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The microbial life in the soil is essential for providing a functioning habitat for plants to grow. A literature study was conducted to investigate the knowledge and science behind soil biology. The purpose of this study was to define what is soil health and how it is influenced by the soil microbial communities. The literature study concluded that the ability of soil biology to benefit plants includes a variety of aspects. Nutrient availability, soil structure and pest resistance are all greatly influenced by soil microbes.  To practically examine these theories, an experiment was conducted where Brandywine tomatoes where grown in three different scenarios. A commercial potting soil, Hasselfors ekojord, was used as substrate in all groups. In the control group (C) the plants were grown only in the substrate. In the second group (R), the seeds where treated with a microbial inoculum and then planted in the substrate. In the third group (RE), the same treatment as in R was done to the seeds and here, compost extract were also added to the RE group. The plants were grown in separate pots in a greenhouse and the growth rate was observed and documented as well as the total harvest. In the end of the growing season a chemical and biological analysis was done to the soil as well as a sap analysis on the leaves. The plant growth where similar among the groups although R and RE showed slightly higher growth rates in the later stages of the growing season. The harvested fruit was highest in C but not significantly. The microbial contents were high in all soils though more fungi communities in the RE and bacterial communities in C. The chemical analysis showed high nitrate concentrations in the leaves in C. In R and especially RE the nitrate conversion into amino acids and proteins where higher wish indicates that these groups are more resilient to pests like aphids. / Det mikrobiella livet i jorden är avgörande för att skapa en fungerande livsmiljö för växter. En litteraturstudie genomfördes för att undersöka nuvarande kunskap och vetenskap bakom markbiologi. Syftet med denna studie var att definiera markhälsa och hur den påverkas av det mikrobiella livet i jorden. Slutsatsen från denna litteraturstudie var att jordbiologins förmåga att gynna växter innefattar en rad olika aspekter. Näringstillgänglighet, markstruktur och skadedjursbeständighet påverkas starkt av jordmikrober.  För att praktiskt granska dessa teorier genomfördes ett experiment där Brandywine-tomater odlades i tre olika scenarier. En kommersiell plantjord, Hasselfors ekojord, användes som huvudsubstrat i alla grupper. I kontrollgruppen (C) odlades växterna endast i substratet. I den andra gruppen (R) behandlades frön med en mikrobiell ympning innan de såddes i substratet.I den tredje gruppen (RE) utfördes samma fröbehandling som i R och kompostextrakt tillsattes också till RE-gruppen. Växterna odlades i separata krukor i ett växthus och tillväxthastigheten observerades och dokumenterades liksom den totala skörden. I slutet av växtsäsongen gjordes en kemisk och biologisk analys av jorden samt en savanalys på bladen. Tillväxten var likartad bland grupperna även om R och RE visade något högre tillväxttakt i de senare stadierna av växtsäsongen. Skördad frukt per planta var högst i C, dock intesignifikant. Den mikrobiella koncentrationen var hög i alla jordar men mer svamporienterat i RE och bakterieorienterat i C. Den kemiska analysen visade högt nitratinnehåll i bladen i C. I R och särskilt i RE var nitratomvandlingen till aminosyror och proteiner högre vilket indikerar att dessa grupper är mer motståndskraftiga mot skadedjur så som bladlöss.

Fe biofortification of potato is a promising strategy to prevent Fe deficiency worldwide either through traditional breeding or biotechnological approaches. These approaches require the identification of candidate genes to uptake, transport and store Fe in potato tubers. We employed multiple approaches including SNP genotyping, QTL analysis, identifying genes orthologous to Arabidopsis ferrome, yeast complementation assay and genetic transformation to avoid the limitation from a single approach. We revealed several candidate genes potentially associated with potato plant Fe acquisition, PGSC0003DMG400024976 (metal transporter), PGSC0003DMG400013297 (oligopeptide transporter), PGSC0003DMG400021155 (IRT1) and IRTunannotated (an ortholog to the IRT gene that is not annotated in the potato genome). The microorganisms in the rhizosphere react intensely with the various metabolites released by plant roots in a variety of ways such as positive, negative, and neutral. These interactions can influence the uptake and transport of micronutrients in the plant roots. Therefore, the contribution of soil microorganisms in the rhizosphere to improve Fe supply of plants may play a key role in Fe biofortification, especially under real world field-based soil scenarios. We thus investigated rhizosphere microbial community diversity in Andean potato landraces to understand the role of plant-microbial interaction in potato Fe nutrient cycling. From the analysis of the high-throughput Illumina sequences of 16S and ITS region of ribosomal RNA gene, we found that both potato landraces with low and high Fe content in tubers and a landrace on which low or high Fe content fertilizer was applied to the leaf surface had large impacts on the rhizosphere fungal community composition. Indicator species analysis (ISA) indicated that Operational Taxonomic Units (OTUs) contributing most to these impacts were closely related to Eurotiomycetes and Leotiomycetes in the phylum Ascomycota, Glomeromycetes in the phylum Glomeromycota and Microbotryomycetes in the phylum Basidiomycota. Lots of species from these groups have been shown to regulate plant mineral nutrient cycling. Our research revealed potential candidate genes and fungal taxa involved in the potato plant Fe nutrient dynamics, which provides new insights into crop management and breeding strategies for sustainable Fe fortification in agricultural production. / Ph. D.

Early Mortality Syndrome (EMS) is a widespread bacterial infection of shrimp, attributed to pathogenic Vibrio parahaemolyticus strains (VP-EMS). This disease threatens aquaculture production and global food security. A valuable and alternative approach to using antibiotics for pathogen control, is the practice of incorporating direct-fed microbes (DFM) or probiotics. In order to evaluate the hypothesis that probiotics (specific strains of Bacillus subtilis spores) are able to provide shrimp, Litopenaeus vannamei, protection to the EMS disease, a pathogen growth model, disease challenge model, and probiotic feed coating methodologies were developed and refined, allowing independent shrimp probiotic trials to be piloted. A single probiotic strain of Bacillus subtilis: O14VRQ and a blend of Bacillus subtilis strains: Plus10, were evaluated as feed additives or as water additions, for their efficacy. Accordingly, two independent trials were conducted in which shrimp were fed daily with a probiotic-coated feed for seven days, before a challenge with VP-EMS. Each trial consisted of a negative control (no VP-EMS exposure, no probiotic) and positive control (VP-EMS exposure, no probiotic), with five additional probiotic treatment groups, which were fed and exposed to VP-EMS in the same manner as the positive control. Shrimp were observed for clinical signs of disease after the initial exposure and were continuously exposed every 24 hours until 50% of the population remained in the positive control treatment. Both probiotics studied were shown to significantly (p < 0.05) improve shrimp survival. Overall the data presented in this work demonstrates that probiotic prophylaxis is reliant upon probiotic dose, regardless of application. / Master of Science in Life Sciences / Aquaculture is one of the fastest growing agricultural sectors in the world allowing it to greatly contribute to global food security. Seafood products are known for their excellent health benefits, providing good sources of protein, fatty acids, and vitamins. However, the animals raised in this industry, like in many facets of animal agriculture, are susceptible to disease. Diseases can be costly to treat and if no treatment exists, can be detrimental to farms, especially to highly valued species such as shrimp. Traditionally, many diseases have been treated with antibiotics, however this can promote the growth of antibiotic resistant bacteria, which is a public health concern especially when involving animals fit for human consumption. An alternative to this approach is administering probiotics or beneficial bacteria to these animals. When incorporated with feed or applied to water, these beneficial bacteria can prevent diseases and help promote the growth of healthy animals. Two novel probiotics were fed to shrimp, before exposing them to the bacteria, Vibrio parahaemolyticus, which causes Early Mortality Syndrome, and is responsible for annual shrimp losses of more than $1 billion USD. Signs of this disease and survival were observed to assess if this probiotic could provide protection against this bacterium. Results from these studies show that these probiotics were capable of offering protection to shrimp when they were fed or introduced into tank water in high concentrations. Such probiotic applications could have beneficial effects on intensive shrimp aquaculture and help prevent this disease.

Soil organic matter (SOM) is a critical biogeochemical pool that can be managed as part of global efforts to conserve nutrients and enhance carbon (C) sequestration. But reliably increasing SOM has proven difficult because most of the organic matter that enters soil as plant litter and organic amendments (i.e., compost, manure) is susceptible to decomposition by soil microorganisms and eventually is lost to the environment as greenhouse gases and non-point source pollution. Many soils lack the physical and/or chemical properties that enable some human-modified soils (e.g., terra preta soils in the Amazon Basin) to stabilize and retain C and nutrients in SOM while maintaining relatively high levels of productivity compared to surrounding natural soils that formed under similar conditions. I hypothesized that two of the major stabilizers of organic matter common to terra preta soils of the Amazon basin – black carbon (biochar) and poorly crystalline, reactive iron (Fe) minerals – could be applied to a fine-textured soil from Southwest Virginia to improve the accumulation and retention of C and nitrogen (N). I used a field experiment to compare the effects of three types of locally-produced biochars applied with and without an organic N fertilizer (blood meal) on soil C and N availability. I then used an incubation experiment featuring the soils from the aforementioned field experiment to examine the effects of applying Fe2+ -treated manure effluent on the retention of C and N in unamended and hardwood biochar-amended soils. I found that biochar adsorbed inorganic N in all cases, while providing a reliable, stable increase in SOM due to its recalcitrant nature. However, the manure effluent used in the incubation experiment stimulated the decomposition of mineral-associated organic matter (MAOM), with the addition of Fe2+ to the manure mitigating this apparent positive priming effect and the presence of biochar actually reversing this effect and promoting an increase in MAOM following manure application to biochar-amended soil. Overall, biochar stimulated the retention of N by decreasing the leachable inorganic N in the soil and enhanced soil C stocks. Additionally, biochar applications had the added benefit of promoting the accumulation of manure in soil as stable, microbially-processed MAOM, while co-applying Fe2+ with manure only served to inhibit the priming of native soil C. / Master of Science / Organic matter is an important constituent of all soils. Farmers and gardeners would like to increase the organic matter on their lands to improve their crop yields and health of their soils, yet people in many regions of the world struggle with actually getting long-lasting forms of organic matter to accumulate in soils. Moreover, managing soils to increase the amount of carbon stored in these long-lasting forms has the benefit of offsetting human contributions to atmospheric carbon dioxide and global warming. Some soils stabilize and build up organic matter more efficiently than others, and I hypothesized that if two well-known soil materials that help to stabilize organic matter – charcoal and iron – were added to a soil, then the accumulation of organic matter in the soil could be improved. The first part of my research was a field experiment in which three different kinds of charcoal were added either with or without an organic fertilizer to the soil in a Southwest Virginia pasture. I then measured the amount of carbon in the soil and determined that charcoal additions increased soil carbon and helped to retain mobile forms of plant nutrients. The second part of my research used the charcoal-treated and untreated soils from the field experiment for a project where cow manure was co-applied with three levels of iron and added to soils in jars in a controlled laboratory setting. The jars were then maintained at an ideal moisture and temperature for the growth of microbes for 70 days and analyzed afterwards. I found that the manure caused the organic matter in the soil to be consumed by microbes, while charcoal caused the organic matter from the manure to accumulate and remain. Adding iron with the manure prevented the microbes from consuming the pre-existing organic matter in the soil, but did not contribute to the retention of the manure in the soil. Overall, while both iron and charcoal influenced the retention of organic matter in soil, biochar proved to be more effective at stabilizing manure organic matter than the iron additions.

Une hernie abdominale survient lorsqu’un organe émerge de la cavité abdominale à travers une faiblesse musculaire. La cure de hernie est une des procédures chirurgicales les plus fréquemment réalisée. Une prothèse synthétique est souvent utilisée lors des procédures pour diminuer le taux de récidives. L’implantation de prothèse peut entraîner certaines complications, dont les infections chroniques. Certains facteurs dans la conception de la prothèse peuvent diminuer les taux d’infections. Plusieurs études ont montré que le Nitinol et certaines nanoparticules possèdent des propriétés antimicrobiennes. Les objectifs de cette étude sont d’examiner les surfaces d’échantillons de prothèses en Nitinol revêtis de nanoparticules d’argent et cuivre, ainsi que d’évaluer préliminairement leurs propriétés antimicrobiennes. Trois échantillons de prothèses ont été examinés : une en Nitinol seul et deux autres avec un revêtement de nanoparticules d’argent et cuivre, KJ103 et KJ501. L’étude de surface fut réalisée à l’École Polytechnique de Montréal. L’étude des propriétés antimicrobiennes fut réalisée dans les laboratoires de l’Institut de Cardiologie de Montréal. Les échantillons en Nitinol et une prothèse commerciale en polypropylène ont été exposés à trois micro-organismes habituellement retrouvés dans les infections chroniques : Staphylococcus aureus, Staphylococcus epidermidis et Candida albicans. Après une période d’incubation, des biofilms étaient visibles sur toutes les prothèses. Qualitativement, les prothèses en Nitinol semblaient moins susceptibles aux micro-organismes, en particulier l’échantillon KJ501. Les hernies abdominales sont fréquemment diagnostiquées en médecine. Les prothèses utilisées lors des chirurgies servent à prévenir les récidives. Par contre, les prothèses sont à risque de causer des infections chroniques. Cette expérience préliminaire suggère que les prothèses expérimentales en Nitinol ayant des nanoparticules d’argent et cuivres semblent moins susceptibles aux micro-organismes comparativement à une prothèse en polypropylène. / An abdominal hernia occurs when an organ protrudes through a weakness in the abdominal wall. Hernia repair is one of the most frequently performed surgeries. During the repair, a synthetic mesh is often used to decrease recurrence rates. Meshes can be associated with complications, such as chronic infections. Certain properties of the mesh itself can decrease infection rates. Several studies have shown that Nitinol, as well as silver and copper nanoparticles, have anti-microbial properties. The objectives of this study were to examine some surface properties of samples of Nitinol mesh with silver and copper nanoparticles and to preliminarily evaluate their antimicrobial properties. Three mesh samples were examined; one made uniquely with Nitinol and two others with silver and copper nanoparticle coatings, KJ103 and KJ501. The surface study was done at the École Polytechnique of Montréal. The study of the antimicrobial properties was performed at the laboratories of the Institut de Cardiologie de Montréal. The Nitinol samples and a commercially sold polypropylene mesh were exposed to three micro-organisms commonly found in mesh infection: Staphylococcus aureus, Staphylococcus epidermidis and Candida albicans. After the incubation period, biofilms were visible on all the meshes. Qualitatively, the Nitinol mesh showed less biofilm growth, in particular the KJ501 sample. Hernias are frequently diagnosed in medicine. Meshes are used during surgery to prevent recurrences. However, meshes are at risk of chronic infections. This preliminary experiment suggests that the Nitinol mesh with silver and copper nanoparticles are less prone to develop microbial biofilms when compared with a polypropylene mesh.

La compréhension des interactions qui associent les plantes et les microorganismes du sol est une étape incontournable pour une gestion durable de nos écosystèmes notamment en agriculture. Parmi les services écosystémiques résultant de leurs interactions, on peut citer la productivité végétale répondant, en partie, aux besoins alimentaires de la population mondiale et la régulation des cycles biogéochimiques. Les services écosystémiques, qui émergent de telles interactions, reposent sur des liens trophiques pouvant être représentés par un compromis entre coûts et bénéfices pour les différents partenaires de l’interaction. Les plantes, organismes autotrophes ou producteurs primaires, sont des organismes clefs qui font entrer le carbone dans l’écosystème, via la photosynthèse. Une partie de ce carbone est libérée sous forme de molécules plus ou moins complexes, au niveau de leurs racines, par le processus de rhizodéposition. Ces composés servent de molécules signal et de nutriments pour les microorganismes du sol, essentiellement hétérotrophes, c’est l’effet rhizosphère. Ce processus est donc coûteux pour la plante mais bénéfique aux microorganismes. Les microorganismes contribuent, en retour, à la nutrition et la santé des plantes ce qui est coûteux mais leur assure une source bénéfique de nutriments. Ces échanges trophiques reposent néanmoins sur un équilibre dépendant des conditions biotiques et abiotiques qui affectent chaque partenaire. La biodiversité microbienne, de par la multitude d’interactions au sein des communautés microbiennes, est un facteur biotique important. Parmi les facteurs abiotiques, le contexte environnemental actuel, soumis aux changements globaux, est propice à une déstabilisation de ces interactions. L’objectif de ce travail est donc de comprendre comment vont varier les coûts et bénéfices, pour chaque partenaire, suite à des modifications de l’environnement affectant l’un ou l’autre. L’intérêt étant de savoir si les bénéfices pour les plantes et les microorganismes, qui permettent les services écosystémiques, seront affectés. Pour répondre à cet objectif, un cadre d’interaction plantes-microbes simplifié a été choisi et une déstabilisation, au niveau de la plante, a été effectuée au moyen d’une augmentation en CO2 atmosphérique. L’interaction entre Medicago truncatula et Pseudomonas fluorescens a ainsi été étudiée. Les interactions ont ensuite été complexifiées en utilisant une communauté microbienne dans son ensemble et, cette fois, la modification a été appliquée au compartiment microbien soumis à une dilution de sa diversité. L’effet du gradient de diversité microbienne obtenu a été mesuré sur la croissance et la reproduction de trois espèces végétales modèles (Medicago truncatula, Brachypodium distachyon et Arabidopsis thaliana). Enfin, l’analyse s’est focalisée sur la communauté microbienne en identifiant la part active, c'est-à-dire les microorganismes qui utilisent les composés libérés par la plante. Ces microorganismes, qui interagissent réellement avec la plante, ont été détectés grâce à une analyse ADN SIP utilisant l’isotope 13C. Les principaux résultats observés, que la modification affecte l’un ou l’autre des partenaires, sont une déstabilisation des coûts et bénéfices. La première étude montre une variation temporaire des interactions en faveur de la plante en condition de CO2 augmenté. Dans le cas d’une dilution de la diversité microbienne, les coûts pour la plante sont conditionnés par la dépendance naturelle des plantes vis-à-vis des microorganismes symbiotiques qui interagissent avec le reste de la communauté. Cela est confirmé par la dernière expérimentation qui met en évidence les interactions microbes-microbes qui conditionnent la structure de la communauté microbienne interagissant avec la plante. [...] / Understanding the interactions that bind plants and soil microorganisms is an essential step for the sustainable management of ecosystems, especially in agriculture. The ecosystem services resulting from such interactions include plant productivity which responds, in part, to the food requirements of the world's population and the regulation of biogeochemical cycles. These ecosystem services depend on trophic links between the two partners in the interaction and can be represented by a tradeoff between the costs and benefits for each partner. Plants, being autotrophic organisms or primary producers, are key organisms which introduce carbon into the ecosystem, through photosynthesis. Part of this carbon is released as more or less complex molecules at the roots level, thanks to the rhizodeposition process. These compounds act as signal molecules and nutrients for soil microorganisms, which are mainly heterotrophic, in the so-called rhizosphere effect. This process is costly for the plant but beneficial to the microorganisms. In return, microorganisms contribute to plant nutrition and health, which is costly but provides them with a beneficial source of nutrients. These trophic exchanges, however, are based on a balance which depends on the biotic and abiotic conditions that affect each partner. Microbial biodiversity, through the multitude of interactions occurring within microbial communities, is a significant biotic factor. Among the abiotic factors, the current environmental context, subject to global change, is tending to destabilize these interactions. The objective of this work was to understand how environmental changes affect the costs and benefits for each partner by applying changes to one or the other, the aim being to determine whether these changes would affect the benefits for plants and microorganisms that provide ecosystem services. To achieve this objective, a simplified framework for plants-microbes interaction was first chosen. Destabilization at the plant level was carried out by increasing the atmospheric CO2 and studying the interaction between Medicago truncatula and Pseudomonas fluorescens. The interactions were then made more complex by using a whole microbial community but this time the change was applied to the microbial compartment by subjecting it to diversity dilution. The effect of the resulting microbial diversity gradient was measured on the growth and reproduction of three model plant species (Medicago truncatula, Brachypodium distachyon and Arabidopsis thaliana). Finally, the microbial community was subjected to a DNA SIP analysis, with the isotope 13C, to identify the active portion, i.e., those microorganisms which really interacted with the plant and used compounds released by it. The main result, when the change affected one or other partner, was a destabilization of the costs and benefits. The first study showed a transient variation in the interactions in favour of the plant under increased CO2 conditions. In the case of a dilution of microbial diversity, the costs for the plant are conditioned by the natural dependency of plants on symbiotic microorganisms that interact with the rest of the community. This was confirmed by the last experiment that highlighted the between-microbes interactions which determined the composition of the microbial community that interacted with the plant. This work has helped to clarify the functioning of relationships between plants and soil microbes and the factors that contribute to their maintenance which is essential to the functioning of ecosystems. These studies also provide ways for predicting the impacts of global change on ecosystems. The conservation or restoration of ecosystem services is essential for human well-being

Le microbiome de la rhizosphère fait généralement référence aux communautés bactériennes, archées et fongiques ainsi qu'à leur matériel génétique entourant étroitement les systèmes racinaires des plantes. Le métagénome de ce microbiome a été appelé le deuxième génome de la plante puisqu’elle est capable de profiter de plusieurs fonctions dont elle manque. La communauté microbienne de la rhizosphère inclue entre autres des microorganismes ayant développé des interactions intimes et spécifiques de longue durée avec les racines des plantes. Il s'agit d'une communauté dynamique de microorganismes, à partir de laquelle une partie d’espèces a développé des interactions intimes et spécifiques de longue durée avec les racines des plantes. Les progrès récents dans l’étude des interactions plantes-microbes ont démontré leur impact considérable sur la croissance, la nutrition et la santé des plantes. Le microbiote de la rhizosphère est complexe avec une structure spatio-temporelle dynamique qui s'adapte rapidement en fonction des stress biotiques et abiotiques. Considérant l’importance du microbiome de la rhizosphère pour la santé des plantes, des informations précises sur leurs microbes associés sont d'une importance capitale pour déchiffrer les mécanismes d'adaptation des plantes aux stress médiés par le microbiome et comprendre comment les plantes recrutent des taxons microbiens clés pour mieux faire face aux conditions stressantes. Pour ce faire, nous avons mené trois études afin de faire la lumière sur les facteurs qui jouent un rôle dans le recrutement et la structure du microbiome de la rhizosphère de plantes dans les milieux stressés. Dans un premier lieu, nous avons testé si des inoculations répétées avec des protéobactéries influençaient la productivité des plantes et les communautés microbiennes associées à la rhizosphère de quatre espèces végétales poussant dans des sédiments contaminés par des hydrocarbures pétroliers. Une expérience de mésocosme a été réalisée en conception de blocs randomisés avec deux facteurs : 1) la présence ou l'absence de quatre espèces végétales collectées dans un bassin de sédimentation d'une ancienne usine pétrochimique, et 2) l'inoculation ou non avec un consortium bactérien composé de dix isolats de Protéobactéries. Les plantes ont été cultivées en serre pendant quatre mois. Le séquençage d'amplicon MiSeq, ciblant le gène de l'ARNr 16S bactérien l’ITS fongique, a été utilisé pour évaluer les structures de la communauté microbienne des sédiments provenant de mesocosmes plantés ou non plantés. Nos résultats ont montré qu’alors que l'inoculation provoquait un changement significatif dans les communautés microbiennes, la présence de la plante et de son identité spécifique avait une influence plus forte sur la structure du microbiome dans les sédiments contaminés par les hydrocarbures pétroliers. Ensuite, en utilisant le même dispositif expérimental, nous avons utilisé le séquençage d'amplicon MiSeq ciblant le gène de l'ARNr 18S pour évaluer les structures communautaires AMF dans les racines et la rhizosphère de plantes poussant dans des substrats contaminés et non contaminés. Nous avons également étudié la contribution de l'identité spécifique des plantes et du biotope (racines des plantes et sol rhizosphérique) dans la formation des assemblages AMF associés. Nos résultats ont montré que si l'inoculation provoquait un changement significatif dans les communautés AMF, la contamination du substrat avait une influence beaucoup plus forte sur leur structure, suivie par le biotope et l'identité végétale dans une moindre mesure. De plus, l'inoculation augmentait considérablement la production de biomasse végétale et était associée à une diminution de la dissipation des hydrocarbures pétroliers dans le sol contaminé. Le résultat de cette étude fournit des connaissances sur les facteurs influençant la diversité et la structure communautaire de l'AMF associée aux plantes en milieux stressés à la suite d’inoculations répétées d'un consortium bactérien. Finalement, nous avons testé l’effet d’une inoculation d’arbres avec des champignons mycorhiziens spécifiques sur leur survie et croissance, ainsi que l’extraction de métaux traces. Pour ce faire, une expérience sur le terrain a été menée dans laquelle nous avons cultivé le clone de Salix miyabeana "SX67" sur le site d'une décharge industrielle déclassée, et inoculé les arbustes avec le champignon arbusculaire mycorhizien Rhizophagus irregularis, le champignon ectomycorhizien Sphaerosporella brunnea, ou un mélange des deux. Après deux saisons de croissance, les saules inoculés avec le champignon S. brunnea ont produit une biomasse significativement plus élevée. Le Ba, le Cd et le Zn se sont avérés être accumulés dans les parties aériennes des plantes, où le Cd présentait les valeurs de facteur de bioconcentration les plus élevées dans tous les traitements. De plus, les parcelles où les saules ont reçu l'inoculation de S. brunnea ont montré une diminution significative des concentrations de Cu, Pb et Sn dans le sol. L'inoculation avec R. irregularis ainsi que la double inoculation n'ont pas influencé de manière significative la production de biomasse et les niveaux d’éléments traces du sol. Le résultat de cette étude apporte des connaissances sur la diversité et l’écophysiologie des microbes de la rhizosphère associés aux plantes de croissance spontanée à la suite d’inoculations répétées. De plus ils montrent le potentiel de l’utilisation de champignons mycorhiziens afin d’améliorer la santé et croissance des plantes dans des milieux pollués et toxiques. Ils soulignent aussi l'importance de la sélection des plantes afin de faciliter leur gestion efficace et accélérer les processus de remise en état des terres. / The rhizosphere microbiome generally refers to the bacterial, archaea, and fungal communities and their genetic material that closely surrounds the root systems of plants. The metagenome of this microbiome has been called the second genome of the plant because it is able to take advantage of several functions that it lacks. It is a vibrant community of microorganisms, from which part of the species has developed long-lasting, specific and intimate interactions with plant roots. Recent advances in the study of plant-microbe interactions have demonstrated their considerable impact on plant growth, nutrition and health. The rhizosphere microbiota is complex with a dynamic spatio-temporal structure which adapts rapidly to biotic and abiotic stresses. Considering the importance of the rhizosphere microbiome to plant health, accurate information about their associated microbes is of utmost importance in deciphering the mechanisms of plant adaptation to microbiome-mediated stress, and understanding how plants recruit key microbial taxa to better cope with stressful conditions. To do this, we conducted three studies to shed light on the factors that play a role in the recruitment and structure of the microbiome of the rhizosphere of plants in stressed environments. First, we tested whether repeated inoculations with Proteobacteria influenced the productivity of plants and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons. A mesocosm experiment was carried out in design of randomized blocks with two factors: 1) the presence or absence of four plant species collected in a sedimentation basin of a former petrochemical plant, and 2) inoculation or not with a bacterial consortium made up of ten isolates of Proteobacteria. The plants were grown in the greenhouse for four months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess the microbial community structures of sediments from planted and unplanted microcosms. Our results showed that while inoculation caused a significant change in microbial communities, the presence of the plant and its specific identity had a stronger influence on the structure of the microbiome in sediments contaminated with petroleum hydrocarbons. Next, using the same experimental setup, we used MiSeq amplicon sequencing targeting the 18S rRNA gene to assess AMF community structures in the roots and rhizosphere of plants growing in contaminated and uncontaminated substrates. We also studied the contribution of the specific identity of plants and the biotope (plant roots and rhizospheric soil) in the formation of associated AMF assemblages. Our results showed that while inoculation caused a significant change in AMF communities, substrate contamination had a much stronger influence on their structure, followed by biotope and plant identity to a lesser extent. In addition, inoculation dramatically increased plant biomass production and was associated with decreased dissipation of petroleum hydrocarbons in contaminated soil. The result of this study provides knowledge on the factors influencing the diversity and community structure of AMF associated with plants in stressed environments following repeated inoculations of a bacterial consortium. Finally, we tested the effect of inoculating trees with specific mycorrhizal fungi on their survival and growth, as well as the extraction of trace metals. To do this, a field experiment was carried out in which we cultivated the Salix miyabeana "SX67" clone on the site of a decommissioned industrial landfill and inoculated the shrubs with the arbuscular mycorrhizal fungus Rhizophagus irregularis, the ectomycorrhizal fungus Sphaerosporella brunnea, or a mixture of both. After two growing seasons, willows inoculated with the fungus S. brunnea produced a significantly higher biomass. Ba, Cd and Zn were found to accumulate in the aerial parts of plants, where Cd had the highest bioconcentration factor values in all treatments. In addition, the plots where the willows were inoculated with S. brunnea showed a significant decrease in the concentrations of Cu, Pb and Sn in the soil. The inoculation with R. irregularis as well as the double inoculation did not significantly influence the biomass production and the soil trace elements levels The result of this study provides insight into the diversity and ecophysiology of rhizosphere microbes associated with spontaneously growing plants following repeated inoculations. In addition, they show the potential of using mycorrhizal fungi to improve plant health and growth in polluted and toxic environments. They also stress the importance of plant selection to facilitate their efficient management, in order to speed up land reclamation processes.

L’utilisation d’inoculants de champignon mycorhizien arbusculaire (CMA) et de bactéries promotrices de la croissance de la plante (PGPR) comme biofertilisants pour améliorer la croissance de la plante et augmenter les rendements des cultures connait de plus en plus un intérêt remarquable. Ces inoculants peuvent influencer les relations trophiques à travers les changements induits au niveau de la plante. Cependant, en contexte agroécologique, il est difficile de prédire les effets de leur application sur les niveaux trophiques supérieurs, notamment sur les insectes phytophages et leurs ennemis naturels. Ainsi, l’objectif de ce projet de thèse était d’évaluer les effets des inoculants de champignon mycorhizien et bactériens sur les insectes du soja. Spécifiquement il est question : 1) d’évaluer l’influence sur le puceron du soja Aphis glycines (2e niveau trophique), de la symbiose tripartite entre un CMA Rhizophagus irregularis, une bactérie rhizobium Bradyrhizobium japonicum et le soja Glycine max ; 2) de déterminer l’impact des inoculants de R. irregularis et de B. japonicum associés au soja sur les ennemis naturels du puceron de soja, la coccinelle Coleomegilla maculata et le parasitoïde Aphelinus certus (3e niveau trophique) ; 3) d’évaluer les effets de la co-inoculation des inoculants de R. irregularis, B. japonicum et de Bacillus pumilus sur les insectes phytophages et leurs ennemis naturels associés au soja au champ. Les expériences en chambre de croissance (objectifs 1 et 2) ont montré une altération des traits de performance des plantes en présence des inoculants comparées aux plantes témoins. Les différences de colonisation mycorhizienne et de nodulation, observées entre les traitements sont une preuve du fonctionnement de l’inoculation. Avec le double inoculant, j’ai observé une augmentation de la biomasse de la plante, des concentrations en azote et carbone, et une diminution de la concentration en phosphore. Avec le rhizobium seul, j’ai obtenu les mêmes effets, sauf pour la biomasse racinaire qui n’a pas été affectée. Avec le CMA seul, une augmentation de la concentration en phosphore a été observée, mais aucun des autres paramètres de la plante n'a été affecté. Au deuxième niveau trophique sur le puceron du soja, le soja inoculé avec le double inoculant CMA+rhizobium, suivi du rhizobium seul, ont augmenté significativement la densité de la population de pucerons, alors qu’aucun des inoculants n’a eu un effet sur le fitness du puceron. En revanche, aucun des traits de performance du puceron (fécondité et taille des individus) n’a été affecté par la présence de l’inoculant CMA seul. D’autre part, j’ai noté une corrélation positive entre la concentration en azote et le taux de reproduction des pucerons, alors qu’avec la concentration en phosphore, la corrélation avec la colonie des pucerons est négative. Quant au troisième niveau trophique, une réduction significative du taux de parasitisme chez A. certus a été observée en présence du rhizobium seul, mais aucun autre paramètre n’a été affecté comparativement aux autres traitements : contrôle, CMA et double inoculant (CMA+rhizobium). Avec le prédateur C. maculata, aucun paramètre mesuré n’a été affecté par les effets indirects des inoculants. Il ressort de l’évaluation que j’ai faite au champ (objectif 3), une augmentation de l'abondance des insectes piqueurs-suceurs avec le triple inoculant (CMA+rhizobium+Bacillus), mais aucune différence entre les traitements pour les autres groupes d'insectes (broyeurs, et ennemis naturels des pucerons). Aucun groupe fonctionnel n’a été affecté en présence du double inoculant CMA+rhizobium sauf le puceron du soja, A. glycines, qui a vu sa population décroître mais seulement dans les parcelles fertilisées en potassium. J’ai également montré que les abondances des insectes piqueurs-suceurs et des insectes broyeurs, et la diversité alpha des insectes phytophages étaient toutes corrélées négativement avec la colonisation mycorhizienne globale. Ces résultats confirment que la co-inoculation de deux symbiotes peut non seulement améliorer les performances des plantes mais aussi celles des insectes phytophages au-delà de ce que chaque symbiote peut apporter seul. Au moins dans notre système d'étude en chambre de croissance, il semble que les avantages que les symbioses microbe-plante confèrent au deuxième niveau trophique avec une augmentation de la population de pucerons sont peu transférés au troisième niveau sur les ennemis naturels du puceron. Dans un système agricole où les agriculteurs veulent bénéficier des retombées de ces inoculants, notamment dans la gestion des insectes associés aux cultures, les CMA semblent favorables s’ils sont utilisés seuls et du fait de leur potentiel à réduire les insectes ravageurs. / The use of arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPR) inoculants, as biofertilizers to boost plant growth and increase crop yields, is gaining interest. These inoculants can also influence trophic relationships through changes on plant. However, in an agroecological context, it is difficult to predict the effects of their application on higher trophic levels, namely phytophagous insects, and their natural enemies. The objective of this thesis research is to evaluate the effects of mycorrhizal fungi and bacterial inoculants on soybean-associated insects. Specifically, it is to: 1) evaluate the influence on the soybean aphid, Aphis glycines (2nd trophic level), of the tripartite symbiosis between an AMF, Rhizophagus irregularis, a rhizobium bacterium, Bradyrhizobium japonicum, and the soybean, Glycine max; 2) determinate the impact of R. irregularis and B. japonicum inoculants associated with soybean on the natural enemies of soybean aphid, the ladybug Coleomegilla maculata and the parasitoid wasp Aphelinus certus (3rd trophic level); 3) evaluate the effects of co-inoculation of R. irregularis, B. japonicum and Bacillus pumilus inoculants on soybean-associated phytophagous insects and their natural enemies in an agricultural field conditions. The walk-in growth room experiments (objectives 1 and 2) showed an alteration of the performance traits of the plants in the presence of the inoculants compared to control plants. The differences in mycorrhizal colonization and nodulation, observed between treatments, are evidence that the inoculation works. With the double inoculant, I observed an increase in plant biomass, nitrogen and carbon concentrations, and a decrease in phosphorus concentration. With rhizobium inoculation alone, without AMF, I obtained the same effects, except the root biomass that was not affected. With AMF alone, an increase in phosphorus concentration was observed, but none of the other plant parameters were affected. At second trophic level, inoculation of soybeans with the dual inoculant AMF-rhizobium, followed by rhizobium alone, significantly increased aphid population density, while none of inoculant influenced the fitness of the aphid. However, AMF alone did not affect any parameter traits (reproduction and fitness) of the aphid. I noted a positive correlation between nitrogen concentration and aphid reproductive rate, whereas the correlation between phosphorus concentration and aphid colony growth was negative. At the third trophic level, a significant reduction in the rate of parasitism of A. certus was observed in the presence of rhizobium inoculant alone, but no other parameters were affected with any other treatments, namely the control, the AMF inoculant, or the double inoculant (AMF+rhizobium). With the predator C. maculata, no measured parameters were affected by the indirect effects of any of the inoculant treatments. During my field assessment (objective 3), I observed an increase in the abundance of piercing-sucking insects with the triple inoculant (AMF+rhizobium+Bacillus), but no differences between treatments for other insect groups (chewing insects, or natural enemies of aphids). No functional group was affected by the presence of the double inoculant, CMA+rhizobium except the soybean aphid, A. glycines, which saw its population decrease in potassium-fertilized plots. I also showed that the abundance of piercing-sucking insects, chewing insects, and the alpha diversity of phytophagous insects were all negatively correlated with mycorrhizal colonization. The results of my studies confirm that co-inoculation of two symbionts can not only improve plant performance but also that of phytophagous insects beyond what each symbiont can provide alone. At least in our growth chamber study system, it appears that the benefits that microbe-plant symbioses confer to the second trophic level, with an increase in aphid population, are little transferred to the third level on the natural enemies of the soybean aphid. In agricultural system where farmers seek the benefits of these inoculants, especially in the management of insects associated with crops, AMF seem favorable when they are used alone and because of their potential to reduce insect pests.

Background: MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. Results: MicrO currently has similar to 14550 classes (similar to 2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by similar to 24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. Conclusions: By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.