Interactions between plant roots and soil microorganisms in the rhizosphere are critical for plant growth. However, understanding of precisely how root exudates influence the diversity and activity of rhizosphere microorganisms is limited. The main objective of this study was to investigate the effect of radiata pine (Pinus radiata) root exudates on rhizosphere soil microbial communities, with an emphasis on the role of low molecular weight organic anions. The study involved the development and validation of new methods for investigating rhizosphere processes in a purpose-built facility. This included development of an in situ sampling technique using an anion exchange membrane strip to collect a range of organic anions exuded from radiata pine roots grown in large-scale rhizotrons. These included tartarate, quinate, formate, malate, malonate, shikimate, lactate, acetate, maleate, citrate, succinate and fumarate. Soil microbial activity and diversity were determined using dehydrogenase activity and denaturing gradient gel electrophoresis. Links between organic anions in root exudates and rhizosphere soil microbial community structures were investigated by comparing wild type and genetically modified radiata pine trees which were grown in rhizotrons for 10 months. As expected, there was considerable temporal and spatial variability in the amounts and composition of organic anions collected, and there were no consistent or significant differences determined between the two tree lines. Significant differences in rhizosphere microbial communities were detected between wild type and genetically modified pine trees; however, they were inconsistent throughout the experiment. The shifts in microbial communities could have been related to changes in exudate production and composition. Based on results from the main rhizotron experiment, a microcosm study was carried out to investigate the influence of selected pine root exudate sugars (glucose, sucrose and fructose) and organic anions (quinate, lactate and maleate) on soil microbial activity and diversity. Soil microbial activity increased up to 3-fold in all of the sugar and organic anion treatments compared to the control, except for a mixture of sugars and maleate where it decreased. The corresponding impacts on soil microbial diversity were assessed using denaturing gradient gel electrophoresis and 16S rRNA phylochips. Addition of the exudate compounds had a dramatic impact on the composition and diversity of the soil microbial community. A large number of bacterial taxa (88 to 1043) responded positively to the presence of exudate compounds, although some taxa (12 to 24) responded negatively. Organic anions had a greater impact on microbial communities than sugars, which indicated that they may have important roles in rhizosphere ecology of radiata pine. In addition, a diverse range of potentially beneficial bacterial taxa were detected in soil amended with organic anions, indicating specific regulation of rhizosphere microbial communities by root exudates. This project highlighted the considerable challenges and difficulties involved in detailed investigation of in situ rhizosphere processes. Nonetheless, the findings of this study represent a significant contribution to advancing understanding of relationships between root exudates and soil microbial diversity, which will be further enhanced by refinement and application of the specific methodologies and techniques developed.

No description available.

Les sols de montagne constituent un réservoir majeur de carbone stocké sous forme de matière organique (carbone organique du sol, COS), potentiellement hautement vulnérable aux changements des conditions climatiques. Afin de comprendre les répercussions des changements des conditions climatiques sur la dynamique du COS des sols de montagne, cette thèse s'appuie sur une expérimentation de transplantation altitudinale de monolithes de sol de prairie subalpine calcaire, mise en place dans le Jura Suisse en 2009. Cette expérimentation permet de simuler deux scénarios réalistes de changements climatiques attendus au cours du 21éme siècle, visant à réchauffer et assécher le climat (+2°C et +4°C ; -20% et -40% de précipitations).La démarche conceptuelle de cette thèse a été d'étudier les effets des changements des conditions climatiques (variations saisonnières et manipulation climatique) au bout de quatre années d'expérimentation sur (i) la dynamique des communautés microbiennes et de leur activité enzymatique de décomposition du COS, (ii) la dynamique de différents pools de COS qui constituent la ressource énergétique des micro-organismes décomposeurs, (iii) les interactions s'établissant entre les communautés microbiennes et leurs ressources énergétiques et (iv) les stocks de COS du sol.Nos résultats montrent une très forte dynamique saisonnière du processus de décomposition microbienne se traduisant par de fortes activités enzymatiques de décomposition, une biomasse microbienne plus importante et une structure des communautés microbienne différente lors de la saison hivernale par rapport à la saison estivale. Ces résultats sont en lien avec la dynamique observée des pools les plus labiles du COS (C organique extractible à l'eau et C organique particulaire libre), et des modèles d'équations structurelles montrent que les conditions climatiques (variations saisonnières et manipulation climatique) modifient les interactions s'établissant entre les communautés microbiennes et leurs ressources pour contrôler la décomposition enzymatique du COS.Enfin, ce travail de thèse montre une forte diminution des concentrations en COS sous l'effet de la manipulation climatique, qui ne peut être expliquée par une décomposition microbienne accrue du COS. Au contraire, nos résultats suggèrent que la diminution de la concentration en COS pourrait être due à l'accélération des processus pédologiques naturels sous les scénarios de changement climatique au sein de ces sols calcaires de prairies subalpines, avec une décarbonatation accrue favorisant la lixiviation du carbone organique dissous et le lessivage du pool de COS associé aux argiles. Ces résultats inédits offrent de nouvelles perspectives de recherche sur les effets des changements climatiques sur l'évolution des stocks de COS. / Mountain soils stocks huge quantities of carbon as soil organic matter (SOM) which may be highly vulnerable to climate change and thus alter the atmospheric greenhouse gases concentration at a decadal timescale. To understand the effect of climate conditions on the dynamics of mountain soil organic carbon (SOC), a climate change experiment was set up in October 2009 in Swiss Jura subalpine grassland soils. The climate change experiment (soil transplantation) simulated two realistic climate change scenarios, with increased air temperatures ranging between 2 °C and 4 °C and decreased precipitation ranging between 20% and 40%. These changes reflect current predictions of climate change for the 21th century in temperate mountain regions.We studied the effect of climate conditions (climate manipulation and seasonal changes) after four years of climate experiment on (i) the dynamic of microbial decomposition, microbial abundance and community structure, (ii) the dynamic soil organic matter pools with contrasted turnover rate and representing the energetic resource of microbial communities, (iii) the interactions between microbial communities and soil organic matter pools and (iv) the soil organic carbon stocks.This work shows a strong seasonal dynamics of microbial decomposition with higher enzymatic activities, higher microbial abundance and shift of microbial community structure in winter than in summer. These results were linked to the seasonal organic matter labile pools dynamics. Moreover structural equation modeling shows that climate manipulation differently influences the drivers of SOC enzymatic decomposition in summer and winter.Finally, this work shows a strong decrease of soil organic carbon concentration under the climate change manipulation which cannot be explained by an increase of microbial activities. In contrast, our results suggest that the observed climate-induced decrease in bulk soil organic C content was due a SOC decrease in the most biogeochemically stable SOM fraction associated with a decrease in clay content and a decrease of soil calcareous concentration. Thus, our results hint more so towards an effect of SOM leaching (Gavazov, 2013) to explain the climate effect on SOC content than an effect of microbial and/or plant activities.

De nombreux cours d’eau sont exposés aux polluants métalliques. Dans ces milieux, les communautés microbiennes structurées sous forme de biofilms peuvent être affectées par ces polluants. Or, une des questions prégnantes en écotoxicologie concerne l’évaluation des impacts toxiques dans le cas de combinaisons multi-stress. Dans ce contexte, l’objectif principal de ce travail était d’évaluer l’influence de la température sur la réponse du biofilm à une exposition au cuivre (Cu). Cet objectif a été abordé en considérant l’influence de la température, d’une part, sur la sensibilité des communautés au Cu, et d’autre part, sur l’exposition des communautés de biofilm à ce métal. Ces travaux ont été réalisés en microcosmes de laboratoires et menés sur des biofilms prélevés à différentes saisons. Nous avons tout d’abord optimisé les protocoles utilisés pour mesurer i) les niveaux de tolérance des communautés au Cu et ii) la bioaccumulation du Cu dans les biofilms. Les résultats des expérimentations ont révélé que la température pouvait moduler l’impact structural et fonctionnel du Cu sur les biofilms, du fait notamment d’une diminution de la bioaccumulation aux plus fortes températures. En complément, les résultats ont mis en évidence l’influence d’une hausse de la température sur la sensibilité des communautés au Cu, qu’elles aient été préalablement exposées (PICT) ou non à ce métal. Cependant, nous avons observé que les effets de la température sur la réponse du biofilm étaient variables d’une étude à l’autre, suggérant une influence de nombreux paramètres, tels que la composition initiale de la communauté, les niveaux de stress appliqués (température et Cu), le compartiment microbien étudié (phototrophe ou hétérotrophe), ou les fonctions considérées / Many streams are impacted by metallic pollution. In such ecosystems, microbial communities, which grow preferentially as biofilms, can be affected by these pollutants. However, there is a need to better assess the impact of toxic substances under multi-stress interactions. In this context, the main aim of this work was to evaluate the effect of temperature on biofilm response to copper (Cu) exposure. Accordingly, we addressed the influence of temperature on microbial community sensitivity to Cu on the one hand, and its influence on biofilm exposure to this metal on the other hand. Microcosm experiments were performed under laboratory conditions using biofilms sampled in winter or summer. This work allowed us to set up new methodological developments, which were applied to improve the protocols used to measure (i) Cu tolerance levels of biofilm microbial communities and (ii) Cu bioaccumulation in biofilms. Results showed that temperature could modulate structural and functional effects of Cu on biofilms, notably due to a decrease in Cu bioaccumulation at higher temperatures. In addition, our findings indicate that temperature increase could influence the sensitivity of microbial communities to Cu, whether they have been previously chronically exposed (PICT) or not to this metal. Nonetheless, temperature effects on biofilms varied among experiments, revealing that the influence of temperature on the effects of Cu on microbial biofilms depends on many parameters, such as the initial composition of communities, the level of the applied stresses (temperature and Cu), the microbial compartment studied (i.e. phototrophic or heterotrophic), or the measured functional parameters

No description available.

Of concern in this research were the ecological parameters associated with the establishment of a model invasive plant species, Imperata cylindrica, across a scale of ecological organization. Specifically, the study addressed the species’ ability to: differentially respond to abiotic and biotic constraints during seedling establishment, exhibit a novel underground competitive interference mechanism, and alter the decomposition dynamics in newly invaded ecosystems. Finally, the last portion of the research was centered around creating a predictive habitat model that will provide information on the most important variables responsible for creating habitat for this species. The population level seedling study indicated that soil characteristics and light availability play a significant role in seedling establishment. There were large trends in biomass allocation attributable to soil type with seedlings performing best in high nutrient soils representative of the Mississippi Alluvial Valley physiographic region. I. cylindrica seedlings also showed a positive response to increased seedling density during the initial stages of seedling establishment. The community level research examining a hypothesized novel interference mechanism deployed by I. cylindrica showed a significant and robust pattern of I. cylindrica damaging its own belowground tissue more often than that of its surrounding neighbors. Therefore, it is highly unlikely that I. cylindrica gains a competitive advantage by exposing the native plant assemblage to pathogen invasion (via ruptured tissue) as the plant would expose itself to these pathogens (to which it is evolutionarily naive) at much higher volumes. The ecosystem level examination of this globally important invasive species indicated that I. cylindrica invasion into native systems will significantly accelerate ambient rates of decomposition. Furthermore, fungal community composition in invaded areas was drastically altered as well as bacterial community functional activity in relation to several key enzymes responsible for the decomposition of plant tissue which were produced more abundantly in invaded areas.The landscape-scale analyses and modeling work validated decades of anecdotal evidence and indicated that anthropogenic disturbance factors associated with road maintenance and construction (soil disturbance and vegetation removal) are the principal factors responsible for creating habitat suitable for invasion by this species.

No description available.

<p>  </p> <p>Plant roots form an intimate relationship with a diversity of soil microorganisms. Some soil-borne microbes cause harmful diseases on crops, but others promote plant growth and enhance host resilience against stressors. Beneficial bacteria have a high potential as a strategy for sustainable agricultural management, many of which have been recognized and commercialized for improving crop growth. Unfortunately, field inoculants of beneficial bacteria often give inconsistent results due to various environmental factors hindering their beneficial properties. Improving crop production utilizing beneficial bacteria requires two approaches: 1) breeding for crops with the enhanced association for beneficial bacteria and 2) improving formulation methods for producing more potent microbial products. To contribute to these goals, we address three critical questions utilizing the tomato root microbiome as a model system. First, we asked how beneficial root-associated bacteria could be efficiently identified. We developed a strategy to select beneficial bacteria from a novel collection of 183 bacterial endophytes isolated from roots of two field-grown tomato species. The results suggest that isolates with similar traits impact plant growth at the same levels, regardless of their taxonomic classification or host origin. Next, we asked whether host genetics contribute to the root microbiome assembly and response to beneficial microbes. An assessment of the root microbiome profile and plant binary interaction experiments suggested the role of host genetics in influencing root recruitment and response to beneficial bacteria. Subsequently, we asked whether root-associated bacteria induce physiological changes in root tissues in the host. We identified two isolates from our bacterial endophyte collection that significantly promoted the growth of tomato genotype H7996 (<em>Solanum lycopersicum</em>). Plant-binary interaction experiments suggested a significant increase of cell wall lignification in the root vasculature starting 96-hour post-inoculation with beneficial bacteria. Additional studies are needed to uncover a possible correlation between the induced vasculature lignification and the growth-promoting effects of the two isolates on H7996. Altogether, our findings highlight the multi-faceted role of root-associated bacteria in promoting plant growth and support the development of crop improvement strategies in optimizing host association with soil bacteria.</p>

Les interactions entre les végétaux et les organismes telluriques sont déterminantes pour la décomposition des matières organiques et la nutrition minérale des plantes. L’objectif général de la thèse était de comprendre comment les interactions multi-trophiques dans la rhizosphere agissent sur la disponibilité en azote minéral et l’allocation en carbone dans la plante. Nous avons mis au point des dispositifs de culture de plante, permettant de contrôler l’environnement biotique des racines (inoculation par des espèces symbiotiques modèles : un protozoaire bactériophage et/ou une espèce mycorhizienne à arbuscules). Nous avons utilisé l’azote 15N et le carbone 13C pour tracer le cheminement de l’azote du sol vers la plante et le carbone assimilé par photosynthèse, de la plante vers le sol et les microorganismes du sol. L’allocation de C vers les racines et la rhizosphère est dépendante de la qualité de la litière foliaire enfouie. La structure de la communauté microbienne déterminée par l’analyse des profils d’acides gras (PLFA) est modifiée par la présence de protozoaires pour la litière à C/N élevé. Les mycorhizes à arbuscules et les protozoaires présentent une complémentarité pour l’acquisition du C et de N par la plante. Les protozoaires remobilisent l’azote de la biomasse microbienne par leur activité de prédation. Les hyphes fongiques transportent du C récent issu de la plante vers des sites riches en matière organique non accessibles aux racines. Ainsi, l’activité de la communauté microbienne est stimulée et la disponibilité en N augmentée lorsque des protozoaires sont présents. Les perspectives de ce travail sont de déterminer si (i) les interactions étudiées dans ce dispositif modèle peuvent être généralisées à d’autres interactions impliquant d’autres espèces de champignons mycorhiziens et de protozoaires (ii) la phénologie de la plante et la composition des communautés végétales influence la nature et l’intensité des réponses obtenues / Plants interact with multiple root symbionts for fostering uptake of growth-limiting nutrients. In turn, plants allocate a variety of organic resources in form of energy-rich rhizodeposits into the rhizosphere, stimulating activity, growth and modifying diversity of microorganisms. The aim of my study was to understand how multitrophic rhizosphere interactions feed back to plant N nutrition, assimilate partitioning and growth. Multitrophic interactions were assessed in a single-plant microcosm approach, with arbuscular mycorrhizal fungi (Glomus intraradices) and bacterial feeding protozoa (Acanthamoeba castellanii) as model root symbionts. Stable isotopes enabled tracing C (13C) and N (15N) allocation in the plant and into the rhizosphere. Plant species identity is a major factor affecting plant-protozoa interactions in terms of N uptake and roots and shoot morphology. Plants adjusted C allocation to roots and into the rhizosphere depending on litter quality and the presence of bacterial grazers for increasing plant growth. The effect of protozoa on the structure of microbial community supplied with both, plant C and litter N, varied with litter quality added to soil. AM-fungi and protozoa interact to complement each other for plant benefit in C and N acquisition. Protozoa re-mobilized N from fast growing rhizobacteria and by enhancing microbial activity. Hyphae of AM fungi acted as pipe system, translocating plant derived C and protozoan remobilized N from source to sink regions. Major perspectives of this work will be to investigate whether (i) multitrophic interactions in our model system can be generalized to other protozoa-mycorrhiza-plant interactions (ii) these interactions are depending on plant phenology and plant community composition

To date, there has been little research into the role of microbial community structure in the functioning of the soil ecosystem and on the links between microbial biomass size, microbial activity and key soil processes that drive nutrient availability. The maintenance of structural and functional diversity of the soil microbial community is essential to ensure the sustainability of agricultural production systems. Soils of the same type with similar fertility that had been under long-term organic and conventional crop management in Canterbury, New Zealand, were selected to investigate relationships between microbial community composition, function and potential environmental impacts. The effects of different fertilisation strategies on soil biology and nitrogen (N) dynamics were investigated under field (farm site comparison), semi-controlled (lysimeter study) and controlled (incubation experiments) conditions by determining soil microbial biomass carbon (C) and N, enzyme activities (dehydrogenase, arginine deaminase, fluorescein diacetate hydrolysis), microbial community structure (denaturing gradient gel electrophoresis following PCR amplification of 16S and 18S rDNA fragments using selected primer sets) and N dynamics (mineralisation and leaching). The farm site comparison revealed distinct differences between the soils in microbial community structure, microbial biomass C (conventional>organic) and arginine deaminase activity (organic>conventional). In the lysimeter study, the soils were subjected to the same crop rotation (barley (Hordeum vulgare L.), maize (Zea mais L.), rape (Brassica napus L. ssp. oleifera (Moench)) plus a lupin green manure (Lupinus angustifolius L.) and two fertiliser regimes (following common organic and conventional practice). Soil biological properties, microbial community structure and mineral N leaching losses were determined over 2½ years. Differences in mineral leaching losses were not significant between treatments (total organic management: 24.2 kg N ha⁻¹; conventional management: 28.6 kg N ha⁻¹). Crop rotation and plant type had a larger influence on the microbial biomass, activity and community structure than fertilisation. Initial differences between soils decreased over time for most biological soil properties, while they persisted for the enzyme activities (e.g. dehydrogenase activity: 4.0 and 2.9 µg g⁻¹ h⁻¹ for organic and conventional management history, respectively). A lack of consistent positive links between enzyme activities and microbial biomass size indicated that similarly sized and structured microbial communities can express varying rates of activity. In two successive incubation experiments, the soils were amended with different rates of a lupin green manure (4 or 8t dry matter ha⁻¹), and different forms of N at 100 kg ha⁻¹ (urea and lupin) and incubated for 3 months. Samples were taken periodically, and in addition to soil biological properties and community structure, gross N mineralisation was determined. The form of N had a strong effect on microbial soil properties. Organic amendment resulted in a 2 to 5-fold increase in microbial biomass and enzyme activities, while microbial community structure was influenced by the addition or lack of C or N substrate. Correlation analyses suggested treatment-related differences in nutrient availability, microbial structural diversity (species richness or evenness) and physiological properties of the microbial community. The findings of this thesis showed that using green manures and crop rotations improved soil biology in both production systems, that no relationships existed between microbial structure, enzyme activities and N mineralisation, and that enzyme activities and microbial community structure are more closely associated with inherent soil and environmental factors, which makes them less useful as early indicators of changes in soil quality.