Microbiology

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.

• 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
• 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 Article (Details)
• Genomic features of bacterial adaptation to plants 
  Levy, Asaf; Gonzalez, Isai Salas; Mittelviefhaus, Maximilian; et al. 
  NATURE GENETICS, 50 (1): 138-+ JAN 2018  Article (Details)
• 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 
  Article (Details)
• 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 Article (Details)
• 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 Review (Details)

• 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