Molecular analysis of the biodiversity of protists in hydrocarbon-polluted and pristine soils

Eukaryotic microorganisms are an essential component of the Earth's global diversity. It is believed that the number of protistan taxa far outnumbers the one of viruses and bacteria. The taxonomic classification of these organisms, which also represent the major part of the total eukaryotic diversity, is still not very well known. It is only lately that the main phylogenetically consistent eukaryotic super assemblages (also called "kingdoms") have been defined. Inside these kingdoms, lateral branches represent the main multicellular taxa, the plants, animals and fungi. Protists are present in virtually all environments; in this thesis, attention was focused on the soil as habitat for the eukaryotic microorganisms. The communities inhabiting soil are characterized by adaptations to drought (the capacity to form cysts). Moreover, certain groups are found exclusively in this environment, to which they are morphologically adapted, whereas others are absent and exclusively found in aquatic systems. Detailed studies on the ecology of certain groups have been performed, and it is possible to define amongst them typical fast reproducing, early colonizers for new environments (r-specialists), whereas others can be found only in stable and highly productive habitats (K-specialists). All these organisms are distributed in a heterogeneous manner in the soil, being usually more frequent in the top horizon and around hotspots such as, for instance, root tips. Prokaryotes have drawn most of the attention of microbial ecologists, who almost neglected the eukaryotic microbes with the exception of fungi. Ecologists usually define four categories ("guilds") of protists in soil: Flagellates, naked amoebae, testate amoebae and ciliates. The importance of protistan activity in soil ecosystems has been shown with the concept of microbial loop: nutrients, produced by autotrophic organisms, are taken up by decomposers (bacteria and fungi) to produce their own biomass. Heterotrophic protists, by preying on them, release these compounds in a form which can be directly used by the autotrophs ("mineralization"), thus closing the loop. This phenomenon is of major significance, because protistan grazing controls the composition and activity of the prokaryotic community, and also the growth of the autotrophs. In soil, this phenomenon takes mainly place at the tip of the roots of vascular plants, where exudates are released. When soils are exposed to an organic pollution, the protistan communities and thus also their impact on the microbial loop, are influenced in two different ways: either by the direct toxic effects of the pollutant and or the indirect effects on their bacterial preys. A detailed study on the negative effects of environmental pollution, however, requires reliable methods to study protists. Molecular approaches offer the possibility to study protists in situ without the limitations inherent to cultivation dependent approaches. The aim of this thesis was to deve