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.

• 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

• 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