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.

• Methanol-dependent Escherichia coli strains with a complete ribulose monophosphate cycle
  Keller, Philipp; Noor, Elad; Meyer, Fabian; Reiter, Michael A.; Anastassov, Stanislav; Kiefer, Patrick; Vorholt, Julia A
  Nature Communications   DOI: 10.1038/s41467-020-19235-5  OCT 26 2020
• Reciprocal growth control by competitive binding of nucleotide second messengers to a metabolic switch in Caulobacter crescentus
  Shyp, Viktoriya; Dubey, Badri Nath; Bohm, Raphael; Hartl, Johannes; Nesper, Jutta; Vorholt, Julia A; Hiller, Sebastian; Schirmer, Tilman; Jenal, Urs
  Nature Microbiology  DOI: 10.1038/s41564-020-00809-4  NOV 2020
• Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins
  Snelders, Nick C.; Rovenich, Hanna; Petti, Gabriella C.; Rocafort, Mercedes; van den Berg, Grardy C. M.; et al.
  Nature Plants  DOI: 10.1038/s41477-020-00799-5  Published: NOV 2020
• Import of Aspartate and Malate by DcuABC Drives H-2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice
  Nguyen, Bidong D.; Cuenca, Miguelangel, V; Hartl, Johannes; Guel, Ersin; Bauer, Rebekka; et al.
  Cell Host & Microbe  DOI: 10.1016/j.chom.2020.04.013  Published: JUN 10 2020
• ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks
  Millard, Pierre; Schmitt, Uwe; Kiefer, Patrick; Vorholt, Julia A.; Heux, Stephanie; et al.
  Plos Computational Biology  https://doi.org/10.1371/journal.pcbi.1007799 APR 2020
• 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
• …

• 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