea M.; Christen, Matthias; Hemmerle, Lucas; et al. 
    CURRENT BIOLOGY, 27 (17): 2579-+ SEP 11 2017
  • Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research 
    Vorholt, Julia A.; Vogel, Christine; Carlstrom, Charlotte I.; et al. 
    CELL HOST & MICROBE, 22 (2): 142-155 AUG 9 2017
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