Les écosystèmes dunaires remplissent plusieurs fonctions écologiques essentielles comme celle de protéger le littoral grâce à leur capacité d’amortissement face aux vents et vagues des tempêtes. Les dunes jouent aussi un rôle dans la filtration de l’eau, la recharge de la nappe phréatique, le maintien de la biodiversité, en plus de présenter un attrait culturel, récréatif et touristique. Les milieux dunaires sont très dynamiques et incluent plusieurs stades de succession végétale, passant de la plage de sable nu à la dune bordière stabilisée par l’ammophile à ligule courte, laquelle permet aussi l’établissement d’autres herbacées, d’arbustes et, éventuellement, d’arbres. Or, la survie de ces végétaux est intimement liée aux microorganismes du sol. Les champignons du sol interagissent intimement avec les racines des plantes, modifient la structure des sols, et contribuent à la décomposition de la matière organique et à la disponibilité des nutriments. Ils sont donc des acteurs clés de l’écologie des sols et contribuent à la stabilisation des dunes. Malgré cela, la diversité et la structure des communautés fongiques, ainsi que les mécanismes influençant leur dynamique écologique, demeurent relativement méconnus. Le travail présenté dans cette thèse explore la diversité des communautés fongiques à travers le gradient de succession et de conditions édaphiques d’un écosystème dunaire côtier afin d’améliorer la compréhension de la dynamique des sols en milieux dunaires. Une vaste collecte de données sur le terrain a été réalisée sur une plaine de dunes reliques se trouvant aux Îles de la Madeleine, Qc. J’ai échantillonné plus de 80 sites répartis sur l’ensemble de ce système dunaire et caractérisé les champignons du sol grâce au séquençage à haut débit. Dans un premier temps, j’ai dressé un portait d’ensemble des communautés fongiques du sol à travers les différentes zones des dunes. En plus d’une description taxonomique, les modes de vie fongiques ont été prédits afin de mieux comprendre comment les variations au niveau des communautés de champignons du sol peuvent se traduire en changements fonctionnels. J’ai observé un niveau de diversité fongique élevé (plus de 3400 unités taxonomiques opérationnelles au total) et des communautés taxonomiquement et fonctionnellement distinctes à travers un gradient de succession et de conditions édaphiques. Ces résultats ont aussi indiqué que toutes les zones des dunes, incluant la zone pionière, supportent des communautés fongiques diversifiées. Ensuite, le lien entre les communautés végétales et fongiques a été étudié à travers l’ensemble de la séquence dunaire. Ces résultats ont montré une augmentation claire de la richesse spécifique végétale, ainsi qu’une augmentation de la diversité des stratégies d’acquisition de nutriments (traits souterrains lié à la nutrition des plantes, soit mycorhizien à arbuscule, ectomycorhizien, mycorhizien éricoide, fixateur d’azote ou non spécialisé). J’ai aussi pu établir une forte corrélation entre les champignons du sol et la végétation, qui semblent tous deux réagir de façon similaire aux conditions physicochimiques du sol. Le pH du sol influençait fortement les communautés végétales et fongiques. Le lien observé entre les communautés végétales et fongiques met l’emphase sur l’importance des interactions biotiques positives au fil de la succession dans les environnements pauvres en nutriments. Finalement, j’ai comparé les communautés de champignons ectomycorhiziens associées aux principales espèces arborescentes dans les forêts dunaires. J’ai observé une richesse importante, avec un total de 200 unités taxonomiques opérationnelles ectomycorhiziennes, appartenant principalement aux Agaricomycètes. Une analyse de réseaux n’a pas permis de détecter de modules (c'est-à-dire des sous-groupes d’espèces en interaction), ce qui indique un faible niveau de spécificité des associations ectomycorhiziennes. De plus, je n’ai pas observé de différences en termes de richesse ou de structure des communautés entre les quatre espèces hôtes. En conclusion, j’ai pu observer à travers la succession dunaire des communautés diversifiées et des structures distinctes selon la zone de la dune, tant chez les champignons que chez les plantes. La succession semble toutefois moins marquée au niveau des communautés fongiques, par rapport aux patrons observés chez les plantes. Ces résultats ont alimenté une réflexion sur le potentiel et les perspectives, mais aussi sur les limitations des approches reposant sur le séquençage à haut-débit en écologie microbienne. / Coastal dunes provide several key ecosystem services, such as erosion mitigation and protection of the littoral by forming a barrier against wind and wave action. These ecosystems also importantly contribute to water filtering, groundwater replenishment, maintenance of biodiversity, and have a cultural, aesthetic and recreational importance. Dune ecosystems are highly dynamic and characterized by stark ecological successional gradients. The sequence of plant communities along the gradient extends from upper beach to the foredune stabilized by pioneer species such as beach grass, which facilitates the establishment of other herbs, shrubs and eventually, trees. Plant growth and survival can be limited by environmental factors such as wind, salinity, drought and nutrient deficiency, and is therefore strongly linked to the presence of soil microorganisms. Soil fungi in particular are important plant symbionts and major regulators of organic matter decomposition, nutrient cycling and soil structure. Hence, they are key drivers of soil and vegetation dynamics, as well as important contributors to dune stabilisation. Still, the diversity and structure of soil fungal communities, as well as the mechanisms responsible for their ecological dynamic, remain incompletely understood. In this thesis, I aimed to characterize fungal communities along a successional and edaphic gradient in a coastal dune in order to improve our understanding of soil dynamics in sand dunes ecosystems. I performed a comprehensive sampling of soils and aboveground vegetation at over 80 sites on a relic foredune plain. Soil fungi were characterized using high-throughput sequencing. A general description of soil fungal communities across dune zones was produced and, in addition to a taxonomic description, I assigned putative roles to all fungal genera to determine how variations in fungal community can be translated in functional changes. I recorded high level of fungal diversity (over 3400 operational taxonomic units) and described distinct communities along the successional and edaphic gradient. These results demonstrated the presence of taxonomically and functionally diverse communities across the dune sequence, including in the barren foredunes. I also investigated the links between plant and fungal communities across the edaphic and successional gradient. These results showed a clear increase in plant species richness, as well as in the diversity of nutrient-acquisition strategies (belowground trait related to plant nutrition: arbuscular mycorrhizal, ectomycorrhizal, ericoid mycorrhizal, nitrogen-fixing or unspecialized). I also found a very strong correlation between aboveground vegetation and soil fungal communities, which both responded to soil physicochemical properties. Soil pH importantly shaped plant and fungal communities, and could act as an important environmental filter along this relic foredune plain. The coordinated changes in soil microbial and plant communities highlight the importance of aboveground-belowground linkages and of positive biotic interactions during ecological succession in nutrient-poor environments. Finally, I compared the ectomycorrhizal fungal communities associated with four co-occuring tree species in the forested zone of the relic foredune plain. High ectomycorrhizal fungal richness was observed across the four hosts, with a total of 200 ectomycorrhizal operational taxonomic units, mainly belonging to the Agaricomycetes. Network analysis did not detect modules (i.e. subgroups of interacting species), indicating a low level of specificity in these ectomycorrhizal associations. In addition, there were no differences in ectomycorrhizal diversity or community structure among the four tree species. To conclude, I was able to describe diverse communities and distinct community structures across the dune sequence, for both plants and fungi. Succession however seemed less pronounced in fungal communities compared to patterns observed in plants. These results fueled a reflection on the potential and perspectives, as well as the limitations, of high-throughput sequencing approaches in the field of microbial ecology.

Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this dissertation were to characterize and examine the fungal and bacterial communities associated with EcM mats in old-growth forests of the H.J. Andrews Experimental Forest located in the Oregon Cascades. Additionally, this work assessed the application of traditional, emerging, and novel molecular sampling techniques for determining microbial communities of environmental samples. This research investigated the microbial communities associated with two common EcM mat genera found in old-growth Douglas fir stands in the Pacific Northwest; Piloderma (Atheliales, Basidiomycota) and Ramaria (Gomphales, Basidiomycota). Soil samples were collected from Piloderma and Ramaria mats and surrounding non- mat soil for molecular analysis of nucleic acids. First, a comparative study was conducted to determine the most appropriate rDNA molecular sampling technique for microbial community characterization. Two next-generation sequencing methods, Roche 454 pyrosequencing and Illumina-based environmental sequencing, the latter developed by the author, were compared to a more traditional sequencing approach, i.e., Sanger sequencing of clone libraries. These findings informed the subsequent sampling of the fungal ITS and bacterial 16S rDNA fragment with 454 pyrosequencing to determine the microbial communities within mat and non-mat soils. Second, this work utilized a pyrosequencing approach to explore fungal community structure in EcM mat and non-mat soils. This work concluded that differences in microbial communities do exist between Piloderma mat, Ramaria mat, and non-mat soils, but the differences are largely quantitative with relatively few distinct taxonomic shifts in microbial constituents. Piloderma, Ramaria and Russula, in addition to being the dominant taxa found on mycorrhizal root tips, were found to be the most abundant taxa in bulk soils within their respective mat types or non-mat sample. The background fungal communities within the EcM mats in this study exhibited considerable taxonomic overlap with the exception of Piloderma vs. non-mat comparisons; Russula species dominated nonmat soils but tended to be excluded or significantly underrepresented in Piloderma mats. Lastly, this study explored the bacterial communities associated with Piloderma and Ramaria mats using lower- coverage 454-Jr pyrosequencing. Bacterial communities exhibited significant structure as a function of mat-type, soil horizon and pH, but this finding should be interpreted with respect to the nonrandom distribution of Piloderma-mats in the O- horizon and the Ramaria-mats in the A-horizon, and the tendancy for EcM mats to be more acidic than surrounding soils. Nonetheless, the total microbial (bacterial and fungal) community was typically dominated by the mat-forming taxa, or Russula, in the case of non-mat soils. While the presence of Piloderma mats did enrich or restrict some bacterial groups, soil pH was also found to be a significant driver of bacterial richness and taxonomic diversity. Fungal and bacterial richness were also found to be positively related to one another, regardless of soil horizon or EcM mat type. This work, taken together, contributes to the understanding of hyperdiversity and heterogeneity of microbial communities of temperate forest soils and highlights the potential for fungal and bacterial communities to be influenced by the presence of EcM mats. / Graduation date: 2012

From the Proceedings of the 1976 Meetings of the Arizona Section - American Water Resources Assn. and the Hydrology Section - Arizona Academy of Science - April 29-May 1, 1976, Tucson, Arizona / The general hydrologic characteristics, selected climatic factors, and soil properties of the high-elevation grasslands are compared to the surrounding forest. Evidence shows that water yield could be increased by 1-1/2 to 2 inches if snow could be held where it falls. It may be possible to establish tree windbreaks in the grassland by altering the microclimate during establishment, and introducing mycorrhiza with the planted seedlings. This conclusion is supported by good survival in a 2-year planting trial.