Ce projet concerne l’analyse de l’organisation de populations microbiennes au sein de structures complexescomme des dépôts ou des biofilms.Si différentes méthodes sont couramment utilisées pour étudier la structure globale ou l’organisation localed’agrégats microbiens, peu d’entre elles, permettent de réaliser simultanément ces deux analyses et nécessitentsouvent des étapes de préparation qui pénalisent un approche in-vivo et en dynamique.La stratégie proposée repose sur la mise en oeuvre de micro-organismes modèles autofluorescents (levures etbactéries) qui peuvent sans aucun traitement être directement observés en microscopie. La similitude ducomportement physiologique de ces micro-organismes avec celui des souches sauvages a été démontrée. Lesconditions d’acquisition des images en microscopie confocale ont été optimisées. Des dispositifs spécifiques ontété conçus pour générer des dépôts ou des biofilms dans des conditions de contraintes physico-mécaniques etbiochimiques maîtrisées afin d’analyser simultanément leurs caractéristiques et les performances du bioprocédé.Ainsi les dépôts ont pu être observés in-vivo et in-situ grâce à une cellule de filtration équipée d’une fenêtred’observation. Le développement d’un biofilm mixte composé de levures et bactéries modèles autofluorescentes,dans un réacteur continu spécifique, a également été analysé par microscopie confocale.Le traitement et les analyses des images acquises au cours des expériences ont été effectués et ont permisd‘étudier la structure globale des agrégats biologiques et l’organisation tridimensionnelle des micro-organismesdans ces structures, en mettant par exemple en évidence une répartition hétérogène de deux populationsmicrobiennes dans des dépôts de filtration ou en comparant la capacité de deux espèces microbiennes à formerdes biofilms en étudiant in-vivo la dynamique de croissance de chacune des espèces.Cette étude a en outre permis de démontrer la pertinence de la méthode proposée, de définir ses limites et sonchamp d’application / The aim of this project deals with the analysis of both the local localization and organization of microbialpopulations in complex structures such as deposits or biofilms. Different methods are currently used to study theglobal structure or the local organization of biological aggregates but only few ones allow a combined approachand require ex-vivo analyses.The proposed strategy uses home-designed model auto-fluorescent microorganisms (yeasts and bacteria) whichcan be observed directly by microscopy without any dying treatment. Same kinetic behaviours between the wildstrains and their recombinant ones were demonstrated. The confocal microscopy conditions were optimised.Specific devices were developed to generate deposits or biofilms under controlled and known hydrodynamic orbiochemical environment conditions to analyse their structure characteristics linked to the bioprocessperformances.Based on the proposed strategy, microbial deposits modifications due to pressure constraints were observed invivo in a specifically designed flow cell equipped with a microscope glass coverslip. A mixed biofilm composedby our auto-fluorescent yeasts and bacteria was carried out in a specific bioreactor allowing the sampling ofbiofilms during their development to be analysed by confocal microscopy. Both studies have shown specificorganisations between yeasts and bacteria mainly depending on their size and on the environment conditions(pressure or dilution rate).These studies of both local and global structure of biological aggregates and 3D-organisation of themicroorganisms within theses structures demonstrated the relevance of the proposed strategy defining the limitsof the method and proposing various perspectives for further characterizations and applications

Made available in DSpace on 2015-05-14T12:14:00Z (GMT). No. of bitstreams: 1 parte1.pdf: 2310445 bytes, checksum: 3cfca25ce861a7301fea8d5aa8526310 (MD5) Previous issue date: 2011-02-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In this work, we study the collective behaviour of living systems whose aggregates form organized groups such as flocks of birds, herds of mamals and schools of fishes. Through numerical simulations, we model the collective movement of a school of fishes using behavioural rules similar to the ones proposed by Couzin et al. [23], that investigates the spatial dynamics of animals groups. The model presents three interaction zones: repulsion, orientation and attraction. Our results for the distributions of nearest neighbour distance, the diference of orientation between the velocities of neighbour fishes and the cooperativeness of the school are in good agreement with experimental measurements. A simpler way to describe the collective motion of several groups of organisms was introduced by Vicsek et al. [10]. This model presents only one interaction region, called orientation zone and considers point particles moving off lattice at constant speed adjusting their direction of motion to that of the average velocity of their neighbors, being subject to some noisy term. A second-order transition between an ordered state and a disordered regime was found. However, Gregoire and Chate [12] contest the nature of such phase transition as being of first order. Indeed, this transition is related to the way of introducing the noise into the system. In this sense, we present a comparative study on noise in two system of self-propelled particle (Vicsek model and Gregoire model) with the aim of understanding the role of the noise on some observables such as polarization, distributions of the nearest neighbour distances, difference of orientations between neighbour particles, the order parameter and the Binder cumulant. / Neste trabalho, estudamos o comportamento coletivo de sistemas vivos cujos agregados formam grupos organizados tais como bandos de pássaros, rebanhos de mamíferos e cardumes de peixes. Através de simulações numéricas, modelamos o movimento coletivo de cardumes de peixes usando regras comportamentais similares áquelas propostas por Cousin et al.[23], que investigam a dinâmica espacial de grupos de animais. O modelo apresenta três zonas de interação: repulsão, orientação e atração. Nossos resultados para as distribuições das distâncias entre vizinhos mais próximos, a diferença de orientação entre as velocidades de peixes vizinhos e a cooperatividade do cardume estão de bom acordo com medidas experimentais. Uma maneira mais simples para descrever o movimento coletivo de vários grupos de organismos foi introduzido por Vicsek et al. [10]. Este modelo apresenta somente uma região de interação, chamada zona de orientação e considera partículas pontuais movendo na rede com uma velocidade constante ajustando sua direção de movimento à velocidade média de seus vizinhos, estando sujeita a algum termo ruidoso. Uma transição de segunda ordem entre um estado ordenado e um regime desordenado foi encontrado. Porém, Gregoire e Chaté [12] contestam a natureza da transição de fase como sendo de primeira ordem. Na verdade, está transição está relacionada à forma de introduzir o ruído no sistema. Neste sentido, apresentamos um estudo comparativo sobre o ruído em dois sistemas de partículas auto-propelidas (modelo de Vicsek e modelo de Gregoire) com o objetivo de compreender o papel do ruído em alguns observáveis tais como a polarização, distribuições das distâncias entre vizinhos mais próximos, diferença de orientação entre partículas vizinhas, o parâmetro de ordem e o cumulante de Binder.