Dans cette étude, nous avons isolé et cultivé des bactéries intimement liées aux spores du champignon mycorhizien Glomus irregulare prélevées dans la rhizosphère de plants d’Agrostis stolonifera L. récoltés dans un sol naturel. Le séquençage des 29 morphotypes isolés a révélé la présence de seulement sept taxons bactériens (Variovorax paradoxus, Microbacterium ginsengiosoli, Sphingomonas sp., Bacillus megaterium, B. simplex, B. cereus et Kocuria rhizophila). Des isolats de chacun de ces sept taxons ont ensuite été cultivés in vitro sur le mycélium de G. irregulare afin d’observer par microscopie leur capacité à croitre et à s’attacher au mycélium en absence d’éléments nutritifs autres que ceux fournis par le champignon. Tous les isolats, sauf B. cereus, ont été capables de bien croitre dans le système expérimental et de s’attacher au mycélium en formant des structures ressemblant à des biofilms sur la surface du champignon. Toutefois, B. simplex formait ces structures plus rapidement, soit en 15 jours, alors que les autres isolats les ont formés après 30 jours (K. rhizophila et B. megaterium) ou 45 jours (V. paradoxus, M. ginsengiosoli et Sphingomonas sp.). D’autre part, la technique PCR-DGGE a permis d’analyser la diversité bactérienne associée aux spores. La diversité des taxons associés aux spores de G. irregulare qu’il a été possible d’isoler et de cultiver in vitro a été nettement moindre que celle qui était présente sur la surface des spores, alors que la biodiversité bactérienne totale du sol a été encore beaucoup plus élevée. Les bactéries associées aux champignons mycorhiziens jouent probablement un rôle important dans la capacité des plantes à résister aux stress biotiques et abiotiques auxquels elles sont soumises. / In this study, we isolated and cultivated bacterial cells intimately associated with Glomus irregulare spores in a natural soil Agrostis stolonifera rhizosphere. Sequencing of the 29 morphotypes isolated revealed the presence of only seven bacterial taxa (Variovorax paradoxus, Microbacterium ginsengiosoli, Sphingomonas sp., Bacillus megaterium, B. simplex, B. cereus and Kocuria rhizophila). These seven isolates were cultivated in vitro on the mycelium of G. irregulare to allow microscopic observation of growth and attachment to the mycelium in absence of nutritive sources other than those derived from the fungal mycelium. All isolates but B. cereus were able to grow on the experimental system and to attach to the mycelium to form biofilm-like structures on their surface. However, B. simplex formed these structures more quickly, in 15 days, than the remaining isolates that have formed them only after 30 days (K. rhizophila and B. megaterium) or 45 days (V. paradoxus, M. ginsengiosoli and Sphingomonas sp.). In addition, PCR-DGGE was used to compare bacterial diversity. The bacterial biodiversity associated with spores of G. irregulare that were isolated and cultured in vitro was significantly lower than that present on the spore surface, while total soil bacterial diversity was much higher. The bacteria associated with mycorrhizal fungi probably have an important role in the ability of plants to withstand biotic and abiotic stresses to which they are submitted.

Les métaux lourds (ML) s’accumulent de plus en plus dans les sols à l’échelle mondiale, d’une part à cause des engrais minéraux et divers produits chimiques utilisés en agriculture intensive, et d’autre part à cause des activités industrielles. Toutes ces activités génèrent des déchets toxiques qui s’accumulent dans l’environnement. Les ML ne sont pas biodégradables et leur accumulation cause donc des problèmes de toxicité des sols et affecte la biodiversité des microorganismes qui y vivent. La fertilisation en azote (N) est une pratique courante en agriculture à grande échelle qui permet d’augmenter la fertilité des sols et la productivité des cultures. Cependant, son utilisation à long terme cause plusieurs effets néfastes pour l'environnement. Par exemple, elle augmente la quantité des ML dans les sols, les nappes phréatiques et les plantes. En outre, ces effets néfastes réduisent et changent considérablement la biodiversité des écosystèmes terrestres. La structure des communautés des champignons mycorhiziens à arbuscules (CMA) a été étudiée dans des sols contaminés par des ML issus de la fertilisation à long terme en N. Le rôle des différentes espèces de CMA dans l'absorption et la séquestration des ML a été aussi investigué. Dans une première expérience, la structure des communautés de CMA a été analysée à partir d’échantillons de sols de sites contaminés par des ML et de sites témoins non-contaminés. Nous avons constaté que la diversité des CMA indigènes a été plus faible dans les sols et les racines des plantes récoltées à partir de sites contaminés par rapport aux sites noncontaminés. Nous avons également constaté que la structure de la communauté d'AMF a été modifiée par la présence des ML dans les sols. Certains ribotypes des CMA ont été plus souvent associés aux sites contaminés, alors que d’autres ribotypes ont été associés aux sites non-contaminés. Cependant, certains ribotypes ont été observés aussi bien dans les sols pollués que non-pollués. Dans une deuxième expérience, les effets de la fertilisation organique et minérale (N) sur les différentes structures des communautés des CMA ont été étudiés. La variation de la structure de la communauté de CMA colonisant les racines a été analysée en fonction du type de fertilisation. Certains ribotypes de CMA étaient associés à la fertilisation organique et d'autres à la fertilisation minérale. En revanche, la fertilisation minérale a réduit le nombre de ribotypes de CMA alors que la fertilisation organique l’a augmenté. Dans cette expérience, j’ai démontré que le changement de structure des communautés de CMA colonisant des racines a eu un effet significatif sur la productivité des plantes. Dans une troisième expérience, le rôle de deux espèces de CMA (Glomus irregulare et G. mosseae) dans l'absorption du cadmium (Cd) par des plants de tournesol cultivés dans des sols amendés avec trois niveaux différents de Cd a été évalué. J’ai démontré que les deux espèces de CMA affectent différemment l’absorption ou la séquestration de ce ML par les plants de tournesol. Cette expérience a permis de mieux comprendre le rôle potentiel des CMA dans l'absorption des ML selon la concentration de cadmium dans le sol et les espèces de CMA. Mes recherches de doctorat démontrent donc que la fertilisation en N affecte la structure des communautés des CMA dans les racines et le sol. Le changement de structure de la communauté de CMA colonisant les racines affecte de manière significative la productivité des plantes. J’ai aussi démontré que, sous nos conditions expériemntales, l’espèce de CMA G. irregulare a été observée dans tous les sites (pollués et non-pollués), tandis que le G. mosseae n’a été observé en abondance que dans les sites contaminés. Par conséquent, j’ai étudié le rôle de ces deux espèces (G. irregulare et G. mosseae) dans l'absorption du Cd par le tournesol cultivé dans des sols amendés avec trois différents niveaux de Cd en serre. Les résultats indiquent que les espèces de CMA ont un potentiel différent pour atténuer la toxicité des ML dans les plantes hôtes, selon le niveau de concentration en Cd. En conclusion, mes travaux suggèrent que le G. irregulare est une espèce potentiellement importante pour la phytoextration du Cd, alors que le G. mosseae pourrait être une espèce appropriée pour phytostabilisation du Cd et du Zn. / Trace metals (TM) are continually world-wide added to soils through the intensive use of mineral fertilizers and agriculture chemicals, together with industrial and other activities generating toxic wastes. Problems associated with metal-contaminated soil exists because TM are not biodegradable. TM that accumulate in soils affect the biodiversity of soil microorganisms. Nitrogen (N) fertilization is a widespread practice to increase soil fertility and crop production. However, the long-term use of N fertilization causes many detrimental effects in the environment. The intensive use of N fertilization increase TM input in soils, and in extreme cases, N fertilization result in TM pollution of the surrounding soil and water and increase TM concentration in plant tissues. In addition, the long-term use of N fertilizers changes and declines the biodiversity of above and underground ecosystems. The community structure of arbuscular mycorrhizal fungi (AMF) was investigated in TM contaminated and long-term N fertilized soils. In addition, the role of different AMF species in TM uptake or sequestration was investigated. In the first experiment, AMF community structure was analyzed from non-contaminated and TM contaminated sites. We found the diversity of native AMF was lower in soils and plant roots harvested from TM polluted soils than from unpolluted soils. We also found that the community structure of AMF was modified by TM contamination. Some AMF ribotypes were more often associated with TM contaminated sites, other ribotypes with uncontaminated sites, while still other ribotypes were found both in polluted and unpolluted soils. In the second experiment, the effect of different organic and mineral N fertilization on AMF community structure was investigated. Variation in root-colonizing AMF community structure was observed in both organic and mineral fertilization. Some AMF ribotypes were more affiliated to organic fertilization and other to mineral fertilization. In addition, mineral fertilization reduced AMF ribotypes number while organic fertilization increased AMF ribotypes number. In this experiment, it was demonstrated that change in root-colonizing AMF community structure had a significant effect on plant productivity. In the third experiment, the role of different AMF species (G. irregulare and G. mosseae) in TM uptake by sunflower plants grown in soil amended with three different Cd levels was evaluated. It was demonstrated that AMF species differentially affected TM uptake or sequestration by sunflower plants. This experiment supported a different effect of AMF in TM uptake based on Cd concentration in soil and the AMF species involved. Our research demonstrated that TM and N fertilization affected and shifted AMF community structure within roots and soils. It was shown that change in root-colonizing AMF community structure significantly affected plant productivity. In this study, it was showed that the AMF species G. irregulare was recorded in all uncontaminated sites while G. mosseae was the most abundant AMF species in TM contaminated sites. Therefore, the role of G. irregulare and G. mosseae in Cd uptake by sunflower plants grown in soils amended with three different Cd levels was investigated. The results indicated that AMF species mediate different mechanisms to alleviate TM toxicity in host plants, depending on AMF species and soil Cd level involved. We hypothesize that G. irregulare is a potentially important species for Cd phytoextration processes, while G. mosseae might be a suitable candidate for Cd and Zn phytostabilization processes.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Pas de résumé en français / In plants, long distance transport of sugars from photosynthetic source leaves to sink organs comprises different crucial steps depending on the species and organ types. Sucrose, the main carbohydrate for long distance transport is synthesized in the mesophyll and then loaded into the phloem. After long distance transport through the phloem vessels, sucrose is finally unloaded towards sink organs. Alternatively, sugar can also be transferred to non‐plant sinks and plant colonization by heterotrophic organisms increases the sink strength and creates an additional sugar demand for the host plant. These sugar fluxes are coordinated by transport systems. Main sugar transporters in plants comprise sucrose (SUTs) and monosaccharide (MSTs) transporters which constitute key components for carbon partitioning at the whole plant level and in interactions with fungi. Although complete SUTs and MSTs gene families have been identified from the reference Dicot Arabidopsis thaliana and Monocot rice (Oriza sativa), sugar transporter families of the leguminous plant Medicago truncatula, which represents a widely used model for studying plant-fungal interactions in arbuscular mycorrhiza (AM), have not yet been investigated.With the recent completion of the M. truncatula genome sequencing as well as the release of transcriptomic databases, monosaccharide and sucrose transporter families of M. truncatula were identified and now comprise 62 MtMSTs and 6 MtSUTs. I focused on the study of the newly identified MtSUTs at a full family scale; phylogenetic analyses showed that the 6 members of the MtSUT family distributed in all three Dicotyledonous SUT clades; they were named upon phylogenetic grouping into particular clades: MtSUT1-1, MtSUT1-2, MtSUT1-3, MtSUT2, MtSUT4-1 and MtSUT4-2. Functional analyses by yeast complementation and expression profiles obtained by quantitative RT-PCR revealed that MtSUT1-1 and MtSUT4-1 are H+/sucrose symporters and represent key members of the MtSUT family. Conservation of transport capacity between orthologous leguminous proteins, expression profiles and subcellular localization compared to previously characterized plant SUTs indicate that MtSUT1-1 is the main protein involved in phloem loading in source leaves whilst MtSUT4-1 mediates vacuolar sucrose export for remobilization of intracellular reserve.The AM symbiosis between plants and fungi from the phylum Glomeromycota is characterized by trophic exchanges between the two partners. The fungus supplies the autotrophic host with nutrients and thereby promotes plant growth. In return, the host plant provides photosynthate (sugars) to the heterotrophic symbiont. Here, sugar fluxes from plant source leaves towards colonized sink roots in the association between the model leguminous plant M. truncatula and the arbuscular mycorrhizal fungus (AMF) Glomus intraradices were investigated. Sugar transporter candidates from both the plant and fungal partners presenting differential expression profiles using available transcriptomic tools were pinpointed. Gene expression profiles of MtSUTs and sugar quantification analyses upon high and low phosphorus nutrient supply and inoculation by the AMF suggest a mycorrhiza-driven stronger sink in AM roots with a fine-tuning regulation of MtSUT gene expression. Conserved regulation patterns were observed for orthologous SUTs in response to colonization by glomeromycotan fungi.In parallel, a non-targeted strategy consisting in the development of a M. truncatula - G. intraradices expression library suitable for yeast functional complementation and screening of symbiotic marker genes, similar to the approach that led to the identification of the first glomeromycotan hexose transporter (GpMST1), has been developed in this study. [...]

Sustainable agriculture practices include a better exploitation of soil natural resources. Arbuscular mycorrhizal fungi (AMF) plays an important role in this context, with native communities in soils that establishes a mutualistic association with most plant species and maximizes their access to mineral nutrients, especially phosphorus. Seed treatment may consist in a good alternative to stimulate AMF root colonization, since early stages of crop growth, by using biostimulant formulations applied to seeds. This research had the objective to evaluate the early mycorrhization of soybean plants in response to seaweed extracts applied to seeds. The treatments consisted of a control (CTR, distilled water), two seaweed extracts, from Ascophyllum nodosum (ANE) and Ecklonia maxima (EME) species and a synthetic formulation containing formononetin (FOR), commercially used as mycorrhization stimulant. The first experiment was conducted in greenhouse, with the aim to evaluate different parameters of soybean early growth and development and AMF root colonization in response to the seed treatments, under different rates of phosphorus added to the soil (0, 50, 100 and 200 mg.dm-3). The second experiment was conducted in growth chamber, with the objective to evaluate qualitative and quantitative aspects of mycorrhization in response to the seed treatments with biostimulants, at early plant growth stages. In this experiment, the influence of treatments on the structure of AMF, bacterial and fungal communities in the soybean rhizosphere were analyzed, through PCR/T- RFLP fingerprinting. Phosphorus rates applied to soil significantly influenced (P<0.10) biometric and physiological parameters of soybean plants, while the seed treatments only influenced leaf chlorophyll content and nitrogen balance at a significant level, despite some trends to increase leaf area, shoot dry mass and nodulation. Formononetin applied to soybean seeds increases AMF root colonization compared to control, independently of P rate applied to soil, while ANE and EME presented intermediate values for this parameter, not differing from both control and formononetin. When considered some qualitative parameters of mycorrhiza establishment, such as frequency and intensity of mycorrhization, both synthetic and natural biostimulants presented significant improvements, with EME and FOR providing higher values in general. The phenological stage of soybean significantly influenced AMF, bacterial and fungal community structures in rizosphere, while the biostimulant seed treatments only significantly influenced the bacterial community. However, a relatively large variation in the microbial community structures could be attributed to the interaction between phenological stage of plants and the seed treatment with biostimulants. / Práticas agrícolas sustentáveis incluem uma melhor exploração dos recursos naturais do solo. Os fungos micorrízicos arbusculares (FMA) desempenham um papel importante neste contexto, com comunidades nativas nos solos que estabelecem uma associação mutualística com a maioria das espécies cultivadas e maximizam o acesso a nutrientes minerais, especialmente o fósforo. O tratamento de sementes pode consistir em uma alternativa interessante para estimular a colonização por FMA, desde estádios iniciais de crescimento da cultura, utilizando formulações de bioestimulantes aplicadas às sementes. Esta pesquisa teve como objetivo avaliar a micorrização precoce de plantas de soja em resposta a extratos de algas aplicados nas sementes. Os tratamentos consistiram de uma testemunha (CTR, água destilada), dois extratos de algas marinhas, das espécies Ascophyllum nodosum (ANE) e Ecklonia máxima (EME) e uma formulação sintética contendo formononetina (FOR), comercialmente utilizada como estimulante de micorrização. O primeiro experimento foi conduzido em casa de vegetação, com o objetivo de avaliar diferentes parâmetros de crescimento e desenvolvimento inicial das plantas de soja e a colonização de raízes por FMA, em resposta aos tratamentos de sementes; estas avaliações foram realizadas sob diferentes doses de fósforo adicionadas ao solo (0, 50, 100 e 200 mg.dm-3). O segundo experimento foi conduzido em câmara de crescimento, com o objetivo de avaliar aspectos qualitativos e quantitativos da micorrização em resposta ao tratamento de sementes com bioestimulantes, nas fases iniciais de crescimento das plantas. Neste experimento, analisou-se a influência dos tratamentos na estrutura de comunidades de FMA, bactérias e fungos na rizosfera das plantas de soja, através de PCR/T-RFLP. As doses de fósforo aplicadas no solo influenciaram significativamente (P<0,10) nos parâmetros biométricos e fisiológicos das plantas de soja, enquanto os tratamentos de sementes influenciaram significativamente apenas o teor de clorofila e o balanço de nitrogênio. A formononetina aplicada nas sementes de soja aumentou a colonização da raiz por FMA em relação ao controle, independentemente da dose de P aplicada ao solo, enquanto ANE e EME apresentaram valores intermediários para este parâmetro, não diferindo tanto da testemunha como da formononetina. Quando considerados alguns parâmetros qualitativos do estabelecimento de micorrizas, tanto os bioestimulantes sintéticos como os naturais apresentaram melhorias significativas. O estádio fenológico da soja influenciou significativamente as estruturas de comunidades de FMA, bactérias e fungos na rizosfera das plantas de soja, enquanto os tratamentos de sementes com bioestimulantes somente influenciaram significativamente a comunidade bacteriana. No entanto, uma variação relativamente grande nas estruturas da comunidade microbiana pôde ser atribuída à interação entre estádio fenológico das plantas e o tratamento de sementes com bioestimulantes.

Os hormônios vegetais etileno e ABA são possíveis reguladores chave do desenvolvimento das micorrizas arbusculares (MAs). O primeiro objetivo deste trabalho foi avaliar o desenvolvimento da MA em mutantes superprodutores e insensíveis ao etileno (epinastic e Never ripe, respectivamente) e verificar se enzimas relacionadas ao sistema de defesa vegetal são reguladas diferencialmente pelo etileno durante o desenvolvimento da simbiose A colonização de raízes de epinastic (epi) por G. clarum foi significativamente reduzida quando comparada com Micro-Tom (MT), além disso, a funcionalidade da simbiose, demonstrada pelo acúmulo de transcritos de LePT4, foi fortemente reduzida quando comparada com MT. Por outro lado, o padrão de colonização e funcionalidade da simbiose no mutante Nr não diferiu de MT. Indução no acúmulo de transcritos de genes que codificam quitinases e enzimas relacionadas ao estresse oxidativo foi observada no mutante epi, enquanto o acúmulo de transcritos de uma -1,3-glucanase foi fortemente induzido no mutante Nr. O segundo objetivo foi verificar se a colonização reduzida observada em mutantes deficientes em ABA é dependente da produção do etileno. Para tanto, mutantes que diferem na deficiência de ABA e produzem diferentes quantidades de etileno (notabilis e sitiens) e o mutante epi foram inoculados com G. clarum e tratados com aminoethoxivinilglicina (AVG), um inibidor de etileno. A colonização intrarradicular de G. clarum nos mutantes epi e notabilis (not) foi significativamente reduzida quando comparada com MT, sendo que o mutante sitiens (sit) foi o menos susceptível à colonização em relação aos demais genótipos. A aplicação de AVG a 10 µM restaurou completamente a colonização em epi, mas não nos mutantes deficientes em ABA. O acúmulo de transcritos de LePT4 confirmou os resultados de colonização. Os genes que codificam enzimas chave na biossíntese do etileno, LeACS2 e LeACO4, foram regulados positivamente pela inoculação com G. clarum, e a restauração do desenvolvimento da MA observada em epi que recebeu AVG, provavelmente envolveu ACC oxidase (LeACO4). O acúmulo de transcritos dos genes que codificam ACC oxidase (LeACO1 e LeACO4) foi induzido significativamente em sit, mostrando que a superprodução de etileno observada neste mutante pode envolver a regulação da ACC oxidase. Por fim, indução no acúmulo de transcritos do gene LeNCED foi observada em todos os genótipos micorrizados e em raízes de epi que receberam AVG, demonstrando que LeNCED é regulado positivamente pela inoculação com G. clarum e que o etileno regula a expressão deste gene. Os resultados demonstram que etileno e ABA estão envolvidos na regulação do desenvolvimento de MA e que etileno modula a expressão de genes relacionados ao sistema de defesa vegetal permitindo o estabelecimento de uma simbiose funcional. / The plant hormones ethylene and ABA are probably key developmental regulators of arbuscular mycorrhizae (AM). The first objective of this work was to evaluate the development of MA in overproducing and insensitive mutants to ethylene (epinastic and Never ripe, respectively) and verify if enzymes related to plant defense system are differentially regulated by ethylene during the symbiosis development. The colonization of epinastic (epi) roots by G. clarum was significantly reduced when compared with Micro-Tom (MT), moreover, the functionality of the symbiosis as demonstrated by transcripts accumulation of LePT4, was strongly reduced when compared with MT. Still, the pattern of colonization and functionality of the symbiosis in the Nr mutant did not differ from MT. Induction in the transcripts accumulation of genes encoding chitinase and enzymes related to oxidative stress was observed in epi mutant, whereas transcripts accumulation of -1, 3-glucanase was strongly induced in the Nr mutant. The second objective was to determine whether the reduced colonization observed in mutants deficient in ABA is dependent on ethylene production. For this purpose, mutants that differ in ABA deficiency and produce different amounts of ethylene (notabilis and sitiens) and the epi mutant were inoculated with G. clarum and treated with an ethylene inhibitor called aminoethoxivinilglicin (AVG). The intraradical colonization of G. clarum in epi and notabilis (not) mutants was significantly reduced when compared with MT and sitiens mutant was less susceptible to colonization in comparison with other genotypes. The application of AVG to 10 µM completely restored the colonization in the epi but not in mutants deficient in ABA. The transcripts accumulation of LePT4 confirmed the results of colonization. The genes that encode key enzymes in the biosynthesis of ethylene, LeACS2 and LeACO4, were positively regulated by inoculation with G. clarum and the restoration in the development of MA observed in epi which received AVG probably involved ACC oxidase (LeACO4). Transcripts accumulation of genes that encode ACC oxidase (LeACO1 and LeACO4) were induced significantly in sit showing that overproduction of ethylene in this mutant can involve ACC oxidase. Finally, the induction in the accumulation of gene transcripts LeNCED was observed in all genotypes and mycorrhizal roots of epi which received AVG demonstrating that LeNCED is regulated positively by the inoculation with G. clarum and that ethylene regulates the expression of this gene. Results show that ethylene and ABA are involved in regulating of MA development and ethylene modulates the expression of genes related to the plant defense system allowing the establishment and functionality of the symbiosis.

Os hormônios vegetais etileno e ABA são possíveis reguladores chave do desenvolvimento das micorrizas arbusculares (MAs). O primeiro objetivo deste trabalho foi avaliar o desenvolvimento da MA em mutantes superprodutores e insensíveis ao etileno (epinastic e Never ripe, respectivamente) e verificar se enzimas relacionadas ao sistema de defesa vegetal são reguladas diferencialmente pelo etileno durante o desenvolvimento da simbiose A colonização de raízes de epinastic (epi) por G. clarum foi significativamente reduzida quando comparada com Micro-Tom (MT), além disso, a funcionalidade da simbiose, demonstrada pelo acúmulo de transcritos de LePT4, foi fortemente reduzida quando comparada com MT. Por outro lado, o padrão de colonização e funcionalidade da simbiose no mutante Nr não diferiu de MT. Indução no acúmulo de transcritos de genes que codificam quitinases e enzimas relacionadas ao estresse oxidativo foi observada no mutante epi, enquanto o acúmulo de transcritos de uma -1,3-glucanase foi fortemente induzido no mutante Nr. O segundo objetivo foi verificar se a colonização reduzida observada em mutantes deficientes em ABA é dependente da produção do etileno. Para tanto, mutantes que diferem na deficiência de ABA e produzem diferentes quantidades de etileno (notabilis e sitiens) e o mutante epi foram inoculados com G. clarum e tratados com aminoethoxivinilglicina (AVG), um inibidor de etileno. A colonização intrarradicular de G. clarum nos mutantes epi e notabilis (not) foi significativamente reduzida quando comparada com MT, sendo que o mutante sitiens (sit) foi o menos susceptível à colonização em relação aos demais genótipos. A aplicação de AVG a 10 µM restaurou completamente a colonização em epi, mas não nos mutantes deficientes em ABA. O acúmulo de transcritos de LePT4 confirmou os resultados de colonização. Os genes que codificam enzimas chave na biossíntese do etileno, LeACS2 e LeACO4, foram regulados positivamente pela inoculação com G. clarum, e a restauração do desenvolvimento da MA observada em epi que recebeu AVG, provavelmente envolveu ACC oxidase (LeACO4). O acúmulo de transcritos dos genes que codificam ACC oxidase (LeACO1 e LeACO4) foi induzido significativamente em sit, mostrando que a superprodução de etileno observada neste mutante pode envolver a regulação da ACC oxidase. Por fim, indução no acúmulo de transcritos do gene LeNCED foi observada em todos os genótipos micorrizados e em raízes de epi que receberam AVG, demonstrando que LeNCED é regulado positivamente pela inoculação com G. clarum e que o etileno regula a expressão deste gene. Os resultados demonstram que etileno e ABA estão envolvidos na regulação do desenvolvimento de MA e que etileno modula a expressão de genes relacionados ao sistema de defesa vegetal permitindo o estabelecimento de uma simbiose funcional. / The plant hormones ethylene and ABA are probably key developmental regulators of arbuscular mycorrhizae (AM). The first objective of this work was to evaluate the development of MA in overproducing and insensitive mutants to ethylene (epinastic and Never ripe, respectively) and verify if enzymes related to plant defense system are differentially regulated by ethylene during the symbiosis development. The colonization of epinastic (epi) roots by G. clarum was significantly reduced when compared with Micro-Tom (MT), moreover, the functionality of the symbiosis as demonstrated by transcripts accumulation of LePT4, was strongly reduced when compared with MT. Still, the pattern of colonization and functionality of the symbiosis in the Nr mutant did not differ from MT. Induction in the transcripts accumulation of genes encoding chitinase and enzymes related to oxidative stress was observed in epi mutant, whereas transcripts accumulation of -1, 3-glucanase was strongly induced in the Nr mutant. The second objective was to determine whether the reduced colonization observed in mutants deficient in ABA is dependent on ethylene production. For this purpose, mutants that differ in ABA deficiency and produce different amounts of ethylene (notabilis and sitiens) and the epi mutant were inoculated with G. clarum and treated with an ethylene inhibitor called aminoethoxivinilglicin (AVG). The intraradical colonization of G. clarum in epi and notabilis (not) mutants was significantly reduced when compared with MT and sitiens mutant was less susceptible to colonization in comparison with other genotypes. The application of AVG to 10 µM completely restored the colonization in the epi but not in mutants deficient in ABA. The transcripts accumulation of LePT4 confirmed the results of colonization. The genes that encode key enzymes in the biosynthesis of ethylene, LeACS2 and LeACO4, were positively regulated by inoculation with G. clarum and the restoration in the development of MA observed in epi which received AVG probably involved ACC oxidase (LeACO4). Transcripts accumulation of genes that encode ACC oxidase (LeACO1 and LeACO4) were induced significantly in sit showing that overproduction of ethylene in this mutant can involve ACC oxidase. Finally, the induction in the accumulation of gene transcripts LeNCED was observed in all genotypes and mycorrhizal roots of epi which received AVG demonstrating that LeNCED is regulated positively by the inoculation with G. clarum and that ethylene regulates the expression of this gene. Results show that ethylene and ABA are involved in regulating of MA development and ethylene modulates the expression of genes related to the plant defense system allowing the establishment and functionality of the symbiosis.

Dans son environnement, la plante interagit sans cesse avec des microorganismes. Elle est confrontée à une variété de microorganismes bénéfiques, neutres ou pathogènes, qui sont fortement dépendants des ressources carbonées que la plante libère dans le sol, leur conférant ainsi un apport de nutriments et d’énergie nécessaire à leur développement. La mycorhize à arbuscules est une symbiose mutualiste formée par 80% des plantes terrestres datant de l’Ordovicien, i.e. environ 450 millions d’années avant notre ère. L’ensemble des travaux de recherche présenté au sein de ce manuscrit, s’inscrit dans le cadre de deux objectifs généraux : (i) acquérir une meilleure compréhension des mécanismes à l’origine des relations trophiques chez la plante mycorhizée, et (ii) étudier l’impact de la mycorhization sur la production végétale tant en terme de quantité que de qualité. Nous avons étudié la réponse à la mycorhization de variétés anciennes de blé afin d’appréhender s’il existait une différence dans un environnement semi-contrôlé (serres) ou dans un environnement non contrôlées (champ), et/ou en fonction de la communauté de champignons mycorhiziens à arbuscules présente. Nos résultats ont mis en évidence que la mycorhization et la nature des champignons mycorhiziens arbusculaires endogènes peuvent influer sur le rendement au stade tallage, même chez des variétés de blé ayant une faible capacité mycorhizogène. Nous avons aussi illustré l’importance de bien choisir les critères utilisés pour mesurer ce gain éventuel. Dans un deuxième axe de recherche nous nous sommes intéressés à l’impact de la mycorhize à arbuscules sur le développement de la tomate Micro-Tom, et les échanges trophiques au cours de l’interaction. Nous avons pu mettre en évidence, grâce à une analyse multivariée, à la fois des différences de comportement parmi les plantes particulièrement aux stades fruit vert mature et fruit rouge mature selon la nature des champignons mycorhiziens à arbuscules présents, et des potentiels phénomènes d’interaction entre deux souches de champignons mycorhiziens à arbuscules; nos résultats confirmant que les arbuscules ne sont pas les seules sites d’échanges dans la mycorhize à arbuscules. Le troisième axe de ce travail a porté sur l’impact potentiel des méthodes de production de semences de variétés anciennes de tomate en condition de sécheresse, à la fois sur la communauté endogène de champignons mycorhiziens au champ, sur la tolérance de la plante au stress hydrique et sur la production végétale en terme de rendement et de qualité des fruits. Le site d’expérimentation se situait au Potager de santé (ferme de production de semences gérée par Pascal Poot). Nos résultats ne montrent aucune différence, en conditions de stress hydrique au champ, entre des variétés cultivées régulièrement sur ce site et des variétés commerciales. Alors, on peut se demander si d’autres facteurs liés au site d’exploitation, tels que les microorganismes interagissant avec les racines de la plante pourraient être à l’origine de la tolérance accrue au stress hydrique. Des travaux sont en cours au laboratoire pour étudier cette hypothèse. L’ensemble de ces travaux ouvrent la voie à de nouvelles recherches visant à élucider les mécanismes moléculaires impliqués dans la régulation des échanges trophiques au cours de la mycorhize à arbuscules et à la valorisation des services écosystémiques rendus par la mycorhize à arbuscules au champ. / In its environment, the plant interacts constantly with microorganisms. It is confronted with a variety of beneficial, neutral or pathogenic microorganisms, which are highly dependent on the carbon resources that the plant releases into the soil, giving them a supply of nutrients and energy necessary for their development. The arbuscular mycorrhiza is a mutualistic symbiosis formed by 80% of terrestrial plants from the Ordovician period, i.e. about 450 million years ago. The research presented in this manuscript was focused on two main goals: (i) to gain a better understanding of the mechanisms underlying trophic relationships in the mycorrhizal plant, and (ii) to study the impact of mycorhization on plant production, both in terms of quantity and quality. We investigated the mycorrhizal response of wheat landraces in order to understand if there were differences in a semi-controlled environment (greenhouses) or in an uncontrolled environment (field), and / or depending on the community of mycorrhizal fungi. Our results showed that mycorrhization and the nature of endogenous arbuscular mycorrhizal fungi can affect yield, even in wheat varieties with low mycorrhizal ability. We also highlighted the importance of choosing the criteria used to measure this potential gain. In a second line of research, we were interested in the impact of arbuscular mycorrhiza on the development of Micro-Tom tomato, and the trophic exchanges during the interaction. Multivariate analysis revealed behavioral differences between plants at mature green fruit and red ripening stages depending on arbuscular mycorrhizal fungal strain, as well as potential interaction event between two arbuscular mycorrhiza fungus trains. Our results confirm that the arbuscules are not the only sites of exchange in arbuscular mycorrhiza. The third axis of this work focused on the potential impact of seed production methods of ancient tomato varieties in drought condition, both on the endogenous community of arbuscular mycorrhizal fungi in the field, on the tolerance of the plant to water stress and on crop production in terms of fruit yield and quality. The experimental site was located in the Potager de santé (seed farm managed by Pascal Poot). Our results show no difference, under conditions of water stress in the field, between varieties regularly cultivated on this site and commercial varieties. Then, one may wonder if other factors related to the exploitation site, such as the beneficial microorganisms interacting with the roots of the plants could be at the origin of the increased tolerance to water stress. Work is underway in the laboratory to study this hypothesis. All of this work paves the way for new research aimed at elucidating the molecular mechanisms involved in the regulation of trophic exchanges during arbuscular mycorrhizae and the valuation of the ecosystem services rendered by arbuscular mycorrhizae in the field.

Situé au sein de la plaine de la Bekaa au Liban, le fleuve du Litani est sujet à divers rejets agricoles, industriels, domestiques et urbain. Lors de l'irrigation des parcelles agricoles, les eaux du fleuve contaminent le sol et les cultures présentant ainsi un risque pour la santé de l'Homme et l’environnement. Parmi les méthodes de remédiation émergentes et en adéquation avec le développement durable figure la phytoremédiation assistée par les champignons mycorhiziens arbusculaires (CMA). Cependant, la rentabilité de ce mode de gestion constitue l'un des principaux freins à son développement et la valorisation de produits biosourcés, à hautes valeurs ajoutées, issus de la biomasse végétale produite sur ces sols contaminés permettrait d'abaisser les coûts globaux de gestion et de requalification de ces sols pollués. Parmi les filières de valorisation éco-innovantes, la culture de plantes à parfums aromatiques et médicinales (PPAM) productrices d'huiles essentielles (HE) à activités biologiques peut être suggérée comme une option prometteuse. Ainsi, l'objectif de ce travail de thèse a consisté tout d'abord à caractériser le sol d'une parcelle expérimentale située à Marj-Bekaa et directement irriguée par les eaux du Litani, puis à proposer un mode de gestion basé sur la production d'HE pouvant ainsi répondre aux attentes environnementales, économiques et sociales. Nos résultats montrent que la parcelle expérimentale, située à Marj-Bekaa et directement irriguée par les eaux du Litani, est principalement contaminée par des éléments traces métalliques [Ni (88 mg.Kgˉ ¹), Cr (122 mg.Kgˉ ¹), V (170 mg.Kgˉ ¹) et Mn (551 mg.Kgˉ ¹) et des polluants organiques [les alcanes (2.5 g.Kgˉ ¹ du sol)]. Cette contamination est à l'origine d'une (1) cytotoxicité vis-à-vis des cellules pulmonaires et hépatiques mise en évidence grâce au dosage de deux activités enzymatiques, la lactate déshydorgénase et la déshydorgénase mithochondriale mais aussi d'une (2) écotoxicité révélée par la réduction (i) des taux de germination des graines (blé, trèfle, luzerne, ray-grass et fétuque), (ii) de la biomasse microbienne du sol [bactéries Gram-positive et Gram-négative, champignons mychoriziens à arbuscules (CMA), champignons saprotrophes et ectomycorhiziens], (iii) de l'abondance et de la diversité des spores de CMA et (iv) de la richesse et de la diversité végétales. Cependant, toutes les plantes indigènes étaient mycorhizées. C'est pourquoi, la faisabilité de la phytoremédiation assistée par les CMA du site expérimental de la Bekaa, a été testée à la fois en microcosmes et in situ en utilisant une plante aromatique productrice d'HE, l'origan (Origanum syriacum L.). Nos résultats ont montré que non seulement l'origan possède un potentiel de dissipation des alcanes mais en plus cette plante ne transfère pas ces polluants dans les HE extraites à partir de sa biomasse aérienne. Par ailleurs, il a été constaté que la mycorhization a une influence sur la composition des HE. En outre, notre étude a permis l'évaluation de diverses activités biologiques (antifongiques, antioxydante et anti-inflammatoire) d'une gamme d'HE extraites de différentes espèces végétales dont l'origan et ce en présence et en absence des cyclodextrines (HP-β-CD), oligosaccharides cycliques qui complexent les HE et augmentent leurs biodisponibilités. / Located in the Bekaa valley in Lebanon, The Litani River is exposed to agricultural, industrial, domestic and urban wastewaters. Through the irrigation of agricultural soils, the river's water contributes to soil and culture contamination and represents a risk for human health and environment. Amongst the emergent sustainable remediation methods, there is arbuscular mycorrhizal fungi (AMF) assisted-phytoremediation. However, one of the limitation in using phytoremediation as depollution method is its socio-economic profitability. Among the eco-innovative valorization processes with high profitability, the cultivation of aromatic and medicinal plants producing essential oils (EO) with biological activities has been suggested as a promising option. Thus, this thesis work aims firstly at characterizing the soil of an experimental site located at Marj-Bekaa and directly irrigated by the Litani's water and secondly at proposing a mode of management of the contaminated soil based on the production of EO that can meet environmental, economic and social expectations. Our findings showed that the soil sampled in Marj-Bekaa is mainly contamined by metal trace elements [Ni (88 mg.Kgˉ ¹), Cr (122 mg.Kgˉ ¹), V (170 mg.Kgˉ ¹) and Mn (551 mg.Kgˉ ¹) and alkanes (2.5 g.Kgˉ ¹ of soil). This contamination is causing (i) cytotoxicity against both bronchial and hepatic human cells revealed by the evaluation of two enzyme activities, extracellular lactate dehydrogenase and mitochondrial dehydrogenase, as well as (2) ecotoxicity pointed out by the reduction of (i) seed germination (wheat, clover, alfalfa, ryegrass and tall fescue), (ii) soil microbial biomass [Gram-positive and Gram-negative bacteria, arbuscular mycorrhizal fungal (AMF), ectomycorrhizal and saprotrophic fungi], (iii) abundance and diversity of AMF spores as well as (iv) the plant diversity and richness. The AMF-assisted phytoremediation of the Bekaa experimental site was evaluated both in microcosms and in situ experiments using an aromatic plant producing EO, oregano (Origanum syriacum L.). Our results revealed that oregano plant possess an alkane's dissipation potential and no polluant transfer is detected in EO. Moreover, the mycorrhization modified the EO composition. On the over hand, our study evaluated several biological (antifungal, antioxidant and anti-inflammatory) activities of a range of EO extracted from many plant species including oregano, in the presence and the absence of cyclodextrines (HP-β-CD), cyclic oligosaccharides that encapsulate EO and enhance their bioavailabilities.

Célèbres depuis l'accident de Seveso en 1976, les dioxines/furanes (PCCD/F) restent, malgré une forte baisse de leurs émissions, un sujet de préoccupation permanent en France et dans le monde. Le rémanence de ces composés organochlorés dans le sol et le risque toxique qu'ils représentent pour l'homme et l'environnement font que la gestion et la remédiation des sols contaminés par les PCDD/F sont devenues une priorité des industriels, législateurs et scientifiques. La phytoremédiation compte parmi les méthodes émergentes de dépollution des sols contaminés en raison de son adéquation avec le développement durable. Elle combine les capacités naturelles des plantes et de leur microbiote rhizosphérique à biodégrader les polluants organiques. Cependant, l'efficacité de cette phytotechnologie est encore souvent limitée, en particulier lorsqu'il s'agit de composés chlorés, à cause de leur récalcitrance, de leur phytotoxicité et leur faible biodisponibilité dans le sol. Ainsi, l'objectif de ce travail de thèse a consisté à étudier les performances de la phytoremédition assistée, en particulier par les champignons mycorhiziens arbusculaires, d'un sol agricole historiquement pollué par les PCDD/F prélevé sur une parcelle expérimentale située à proximité d'un ancien incinérateur. L'ensemble des résultats obtenus mettent en évidence, en particulier, le potentiel de deux espèces végétales, la luzerne et la fétuque, dans la rhizodégradation des PCCDD/F. La végétalisation du sol permet de moduler les communautés microbiennes du sol (bactéries, Archées et champignons) et notamment celles qui semblent impliquées dans la dissipation des PCCDD/F. En revanche, bien que la mycorhization agisse sur les communautés microbiennes du sol, celle-ci n'a pas eu d'impact, dans nos conditions expérimentales, sur la dissipation des PCCDD/F quelles que soit l'origine de l'inoculum utilisé et les espèces mycorhiziennes qui le compose. La dégradation de ces composés organochlorés est plus marquée dans un sol préalablement stérilisé, puis recolonisé par certaines communautés microbiennes spécifiques, impliquées dans la dissipation des PCCDD/F. L'utilisation combinée d'un mélange de rhamnolipides avec l'introduction dans le sol d'une bactérie Sphingomonas wittichii RWI, décrite pour ses capacités de dégradation des PCCDD/F, permet d'accroitre l'efficience de la rhizodégradation des PCDD/F qui se traduit par une baisse significative de la cytotoxicité du sol après phytoremédiation. / Famous since the Seveso accident in 1976, dioxins/furans (PCCD/F) remain, despite a sharp decline in emissions, a subject of permanent concern in France and in the world. The remanence of these organochlored compounds in soil and the toxic risk they represent for humans and the environment mean that the management and remediation of PCDD/F contaminated soil has become a priority for industrialists, legislators and scientists. Phytoremediation is one of the emerging depollution methods of contaminated soils due to Its suitability for sustainable development. It combines the natural capacities of plants and their rhizospheric microbiota to biodegrade organic pollutants. However, the effectiveness of this phytotechnology is still often limited, especially in the case of chlorinated compounds, due to their recalcitrance, phytotoxicity and low bioavailability in the soil. Thus, the thesis aims to study the performance of assisted phytoremission, in particular by mycorrhizal fungi, of an agricultural PCDD / F based-polluted soil from an experimental plot near an old incinerator. The results obtained show the potential of two plant species, alfalfa and tall fescue, in the rhizodegradation of PCCDD/F. Soil vegetation shows to modulate soil microbial communities (bacteria, archaea and fungi) includind those that appear to involved in the dissipation of the PCCDD/F. On the other hand, although mycorrhization affects soil microbial communities, it has not had any impact on the dissipation of PCCDD/F in our experimental conditions, whatever the inoculums origin and the mycorrhizal species which compose it. The degradation of these organochlorined compounds is more significant in a previously sterilized soil and then recolonized by specific microbial communities involved in the PCCDD/Fdissipation. The combined use of rhamnolipids mixture and Sphingomonas wittichii RWI bactrerium described for its degradation capabilities of PCCDD/F makes it possible to increase the efficiency of PCDD/F rhizodegradation which results in a significant decrease in soil cytotoxicity after phytoremediation.