A molecular analysis of the interactions of escherichia coli and macrophages

Escherichia coli (E.coli) is a diverse bacterial species that primarily forms a beneficial symbiotic relationship with the host in the human lower gastrointestinal track (GIT), however it can also be pathogenic in this environment. Furthermore, some strains can diverge from the GIT and occupy niches such as the urinary tract. In all these environments, E. coli interacts with the immune system and macrophages represent the front line of the innate immune system. In this study we characterise the immune response by macrophages to E. coli infection. It was shown that E. coli broadly provoke a similar cytokine response during macrophages infection and furthermore are degraded primarily by the phagocytosis pathway. Recently a new group of E. coli called Adherent Invasive Escherichia coli (AIEC) has been described. AIEC are present in the guts of Crohn’s disease (CD) patients at a higher frequency than in healthy patients. AIEC can replicate in macrophages but the mechanism for this is not fully understood. The processing of AIEC by macrophages was investigated and it was shown that AIEC only replicated in permissive macrophages. Furthermore, even in a permissive macrophages AIEC are trafficked through macrophages in a similar manner to commensal E. coli. This supports the hypothesis that AIEC are highly similar to commensal E. coli and only cause pathogenicity when present in the permissive environment of the gut of CD patients. Replication in macrophages requires functioning metabolic pathways and it was identified that glycolysis is important for AIEC survival in macrophages. AIEC mutants without a fully functioning glycolysis pathway induced less IL-1β cytokine release from macrophages than wild type strain suggesting that metabolism plays a role in inflammasome activation. Furthermore, AIEC mutants that could not produce the glycolytic end product acetate induced significantly reduced IL-1β release during infection. This suggest that the acetate molecule or a phenotypic effect of its production may be a driver of IL-1β release from AIEC infected macrophages. The interaction of uropathogenic E. coli (UPEC) with macrophages was also investigated. UPEC induced very high levels of cytotoxicity in human macrophages which was shown to be dependent on the production of the pore forming toxin α-hemolysin. However, UPEC did not induced high levels of cytotoxicity in murine macrophages suggesting there are species specific sensitivity to α-hemolysin that should be considered when studying UPEC pathogenicity in murine models.

Elevated CO2 affects predator-prey interactions through altered performance

Recent research has shown that exposure to elevated carbon dioxide (CO2) affects how fishes perceive their environment, affecting behavioral and cognitive processes leading to increased prey mortality. However, it is unclear if increased mortality results from changes in the dynamics of predator-prey interactions or due to prey increasing activity levels. Here we demonstrate that ocean pCO2 projected to occur by 2100 significantly effects the interactions of a predator-prey pair of common reef fish: the planktivorous damselfish Pomacentrus amboinensis and the piscivorous dottyback Pseudochromis fuscus. Prey exposed to elevated CO2 (880 µatm) or a present-day control (440 µatm) interacted with similarly exposed predators in a cross-factored design. Predators had the lowest capture success when exposed to elevated CO2 and interacting with prey exposed to present-day CO2. Prey exposed to elevated CO2 had reduced escape distances and longer reaction distances compared to prey exposed to present-day CO2 conditions, but this was dependent on whether the prey was paired with a CO2 exposed predator or not. This suggests that the dynamics of predator-prey interactions under future CO2 environments will depend on the extent to which the interacting species are affected and can adapt to the adverse effects of elevated CO2.

Collection of aboveground community and species-specific plant biomass from the Jena Experiment (time series since 2002).

This data set comprises time series of aboveground community plant biomass (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of several experiments at the field site of a large grassland biodiversity experiment (the Jena Experiment; see further details below). Aboveground community biomass was normally harvested twice a year just prior to mowing (during peak standing biomass twice a year, generally in May and August; in 2002 only once in September) on all experimental plots in the Jena Experiment. This was done by clipping the vegetation at 3 cm above ground in up to four rectangles of 0.2 x 0.5 m per large plot. The location of these rectangles was assigned by random selection of new coordinates every year within the core area of the plots. The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The data for individual samples and the mean over samples for the biomass measures on the community level are given. Overall, analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity-productivity relationship. The following series of datasets are contained in this collection: 1. Plant biomass form the Main Experiment: In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). 2. Plant biomass from the Dominance Experiment: In the Dominance Experiment, 206 grassland plots of 3.5 x 3.5 m were established from a pool of 9 species that can be dominant in semi-natural grassland communities of the study region. In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 3, 4, 6, and 9 species). 3. Plant biomass from the monoculture plots: In the monoculture plots the sown plant community contains only a single species per plot and this species is a different one for each plot. Which species has been sown in which plot is stated in the plot information table for monocultures (see further details below). The monoculture plots of 3.5 x 3.5 m were established for all of the 60 plant species of the Jena Experiment species pool with two replicates per species like the other experiments in May 2002. All plots were maintained by bi-annual weeding and mowing.

Aboveground community and species-specific plant biomass from the Jena Experiment (Dominance Experiment, year 2008)

This data set contains aboveground community plant biomass (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of the dominance experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the dominance experiment, 206 grassland plots of 3.5 x 3.5 m were established from a pool of 9 plant species that can be dominant in semi-natural grassland communities of the study region. In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 3, 4, 6, and 9 species). Plots were maintained by bi-annual weeding and mowing. Aboveground community biomass was harvested twice in May and August 2008 on all experimental plots of the dominance experiment. This was done by clipping the vegetation at 3 cm above ground in two rectangles of 0.2 x 0.5 m per experimental plot. The location of these rectangles was assigned by random selection of coordinates within the central area of the plots (excluding an outer edge of 50cm). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material, and remaining plant material that could not be assigned to any category. All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The mean of both samples per plot and the individual measurements are provided in the data file. Overall, analyses of the community biomass data have identified species richness and the presence of particular species as an important driver of a positive biodiversity-productivity relationship.

Aboveground community and species-specific plant biomass from the Jena Experiment (Main Experiment, year 2009)

This data set contains aboveground community biomass in 2009 (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Aboveground community biomass was harvested twice in 2009 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the main experiment. This was done by clipping the vegetation at 3 cm above ground in three rectangles of 0.2 x 0.5 m per large plot. The location of these rectangles was assigned prior to each harvest by random selection of coordinates within the core area of the plots (i.e. the central 10 x 15 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The data for individual samples and the mean over samples for all biomass measures are given. Overall, analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity-productivity relationship.

Aboveground community and species-specific plant biomass from the Jena Experiment (Main Experiment, year 2010)

This data set contains aboveground community biomass in 2010 (Sown plant community, Weed plant community, Dead plant material, and Unidentified plant material; all measured in biomass as dry weight) and species-specific biomass from the sown species of the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Aboveground community biomass was harvested twice in 2010 just prior to mowing (during peak standing biomass in early June and in late August) on all experimental plots of the main experiment. This was done by clipping the vegetation at 3 cm above ground in two rectangles of 0.2 x 0.5 m per large plot. The location of these rectangles was assigned prior to each harvest by random selection of coordinates within the core area of the plots (i.e. the central 10 x 15 m). The positions of the rectangles within plots were identical for all plots. The harvested biomass was sorted into categories: individual species for the sown plant species, weed plant species (species not sown at the particular plot), detached dead plant material (i.e., dead plant material in the data file), and remaining plant material that could not be assigned to any category (i.e., unidentified plant material in the data file). All biomass was dried to constant weight (70°C, >= 48 h) and weighed. Sown plant community biomass was calculated as the sum of the biomass of the individual sown species. The data for individual samples and the mean over samples for all biomass measures are given. Overall, analyses of the community biomass data have identified species richness as well as functional group composition as important drivers of a positive biodiversity-productivity relationship.

Anthropogenic noise affects vocal interactions

Animal communication plays a crucial role in many species, and it involves a sender producing a signal and a receiver responding to that signal. The shape of a signal is determined by selection pressures acting upon it. One factor that exerts selection on acoustic signals is the acoustic environment through which the signal is transmitted. Recent experimental studies clearly show that senders adjust their signals in response to increased levels of anthropogenic noise. However, to understand how noise affects the whole process of communication, it is vital to know how noise affects the receiver’s response during vocal interactions. Therefore, we experimentally manipulated ambient noise levels to expose male European robins (Erithacus rubecula) to two playback treatments consisting of the same song: one with noise and another one without noise. We found that males responding to a conspecific in a noise polluted environment increased minimum frequency and decreased song complexity and song duration. Thus, we show that the whole process of communication is affected by noise, not just the behaviour of the sender.

La face cachée de la dune : communautés fongiques du sol: dynamique, succession et interactions avec la végétation d’un écosystème dunaire côtier aux Îles de la Madeleine, Qc

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.

Predators on private land: broad-scale socioeconomic interactions influence large predator management

The proliferation of private land conservation areas (PLCAs) is placing increasing pressure on conservation authorities to effectively regulate their ecological management. Many PLCAs depend on tourism for income, and charismatic large mammal species are considered important for attracting international visitors. Broad-scale socioeconomic factors therefore have the potential to drive fine-scale ecological management, creating a systemic scale mismatch that can reduce long-term sustainability in cases where economic and conservation objectives are not perfectly aligned. We assessed the socioeconomic drivers and outcomes of large predator management on 71 PLCAs in South Africa. Owners of PLCAs that are stocking free-roaming large predators identified revenue generation as influencing most or all of their management decisions, and rated profit generation as a more important objective than did the owners of PLCAs that did not stock large predators. Ecotourism revenue increased with increasing lion (Panthera leo) density, which created a potential economic incentive for stocking lion at high densities. Despite this potential mismatch between economic and ecological objectives, lion densities were sustainable relative to available prey. Regional-scale policy guidelines for free-roaming lion management were ecologically sound. By contrast, policy guidelines underestimated the area required to sustain cheetah (Acinonyx jubatus), which occurred at unsustainable densities relative to available prey. Evidence of predator overstocking included predator diet supplementation and frequent reintroduction of game. We conclude that effective facilitation of conservation on private land requires consideration of the strong and not necessarily beneficial multiscale socioeconomic factors that influence private land management.

Bat-plant pollination interactions in southern Thailand

The overwhelming majority of flowering plant species depend on animals for pollination, and such pollinators are important for the reproductive success of many economically and environmentally important plant species. Yet pollinators in the Old World tropics are relatively understudied, particularly paleotropical nectarivorous bats (Pteropodidae), and much is unknown about their interactions with night-blooming plant species. To better understand these bat-plant pollination interactions, I conducted fieldwork in southern Thailand for a total of 20 months, spread across three years. I examined the foraging times of pteropodid bat species (Chapter 1), and found that strictly nectarivorous species foraged earlier, and for a shorter duration, than primarily frugivorous species. I also studied year-long foraging patterns of pteropodid bats to determine how different species track floral resources across seasons (Chapter 2). Larger species capable of flying long distances switched diets seasonally to forage on the most abundant floral species, while smaller species foraged throughout the year on nearby plant species that were low-rewarding but highly reliable. To determine which pteropodid species are potentially important pollinators, I quantified the frequency and effectiveness of their visits to six common bat-pollinated plant taxa for an entire year (Chapter 3). The three strictly nectarivorous species were responsible for almost all pollination, but pollinator importance of each bat species varied across plant species. I further examined the long-term reliability of these pollinators (Chapter 4), and found that pollinator importance values were consistent across the three study years. Lastly, I explored mechanisms that reduce interspecific pollen transfer among bat-pollinated plants, despite having shared pollinators. Using a flight cage experiment, I demonstrated that these plant species deposit pollen on different areas of the bat’s body (mechanical partitioning), resulting in greater pollen transfer between conspecific flowers than heterospecific flowers (Chapter 5). Additionally, while I observed ecological and phenological overlap among flowering plant species, pollinators exhibited high floral constancy within a night, resulting in strong ethological separation (Chapter 6). Collectively, these findings illustrate the importance of understudied Old World bat pollinators within a mixed agricultural-forest system, and their strong, interdependent interactions with bat-pollinated plant species within a night, across seasons, and across years.

An examination of the usefulness of single-species biomass models for the management of Lake Victoria fisheries

Nile perch (Lates niloticus), tilapia (Oreochromis spp), dagaa (Rastrineobola argentea, silver cyprinid), and haplochromines (Tribe Haplochromini) form the backbone of the commercial fishery on Lake Victoria. These fish stocks account for about 70% of the total catch in the three riparian states Uganda, Kenya, and Tanzania. The lake fisheries have been poorly managed, in part due to inadequate scientific analysis and management advice. The overall objective of this project was to model the stocks of the commercial fisheries of Lake Victoria with the view of determining reference points and current stock status. The Schaefer biomass model was fitted to available data for each stock (starting in the 1960s or later) in the form of landings, catch per unit effort, acoustic survey indices, and trawl survey indices. In most cases, the Schaefer model did not fit all data components very well, but attempts were made to find the best model for each stock. When the model was fitted to the Nile perch data starting from 1996, the estimated current biomass is 654 kt (95% CI 466–763); below the optimum of 692 kt and current harvest rate is 38% (33–73%), close to the optimum of 35%. At best, these can be used as tentative guidelines for the management of these fisheries. The results indicate that there have been strong multispecies interactions in the lake ecosystem. The findings from our study can be used as a baseline reference for future studies using more complex models, which could take these multispecies interactions into account.

Agonistic interactions elicit rapid changes in brain nonapeptide levels in zebrafish

The teleost fish nonapeptides, arginine vasotocin (AVT) and isotocin (IT), have been implicated in the regulation of social behavior. These peptides are expected to be involved in acute and transient changes in social context, in order to be efficient in modulating the expression of social behavior according to changes in the social environment. Here we tested the hypothesis that short-term social interactions are related to changes in the level of both nonapeptides across different brain regions. For this purpose we exposed male zebrafish to two types of social interactions: (1) real opponent interactions, from which a Winner and a Loser emerged; and (2) mirror-elicited interactions, that produced individuals that did not experience a change in social status despite expressing similar levels of aggressive behavior to those of participants in real-opponent fights. Non-interacting individuals were used as a reference group. Each social phenotype (i.e. Winners, Losers, Mirror-fighters) presented a specific brain profile of nonapeptides when compared to the reference group. Moreover, the comparison between the different social phenotypes allowed to address the specific aspects of the interaction (e.g. assessment of opponent aggressive behavior vs. self-assessment of expressed aggressive behavior) that are linked with neuropeptide responses. Overall, agonistic interactions seem to be more associated with the changes in brain AVT than IT, which highlights the preferential role of AVT in the regulation of aggressive behavior already described for other species.

Report of the Workshop on Growth-increment Chronologies in Marine Fish: climate-ecosystem interactions in the North Atlantic 2 (WKGIC2). 18-22 April 2016 Esporles, Mallorca, Spain

Over the past several decades, thousands of otoliths, bivalve shells, and scales have been collected for the purposes of age determination and remain archived in European and North American fisheries laboratories. Advances in digital imaging and computer software combined with techniques developed by tree-ring scientists provide a means by which to extract additional levels of information in these calcified structures and generate annually resolved (one value per year), multidecadal time-series of population-level growth anomalies. Chemical and isotopic properties may also be extracted to provide additional information regarding the environmental conditions these organisms experienced.Given that they are exactly placed in time, chronologies can be directly compared to instrumental climate records, chronologies from other regions or species, or time-seriesof other biological phenomena. In this way, chronologies may be used to reconstruct historical ranges of environmental variability, identify climatic drivers of growth, establish linkages within and among species, and generate ecosystem-level indicators. Following the first workshop in Hamburg, Germany, in December 2014, the second workshop on Growth increment Chronologies in Marine Fish: climate-ecosystem interactions in the North Atlantic (WKGIC2) met at the Mediterranean Institute for Advanced Studies headquarters in Esporles, Spain, on 18–22 April 2016, chaired by Bryan Black (USA) and Christoph Stransky (Germany).Thirty-six participants from fifteen different countries attended. Objectives were to i) review the applications of chronologies developed from growth-increment widths in the hard parts (otoliths, shells, scales) of marine fish and bivalve species ii) review the fundamentals of crossdating and chronology development, iii) discuss assumptions and limitations of these approaches, iv) measure otolith growth-increment widths in image analysis software, v) learn software to statistically check increment dating accuracy, vi) generate a growth increment chronology and relate it to climate indices, and vii) initiate cooperative projects or training exercises to commence after the workshop.The workshop began with an overview of tree-ring techniques of chronology development, including a hands-on exercise in cross dating. Next, we discussed the applications of fish and bivalve biochronologies and the range of issues that could be addressed. We then reviewed key assumptions and limitations, especially those associated with short-lived species for which there are numerous and extensive otolith archives in European fisheries labs. Next, participants were provided with images of European plaice otoliths from the North Sea and taught to measure increment widths in image analysis software. Upon completion of measurements, techniques of chronology development were discussed and contrasted to those that have been applied for long-lived species. Plaice growth time-series were then related to environmental variability using the KNMI Climate Explorer. Finally, potential future collaborations and funding opportunities were discussed, and there was a clear desire to meet again to compare various statistical techniques for chronology development using a range existing fish, bivalve, and tree growth-increment datasets. Overall, we hope to increase the use of these techniques, and over the long term, develop networks of biochronologies for integrative analyses of ecosystem functioning and relationships to long-term climate variability and fishing pressure.

La face cachée de la dune : communautés fongiques du sol: dynamique, succession et interactions avec la végétation d’un écosystème dunaire côtier aux Îles de la Madeleine, Qc

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.