Thomas Julou, Nicolas Desprat, Vincent Croquette, David Bensimon

Evolution, competition,cooperation in bacteriaThomas Julou, Nicolas Desprat, Vincent Croquette, David BensimonJournées du LPS - 2008 june 17 th

“Adaptive evolution”definition: process by which a unit of an evolvingsystem (e.g. an organism or species) becomes bettersuited to its environment.Journées du LPS - 17 juin 20082

“Adaptive evolution”definition: process by which a unit of an evolvingsystem (e.g. an organism or species) becomes bettersuited to its environmentJournées du LPS - 17 juin 20083

“Adaptive evolution”Several levels of selection(DNA, cells, organisms, colonies, populations)Journées du LPS - 17 juin 20084

Experimental evolution milestones๏ “Long Term Experimental Evolution”with Escherichia coli (R.E. Lenski)markerara-Overnight growth(t=24h, 6.7 divisions)1:100dilutionOvernight growth(t=24h, 6.7 divisions)1:100dilutionmarkerara+Journées du LPS - 17 juin 20086

Experimental evolution milestones๏ “Long Term Experimental Evolution”with Escherichia coli (R.E. Lenski 2004)๏ Main breakthroughs:• at the ecological level๏ Limitations• Discontinuous culture• Daily catastrophe(every 7 generations)• Uniform environment• at the genetic levelJournées du LPS - 17 juin 20087

Requirements๏ Our aim: focus on the effect of ecologicalinteractions (competition) in adaptation.• Structured environment• Long timescale• Contamination-proofautomated continuousculture devicei.e. chemostatJournées du LPS - 17 juin 20088

Experimental designnutrient + air๏ an automated continuousculture: a chemostat55°C๏ a gradient of selectivepressure:a temperature gradient35°CwasteJournées du LPS - 17 juin 20089

Experimental design∂E∂t = c E. ∂E∂x∂N∂t = c N . ∂N∂x}{{}flow+D E . ∂2 EN∂x+E(γ.α. 2 N+N 0)+D N . ∂2 NN∂x−E(γ.α. 2 N+N 0)} {{ }diffusion} {{ }growth / uptakeJournées du LPS - 17 juin 200810

Experimental design๏ get rid of bacterialbiofilms: usingMarlière’s device๏ automated device:battery-powered,washing cyclespiloted by amicrocontrollerJournées du LPS - 17 juin 200811

Monitoring adaptation๏ Real-time monitoring of population densitiesand detection of colonization events๏ Sample analysis• adaptive dynamics of growth rate in functionof temperature• adaptive dynamics of fitness๏ Genomics analysis: sequence and expressionJournées du LPS - 17 juin 200812

Towards a cell-level description๏ Phenotypic variability ishigh within a clone๏ Spatial structure stronglyaffects the cooperativedynamicsJournées du LPS - 17 juin 200813

An alive “game of life”๏ Our aim: study ecological dynamics overintermediate timescales at the single-cell precisionWikipedia life movieJournées du LPS - 17 juin 200814

Experimental design๏ Microfluidic device allowing to control the environment๏ Laser optocuting to keep constant bacteria densityyx11 J.cm -2Journées du LPS - 17 juin 200815

Cooperation at the single cell level๏ Antibiotics / resistance systemJournées du LPS - 17 juin 200816