Publications

ZORA Publication List

Publications

• 2025

  • Schnyder, Anya; Kalawong, Ratchara; Eberl, Leo; Agnoli, Kirsty (2025). $Pseudomonas$ $fungipugnans$ sp. nov., a potently antifungal bacterium isolated from moss. International Journal of Systematic and Evolutionary Microbiology, 75(1):online.

• 2024

  • Bellés-Sancho, Paula; Golaz, Daphné; Paszti, Sarah; Vitale, Alessandra; Liu, Yilei; Bailly, Aurélien; Eberl, Leo; James, Euan K; Pessi, Gabriella (2024). Tn-seq profiling reveals that NodS of the beta-rhizobium Paraburkholderia phymatum is detrimental for nodulating soybean. Communications Biology, 7(1):1706.
  • Ren, Jiajun; Mathew, Anugraha; Rodríguez-García, María; Kohler, Tobias; Blacque, Olivier; Linden, Anthony; Eberl, Leo; Sieber, Simon; Gademann, Karl (2024). Functional biosynthetic stereodivergence in a gene cluster via a dihydrosydnone N-oxide. Communications Chemistry, 7(1):301.
  • Leinweber, Anne; Laffont, Clémentine; Lardi, Martina; Eberl, Leo; Pessi, Gabriella; Kümmerli, Rolf (2024). RNA-Seq reveals that Pseudomonas aeruginosa mounts growth medium-dependent competitive responses when sensing diffusible cues from Burkholderia cenocepacia. Communications Biology, 7(1):995.
  • Paganini, Leonardo. Untangling a Regulatory Network Involving a Novel Diazeniumdiolate Signal in $\textit{Pseudomonas syringae}$. 2024, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Torres, Marta; Paszti, Sarah; Eberl, Leo (2024). Shedding light on bacteria–host interactions with the aid of TnSeq approaches. mBio, 15(6):e0039024.
  • Neubauer, Anna. Molecular Insights into the Mutualistic Association between the Hornwort Plant Host $Anthoceros Agrestis$ and its Symbiont $Nostoc Punctiforme$. 2024, University of Zurich, Faculty of Science.

• 2023

  • Heredia-Ponce, Zaira; Secchi, Eleonora; Toyofuku, Masanori; Marinova, Gabriela; Savorana, Giovanni; Eberl, Leo (2023). Genotoxic stress stimulates eDNA release via explosive cell lysis and thereby promotes streamer formation of Burkholderia cenocepacia H111 cultured in a microfluidic device. npj Biofilms and Microbiomes, 9(1):96.
  • Hug, Sebastian; Heiniger, Benjamin; Bolli, Kim; Paszti, Sarah; Eberl, Leo; Ahrens, Christian H; Pessi, Gabriella (2023). Paraburkholderia sabiae Uses One Type VI Secretion System (T6SS-1) as a Powerful Weapon against Notorious Plant Pathogens. Microbiology Spectrum:online.
  • Toyofuku, Masanori; Schild, Stefan; Kaparakis-Liaskos, Maria; Eberl, Leo (2023). Composition and functions of bacterial membrane vesicles. Nature Reviews. Microbiology, 21(7):415-430.
  • Grayfer, Tatyana D; Yamani, Khalil; Jung, Erik; Chesnokov, Gleb A; Ferrara, Isabella; Hsiao, Chien-Chi; Georgiou, Antri; Michel, Jeremy; Bailly, Aurélien; Sieber, Simon; Eberl, Leo; Gademann, Karl (2023). Allylic Carbocyclic Inhibitors Covalently Bind Glycoside Hydrolases. JACS Au, 3(4):1151-1161.
  • Straub, Hervé; Zuber, Flavia; Eberl, Leo; Maniura-Weber, Katharina; Ren, Qun (2023). In Situ Investigation of Pseudomonas aeruginosa Biofilm Development: Interplay between Flow, Growth Medium, and Mechanical Properties of Substrate. ACS applied materials & interfaces, 15(2):2781-2791.
  • Eberl, Leo (2023). Rehabilitation of the ‘bad guys’ for biocontrol applications. Environmental Microbiology, 25(1):97-101.
  • Oi, Kathryn K. Structural and biophysical characterization ot thanatin peptidomimetics binding to LpA of critical gram-negative pathogens. 2023, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Wiehlmann, Lutz; Klockgether, Jens; Hammerbacher, Anna-Silke; Salunkhe, Prabhakar; Horatzek, Sonja; Munder, Antje; Peilert, Janno Florian; Gulbins, Erich; Eberl, Leo; Tümmler, Burkhard (2023). A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839. Frontiers in Cellular and Infection Microbiology, 13:1234420.
  • Shilling, Rebecca Elizabeth. Inhibition of BerB within B. cenocepacia H111 single cells and its consequences on the macrolony. 2023, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Bellés-Sancho, Paula. Elucidation of the genetic determinants underlying Paraburkholderia phymatum's symbiotic ability and its high competitiveness in legume root infection. 2023, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Straub, Hervé Jean. Should I stay or should I flow: Pseudomonas aeruginosa biofilm formation under flow in a microfluidic platform. 2023, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2022

  • Schnyder, Anya; Eberl, Leo; Agnoli, Kirsty (2022). Investigating the Biocontrol Potential of the Natural Microbiota of the Apple Blossom. Microorganisms, 10(12):2480.
  • Steiner, Elisabeth; Shilling, Rebecca E; Richter, Anja M; Schmid, Nadine; Fazli, Mustafa; Kaever, Volkhard; Jenal, Urs; Tolker-Nielsen, Tim; Eberl, Leo (2022). The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB. npj Biofilms and Microbiomes, 8:93.
  • Bellés-Sancho, Paula; Liu, Yilei; Heiniger, Benjamin; von Salis, Elia; Eberl, Leo; Ahrens, Christian H; Zamboni, Nicola; Bailly, Aurélien; Pessi, Gabriella (2022). A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis. Frontiers in Plant Science, 13:991548.
  • Purtschert-Montenegro, Gabriela; Cárcamo-Oyarce, Gerardo; Pinto-Carbó, Marta; Agnoli, Kirsty; Bailly, Aurélien; Eberl, Leo (2022). Pseudomonas putida mediates bacterial killing, biofilm invasion and biocontrol with a type IVB secretion system. Nature Microbiology, 7(10):1547-1557.
  • Paszti, Sarah; Vitale, Alessandra; Liu, Yilei; Braunwalder, Rubina; Kalawong, Ratchara; Biner, Olivier; Pessi, Gabriella; Eberl, Leo (2022). Identification of Key Factors for Anoxic Survival of B. cenocepacia H111. International Journal of Molecular Sciences, 23(9):4560.
  • Secchi, Eleonora; Savorana, Giovanni; Vitale, Alessandra; Eberl, Leo; Stocker, Roman; Rusconi, Roberto (2022). The structural role of bacterial eDNA in the formation of biofilm streamers. Proceedings of the National Academy of Sciences of the United States of America, 119(12):e2113723119.
  • Gualdi, Stefano; Agnoli, Kirsty; Vitale, Alessandra; Higgins, Steven; Eberl, Leo (2022). Identification of genes required for gold and silver tolerance in Burkholderia cenocepacia H111 by transposon sequencing. Environmental Microbiology, 24(2):737-751.
  • Schweizer, Tiziano A. Die another cell : implications of regulated cell death during infection and inflammation. 2022, University of Zurich, Faculty of Science.
  • Kalawong, Ratchara. Influence of putisolvin on membrane vesicle and nanotube formation in Pseudomonas putida IsoF. 2022, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Gschwend, Florian. Next-generation soil quality monitoring : metabarcoding of soil bacterial and fungal communities for long-term soil quality monitoring. 2022, University of Zurich, Faculty of Science.
  • Purtschert-Montenegro, Gabriela. Identification of a novel bacterial killing nanomachine in Pseudomonas putida IsoF. 2022, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2021

  • Georgiou, Antri; Sieber, Simon; Hsiao, Chien-Chi; Grayfer, Tatyana; Gorenflos López, Jacob L; Gademann, Karl; Eberl, Leo; Bailly, Aurélien (2021). Leaf nodule endosymbiotic Burkholderia confer targeted allelopathy to their Psychotria hosts. Scientific Reports, 11:22465.
  • Sieber, Simon; Mathew, Anugraha; Jenul, Christian; Kohler, Tobias; Bär, Max; Carrión, Víctor J; Cazorla, Francisco M; Stalder, Urs; Hsieh, Ya-Chu; Bigler, Laurent; Eberl, Leo; Gademann, Karl (2021). Mitigation of Pseudomonas syringae virulence by signal inactivation. Science Advances, 7(37):eabg2293.
  • Wong, Gerard C L; Antani, Jyot D; Lele, Pushkar P; Chen, Jing; et al; Carrara, Francesco; Stocker, Roman; Eberl, Leo (2021). Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Physical Biology, 18(5):051501.
  • Georgieva, Maria; Heinonen, Tytti; Vitale, Alessandra; Hargraves, Simone; Causevic, Senka; Pillonel, Trestan; Eberl, Leo; Widmann, Christian; Jacquier, Nicolas (2021). Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide. iScience, 24:102923.
  • Hug, Sebastian; Liu, Yilei; Heiniger, Benjamin; Bailly, Aurélien; Ahrens, Christian H; Eberl, Leo; Pessi, Gabriella (2021). Differential Expression of Paraburkholderia phymatum Type VI Secretion Systems (T6SS) Suggests a Role of T6SS-b in Early Symbiotic Interaction. Frontiers in Plant Science, 12:699590.
  • Bellés-Sancho, Paula; Lardi, Martina; Liu, Yilei; Eberl, Leo; Zamboni, Nicola; Bailly, Aurélien; Pessi, Gabriella (2021). Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by Paraburkholderia phymatum NifA. Metabolites, 11(7):455.
  • Mannweiler, Olga; Pinto-Carbó, Marta; Lardi, Martina; Agnoli, Kirsty; Eberl, Leo (2021). Investigation of Burkholderia cepacia Complex Methylomes via Single-Molecule, Real-Time Sequencing and Mutant Analysis. Journal of Bacteriology, 203(12):00683-20.
  • Fenn, Samuel; Dubern, Jean-Frédéric; Cigana, Cristina; De Simone, Maura; Lazenby, James; Juhas, Mario; Schwager, Stephan; Bianconi, Irene; Döring, Gerd; Elmsley, Jonas; Eberl, Leo; Williams, Paul; Bragonzi, Alessandra; Cámara, Miguel (2021). NirA is an alternative nitrite reductase from Pseudomonas aeruginosa with potential as an antivirulence target. mBio, 12(2):e00207-21.
  • Bernal, Patricia; Eberl, Leo; de Jonge, Ronnie; Lepek, Viviana C; Malone, Jacob G (2021). Understanding plant–microorganism interactions to envision a future of sustainable agriculture. Environmental Microbiology, 23(4):1809-1811.
  • Heredia‐Ponce, Zaira; Gutiérrez‐Barranquero, José Antonio; Purtschert‐Montenegro, Gabriela; Eberl, Leo; de Vicente, Antonio; Cazorla, Francisco M (2021). Role of extracellular matrix components in the formation of biofilms and their contribution to the biocontrol activity of Pseudomonas chlororaphis PCL1606. Environmental Microbiology, 23(4):2086-2101.
  • Vandenbussche, Ian; Sass, Andrea; Van Nieuwerburgh, Filip; Pinto-Carbó, Marta; Mannweiler, Olga; Eberl, Leo; Coenye, Tom (2021). Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing. Microbiology, 167(3):001027.
  • Cadot, Selma Florence. Plant root exudates shape the rizosphere microbiome and mediate context-specific plant-soil feedback. 2021, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.
  • Gualdi, Stefano. Identification of fitness determinants in Burkholderia cenocepacia H111 by transposon sequencing. 2021, University of Zurich, Mathematisch-naturwissenschaftliche Fakultät.

• 2020

  • Secchi, Eleonora; Vitale, Alessandra; Miño, Gastón L; Kantsler, Vasily; Eberl, Leo; Rusconi, Roberto; Stocker, Roman (2020). The effect of flow on swimming bacteria controls the initial colonization of curved surfaces. Nature Communications, 11:2851.
  • Heredia-Ponce, Zaira; Gutiérrez-Barranquero, Jose Antonio; Purtschert-Montenegro, Gabriela; Eberl, Leo; Cazorla, Francisco M; de Vicente, Antonio (2020). Biological role of EPS from Pseudomonas syringae pv. syringae UMAF0158 extracellular matrix, focusing on a Psl-like polysaccharide. npj Biofilms and Microbiomes, 6:875.
  • Straub, Hervé; Eberl, Leo; Zinn, Manfred; Rossi, René M; Maniura-Weber, Katharina; Ren, Qun (2020). A microfluidic platform for in situ investigation of biofilm formation and its treatment under controlled conditions. Journal of Nanobiotechnology, 18:166.
  • Vitale, Alessandra; Paszti, Sarah; Takahashi, Kohei; Toyofuku, Masanori; Pessi, Gabriella; Eberl, Leo (2020). Mapping of the denitrification pathway in Burkholderia thailandensis by genome-wide mutant profiling. Journal of Bacteriology, 202(23):00304-20.
  • Vandenbussche, Ian; Sass, Andrea; Pinto-Carbó, Marta; Mannweiler, Olga; Eberl, Leo; Coenye, Tom (2020). DNA methylation epigenetically regulates gene expression in Burkholderia cenocepacia and controls biofilm formation, cell aggregation, and motility. mSphere, 5(4):00455-20.
  • Vitale, Alessandra; Pessi, Gabriella; Urfer, Matthias; Locher, Hans H; Zerbe, Katja; Obrecht, Daniel; Robinson, John A; Eberl, Leo (2020). Identification of genes required for resistance to peptidomimetic antibiotics by transposon sequencing. Frontiers in Microbiology, 11:1681.
  • Liu, Yilei; Bellich, Barbara; Hug, Sebastian; Eberl, Leo; Cescutti, Paola; Pessi, Gabriella (2020). The exopolysaccharide Cepacian plays a role in the establishment of the Paraburkholderia phymatum – Phaseolus vulgaris symbiosis. Frontiers in Microbiology, 11:1600.
  • Higgins, Steven; Gualdi, Stefano; Pinto‐Carbó, Marta; Eberl, Leo (2020). Copper resistance genes of Burkholderia cenocepacia H111 identified by transposon sequencing. Environmental Microbiology Reports, 12(2):241-249.
  • Lardi, Martina; Liu, Yilei; Hug, Sebastian; Bolzan de Campos, Samanta; Eberl, Leo; Pessi, Gabriella (2020). Paraburkholderia phymatum STM815 σ54 controls utilization of Dicarboxylates, motility, and T6SS-b expression. Nitrogen, 1(2):81-98.

• 2019

  • Andreoni, Federica; Toyofuku, Masanori; Menzi, Carmen; Kalawong, Ratchara; Mairpady Shambat, Srikanth; François, Patrice; Zinkernagel, Annelies S; Eberl, Leo (2019). Antibiotics Stimulate Formation of Vesicles in Staphylococcus aureus in both Phage-Dependent and -Independent Fashions and via Different Routes. Antimicrobial Agents and Chemotherapy, 63(2):e01439-18.
  • Sathe, Santosh; Mathew, Anugraha; Agnoli, Kirsty; Eberl, Leo; Kümmerli, Rolf (2019). Genetic architecture constrains exploitation of siderophore cooperation in the bacterium Burkholderia cenocepacia. Evolution Letters, 3(6):610-622.
  • Luther, Anatol; Urfer, Matthias; Zahn, Michael; Müller, Maik; Wang, Shuang-Yan; Mondal, Milon; Vitale, Alessandra; Hartmann, Jean-Baptiste; Sharpe, Timothy; Monte, Fabio Lo; Kocherla, Harsha; Cline, Elizabeth; Pessi, Gabriella; Rath, Parthasarathi; Modaresi, Seyed Majed; Chiquet, Petra; Stiegeler, Sarah; Verbree, Carolin; Remus, Tobias; Schmitt, Michel; Kolopp, Caroline; Westwood, Marie-Anne; Desjonquères, Nicolas; Brabet, Emile; Hell, Sophie; LePoupon, Karen; Vermeulen, Annie; Jaisson, Régis; Rithié, Virginie; Upert, Grégory; Lederer, A; Zbinden, P; Wach, A; Moehle, Kerstin; Zerbe, Katja; Locher, H H; Bernardini, Federico; Dale, G E; Eberl, Leo; Wollscheid, Bernd; Hiller, Sebastian; Robinson, J A; Obrecht, D (2019). Chimeric peptidomimetic antibiotics against Gram-negative bacteria. Nature, 576(7787):452-458.
  • Straub, Hervé; Bigger, Claudio M; Valentin, Jules; Abt, Dominik; Qin, Xiao-Hua; Eberl, Leo; Maniura-Weber, Katharina; Ren, Qun (2019). Bacterial Adhesion on Soft Materials: Passive Physicochemical Interactions or Active Bacterial Mechanosensing?. Advanced Healthcare Materials, 8(8):e1801323.
  • Spiewak, Helena L; Shastri, Sravanthi; Zhang, Lili; Schwager, Stephan; Eberl, Leo; Vergunst, Annette C; Thomas, Mark S (2019). Burkholderia cenocepacia utilizes a type VI secretion system for bacterial competition. MicrobiologyOpen:e774.
  • Toyofuku, Masanori; Nomura, Nobuhiko; Eberl, Leo (2019). Types and origins of bacterial membrane vesicles. Nature Reviews. Microbiology, 17(1):13-24.

• 2018

  • Jenul, Christian; Sieber, Simon; Daeppen, Christophe; Mathew, Anugraha; Lardi, Martina; Pessi, Gabriella; Hoepfner, Dominic; Neuburger, Markus; Linden, Anthony; Gademann, Karl; Eberl, Leo (2018). Biosynthesis of fragin is controlled by a novel quorum sensing signal. Nature Communications, 9:1297.
  • Gomes, Margarida C; Tasrini, Yara; Subramoni, Sujatha; Agnoli, Kirsty; Feliciano, Joana R; Eberl, Leo; Sokol, Pamela; O'Callaghan, David; Vergunst, Annette C (2018). The afc antifungal activity cluster, which is under tight regulatory control of ShvR, is essential for transition from intracellular persistence of Burkholderia cenocepacia to acute pro-inflammatory infection. PLoS Pathogens, 14(12):e1007473.
  • Carrión, Víctor J; Cordovez, Viviane; Tyc, Olaf; Etalo, Desalegn W; de Bruijn, Irene; de Jager, Victor C L; Medema, Marnix H; Eberl, Leo; Raaijmakers, Jos M (2018). Involvement of Burkholderiaceae and sulfurous volatiles in disease-suppressive soils. The ISME journal, 12(9):2307-2321.
  • Vetterli, Stefan U; Zerbe, Katja; Müller, Maik; Urfer, Matthias; Mondal, Milon; Wang, Shuang-Yan; Moehle, Kerstin; Zerbe, Oliver; Vitale, Alessandra; Pessi, Gabriella; Eberl, Leo; Wollscheid, Bernd; Robinson, John A (2018). Thanatin targets the intermembrane protein complex required for lipopolysaccharide transport in Escherichia coli. Science Advances, 4(11):eaau2634.
  • Leinweber, Anne. The struggle for iron: how it affects cooperation, competition and biodiversity in bacterial communities. 2018, University of Zurich, Faculty of Science.

• 2017

  • Higgins, Steven; Sanchez-Contreras, Maria; Gualdi, Stefano; Pinto-Carbó, Marta; Carlier, Aurélien; Eberl, Leo (2017). The Essential Genome of Burkholderia cenocepacia H111. Journal of Bacteriology, 199(22):e00260-17.
  • Toyofuku, Masanori; Cárcamo-Oyarce, Gerardo; Yamamoto, Tatsuya; Eisenstein, Fabian; Hsiao, Chien-Chi; Kurosawa, Masaharu; Gademann, Karl; Pilhofer, Martin; Nomura, Nobuhiko; Eberl, Leo (2017). Prophage-triggered membrane vesicle formation through peptidoglycan damage in Bacillus subtilis. Nature Communications, 8:481.

• 2016

  • Eshwar, Athmanya K. Studying pathogen-host interactions and pathogenesis in Cronobacter and Listeria infections using in vitro and in vivo infection models. 2016, Universität Zürich, Faculty of Science.

• 2015

  • Cárcamo Oyarce, Gerardo. Social behaviors of Pseudomonas putida IsoF. 2015, University of Zurich, Faculty of Science.

• 2013

  • Gomes, José; Grunau, Alexander; Lawrence, Adrien K; Eberl, Leo; Gademann, Karl (2013). Bioinspired Surfaces Against Bacterial Infections. CHIMIA International Journal for Chemistry, 67(4):275-278.

• 2012

  • Dieckmann, Sarah Maria. Analysis of novel haemotrophic mycoplasma isolates with main focus on significance of haemotrophic mycoplasma infections in horses. 2012, University of Zurich, Faculty of Science.

• 2011

  • Polinceusz, Anna Izabela. Molecular characterisation of the Arabidopsis TT12 MATE protein and functional analysis of other plant MATE transporters. 2011, University of Zurich, Faculty of Science.

• 2010

  • Subramanian, Akshay. Sequence variations in the ribosomal decoding and peptidyl transferase sites determine sensitivity to aminoglycosides and macrolides. 2010, University of Zurich, Faculty of Science.

• 2009

  • Zeder, Michael. Development of methods and technology for automated high-throughput multi-parameter analysis of single cells by fluorescence microscopy. 2009, University of Zurich, Faculty of Science.

• 2008

  • Salcher, Michaela Maria. Seasonality of bacterial phylotypes affected by bottom-up and top-down control in Piburger See, Austria. 2008, University of Zurich, Faculty of Science.