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The evolution of social interactions in microbial communities

Applicant Mitri Sara
Number 154736
Funding scheme Ambizione
Research institution Département de Microbiologie Fondamentale Faculté de Biologie et de Médecine Université de Lausanne
Institution of higher education University of Lausanne - LA
Main discipline Experimental Microbiology
Start/End 01.01.2015 - 31.12.2017
Approved amount 599'343.00
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All Disciplines (2)

Discipline
Experimental Microbiology
Mathematics

Keywords (6)

Computational model; Ecosystems; Evolutionary biology; Mathematical model; Community interactions; Microbiology

Lay Summary (French)

Lead
Les microbes sont partout et affectent presque tous les aspects de nos vies : ils vivent sur notre peau, dans nos intestins, dans les hôpitaux et sont utilisés également dans l’industrie, par exemple pour la purification de l’eau. Les communautés microbiennes contiennent souvent des milliers d’espèces différentes qui se rencontrent, se mélangent et qui influencent la croissance et la survie de leurs voisins.
Lay summary

Le but de ce projet est de développer des méthodes pour étudier les interactions entre espèces qui sont fondamentales pour le fonctionnement des écosystèmes microbiens. Ces études vont aider à comprendre ainsi qu’à contrôler ces écosystèmes à notre avantage.

A cette fin, je vais combiner des approches théoriques et expérimentales. Au niveau théorique, je vais développer un model qui décrit les interactions entre espèces et suit l’évolution de ces interactions. Ensuite, je vais tester les prédictions de ce model dans un écosystème bactérien simple, composé de quatre espèces, qui est utilisé pour la purification de l’eau dans les industries. Enfin, je vais utiliser l’ensemble des approches pour prévoir et contrôler l’évolution de cette communauté avec le but de rendre l’écosystème plus efficace pour décontaminer les polluants toxiques. 

A long-terme, j’envisage de continuer le développement de mes modèles mathématiques ainsi que les systèmes expérimentaux pour comprendre et contrôler des écosystèmes microbiens avec un plus grand nombre d’espèces. Cette capacité de manipuler des écosystèmes selon des critères prédeterminés va être important pour résoudre un grand nombre de problèmes environnementaux comme la purification du sol contaminé, pour l’agriculture comme la conception d’engrais, et dans la santé humaine, comme le développement de traitements pour les infections microbiennes et d’autres maladies humaines. 

Direct link to Lay Summary Last update: 06.01.2015

Responsible applicant and co-applicants

Employees

Publications

Publication
The evolution of siderophore production as a competitive trait
Niehus René, Picot Aurore, Oliveira Nuno, Mitri Sara, Foster Kevin Richard (2017), The evolution of siderophore production as a competitive trait, in Evolution, 71(6), 1443-1455.
Highly variable individual donor cell fates characterize robust horizontal gene transfer of an Integrative and Conjugative Element
Delevat François, Mitri Sara, Pelet Serge, van der Meer Jan-Roelof (2016), Highly variable individual donor cell fates characterize robust horizontal gene transfer of an Integrative and Conjugative Element, in PNAS, 113, E3375-E3383.
Pleiotropy and the low cost of individual traits promote cooperation
Mitri Sara, Foster Kevin (2016), Pleiotropy and the low cost of individual traits promote cooperation, in Evolution, 1.
The ecology and evolution of microbial competition
Ghoul Melanie, Mitri Sara (2016), The ecology and evolution of microbial competition, in Trends in Microbiology, 24, 833-845.
The evolution of quorum sensing as a mechanism to infer kinship
Schluter Jonas, Schoech Armin, Foster Kevin, Mitri Sara (2016), The evolution of quorum sensing as a mechanism to infer kinship, in PLoS Computational Biology, 12, e1004848.
Migration and horizontal gene transfer divide microbial genomes into multiple niches
Niehus René, Mitri Sara, Fletcher Alexander, Foster Kevin (2015), Migration and horizontal gene transfer divide microbial genomes into multiple niches, in Nature Communications, 6, 8924.
Resource limitation drives spatial organization in microbial groups
Mitri Sara, Clarke Ellen, Foster Kevin (2015), Resource limitation drives spatial organization in microbial groups, in The ISME Journal, 1.

Collaboration

Group / person Country
Types of collaboration
Pietro de Anna Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure
- Exchange of personnel
Professor Ian Thompson, Engineering Science, University of Oxford Great Britain and Northern Ireland (Europe)
- Research Infrastructure
Gregory Velicer Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
From pathogen evolution to microbiome dynamics Talk given at a conference Ecology and evolution in a small microbial community 27.10.2017 Titisee, Germany Mitri Sara;
Swiss Society for Microbiology Talk given at a conference The evolution of social interactions in small microbial communities 01.09.2017 Basel, Switzerland Mitri Sara;
Swiss Society for Microbiology Talk given at a conference A small community for pollutant degradation 31.08.2017 Basel, Switzerland Piccardi Philippe;
Microbial Population Biology Gordon Research Conference (GRC) Talk given at a conference The evolution of social interactions in small microbial communities 13.07.2017 Andover, New Hampshire, United States of America Mitri Sara;
American Society for Microbiology, Symposium on microbial communities Talk given at a conference Social evolution in microbial communities 03.06.2017 New Orleans, United States of America Mitri Sara;
Departmental seminar at the University of Neuchâtel Individual talk The evolution of social interactions in microbial communities 02.03.2017 Neuchâtel, Switzerland Mitri Sara;
EMBO conference on bacterial morphogenesis, survival and virulence Talk given at a conference The evolution of social interactions in microbial communities 29.11.2016 Kerala, India Mitri Sara;
Departmental seminar at CHUV Individual talk The ecology and evolution of microbial social interactions 24.11.2016 Lausanne, Switzerland Mitri Sara;
Departmental seminar at Geosciences department, University of Lausanne Individual talk Understanding microbial communities as they evolve in space and time 22.11.2016 Lausanne, Switzerland Mitri Sara;
1st Lausanne CompBio meeting Talk given at a conference The evolution of social interactions in microbial communities 03.05.2016 Lausanne, Switzerland Mitri Sara;
Departmental seminar Individual talk The evolution of social interactions in multi-species microbial communities 23.10.2015 Zurich, Switzerland Mitri Sara;
European Society of Evolutionary Biology bi-annual conference Poster The genotypic view of social interactions in multispecies microbial communities 10.08.2015 Lausanne, Switzerland Mitri Sara;
DMF-IMUL joint meeting Individual talk The evolution of social interactions in multi-species microbial communities 01.05.2015 University of Lausanne, Switzerland Mitri Sara;
Departmental seminar Individual talk The evolution of social interactions in multi-species microbial communities 02.03.2015 Institute for Evolutionary Biology, Barcelona, Spain Mitri Sara;
MicroscapesX meeting Individual talk The evolution of social interactions in microbial communities 02.02.2015 University of Lausanne, CHUV, Switzerland Mitri Sara;


Self-organised

Title Date Place
Ecology and evolution in microbial communities 06.11.2015 University of Lausanne, Switzerland
Evolving microbial communities workshop for PhD students 05.11.2015 University of Lausanne, Switzerland

Communication with the public

Communication Title Media Place Year
New media (web, blogs, podcasts, news feeds etc.) “The social lives of Microbes” Public panel discussion and podcast at the London School of Economics International 2017

Associated projects

Number Title Start Funding scheme
181272 Controlling species embedded within a small microbial community 01.09.2019 Eccellenza grant

Abstract

Traditionally, microbes were viewed as solitary organisms swimming in liquid. It is becoming increasingly clear, however, that the dominant form of microbial life takes place in dense and genetically-diverse surface-attached communities where each cell's ability to survive and divide can be influenced by its neighbours. These intercellular interactions are mediated by "social phenotypes", which may have positive or negative effects on neighbouring cells, such as the construction of protective structures, or the secretion of lethal antibiotics, respectively. Because these phenotypes can result in some species dominating a community while others go extinct, social interactions are key to determining a community's species composition, and consequently, its stability and productivity. If we are to understand the microbial communities that are ubiquitous in our lives, it is of great importance that we develop the research methods to disentangle the complex interactions taking place between the strains and species living within them. I am proposing to develop the necessary theoretical and empirical tools to study and control microbial communities. My work will bridge two areas of biology that have mainly been developed independently: social evolution theory, which considers the evolution of social phenotypes within a species, and microbial ecology, where the focus is on ecosystems as a whole, which are typically modelled as networks of non-evolving species. To understand the evolution of social traits in microbial communities, then, I will begin with an existing spatially-explicit individual-based computational model of social interactions between two co-evolving microbial species, and proceed by adding species to an increasingly abstract model. This will result in a novel, multi-species network model that combines the evolution of social phenotypes within and between microbial species, while taking ecological factors, such as spatial structures, into account. I will then apply the resulting theoretical framework to studying and optimising natural microbial ecosystems, beginning with a community used for bioremediation. Together with collaborators, I will develop a simple laboratory system: a four-species microbial community designed to digest toxic chemicals in metal-working fluids (MWF), which are used in large manufacturing facilities, and are later disposed to landfill. In the laboratory, I will first characterise the social interactions within and between the four species in this community. By applying these parameter estimates to the theoretical model, I will then make predictions on how each of the species will evolve, which I will verify by conducting evolutionary selection experiments in the lab. Finally, using both the model and the experimental system, I will investigate how to manipulate the microbial community towards higher productivity and evolutionary stability. As a result, the experimental system will inform and improve the theoretical model, and in return, a clear theoretical understanding of the experimental system will allow me to make concrete suggestions to my industrial collaborators on how to consistently improve MWF bioremediation, which has been identified as a major target for reducing toxic chemicals in industrial waste. The development of the proposed toolkit of theoretical and experimental techniques for the comparatively simple microbial ecosystem, is the foundational piece of my vision to improve our scientific understanding of more complex communities. Accordingly, in the future, I plan to apply my framework to other microbial systems, including gut microbial communities, potentially providing insights for the treatment of human diseases, and communities in sewage treatment plants, leading to improved strategies for water purification and sustainable energy production. Taken together, my research will increase our basic scientific understanding of complex ecosystems, while simultaneously contributing to economically, medically and environmentally important practical applications. This interdisciplinary work requires a tight coupling between theory and experiments. My unique background in computational biology, evolutionary theory and microbiology, has provided me with the necessary expertise, both as a theoretician and an experimental biologist, to take this line of research from the drawing board towards its many practical applications.
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