Abstract Mycorrhizal symbiosis is generally advantageous for plants in nutrient-poor soils. Arcto-alpine areas are relatively nutrient-poor, but abundantly inhabited by non-mycorrhizal species. Possibly, mycorrhizal symbiosis is not favoured due to the harsh climatic conditions and the short growing season, which constrain the photosynthetic gain and growth of the arcto-alpine plants. This hypothesis was theoretically evaluated by assuming that optimal mycorrhizal colonization maximizes the net carbon gain of the host plant. In addition, the prevalence of arbuscular mycorrhizal (AM) and dark-septate endophytic (DSE) fungi along an altitudinal gradient was studied in the field, and their effects on the plant performance were tested in the laboratory. In the model, the photosynthetic nutrient use efficiency (PNUE) had a key role in determining whether mycorrhizal strategy would be optimal for the plant net carbon gain. The model generated several colonization patterns depending on possible changes in PNUE and soil nutrient concentrations along altitudinal gradients. Field studies indicated that species-level colonizations do not yield a consistent pattern along the altitude except for fine endophyte, which increased along an altitudinal gradient. In a high-alpine field site root fungal colonizations were rare. Seasonal shifts in colonizations in low-alpine conditions were not found. DSE fungi were common root-associates in the field. In the laboratory, AM had a positive impact on the performance of Gnaphalium norvegicum at 15°C, but not at 8°C. DSE-inoculation did not colonize the roots, but it had a positive impact on seedling performance, which may be due to the saprophytic activity of the fungus in the substrate. Additionally, mycorrhizal inoculum was found to decrease the performance of a non-mycorrhizal plant in a competition experiment. Species-level mycorrhizal colonization patterns may differ from community-level pattern along altitudinal gradients and the relative abundance of different fungal symbionts may change along with the altitude. The performance of mycorrhizal plants in high-alpine conditions may be decreased due to several factors e.g. low temperature constraints on plant and fungal physiology and allocation, soil disturbances and low availability of inoculum. Climatic constraints for plant photosynthesis may thus affect the mycorrhizal colonization patterns in arcto-alpine conditions, but are not necessarily the primary cause for lower performance of mycorrhizal plants at higher altitudes.

10 Abstract All plants live in symbiosis with fungal endophytes - they can form mutualistic, commensal or parasitic symbioses. Symbiosis of root endophytes, called for their darkly pigmented and septated hyphae dark septate endophytes (DSE), and plants has been often overlooked although its role for plant communities can be very important. Despite their ubiquitous presence in roots of terrestrial and also aquatic plants the influence of DSE on their host plants is still unresolved. Results of previous studies are inconsistent - some reported that DSE have positive effects on their host plant growth and some negative. The main reason for this inconsistency might be their complicated taxonomy and difficult identification of different cryptic species which are morphologically indistinguishable. We were able to complete a unique collection of the most common DSE species, mainly members of the Phialocephala fortinii - Acephala applanata species complex. The collection includes the most common DSE species isolated from roots of forest plant communities. The goal of my thesis was to describe behaviour of DSE in roots of typical forest plants and elucidate their physiological influence on host plants. In vitro resynthesis experiments were used to observe root colonization patterns. Nutrient flow between the plant...

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2018-05-11T19:39:26Z No. of bitstreams: 1 2016 - Rosalba Ortega Fors.pdf: 2620047 bytes, checksum: d7b3d78fdeae080e9bee983dad584881 (MD5) / Made available in DSpace on 2018-05-11T19:39:26Z (GMT). No. of bitstreams: 1 2016 - Rosalba Ortega Fors.pdf: 2620047 bytes, checksum: d7b3d78fdeae080e9bee983dad584881 (MD5) Previous issue date: 2016-02-18 / CNPq / Brazil is the main sugarcane producer worldwide, with the crop accounting for 15% of the total fertilizers used in the country. In this context, the development and application of arbuscular mycorrhizal fungi (AMF) (Phylum Glomeromycota) inoculants represents a promising alternative for increasing the utilization eficiency of chemical fertilizers, mainly the phosphates In the present work a survey of the AMF community was carried out before planting and after harvesting of the "plant cane" in renewal (rotated or not with Brachiaria ruziziensis) and expansion (previously under pasture) areas. A similar assessment was carried out in sugarcane renovation and expansion areas where two experiments of inoculation with diazotrophic bacterias were being conducted. Under greenhouse conditions, two experiments for selecting AMF strains for sugarcane (Variety SP81-3250) in different soils and substrates were carried out. In renewal areas, after maintained sugarcane monocropping, a rotation cycle with B. ruziziensis between the ratoon removal and the new cane planting doesnot influence the AMF species richness. Prolonged monoculture of sugarcane tends to reduce the AMF diversity after the renewal of the sugarcane plantation, but stills quite high compared to other agricultural systems. In pasture areas converted to sugarcane plantation (expansion) the AMF species richness tends to be higher in the first year after the conversion (plant cane) compared to sugarcane renovation areas. The spore density reached the highest values after the "plant cane" harvesting. The AMF isolates with potentiality to compose a mycorrhizal inoculant for sugarcane areAcaulospora colombiana and Claroideoglomus etunicatum which favoured the development of the pre-sprouted seedlings of sugarcane in soil and substrate. Other isolates that promoted the sugarcane seedlings' development ou nutrition, but still need additional studies are Gigaspora margarita, Scutellospora calospora and Rhizophagus clarus. The expansion area soil (with moderate P content) was the most favorable for the sugarcane growth. The Multiplant substrate promoted the highest growth of the seedlings and favored the AMF colonization. The fertillization recommended for sugarcane seedling production inhibited the plants growth, particularly in the substrate Turfa F?rtil. The Sugar Mill substrate stimulated the seedlings growth the least. The rate of dark septate endophytes colonization (DSE) in the sugarcane seedlings of the cultivar SP81-3250 was high, independently of the inoculated AMF isolate. All the AMF isolates tested showed simultaneus colonization with DSE. / O Brasil ? o maior produtor mundial de cana-de-a??car, sendo a cultura respons?vel por 15% dos fertilizantes utilizados no pa?s. Nesse contexto, o desenvolvimento e aplica??o de inoculantes de fungos micorr?zicos arbusculares (FMAs) (Phylum Glomeromycota) representa uma promissora alternativa para incrementara efici?ncia de aproveitamento dos fertilizantes, principalmente os sfatados. No presente trabalho foi realizado um levantamento da comunidade de FMAs pr?-plantio e p?s-colheita da "cana planta" em ?reas de renova??o (rotacionadas ou n?o com Brachiaria ruzizensis) e expans?o (previamente sobre pastagem) do canavial. Uma avalia??o similar foi realizada em ?reas correspondentes a dois experimentos de inocula??o com bact?rias diazotr?ficas. Foram conduzidos, em casa de vegeta??o, dois experimentos de sele??o de linhagens de FMAs para cana-de-a??car (Cultivar SP81-3250) em diferentes solos e substratos. Em ?reas de monocultivo prolongado de cana-de-a??car uma rota??o com B. ruziziensis na ?poca da renova??o n?o influencia a riqueza da comunidade de FMAs. Por?m, a riqueza de FMAs diminui em monocultura prolongada de cana, mas ainda ? elevada comparada com outros sistemas agr?colas. A riqueza de FMAs em pastagem convertida a canavial ? maior na ?cana planta? comparada ? ?reas de renova??o de canavial. As maiores densidades de esporos nas ?reas canavieiras ocorrem ap?s a colheita da ?cana planta?. As linhagens de FMAs com potencialidade para compor um inoculante micorr?zico para cana-de-a??car s?o Acaulospora colombiana Claroideoglomus etunicatum as quais favorecem o desenvolvimento de mudas pr?-brotadas de cana tanto em solo como em substrato. Outras linhagens que precisam de estudos adicionais por promoverem crescimento ou nutri??o de mudas de cana s?o Gigaspora margarita, Scutellospora calospora e Rhizophagus clarus. O solo da ?rea de expans?o, com teores intermedi?rios de P, ? o mais favor?vel para o crescimento da cana-de-a??car. O substrato Multiplant foi o que mais estimulou o crescimento de mudas pr?-brotadas e promove a maior coloniza??o por FMAs. A aduba??o completa recomendada para a produ??o de mudas pr?-brotadas de cana-de-a??car inibiu o crescimento das plantas, particularmente no substrato Turfa F?rtil. O substrato da Usina promoveu o menor crescimento de mudas de cana-de-a??car. A taxa de coloniza??o radicular por DSE nas mudas da cultivar SP81-3250 foi elevada, independentemente da linhagem de FMA inoculada. Todas as linhagens de FMAs avaliadas apresentaram coloniza??o conjunta com DSE.

Le phytomanagement est une méthode de gestion de sites pollués basée sur la capacité des plantes à séquestrer les polluants. L’utilisation de symbiotes fongiques peut représenter un atout afin d’augmenter la production de biomasse. Les endophytes bruns septés (DSE) pourraient stimuler la croissance végétale et augmenter leur protection contre les éléments-traces-métalliques (ETM). Cette thèse se déroule dans le cadre du projet LORVER et vise à comprendre l’interaction « plantes-DSE-sols pollués ». A ces fins, des champignons DSE isolés de racines de peupliers issues de sols pollués par des ETM ont été caractérisés. Ils appartiennent aux genres Leptodontidium, Phialophora, Cadophora et Phialocephala. Trois de ces souches ont ensuite été inoculées à des plantes en présence d’ETM. Dans certains cas, la croissance végétale a été stimulée et une augmentation de la teneur en chlorophylles, en P et en K, ou une réduction de la teneur en Cd dans les parties aériennes ont été mises en évidence. Puis, la souche la plus efficace sur la croissance végétale, Cadophora sp. Fe06, a été utilisée dans un double inoculum avec une souche endomycorhizienne, chez du ray-grass en présence d’ETM. Cette association diminue la teneur en Cd dans les feuilles. Enfin, les mécanismes impliqués dans la tolérance aux ETM chez les DSE ont été examinés via le criblage d’une banque de mutants d’insertions aléatoires, et via l’étude du rôle de la mélanine. Ce travail met en évidence que l’utilisation de DSE, de part leur capacité à coloniser de nombreuses plantes dans différents sols et à stimuler leur croissance, pourrait représenter un atout considérable pour des opérations de phytomanagement / Phytomanagement is a handling method of contaminated sites based on the ability of plants to sequester pollutants. Fungi could favor plant growth in contaminated sites but were far less studied in the context of phytomanagement. Dark septate endophytes (DSE) were reported to improve plant tolerance against metallic trace elements (TE). The present work is part of the LORVER project and aims to understand the “plant-DSE-TE”. DSE were isolated from poplar roots growing on TE-contaminated soils and characterized. They belong to Leptodontidium, Phialophora, Cadophora and Phialocephala genera. Three strains were inoculated to birch and poplar in TE-contaminated soils. Leptodontidium sp. improved plant growth with an increase in chlorophyll, P and K concentrations, whereas Cadophora sp. decreased Cd concentration in shoots of birch. Then, Cadophora sp. Fe06, was used with an endomycorrhizal fungus, to co-inoculate ryegrass in a TE-polluted soil. The co-inoculation leads to the decrease of Cd concentration in shoots. Finally, the mechanisms involved in TE-tolerance by DSE were studied through the screening of a library of Leptondontidium sp. insertional random-mutants and an evaluation of the role of melanin against TE stress. The present work highlights the complexity of the interactions between DSE and plants under TE stress. These interactions were influenced by different parameters including plant species, DSE strains, and soil properties. Nevertheless, the ability of DSE to colonize a broad spectrum of plants in different soils and to promote plant growth, suggest that DSE could represent a substantial benefit for the fungus-assisted phytomanagement of polluted soils

Abstract Most plants form symbiotic associations with various fungi in natural ecosystems. Traditionally, many of these associations are viewed as mutually beneficial, but recent studies show that symbiotic interactions can be complex and labile. I studied the variability of interactions between grasses and fungi, using root-associated fungi and foliar endophytes in grasses as study systems. First, I studied experimentally how root-associated fungi colonize their host grasses in different natural and artificial conditions. I then investigated experimentally how foliar endophytes affect their host grasses, and whether the endophyte contributes to the host’s adaptation to local and/or foreign habitats. Finally, I reviewed the current use of foliar endophytes in agriculture, with a particular focus on Europe, and critically considered their potential for practices beyond agriculture. I found root fungi to be common, but different types of root fungi had contrasting colonization patterns in natural environments. However, I found that grasses lose almost all of their root fungi in controlled and more favourable conditions, indicating that the associations are fairly loose and conditional to environmental context. My results also showed that foliar endophytes affected the host’s performance in varying ways, depending on plant origin and experimental country, indicating that the associations were context dependent and could represent conditional mutualism. I also found that endophytes contribute to plant adaptation only weakly, but that the grasses were clearly locally adapted to their sites of origin, especially in regard to reproduction. However, the grasses of subalpine origin performed well vegetatively also in Northern Finland, suggesting that they may have high adaptive potential under changing climates. The literary review showed that foliar endophytes are successfully used in agriculture, e.g. in the USA and New Zealand, and that they possess the potential for several practical applications. However, the intentional use of endophyte-enhanced grasses is non-existent in Europe, although many European grass cultivars have great potential for improvement via endophytes. Taken together, these results show that plant–fungal interactions are highly variable along sites, environmental contexts and origins of the symbiotum, making predictions for these interactions difficult. / Tiivistelmä Luonnollisissa ekosysteemeissä melkein kaikilla kasveilla on symbionttisia sienikumppaneita. Perinteisesti monien näiden vuorovaikutusten on oletettu olevan molemmille hyödyllisiä, mutta viimeaikaiset tutkimukset osoittavat symbionttisten yhteyksien olevan vaihtelevia. Väitöskirjassani tutkin tätä heinien ja sienien välisten yhteyksien vaihtelevuutta, käyttäen heinissä esiintyviä juurisieniä ja lehtiendofyyttejä tutkimuskohteinani. Ensiksi tutkin kokeellisesti, kuinka juurisienet kolonisoivat heiniä erilaisissa luonnon- ja kasvihuoneolosuhteissa. Seuraavaksi tutkin kokeellisesti, kuinka lehtiendofyytit vaikuttivat heinien menestymiseen ja edesauttoivatko endofyytit heinien sopeutumista paikallisiin ja/tai vieraisiin elinympäristöihin. Viimeiseksi selvitin kirjallisuuskatsauksen avulla, kuinka lehtiendofyyttejä hyödynnetään maataloudessa ja arvioin endofyyttien potentiaalista käyttöarvoa maatalouden ulkopuolella, erityisesti keskittyen niiden hyödyntämiseen Euroopassa. Tutkimukseni osoitti, että heinien juurisienet ovat yleisiä, mutta niiden keskinäiset runsaussuhteet vaihtelivat luonnollisissa ympäristöissä. Kasvihuoneolosuhteissa heinät kuitenkin menettivät juurisienensä, viitaten siihen, että kyseinen yhteys on melko löyhä ja riippuvainen ympäristöstä. Tutkimukseni osoitti myös, että lehtiendofyytit vaikuttivat heinien menestykseen vaihtelevasti riippuen heinien alkuperästä sekä koemaasta, viitaten siihen, että nämä yhteydet ovat niin ikään olosuhteista riippuvaisia. Endofyytti vaikutti vain heikosti heinien sopeutumiseen, mutta heinät olivat selkeästi paikallisesti sopeutuneita niiden alkuperäisiin elinympäristöihin, erityisesti heinien lisääntymisen suhteen. Alppien heinät kuitenkin menestyivät vegetatiivisesti myös Pohjois-Lapissa, mikä viittaa siihen, että näillä heinillä saattaa olla korkea sopeutumispotentiaali muuttuvissa olosuhteissa. Kirjallisuuskatsaukseni osoitti, että lehtiendofyyttejä käytetään menestyksekkäästi mm. USA:n ja Uudessa-Seelannin maataloudessa. Euroopassa niiden käyttö on kuitenkin lähes olematonta, vaikka endofyyteillä voisi olla monia käyttömahdollisuuksia, sekä maataloudessa että ympäristön hoidossa. Kaiken kaikkiaan tutkimukseni osoittavat, että heinien ja sienten väliset vuorovaikutukset ovat hyvin vaihtelevia riippuen ympäristöstä ja heinien alkuperästä, minkä vuoksi näiden sienien vaikutuksia heiniin on vaikea ennustaa.

réalisé en cotutelle avec la Faculté des Sciences de Tunis, Université Tunis El Manar. / Le pois chiche (Cicer arietinum L.) a l’avantage de pouvoir assimiler l'azote atmosphérique grâce à son association symbiotique avec des bactéries du genre Mesorhizobium. Malgré cet effet bénéfique sur les systèmes culturaux, le pois chiche réduit parfois la productivité du blé qui la suit. Cet effet négatif du pois chiche pourrait provenir d’une réaction allélopathique à ses exsudats racinaires ou résidus, ou de changements inopportuns dans la communauté microbienne du sol induits par la plante. L'amélioration des interactions symbiotiques du pois chiche pourrait améliorer la performance économique et environnementale des systèmes culturaux basés sur le blé. L’objectif à long terme de ce travail est d'améliorer l’influence du pois chiches sur son environnement biologique et sur la productivité du système cultural. À court terme, nous voulons 1) vérifier l'effet des champignons endophytes sur la performance de cultivars de pois chiche de type desi et kabuli, particulièrement en conditions de stress hydrique, ainsi que sur celle d’une culture subséquente de blé dur, 2) identifier des cultivars de pois chiche capables d’améliorer la qualité biologique de sols cultivés, 3) vérifier que des composés biologiquement actifs sont présents dans les racines des différents cultivars de pois chiches et 4) définir la nature de l’activité (stimulation ou inhibition) des ces composés sur les champignons endomycorhiziens à arbuscules (CMA), qui sont des microorganismes bénéfiques du sol reconnus. L’inoculation du pois chiche avec des champignons endophytes indigènes en serre a augmenté la tolérance à la sécheresse du cultivar de type kabuli à feuille simple CDC Xena et amélioré la nutrition azotée et phosphatée d’un cultivar de type desi, cv. CDC Nika, cultivé en conditions de stress hydrique. La germination des graines de blé dur fut meilleure lorsque celles-ci étaient semées dans les débris de pois chiche inoculé de type kabuli. Le sol dans lequel le génotype de pois chiche à feuille simple CDC Xena fut cultivé mais duquel tout le matériel végétal de pois chiche fut retiré a fortement inhibé la germination des semences de blé dur, ce qui suggère un effet des exsudats racinaires sur la communauté microbienne du sol associée à cette variété de pois chiche. En champ, les cultivars de pois chiche ont influencé différemment la composition des communautés de champignons de la rhizosphère. Les espèces de champignons pathogènes étaient infréquentes et les espèces saprotrophiques et de CMA étaient fréquentes dans la zone des racines du cultivar de type desi CDC Anna. L’effet des composés contenus dans les fractions séparées par HPLC et solubles en solution de méthanol à 25% et 50% de l’extrait racinaire de ce cultivar sur la germination de spores de CMA a été testé in vitro. Les deux espèces de CMA utilisées ont répondu différemment à l’exposition aux composés testés, révélant un mécanisme impliqué dans l’association préférentielle entre les plantes hôtes et les CMA qui leurs sont associés. Nous concluons que le génotype de pois chiche influence la composition de la communauté microbienne qui lui est associée et que cette influence est reliée au moins en partie aux molécules bioactives produites par les racines de la plante. D’autre part, la productivité du pois chiche et de la culture subséquente pourrait être favorisée par la manipulation de leurs champignons endophytes par inoculation. / Chickpea (Cicer arietinum L.) has the ability to bring free N into cropping systems, but is only a fair rotation crop, leading to lower yield in following wheat crops, as compared to medic, vetch or lentil. The negative effects of a chickpea plant on the following wheat crops could come from chickpea root exudates, their residues or their influence on the soil microbial community. The identification of chickpea cultivars best able to promote soil biological quality and the growth of a subsequent crop in rotation will help farmers in selecting better crop rotations and, thus, will improve crop management in soil zone growing chickpea. The global objective of this research is to improve the fitness of chickpea crops to their biological environment and to improve the ability of the plant to enhance soil biological quality. The specific objectives were (1) to verify that the productivity of chickpea and subsequent crops could be promoted through the inoculation by some indigenous endophytic fungi particularly under drought stress conditions (2) to verify the existence of variation in the rhizospheric associations of field-grown chickpea, as it is a necessary condition for the selection of genotypes with improved compatibility with beneficial microorganisms. (3) to identify the biologically active compounds present in the root extracts of chickpea cultivars with contrasting phenotypes, and assess their effect on beneficial and pathogenic soil microorganisms. The greenhouse experiments show that inoculation with indigenous endophytes increased drought tolerance of the unifoliate Kabuli chickpea CDC Xena and the N and P nutrition of the drought stressed Desi chickpea CDC Nika. Inoculation of both Kabuli chickpea varieties with indigenous endophytes improved wheat seeds germination in tissues amended soil. Residue-free soil previously growing the unifoliate Kabuli chickpea CDC Xena strongly inhibited durum seed germination suggesting an effect of root exudates on the soil microbial community, with this Kabuli chickpea variety. In a field experiment, the fungal diversity in cultivated Prairie dryland appeared to host a large array of fungal groups known to reduced plant nutrient, water and biotic stresses, and chickpea genotypes influenced differently the composition and biomass of the soil microbial community. The Desi chickpea CDC Anna was associated with high diversity of arbuscular mycorrhizal fungi (AMF) and culturable fungi, favored the proliferation of soil bacteria and fungal genus hosting biocontrol agents, and developed high AM root colonization level, as compared to the three Kabuli genotypes examined. The HPLC fractions of the roots of chickpea cultivar CDC Anna were recovered and the effects of these fractions on AM fungal spore germination were assayed in multi-well plates. Root extract fractions affect in a different ways the percentage of spores’ germination of Glomus etunicatum and Gigaspora Rosea. We concluded that the genotype of chickpea plants influences the composition of the associated microbial community, and this influence may be related to molecular signals produced by the plants. Furthermore, the productivity of chickpea and subsequent crops could be promoted through the inoculation with indigenous endophytic fungi.

Le pois chiche (Cicer arietinum L.) a l’avantage de pouvoir assimiler l'azote atmosphérique grâce à son association symbiotique avec des bactéries du genre Mesorhizobium. Malgré cet effet bénéfique sur les systèmes culturaux, le pois chiche réduit parfois la productivité du blé qui la suit. Cet effet négatif du pois chiche pourrait provenir d’une réaction allélopathique à ses exsudats racinaires ou résidus, ou de changements inopportuns dans la communauté microbienne du sol induits par la plante. L'amélioration des interactions symbiotiques du pois chiche pourrait améliorer la performance économique et environnementale des systèmes culturaux basés sur le blé. L’objectif à long terme de ce travail est d'améliorer l’influence du pois chiches sur son environnement biologique et sur la productivité du système cultural. À court terme, nous voulons 1) vérifier l'effet des champignons endophytes sur la performance de cultivars de pois chiche de type desi et kabuli, particulièrement en conditions de stress hydrique, ainsi que sur celle d’une culture subséquente de blé dur, 2) identifier des cultivars de pois chiche capables d’améliorer la qualité biologique de sols cultivés, 3) vérifier que des composés biologiquement actifs sont présents dans les racines des différents cultivars de pois chiches et 4) définir la nature de l’activité (stimulation ou inhibition) des ces composés sur les champignons endomycorhiziens à arbuscules (CMA), qui sont des microorganismes bénéfiques du sol reconnus. L’inoculation du pois chiche avec des champignons endophytes indigènes en serre a augmenté la tolérance à la sécheresse du cultivar de type kabuli à feuille simple CDC Xena et amélioré la nutrition azotée et phosphatée d’un cultivar de type desi, cv. CDC Nika, cultivé en conditions de stress hydrique. La germination des graines de blé dur fut meilleure lorsque celles-ci étaient semées dans les débris de pois chiche inoculé de type kabuli. Le sol dans lequel le génotype de pois chiche à feuille simple CDC Xena fut cultivé mais duquel tout le matériel végétal de pois chiche fut retiré a fortement inhibé la germination des semences de blé dur, ce qui suggère un effet des exsudats racinaires sur la communauté microbienne du sol associée à cette variété de pois chiche. En champ, les cultivars de pois chiche ont influencé différemment la composition des communautés de champignons de la rhizosphère. Les espèces de champignons pathogènes étaient infréquentes et les espèces saprotrophiques et de CMA étaient fréquentes dans la zone des racines du cultivar de type desi CDC Anna. L’effet des composés contenus dans les fractions séparées par HPLC et solubles en solution de méthanol à 25% et 50% de l’extrait racinaire de ce cultivar sur la germination de spores de CMA a été testé in vitro. Les deux espèces de CMA utilisées ont répondu différemment à l’exposition aux composés testés, révélant un mécanisme impliqué dans l’association préférentielle entre les plantes hôtes et les CMA qui leurs sont associés. Nous concluons que le génotype de pois chiche influence la composition de la communauté microbienne qui lui est associée et que cette influence est reliée au moins en partie aux molécules bioactives produites par les racines de la plante. D’autre part, la productivité du pois chiche et de la culture subséquente pourrait être favorisée par la manipulation de leurs champignons endophytes par inoculation. / Chickpea (Cicer arietinum L.) has the ability to bring free N into cropping systems, but is only a fair rotation crop, leading to lower yield in following wheat crops, as compared to medic, vetch or lentil. The negative effects of a chickpea plant on the following wheat crops could come from chickpea root exudates, their residues or their influence on the soil microbial community. The identification of chickpea cultivars best able to promote soil biological quality and the growth of a subsequent crop in rotation will help farmers in selecting better crop rotations and, thus, will improve crop management in soil zone growing chickpea. The global objective of this research is to improve the fitness of chickpea crops to their biological environment and to improve the ability of the plant to enhance soil biological quality. The specific objectives were (1) to verify that the productivity of chickpea and subsequent crops could be promoted through the inoculation by some indigenous endophytic fungi particularly under drought stress conditions (2) to verify the existence of variation in the rhizospheric associations of field-grown chickpea, as it is a necessary condition for the selection of genotypes with improved compatibility with beneficial microorganisms. (3) to identify the biologically active compounds present in the root extracts of chickpea cultivars with contrasting phenotypes, and assess their effect on beneficial and pathogenic soil microorganisms. The greenhouse experiments show that inoculation with indigenous endophytes increased drought tolerance of the unifoliate Kabuli chickpea CDC Xena and the N and P nutrition of the drought stressed Desi chickpea CDC Nika. Inoculation of both Kabuli chickpea varieties with indigenous endophytes improved wheat seeds germination in tissues amended soil. Residue-free soil previously growing the unifoliate Kabuli chickpea CDC Xena strongly inhibited durum seed germination suggesting an effect of root exudates on the soil microbial community, with this Kabuli chickpea variety. In a field experiment, the fungal diversity in cultivated Prairie dryland appeared to host a large array of fungal groups known to reduced plant nutrient, water and biotic stresses, and chickpea genotypes influenced differently the composition and biomass of the soil microbial community. The Desi chickpea CDC Anna was associated with high diversity of arbuscular mycorrhizal fungi (AMF) and culturable fungi, favored the proliferation of soil bacteria and fungal genus hosting biocontrol agents, and developed high AM root colonization level, as compared to the three Kabuli genotypes examined. The HPLC fractions of the roots of chickpea cultivar CDC Anna were recovered and the effects of these fractions on AM fungal spore germination were assayed in multi-well plates. Root extract fractions affect in a different ways the percentage of spores’ germination of Glomus etunicatum and Gigaspora Rosea. We concluded that the genotype of chickpea plants influences the composition of the associated microbial community, and this influence may be related to molecular signals produced by the plants. Furthermore, the productivity of chickpea and subsequent crops could be promoted through the inoculation with indigenous endophytic fungi. / réalisé en cotutelle avec la Faculté des Sciences de Tunis, Université Tunis El Manar.