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The role of ambient flow and physico-chemical microenvironment in determining the microstructure of the biofilm matrix

English title The role of ambient flow and physico-chemical microenvironment in determining the microstructure of the biofilm matrix
Applicant Secchi Eleonora
Number 179834
Funding scheme PRIMA
Research institution Institut für Umweltingenieurwissenschaften ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Condensed Matter Physics
Start/End 01.09.2018 - 31.08.2023
Approved amount 1'390'628.00
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All Disciplines (2)

Discipline
Condensed Matter Physics
Biophysics

Keywords (7)

Rheology; Microfluidics; Biofilms; Microbial imaging; Soft Matter Physics; Hydrodynamics; Pseudomonas aeruginosa

Lay Summary (Italian)

Lead
I biofilm sono aggregati di batteri caratterizzati dalla produzione di una matrice polimerica. Al loro interno, i batteri sono protetti dalle sollecitazioni chimico-fisiche, come essicazione, antibiotici, detergenti e predatori. Inoltre, i biofilm risultano molto difficili da rimuovere. Il loro sviluppo è influenzato da numerosi fattori ambientali, uno dei quali é il flusso, frequentemente presente negli ambienti in cui essi crescono. Nonostante la loro indiscussa importanza, non si sa ancora molto del ruolo delle condizioni ambientali nel determinare la struttura e le proprietà meccaniche dei biofilm.
Lay summary

Soggetto e obiettivo

Il mio obiettivo è comprendere il ruolo del flusso nel determinare la struttura e le proprietà meccaniche dei biofilm e determinare come essi rispondono al cambiamento delle condizioni fisico-chimiche. In particolare, mi ripropongo di testare due ipotesi: (i) biofilm cresciuti in condizioni di flusso diverse hanno una struttura diversa, in termini di proprietà meccaniche e composizione chimica; (ii) biofilm con una struttura diversa rispondono diversamente al cambiamento delle condizioni ambientali.

Contesto socio-scientifico

Il principale risultato scientifico del progetto sarà la comprensione del legame tra le condizioni ambientali e le proprietà fisiche del biofilm. Attraverso lo studio della loro interazione con l’ambiente circostante, il mio progetto renderà possibile lo sviluppo di strategie innovative in ambito industriale e medico per ridurre la formazione di biofilm dannosi, ad esempio all’interno di tubature e cateteri, e per promuovere la loro formazione per fini utili, come sistemi di filtrazione e depurazione.   

Parole chiave

Rheology, Microfluidics, Biofilms, Microbial Imaging, Soft matter Physics, Hydrodynamics, Pseudomonas aeruginosa

Direct link to Lay Summary Last update: 27.08.2018

Responsible applicant and co-applicants

Employees

Publications

Publication
The structural role of bacterial eDNA in the formation of biofilm streamers
Secchi Eleonora, Giovanni Savorana, Alessandra Vitale, Leo Eberl, Roman Stocker, Roberto Rusconi (2021), The structural role of bacterial eDNA in the formation of biofilm streamers, 1-31.
Sequential capillarity-assisted particle assembly in a microfluidic channel
Pioli Roberto, Fernandez-Rodriguez Miguel Angel, Grillo Fabio, Alvarez Laura, Stocker Roman, Isa Lucio, Secchi Eleonora (2021), Sequential capillarity-assisted particle assembly in a microfluidic channel, in Lab on a Chip, 21(5), 888-895.
Localization in Flow of Non-Newtonian Fluids Through Disordered Porous Media
Seybold H. J., Eberhard U., Secchi E., Cisne R. L. C., Jiménez-Martínez J., Andrade R. F. S., Araújo A. D., Holzner M., Andrade J.S. (2021), Localization in Flow of Non-Newtonian Fluids Through Disordered Porous Media, in Frontiers in Physics, 9, 635051.
An interdisciplinary and application-oriented approach to teach microfluidics
Salek M. Mehdi, Fernandez Vicente, D'souza Glen, Puigmartí-Luis Josep, Stocker Roman, Secchi Eleonora (2021), An interdisciplinary and application-oriented approach to teach microfluidics, in Biomicrofluidics, 15(1), 014104-014104.
Dynamic arrest and aging of biomolecular condensates are regulated by low-complexity domains, RNA and biochemical activity
Linsenmeier Miriam, Hondele Maia, Grigolato Fulvio, Secchi Eleonora, Weis Karsten, Arosio Paolo (2021), Dynamic arrest and aging of biomolecular condensates are regulated by low-complexity domains, RNA and biochemical activity, 1-30.
Magnetic cilia carpets with programmable metachronal waves
Gu Hongri, Boehler Quentin, Cui Haoyang, Secchi Eleonora, Savorana Giovanni, De Marco Carmela, Gervasoni Simone, Peyron Quentin, Huang Tian-Yun, Pane Salvador, Hirt Ann M., Ahmed Daniel, Nelson Bradley J. (2020), Magnetic cilia carpets with programmable metachronal waves, in Nature Communications, 11(1), 2637-2637.
Mapping the local viscosity of non-Newtonian fluids flowing through disordered porous structures
Eberhard U., Seybold H. J., Secchi E., Jiménez-Martínez J., Rühs P. A., Ofner A., Andrade J. S., Holzner M. (2020), Mapping the local viscosity of non-Newtonian fluids flowing through disordered porous structures, in Scientific Reports, 10(1), 11733-11733.
The effect of flow on swimming bacteria controls the initial colonization of curved surfaces
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, in Nature Communications, 11(1), 2851-2851.
Encounter rates between bacteria and small sinking particles
Słomka Jonasz, Alcolombri Uria, Secchi Eleonora, Stocker Roman, Fernandez Vicente I (2020), Encounter rates between bacteria and small sinking particles, in New Journal of Physics, 22(4), 043016-043016.
Not Just Going with the Flow: The Effects of Fluid Flow on Bacteria and Plankton
Wheeler Jeanette D., Secchi Eleonora, Rusconi Roberto, Stocker Roman (2019), Not Just Going with the Flow: The Effects of Fluid Flow on Bacteria and Plankton, in Annual Review of Cell and Developmental Biology, 35(1), 213-237.

Collaboration

Group / person Country
Types of collaboration
Prof. Roberto Cerbino / University of Milan Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel
Prof. Idan Duval / IMEDEA, UIB Spain (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
- Exchange of personnel
Dr. Gavin Melaugh, School of Physics and Astronomy, University of Edinburgh Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Marcus Holtzner / WSL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Leo Eberl / University of Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Paolo Arosio / D- CHEM / ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Prof. Dr. Jan Vermant, Soft Material / D-MATL / ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
- Exchange of personnel
Prof. Todd Squires, Microfluidics and Microrheology Lab/ Chemical Engineering / UC Santa Barbara United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Zinkernagel / Department of Infectious Diseases and Hospital Hygiene, University Hospital Zuri Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel
Prof. Peter Kang / University of Minnesota United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Roberto Rusconi / Humanitas Research Hospital Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Dr. Med. Silvio Daniel Brugger / Department of Infectious Diseases and Hospital Hygiene, University Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel
Prof. Luca Heltai, mathlab/SISSA Italy (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Prof. Lucio Isa / D-MATL / ETH Zurich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
- Exchange of personnel
Prof. Marco Polin / Physics Department, University of Warwick. Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
11th Liquid Matter Conference Poster A microfluidic platform for characterizing the structure and rheology of biofilm streamers 19.07.2021 Online conference, Czech Republic Savorana Giovanni;
11th Liquid Matter Conference Talk given at a conference Dynamics of Comamonas denitrificans aggregation: formation of a bacterial gel 19.07.2021 Online conference, Czech Republic Charlton Samuel;
11th Liquid Matter Conference Talk given at a conference The role of eDNA in the formation of biofilm streamers 19.07.2021 Online conference, Czech Republic Secchi Eleonora;
27th Swiss Soft Days Talk given at a conference A microfluidic platform for characterizing the structure and rheology of biofilm streamers 08.06.2021 Online conference, Switzerland Savorana Giovanni;
Interpore2021- MS5 Poster Self-assembly of Comamonas denitrificans: formation of a living bacterial gel 31.05.2021 Online conference, Netherlands Charlton Samuel;
Invited seminar at the University of Melbourne Talk given at a conference Biofilm streamers’ formation: viscoelasticity and biochemical composition at play 05.05.2021 Online/Zoom, Australia Secchi Eleonora;
Annual European Rheology Conference Poster A microfluidic platform for characterizing the structure and rheology of biofilm streamers 15.04.2021 Online conference, Germany Savorana Giovanni;
APS March Meeting 2021- Session E13: Physics of Biological Active Matter II: Cell Colonies Talk given at a conference The role of eDNA in the formation of biofilm streamers 16.03.2021 Online, United States of America Secchi Eleonora;
26th Swiss Soft Days Poster A microfluidic platform for characterizing the structure and rheology of biofilm streamers 06.03.2021 Basel, Switzerland Savorana Giovanni;
Invited talk at ENAC, EPFL Individual talk The effect of fluid flow on motile bacteria controls bacterial transport and initial surface colonization 13.11.2020 Online/Zoom, Switzerland Secchi Eleonora;
Invited talk at the seminar series Physics of Living Systems, EPFL Individual talk Fluid flow and motility control initial bacterial colonization on curved surfaces 16.10.2020 Online/Zoom, Switzerland Secchi Eleonora;
Invited talk at the Institut Charles Sadron, Strasbourg Individual talk Bacteria in flow : surface colonization and biofilm formation 05.10.2020 Online, France Secchi Eleonora;
biofilm 9 Poster A microfluidic platform for characterizing the structure and rheology of biofilm streamers 29.09.2020 Online conference, Germany Savorana Giovanni;
biofilm 9 Talk given at a conference The role of eDNA in the formation of biofilm streamers 29.09.2020 Online/Zoom, Germany Secchi Eleonora;
Italian Matter Days 2020 Talk given at a conference The role of eDNA in the formation of biofilm streamers 21.09.2020 Online/ Zoom, Italy Secchi Eleonora;
Italian Soft Days 2020 Poster A microfluidic platform for characterizing the structure and rheology of biofilm streamers 21.09.2020 Online conference, Italy Savorana Giovanni;
Virtual seminar series organized by the UK Fluids Network Individual talk The effect of flow on swimming bacteria controls the initial colonization of surfaces 15.06.2020 Online/Zoom, Great Britain and Northern Ireland Secchi Eleonora;
Quantitative Methods in Gene Regulation 2019 Talk given at a conference Capillary deposition of microorganisms in a microfluidic channel for the study of cells in spatially controlled environments 09.12.2019 London, Great Britain and Northern Ireland Secchi Eleonora;
Fluid Physics of Life – FPLIFE2019 Talk given at a conference Fluid flow and motility control initial bacterial colonization on curved surfaces 21.10.2019 Dresden, Germany Secchi Eleonora;
Invited talk at the Leiden Institute of Physics (LION) Individual talk Bacteria in flow: surface colonization and biofilm formation 26.09.2019 Leiden, Netherlands Secchi Eleonora;
International Soft Matter Conference 2019 Poster Miscible two-fluid channel flow: velocity profiles and hydrodynamic stability 03.06.2019 Edinburg, Great Britain and Northern Ireland Savorana Giovanni;
International Soft Matter Conference 2019 Talk given at a conference Fluid flow and motility control initial bacterial colonization on curved surfaces 03.06.2019 Edinburgh, Great Britain and Northern Ireland Secchi Eleonora;
Interpore 2019 - 11th annual meeting Talk given at a conference The influence of flow on bacterial transport and surface colonization in a model porous medium 06.05.2019 Valencia, Spain Secchi Eleonora;
Invited talk at Empa, St. Gallen Individual talk Bacteria in flow around a pillar: surface colonization and biofilm streamers growth 26.04.2019 St. Gallen, Switzerland Secchi Eleonora;
Invited talk at the University of Zurich, Zurich Individual talk Bacteria in flow around a pillar: surface colonization and biofilm streamers growth 12.04.2019 Zurich, Switzerland Secchi Eleonora;
Swiss Soft Day - 24th edition Talk given at a conference Fluid flow and motility control initial bacterial colonization on curved surfaces 23.03.2019 Fribourg, Switzerland Secchi Eleonora;
7th Swiss Microbial Ecology Meeting- SME 2019 Talk given at a conference The influence of flow and geometric constraints on bacterial transport and attachment 30.01.2019 Lausanne, Switzerland Secchi Eleonora;


Self-organised

Title Date Place
InterPore2021 - (MS5) Biochemical processes and biofilms in porous media 31.05.2021 Online Conference, Netherlands
AGU - session "Biochemical and Hydrodynamic Processes in Biofilms and Porous Media” 07.12.2020 Online, United States of America
InterPore2020 - (MS5) Biochemical processes and biofilms in porous media 31.08.2020 Online conference, Netherlands

Awards

Title Year
Inviation to submit a paper to the "Soft Matter Emerging Investigators Series", which will highlight the inspiring work being carried out by scientists in the early stages of their independent careers in the field of soft matter. 2021
Invitation to the 4th World Laureates Forum (WLF) as Young Researcher. WLF is a global gathering of the prize-winners of several major prizes, e.g. Nobel Prize. It will be held in Shanghai, China from October 29th – November 1st, 2021. The president of ETH Zurich has been invited to recommend three outstanding young scientists to attend the WLF and, lately, the internal committee lately confirmed the invitation for me. 2021
Invited as Visiting Professor at the Institute of Advanced Mediterranean Studies (IMEDEA) from the University of Balearic Islands (Palma de Mallorca, Spain) for a one-month stay during the month of September 2020 (postponed to September 2021). 2020
Poster Prize for the Best Poster presented at the Italian Soft Days 2020. The prize included the invitation to submit a paper to the journal Soft Matter. 2020

Abstract

Biofilms are consortia of bacteria that grow on surfaces. Most bacteria in moist environments adopt the biofilm lifestyle and biofilms have major environmental, technological and medical impacts. Biofilms consist of dense communities of bacterial cells embedded in a matrix of extracellular material. The matrix can account for over 90% of biofilm mass, is made up of a conglomeration of diverse biopolymers, and provides protection against mechanical and chemical insults. Despite the importance of the matrix to biofilm survival, little is known about how the environment shapes its characteristics and, in turn, how its characteristics shape the biofilm’s response to environmental conditions. Flow is ubiquitous in the aquatic habitats where biofilms are found, and the shear stress resulting from the interaction of flow with surfaces is a fundamental feature of biofilm environments. I will study the influence of flow and shear stress on biofilm matrix development, using the experimental toolbox from soft matter physics to characterize the matrix and elucidate the relation between rheology and chemical composition. I will then use this knowledge to study how matrix structure affects biofilm function, by considering the response to physico-chemical stressors in the form of pH and osmotic pressure gradients. I will use microfluidics to obtain precise control of fluid flow, in combination with microrheology and advanced visualization techniques.This project represents an ambitious step towards understanding the role of the matrix in determining the resistance of biofilms to environmental insults and our efforts to remove them. The knowledge gained from this research will provide fundamental insights relevant for a wide range of applications in the environment, technology and health. By focusing on fundamental mechanisms, this work also has the potential to spark new strategies for biofilm deterrence or eradication, or promote their stability in applications where biofilms are beneficial.
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