This thesis describes the use of centrifugal photosedimentation, for the particle size analysis of soil clays and clay minerals. The instrument that was used is the Horiba, CAPA 500. It has a lower limit to particle size analysis for clays of 20nm (Stokes' diameter) and gives a high degree of size resolution. The initial output is a relationship between turbidity and Stokes' diameter over a limited range of particle sizes. Use of the centrifugal photosedimentometer with materials containing a broad range of particle sizes, such as clays, by combining results from runs with overlapping size ranges is described. In order to maximize sensitivity it was necessary to use higher initial suspension concentrations when analysing for small particles, compared to those used when analysing for larger particles. Typically clays contain particles that are both greater and smaller than the wavelength of light in the dispersing medium (400 nm in this case). It is therefore important to correct for the variation in light extinction with particle size and those aspects of light scattering and absorption theory that are relevant to photosedimentation data analysis are reviewed. For particles that are smaller than 100nm absorption makes a significant contribution to light extinction. Therefore the absorption coefficients of a range of contrasting clays were estimated from reflectance measurements taken from diluted clays (in powder form). These samples provided a set of standards that allowed the absorption coefficients of other clays to be estimated by visual comparison. In very force fields disc-like particles sediment so that they are oriented with their minimum dimension in the direction of motion. Light scattering is sensitive to particle orientation, hence photosedimentation was used to estimate the orientation state of sedimenting particles. Estimates of the maximum advisable centrifugal speed for use with the various particle sizes are given. These were obtained from both simple theory and from experimental results. Although repeatable results were obtained from photosedimentation, the particle size distributions calculated from the relationship between turbidity and Stokes' diameter did not agree with those from gravimetric size analysis, when traditional theories (e.g. Mie) were used to correct the experimentally obtained turbidity data prior to the calculation of particle size distribution. However, satisfactory semi-empirical scattering efficiencies are suggested for the 100nm to 10 μm size range, but they need further testing. Photosedimentation analysis produced the same shape of particle size distribution for TEM size analysed samples, however the positions of these size distributions in terms of mean particle size did not always coincide. Despite the various sources of uncertainty in the particle size distributions that are obtained from photosedimentation data analysis, the high degree of size resolution and good repeatability of the instrument make it suitable for many applictions in Soil Science. Centrifugal photosedimentation was found to be particularly useful for studying the effect of saturating cation on the particle size distributions of dispersed bentonite. Further work is suggested to extend the range of semi-empirical values of extinction efficiency that are given and also to quantify the biasing that can result from samples which have a variation of axial ratio and/or chemical composition with particle size.

Les Streptomyces sont des bactéries de la rhizosphère qui contribuent à la fertilité des sols (recyclage de la matière organique), et à la croissance et la santé des plantes. Elles possèdent parmi les plus grands génomes bactériens (12 Mb) et présentent une variabilité génétique importante. Cette variabilité connue au niveau interspécifique n’a jamais été abordée à l’échelle de la population, c’est-à-dire entre individus sympatriques appartenant à la même espèce (souches sœurs) au sein de la même niche écologique. L’objectif de ce travail est de rechercher cette diversité dans les populations de l’écosystème sol forestier, d’approcher sa dynamique et son rôle fonctionnel. Après séquençage et comparaison des génomes complets, nous avons observé une grande diversité génomique en termes de taille, de présence/absence d’éléments extrachromosomiques, mais également en terme de présence/absence de gènes le long du chromosome. Un grand nombre d’événements d’insertions et délétions (indels) comprenant de 1 à 241 gènes différencient les individus de la population. Au vu des liens phylogénétiques étroits entre les individus, l’ancêtre commun de la population est récent, aussi la diversité génomique résulterait d’un flux massif et rapide de gènes. La forte prévalence d’éléments conjugatifs intégrés dans la population suggère que la conjugaison est le moteur prépondérant de cette diversité génomique. La production différentielle de métabolites spécialisés (antibiotiques) a également été utilisée pour estimer l’impact de la diversité génétique sur le fonctionnement de la population. Nous avons pu montrer que cette production était liée à des gènes spécifiques de souches et qu’elle pouvait constituer un bien commun pour la population. Nous proposons que l’évolution rapide du génome participe au maintien des mécanismes de cohésion sociale chez ces bactéries du sol. / Streptomyces are rhizospheric bacteria that contribute to soil fertility (recycling of organic matter), plant growth and health. They have among the largest bacterial genomes (12 Mb) with a high genetic variability. The genome variability, observed at the interspecific level has never been addressed within a population, i.e. between sympatric individuals belonging to the same species (Conspecific strains) within the same ecological niche. The objective of this work was to investigate this diversity in the forest soil ecosystem, to estimate its dynamics and its potential functional roles. After sequencing and comparison of the complete genomes, we observed a wide genomic diversity in terms of size, presence/absence of extrachromosomal elements, but also in terms of presence/absence of genes along the chromosome. A large number of insertion and deletion events (indels) from 1 to 241 genes differentiate individuals in the population. Given the close phylogenetic relationship of these strains, the common ancestor of the population is recent, hence the genomic diversity would result from a massive and rapid gene flux. The high prevalence of integrative and conjugative elements in the population suggests that conjugation could act as a driving force of this diversity. Differential production of specialized metabolites (antibiotics) was also used to estimate the impact of genetic diversity on population’s ecology. We were able to show that this production was linked to strain specific genes and that it may constitute a « public good » for the population. We propose that the rapid evolution of the genome contributes to the maintenance of social cohesion mechanisms within these soil bacteria.