La réhabilitation des sols pollués par les Hydrocarbures Aromatiques Polycycliques (HAP) est une problématique importante au niveau européen. Afin de développer une technique de bioremédiation, une collection de 30 souches de champignons saprotrophes est constitués à partir d'échantillons de sols historiquement pollués par les HAP provenant du Nord de la France. Ces souches sont caractérisées pour leur capacités de désorption et de dégradation du Benzo[a]pyrène (BaP) en milieu minéral. Quatre souches présentent des taux de dégradation du BaP supérieur à 30% après seulement 9 jours d'incubation en milieu minéral. Des mesures d'activités enzymatiques sur un panel de 14 souches permettent d'observer des concordances intéressantes entre les capacités de dégradation du BaP et des activités enzymatiques extracellulaires ou liées au cytochrome P450. Des essais au laboratoire de bioaugmentation/biostimulation en microcosmes de sols historiquement contaminés en HAP permettent une augmentation d'environ 25% de la dégradation des HAP totaux par rapport aux témoins après inoculation d'une souche de Talaromyceshelicus dans deux sols d'origines et de textures différentes. Le processus d'incorporation du BaP, un HAP à 5 cycles aromatiques, est étudié en microscopie chez une souche de Fusariumsolani. D'après nos résultats, cette molécule serait incorporée dans les cellules fongiques par un processus actif et dépendant du réseau d'actine du cytosquelette. Ce travail de thèse ouvre ainsi de nouvelles perspectives pour la compréhension des mécanismes de dégradation des HAP par les champignons saprotrophes telluriques et le développement de nouveaux protocoles de bioremédiation fongique des sols. / Recovery of soils polluted by Polycyclic Aromatic Hydrocarbons (PAH) is an important problematic at the European scale. In order to develop a bioremediation technique, a collection of 30 saprotrophic fungal strains is constituted using PAH historically contamined soil samples coming from the north of France. These strains are characterized for their capacity of Benzo[a]pyrene (BaP) desorption and degration in mineral medium. Four strains exhibit BaP degradation rates over 30% after 9 days of incubation in mineral medium. Measurements of enzymatic activities within a panel of 14 strains enable to observe interesting correlations between BaP degradation capacities and extracellular or cytochrome P450-linked enzymatic activities. Lab-scale bioaugmentation/biostimulation experiments in microcosms of PAH historically contamined soils enbale to observe an increase of approximately 25% of the total-PAH degradation compared to the blanks after the inoculation of a strain of Talaromyceshelicus in two soils differing by their origins and textures. The incorporation of BaP, a 5 aromatic rings PAH, is studied through microcopy in the strain Fusariumsolani. According to our results, this molecule would be incorporated in fungal cells through an active mechanism depending on the actin network of the cytoskeleton. This PhD thesis draws new perpectives for the understanding of PAH degradations mechanisms in telluric saprotrophic fungi and for the development of new fungal bioremediation protocols in soils.

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<p>Tri soja gljive bukovače, P. ostreatus NS 77, P. ostreatus NS 355 i P. ostreatus 244,<br />gajena su na supstratima četiri biljne vrste, p&scaron;enica, kukuruz, soja i suncokret, kao<br />samostalni supstrati i u kombinaciji sa p&scaron;eničnom slamom. Nakon plodono&scaron;enja<br />vr&scaron;ena su ispitivanja odgajivačkih, morfolo&scaron;kih, hemijskih, svojstva gljiva, kao i<br />hemijske i mikrobiolo&scaron;ke&nbsp;&nbsp;&nbsp; sirovim supstratima u odnosu na sadržaj celuloze u<br />supstratima nakon plodono&scaron;enja sojeva, dok je kod sadržaja pepela obrnuto, u sirovim<br />supstratima je niži u odnosu na supstrate nakon plodono&scaron;enja. Koncentracija ukupnog<br />broja mikroorganizama, brojnost amonifikatora i brojnost saprofitnih gljiva na<br />nesterilisanim supstratima je niža nego na iskori&scaron;tenim supstratima. Dehidrogenazna<br />aktivnost&nbsp; je najvi&scaron;a na supstratima nakon plodono&scaron;enja soja NS 244, dok kod<br />enzimskog kompleksa celulaza varira u zavisnosti od soja i supstrata Kod sva tri soja<br />maksimalni prinosi su bili na supstratu Soja (S5), a minimlni na supstratu P&scaron;enica<br />(S1). Na osnovu morfolo&scaron;kih osobine konstatovana je velika varijabilnist između<br />sojeva. Supstrat Kukuruz (S6) se pokazao kao najbolji, sa aspekta vodnog režima, dok<br />se Suncokret (S7) pokazao kao najlo&scaron;iji. Na supstratu Kukuruz (S6) je najvi&scaron;i, a na<br />supstratu P&scaron;enica (S1) je najniži sadržaj pepela. Sadržaj natrijuma u nožici je veći od<br />sadržaja u &scaron;e&scaron;iru, &scaron;to je obrnuto u odnosu na druge mikroelemente i makroelemente.<br />Sadržaj celuloze je vi&scaron;i u svim&nbsp; sirovim supstratima, dok&nbsp; je kod sadržaja pepela<br />obrnuto. Brojnost svih mikroorgnaizma na nesterilisanim supstratima je niža nego na<br />iskori&scaron;tenim supstratima.&nbsp; Dehidrogenazna&nbsp; je najvi&scaron;a na supstratima nakon<br />plodono&scaron;enja soja NS 244, dok kod enzimskog kompleksa celulaza varira u zavisnosti<br />od soja i supstrata.</p> / <p>Three strains of oyster mushroom (P. ostreatus NS 77, NS 355, and 244) were grown on substrates made from four crops (wheat, maize, soybean, and sunflower), as individual substrates or in combination with wheat straw. After fruit maturity,&nbsp; mushroom growing, morphological, and chemical properties were analysed, as well as chemical and microbiological analyses of fresh and used substrates. All three strains showed maximum yields on soybean substrate (S5), and minimum yields on wheat substrate (S1). A large variability among the strains was observed based on the morphological properties. The strain NS 77 has caps of the smallest weight,&nbsp; width and length, the largest number of fruiting bodies, and the longest stalks. The&nbsp; strain NS 244 have caps of the largest weight, width and length, the lowest number of fruiting bodies and stalk length, but the largest width of the stalks. Regarding water regime, maize substrate (S6) was the best, while sunflower (S7) was the poorest. Ash content was the highest in maize substrate (S6) and the lowest in wheat&nbsp; substrate (S1). Potassium content in the stalk was higher than in the cap, which is opposite from other micro- and macro elements. Cellulose content was higher in all fresh substrates than in the used substrates after the strains have fruited, while ash content was higher in the used substrates. Concentration of total number of microorganisms, abundance of ammonifiers and saprophytic fungi in the unsterilized substrates were lower than in the used ones. Dehydrogenase activity was the highest in substrates after fruiting of NS 244, while cellulose enzyme complex varied regarding the strain and substrate.</p>

Both testate amoebae and fungi are common inhabitants of coniferous litter. Their interactions in this environment were rarely studied, although they reach high biodiversity and can play a significant role in nutrient cycling in this environment. In this study, a cultivation of litter needles in the damp chambers was used to investigate interactions between fungi and testate amoebae. Observation of spruce litter needles in environmental scanning electron microscope was used to better characterize testate amoebae communities directly on the needles. Additionally, two experiments changing the biotic conditions in the microcosm were used to follow a principle of the interactions. Three species of testate amoebae from litter needles were able to colonize the filter paper on the bottom of the damp chambers. Occurrence of Phryganella acropodia and Assulina muscorum on the filter paper was significantly fuelled by the presence of mycelium. Assulina muscorum was associated with the fungal spores and Arcella discoides was attracted by sporulating colonies of Cladosporium spp. in the damp chambers. By contrast, no association of putatively mycophagous Phryganella acropodia with fungal spores was observed. Arcella discoides was attracted both by live and death mycelium in additional experiment. Interestingly, the...

L'association mycorhizienne implique nombre de plantes et de champignons, étant sans doute la symbiose mutualiste la plus importante et la plus répandue au sein des écosystèmes terrestres. Étant donné que la plupart des arbres forment des mycorhizes arbusculaires ou des ectomycorhizes qui se distinguent par leur écophysiologie, il est judicieux de caractériser les forêts en fonction de leur dominance mycorhizienne afin d'en mesurer les impacts sur les processus écologiques. Ainsi, l'objectif de cette thèse est de quantifier les influences de la dominance mycorhizienne en forêt sur les propriétés abiotiques et biotiques du sol ayant un impact à l'échelle locale sur deux processus associés : la décomposition de la matière organique et la régulation de la diversité végétale. Les forêts étudiées, de dominance mycorhizienne très contrastée, présentent des propriétés physico-chimiques et des communautés microbiennes distinctes au niveau du sol, mais des patrons de distribution verticale des microorganismes du sol d'une similarité inattendue. Dans ces forêts nordiques décidues, la décomposition de la matière organique est favorisée dans les couches supérieures du sol, notamment grâce à la présence du réseau fongique et d'autant plus lorsque les ectomycorhizes prédominent, ce qui prouve l'aspect déterminant du contexte local. L'établissement d'arbres mycorhiziens arbusculaires peut être limité par la combinaison des conditions abiotiques et biotiques édaphiques de la forêt boréale, qui est dominée par les ectomycorhizes, contrairement aux forêts à dominance partagée entre mycorhize arbusculaire et ectomycorhize, où la diversité est favorisée à l'échelle de la communauté. Cette thèse démontre le rôle déterminant, au niveau local, exercé par la dominance mycorhizienne sur les processus écologiques, et soulève l'importance de l'hétérogénéité biotique et abiotique du sol pour mieux saisir le fonctionnement des écosystèmes terrestres. / Mycorrhizas, which involve plants and fungi, are probably the most important and widespread mutual symbioses in terrestrial ecosystems. Since most trees form arbuscular mycorrhizas or ectomycorrhizas that are ecophysiologically distinct from each other, it is useful to characterize forests according to their mycorrhizal dominance in order to measure their respective impacts on ecological processes. The objective of this thesis is to quantify the impacts of forest mycorrhizal dominance on the abiotic and biotic properties of the soil, which influence at the local scale two associated processes: the decomposition of organic matter and the maintenance of plant diversity. The forests studied have opposite mycorrhizal dominance exhibit distinct soil physico-chemical properties and microbial communities, but more similar vertical distribution patterns of microorganisms than expected. Decomposition is favored by organic matter in the upper soil layers, but also by the presence of the fungal network, especially when ectomycorrhizas predominate, illustrating the importance of the local environmental context. Establishment of arbuscular mycorrhizal tree may be limited by the combination of abiotic and biotic edaphic factors of the boreal forest, which is ectomycorrhizal-dominated, in contrast to forests with shared dominance between arbuscular mycorrhizas and ectomycorrhizas, where tree species diversity is favored at the community level. This thesis demonstrates the decisive role, at the local scale, played by mycorrhizal dominance on ecological processes, and raises the importance of soil biotic and abiotic heterogeneity to better understand the functioning of terrestrial ecosystems.