Master of Science / Department of Agronomy / Charles W. Rice / Maize (Zea mays L.) is a major staple crop whose wild ancestor was domesticated about 9,000 years ago (Beadle, 1939). Long-term breeding for more desirable traits ultimately resulted in the maize we see today. This long-term breeding likely impacted the processes within the rhizosphere of maize, however, to what extent is not well understood. This study examined the microbial communities between an inbred maize line (B73), a hybrid of two isogenic lines (B73xMo17), and two genetically modified maize hybrids (DKC63-55RIB and DKC64-69RIB) to determine if the plant’s ability to attract beneficial microbes changed with breeding. The hypothesis was that the isogenic cultivar forms better relationships with bacteria and fungi compared to the newer cultivars, especially in low P soil. It was also expected that the greater the difference between the cultivars the more distinct their soil microbiome. To test these hypotheses, experiments were conducted under greenhouse and field conditions. Analyses consisted of root staining to test symbiotic relationships, phospholipid fatty acid analysis (PLFA) for microbial communities, total plant and root biomass, and nutrient content to understand plant responses. Based on the field results, there was no impact on root and shoot biomass and nutrient content by differences in cultivar. Differences in cultivar did impact arbuscular mycorrhizal fungi (AMF) colonization, which decreased over time and depth for all. Soil AMF also saw a significant effect by cultivar. Other microbial groups were not impacted by cultivar, were greatest in the control, and decreased over time. Greenhouse results showed a cultivar by time interaction for root and shoot biomass. Soil P also impacted shoot biomass, but not root biomass. Shoot nutrient content was greater in high P soil, while roots only saw an impact for root P. No cultivar effect was found for soil microbial groups except for fungi, while all microbial groups were reduced in the control soil. Most soil microbial groups were also impacted by soil P as indicated by reduced concentrations in low P soil. AMF was the only microbial group that was not negatively impacted by limited soil P. In addition, all soil microbial groups increased over time, although fungi saw a decrease at R1. No significances were observed for percent AMF colonization.

Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria, Proteobacteria, Planctomycetes, Verrucomicrobia, and Euryarchaeota (Spearman's rank correlation [r(s)] = >0.81; false-discovery rate [q] = <= 0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

The role of individual soil microorganisms changes over the course of a plant's life - microorganisms that have no discernable role at one developmental stage may affect the plant later in its growth. Traditional analysis of the soil microbiome, which has focused principally on the relative abundances (RA) of individual organisms, may be incomplete, as underlying differences in population size cannot be addressed. We conducted a metagenomic analysis of soil microorganisms from various maize (Zea mays L.) fields at two depths, accompanied by crop yield components, to provide insight into influences of edaphic microbes on maize productivity under commercial maize production systems in Missouri. This study assesses the influence of fungi and bacteria, not only in terms of RA, but also in their estimated absolute abundances (EAA), derived by combining the results of Illumina HiSeq sequencing data and phospholipid fatty acid abundance data. Significant interactions were identified between maize yield components and soil microbes at critical developmental states. Most interactions between fungi and yield components were negative, with notable exceptions. Bacterial interactions were more complex, with most interactions during early ear development identified as positive, and most interactions during tasseling identified as negative. In addition to the effects that microbial populations have on yield, plant populations reciprocally changed the microbial community. Plant developmental state was the greatest predictor of bacteria, with the microbial communities present during the active growing season being most similar to each other, whereas the preplant microbiome and post-reproductive microbiome being most similar to each other. Fungal communities were primarily dependent on location.

Soil microorganisms have a variety of beneficial and deleterious effects on plants, impacting such processes as plant growth, soil nutrient cycling, crop yield, disease resistance and tolerance to an array of biotic and abiotic stressors. The disruption of soil microbial community structures, particularly when beneficial soil biota are altered, has been shown to reduce crop yield and leave plants susceptible to disease. Long-term disruption of microbial communities may occur with repeated fumigation, being the application of gaseous pesticides, in agricultural soils. For this reason, we characterized bacterial, fungal, oomycete and nematode populations in paired fumigated and nonfumigated potato fields located in Idaho, Oregon, Washington and Minnesota. Samples were taken at three distinct timepoints: one before a fall fumigation event and two others at important stages in potato production, row closure and vine death. Soil biota populations were assessed by targeting the 16S, 18S and ITS1 gene regions. FunGuild, a database capable of guild and trophic assignment of fungal lineages, was used to sort fungal OTUs in different trophic modes. Fungal analyses indicated an increase in relative abundances of saprotrophic fungal populations and a decrease in pathotrophic fungal populations, both during row closure. Principally, the fungal genera of Humicola and Mortierella were responsible for the increase of saprotrophs while Alternaria decreased the most for pathotrophs. Other fungi occupying multiple trophic modes, such as Fusarium, also decreased during row closure. We found that fumigation treatments, in combination with various pesticide and fertilizer applications, alter both alpha- and beta- bacterial soil diversity although certain treatments, i.e. chloropicrin, may alter bacterial populations more than other treatment types such as metam-sodium. Nematode populations were likewise distinct at each location with soils from Boardman, OR, Minidoka, ID and Pine Point, MN with these having higher levels of nematodes associated with better soil health, i.e. Dorylaimidae. Conversely, nematodes associated with plant pathogenesis were found in higher relative abundances at Minidoka, ID and Quincy, WA. In this study, we characterize the populations of bacteria, fungi, oomycetes and nematodes with an emphasis on fungal taxa. We found that relative abundances of fungal trophic modes vary temporally. Additionally, we catalogue several other high abundance taxa with seasonal differential abundances whose functional capacity in potatoes remain uncharacterized.

Soils harbor a huge diversity of microorganisms, which are dominated by bacteria and fungi. These soil microorganisms, collectively termed as the soil microbiome, are major contributors to soil biodiversity and play essential roles in soil functions (e.g. soil fertility and plant nutrition, organic matter degradation and nutrient cycling, and soil formation). Therefore, many studies in recent decades have explored soil microbial diversity in order to unravel driving forces of its variations. Hence, this thesis reports on spatial and temporal variations of the soil microbiome in response to site specificities, i.e. local climate as well as soil physico-chemistry, and host tree parameters. To avoid effects of intraspecific genetic variations, the pedunculate oak clone DF159 (Quercus robur L.) generated by the project TrophinOak-PhytOakmeter of the Soil Ecology Department at the Helmholtz Centre for Environmental Research (UFZ) was used as phytometer system. In the PhytOakmeter project of which this thesis is a part, saplings regenerated from microcuttings of DF159 were out-planted in grassland, forest and urban field sites in Central Germany and along a European North-South transect. The overall goal of the project is to analyze how the clone adapts to and performs under different regional climatic contexts and changing environment conditions. Pedunculate oak was chosen as a model tree species because it is engaged in highly complex and diverse multitrophic interactions, including soil microorganisms. Q. robur displays an endogenous rhythmic growth with alternating growing flushes in shoot and root, which can be repeated two to four times along a vegetation period. These alternating flushes have been shown to impact on variations of biological activities in soil zones close to the tree roots. Based on the above-described background, the current PhD study investigated changes in the soil microbial communities associated to the pedunculate oak phytometer outplanted in grassland sites at two different spatial scales: (1) the local scale by comparing the soil microbiomes associated to the phytometer in sites located within a close geographic space of Central Germany with similar climatic conditions; and (2) continental scale by making a similar comparison among sites along a European North-South transect, which encompasses a wide range of climatic and soil physico-chemical conditions. Moreover, temporal scale was considered, whereby the variability of the microbiomes intra-annually along a vegetation period was analyzed. Soil samples were taken not only in the tree root zone (RZ), i.e. soil zone containing living roots of the tree, but also in the tree root-free zone (RFZ), i.e. soil zone out of reach of any tree roots, but within the same field plot, to access also the local microbial pools. The analyses used a PCR-based Illumina MiSeq amplicon sequencing approach targeting bacteria and fungi, to assess their diversity, community structure and functionality after assignment of their OTUs to functional groups. In addition to Chapter 1, which introduces the whole work of this PhD research, the findings are presented within Chapters 2-4, of which two studies were already published in international peer-reviewed journals, while another study was published as a conference paper. The thesis is closed by the synopsis Chapter 5 that integrates discussion of all the publication chapters together with an outlook section. Chapter 2 “Tree root zone microbiome: exploring the magnitude of environmental conditions and host tree impact” published in Frontiers in Microbiology investigates the relative contribution of abiotic environmental and host tree parameters among four sites characterized by homogeneous climatic conditions in Central Germany, two years after the tree out-plant. We first compared at each field site the composition of the bacterial and fungal communities between the RZ of the oak clone, called PhytOakmeter in this chapter, and the tree RFZ. The chapter further evaluates the diversity and structure of the microbial communities within the tree RZ among the sites. The results revealed different microbial compositions between the tree RZ and RFZ, whereby the tree RZ-associated microbiome included numerous ectomycorrhizal fungi of the genera Hebeloma, Exophiala, Scleroderma, Tomentella, Trichophaea, and Tuber. This quick recruitment of specific beneficial microbial taxa from the local microbial pool seems to be among the tree strategies to acclimate to local site conditions. However, the overall tree contribution to shape soil microbial communities was lower than the impact of abiotic environmental parameters. The results revealed also a similar level of microbial diversity within the tree RZ among the sites for both the bacteria and fungi, an outcome attributed to the homogeneous climatic conditions within the sites and the common genetic identity of the host trees. In contrast, structure of the microbial communities was site-specific. Chapter 3 “Balance between geographic, soil, and host tree parameters to shape soil microbiomes associated to clonal oak varies across soil zones along a European North-South transect” published in Environmental Microbiology, also examines the relative impact of geographic, soil physico-chemical, and pedunculate oak clone parameters on the variability of the soil microbiome, but at a larger spatial scale from Lapinjärvi (Finland) to Bordeaux (Southwestern France), which is characterized by a broad range of geographic and soil physico-chemical conditions. In addition to the tree RFZ total microbiome and the tree RZ total microbiome, this chapter introduces a new sub-microbiome called tree RZ affine microbiome. The latter was defined as a subset of the RZ bacteria and fungi, significantly enriched in this zone compared to the tree RFZ. The results demonstrated an interplay among abiotic environmental and host tree parameters in shaping bacterial and fungal communities of the tree RZ along the European transect. These parameters showed a descending order of magnitude of their impact on the tree RZ total microbiome: geographic > soil physico-chemical > host tree parameters. However, for the variability of the RZ affine microbiome alone, the impact of the abiotic environmental parameters decreased, while the tree influence was strongly increased, particularly for fungi. Another important result was the highest proportion of the tree RZ affine microbial OTUs shared among all four sites, which was here designated as the tree “core” microbiome. These bacteria and fungi with significant affinity to the host tree, and shared by all the sites because of their ability to cope with diverging environmental conditions across the transect, may be playing a crucial role in supporting the wide distribution of Q. robur across Europe. Interestingly, we found no members of the RZ affine microbiome to be exclusive of only one particular site. Chapter 4 “Temporal changes and alternating host tree root and shoot growth affect soil microbiomes” published in Proceedings as conference paper after “The 1st International Electronic Conference on Microbiology”, considers a temporal scale, and here the variability of the tree RZ and RFZ total microbiomes was analyzed along a vegetation period in two sites of Central Germany. The soil was sampled at different time points coinciding with the tree alternating root and shoot growth, and the fall senescence that concludes the vegetation period. The results show a directional change over time along a vegetation period for the bacterial communities. However, the fungal communities did not show such temporal changes; they rather displayed a fine spatial scale partitioning closely linked to host plant individuals. In addition to the effect of temporal succession, deeper analyses of the generated data set will enable us to specify the impact of the alternating root and shoot growth characteristic of the tree endogenous rhythmic growth in the near future. These further analyses will include for example zooming in the tree RZ affine microbiome and in individual microbial functional groups. The results presented in this thesis evidence the quick impact of pedunculate oak tree clone on the soil microbiome within a two-year time span after the tree out-plant. Also, to different extents, geographic, soil physico-chemical, and host tree concurrently shape the soil bacterial and fungal communities. This thesis shows different spatial and temporal responses to the abiotic environmental and tree parameters between the soil bacterial and fungal communities. The use of tree clonal phytometer to study the tree-related parameters on soil microbiomes was proved to be a promising tool, to unravel the hierarchy of different abiotic and biotic factors in shaping the soil microbiome associated to long live trees. Finally, this work represents a first step toward establishing a long term monitoring of the dynamics of soil microbiomes associated to trees, as a strategy to unravel how these microorganisms participate to the long term acclimation of these long live plants to diverse and changing environments.

Submitted by Caroline Nishisaka (csayurii@hotmail.com) on 2018-06-04T15:38:30Z No. of bitstreams: 2 Dissertação_Caroline_Sayuri_Nishisaka_UFSCar.pdf: 10342020 bytes, checksum: 83fe90894363834291d0f68de806c3ab (MD5) Carta comprovante da versao final de teses e dissertações.pdf: 204209 bytes, checksum: 74667e4b6b3923d66bce39462bb4538f (MD5) / Approved for entry into archive by Milena Rubi ( ri.bso@ufscar.br) on 2018-06-06T17:30:18Z (GMT) No. of bitstreams: 2 Dissertação_Caroline_Sayuri_Nishisaka_UFSCar.pdf: 10342020 bytes, checksum: 83fe90894363834291d0f68de806c3ab (MD5) Carta comprovante da versao final de teses e dissertações.pdf: 204209 bytes, checksum: 74667e4b6b3923d66bce39462bb4538f (MD5) / Approved for entry into archive by Milena Rubi ( ri.bso@ufscar.br) on 2018-06-06T17:30:45Z (GMT) No. of bitstreams: 2 Dissertação_Caroline_Sayuri_Nishisaka_UFSCar.pdf: 10342020 bytes, checksum: 83fe90894363834291d0f68de806c3ab (MD5) Carta comprovante da versao final de teses e dissertações.pdf: 204209 bytes, checksum: 74667e4b6b3923d66bce39462bb4538f (MD5) / Made available in DSpace on 2018-06-06T17:31:01Z (GMT). No. of bitstreams: 2 Dissertação_Caroline_Sayuri_Nishisaka_UFSCar.pdf: 10342020 bytes, checksum: 83fe90894363834291d0f68de806c3ab (MD5) Carta comprovante da versao final de teses e dissertações.pdf: 204209 bytes, checksum: 74667e4b6b3923d66bce39462bb4538f (MD5) Previous issue date: 2018-05-03 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Agriculture is responsible for 80% of nitrous oxide emissions on earth's atmosphere, the most potential greenhouse gas among the three main gases (CO2, CH4 and N2O). Citriculture and silviculture play an important role on Brazilian economics due to the high demand of orange and wood products for exportation. Thus, in order to get a better understand about the role of those cultures on N2O emission, this research aims to evaluate N2O emissions from Citrus sinensis and Eucalyptus spp. crops, adjacent forests of each agriculture field were used as control. Citrus and eucalyptus sites are located in Sorocaba and Salto de Pirapora municipality, both in the state of Sao Paulo, Brazil. In each agriculture field and adjacent forest, eight static chambers were randomly installed, and gas sample were collected during dry and wet region season. Soil samples were collected in each field of study from five random sampling points, for further physicochemical, molecular analysis and microcosm incubation. Gas samples were collected from microcosm after moisture adjustment in 70% of field capacity. All gas samples were analyzed by gas chromatography technique. The number of copies of genes related to denitrifying process (nirK, nirS e nosZ) was determined by quantitative real time PCR. Seasonality had significant (P<0.05) influence on N2O emission in field, and N2O fluxes in incubated soil. It was observed positive correlation among dissolved organic carbon (DOC) concentration on soil, soil and plant residue total carbon and nitrogen content and N2O emissions. High nirK, nirS and nosZ gene abundance was found on soil collected during wet season, comparing to those collected on dry season, in both field and microcosm, which was correlated with DOC content and soil moisture. However, there were not significant differences on genes abundance comparisons between cultivated soils and adjacent forests. In conclusion, the seasonality has influence in both N2O emission and denitrifying bacteria abundance present in citrus- and eucalyptus-cultivated soils, mainly through the effects on soil and plant residue physicochemical characteristics, especially those related to COD and soil moisture. / A agricultura é responsável por 80 % do óxido nitroso (N2O) emitido para a atmosfera terrestre, o qual é considerado, dentre os principais gases causadores do efeito estufa, aquele com maior potencial de aquecimento global. A citricultura e a silvicultura são culturas agrícolas que apresentam importante papel na economia brasileira, devido a alta demanda de exportação de produtos derivados da laranja e da madeira. A fim de entender como essas culturas influenciam na emissão do N2O, esse trabalho teve como objetivo avaliar as emissões de N2O a partir de solos cultivados com Citrus sinensis e Eucalyptus spp. Solos florestais adjacentes às áreas agrícolas foram utilizados como controle. As áreas cultivadas com citros e eucalipto estão localizadas nos municípios de Sorocaba e Salto de Pirapora, respectivamente, ambos no estado de São Paulo, Brasil. Em cada área agrícola e florestal, oito câmaras estáticas foram aleatoriamente instaladas e amostras de gases foram coletadas durante o período seco e úmido. Amostras de solo foram coletadas em cada área de estudo a partir de cinco pontos amostrais, as quais foram submetidas a análises físico-químicas, moleculares e incubação em microcosmo. Amostras de gases também foram coletadas a partir dos ensaios de incubação do solo em microcosmos após ajuste da umidade em 70 % da capacidade de campo. Todas as amostras de gases foram analisadas pela técnica de cromatografia gasosa. O número de cópias de genes relacionados com o processo de desnitrificação (nirK, nirS e nosZ) foi determinado por PCR quantitativo em tempo real. A sazonalidade mostrou efeito significativo (P<0,05) nas emissões de N2O em campo, e nos fluxos de N2O determinados a partir do solo incubado. Foi mostrada correlação positiva entre a concentração de carbono orgânico dissolvido (COD) no solo, o teor de carbono e nitrogênio total em solos e resíduos vegetais e as emissões de N2O. Maior abundância dos genes nirK, nirS e nosZ foi encontrada nas amostras de solo coletadas no período úmido em comparação com aquelas coletadas no período seco, tanto em campo como em microcosmo, a qual foi correlacionada com a concentração de COD e a umidade do solo. Contudo, não houve diferença significativa na abundância de tais genes quando comparadas amostras de solos cultivados e florestais adjacentes. Tomados conjuntamente, os resultados permitiram concluir que a sazonalidade influencia tanto a emissão de N2O quanto a abundância de bactérias desnitrificantes presentes em solos cultivados com citros e eucalipto, mediante, principalmente, os efeitos nas características físicas e químicas do solo e dos resíduos vegetais, especialmente aqueles relacionados com o COD e umidade do solo. / FAPESP: 2016/15289-4 / FAPESP: 2017/17441-0

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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.