Thesis

Richesse et diversité des assemblages de champignons et d'oomycètes de hêtraies, en relation avec des facteurs climatiques et édaphiques : de la parcelle au continent

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Abstract

Les sols forestiers sont des habitats hétérogènes, véritables réservoirs de microorganismes. Parmi ces microorganismes, les eucaryotes filamenteux (champignons et oomycètes) sont très divers et jouent un rôle important dans le fonctionnement et la durabilité des écosystèmes forestiers. Leur diversité et leur répartition spatiale à différentes échelles sont encore peu connues et les facteurs qui sous-tendent cette dispersion sont encore peu étudiés. Aussi, les objectifs étaient (i) d'exploiter le séquençage haut-débit pour des études d'écologie microbienne à large échelle et valider son application aux communautés d'oomycètes pathogènes en milieu forestier, (ii) de décrire ces communautés microbiennes, en termes de diversité et de structure, à différentes échelles spatiales (locale, régionale et continentale), (iii) de caractériser les variables biotiques et abiotiques structurant ces communautés et (iv) d'évaluer la réponse éventuelle des communautés aux variations climatiques. Une première étude pilote à l'échelle de la parcelle a été suivi de deux études à grande échelle spatiale le long de gradients environnementaux. Des gradients d'altitude et un gradient latitudinal, à l'échelle continentale, ont été utilisés comme gradient climatique. L'étude préliminaire a donc validé l'utilisation du pyroséquençage pour les communautés fongiques, et en particulier pour les espèces ectomycorhiziennes, et apporté des éléments pour établir une méthodologie d'échantillonnage couplée à cette technique. L'application de ces outils moléculaires à l'étude des communautés oomycètes pathogènes reste à optimiser. Les résultats obtenus sur les communautés fongiques telluriques suggèrent que dans l'hypothèse d'un réchauffement climatique, la richesse fongique ne serait pas directement affectée mais la composition des communautés le serait. La composition des communautés fongiques est également fortement liée au pH du sol. Ces résultats sont à affiner en étudiant plus en détail divers groupes taxonomiques et écologiques en lien avec des variables climatiques plus précises. Par ailleurs, de nombreuses perspectives sont envisageables pour améliorer la détection des oomycètes dans les sols forestiers, qui reste un challenge en écologie microbienne

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Thesis
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Attempts to assess fungal global species richness are confounded by several problems: uncertainty about the number of described species, incomplete fungal inventories even at a high taxonomic level, high diversity of unknown, often small and elusive taxa, high levels of morphological conservation, and incomplete knowledge of their ecological and biogeographical distributions. The two main bases for estimating total fungal diversity are (1) the number of described species and their taxonomic structure, and (2) extrapolating species-area relationships. We argue that knowledge of fungal taxonomy and environmental sampling of fungi are both too incomplete for either approach to be reliable. However, it is likely that the true number of fungal species on the planet is a seven-digit number, and may even be an order of magnitude higher.
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Recent knowledge about root systems of trees mostly originates from studies in pure stands. But the root systems may change if more than one species is present. The fine root system (d < 2mm) of spruce was characterized for pure stands and for comparable mixed spruce/beech stands to a soil depth of 80 cm. This made it possible to estimate the effects of interspecific competition on stagnic cambisol and on dystric cambisol, respectively. An additional pure beech stand was studied on stagnic cambisol to evaluate the mixture effect also on the root system of beech. The total fine root biomass was greater in each mixed stand compared to the neighbouring pure stand. Fine roots of beech were over-represented in the rooting zone of the mixed stand, which indicates a competitive displacement of fine roots of spruce. In addition, spruce developed a more superficially distributed root system in the mixed compared to the pure stands. The low abundance of spruce roots in mixed stand and the limitation of spruce roots to the uppermost soil layers underlines the high competitive ability of beech in the rooting zone of the investigated mixed stands.
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Temperate black cherry forests may owe their diversity in part to the presence of pathogenic fungi. Black cherry seedlings do not tend to survive beneath... [KEYWORDS: Populations; trees]
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Pyrosequencing analysis was performed on soils from Italian chestnut groves to evaluate the diversity of the resident Phytophthora community. Sequences analysed with a custom-database discriminated 15 pathogenic Phytophthoras including species common to chestnut soils, while a total of 9 species were detected with baiting. The two sites studied differed in Phytophthora diversity and the presence of specific taxa responded to specific ecological traits of the sites. Furthermore, some species not previously recorded were represented by a discrete number of reads; among these species, P. ramorum was detected at both sites. Pyrosequencing demonstrated to be a very sensitive technique to describe Phytophthora community in soil, able to detect species not easy to be isolated from soil with standard baiting techniques. In particular, pyrosequencing is an highly efficient tool for investigating the colonisation of new environments by alien species, and for ecological and adaptive studies coupled to biological detection methods. This study represents the first application of pyrosequencing for describing Phytophthoras in environmental soil samples. This article is protected by copyright. All rights reserved.