Dissertations / Theses on the topic 'Rhizosphere'
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Burton, C. C. "Phosphomonoesterase and phosphodiesterase activities in rhizosphere and non-rhizosphere soil." Thesis, University of Kent, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378637.
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Dartnall, A. M. "Cyanogenesis and the rhizosphere." Thesis, University of Kent, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.383179.
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Bergfield, William Alan. "Rhizosphere bacteria and benomyl interactions /." free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3036805.
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Levy, Avram. "Modelling rhizosphere interactions of Burkholderia species." University of Western Australia. School of Biomedical and Chemical Sciences, 2007. http://theses.library.uwa.edu.au/adt-WU2007.0123.
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[Truncated abstract] Genus Burkholderia encompasses a diverse collection of bacteria that inhabit rhizospheres throughout the world. Species can provide beneficial returns for eukaryotes, such as nitrogen fixation and nodule formation in plants and biocontrol of cropping systems. Burkholderia members can also cause disease in various animals, fungi and plants. These seemingly conflicting characteristics point to the capacity of Burkholderia spp. to interact with diverse eukaryotes. Within terrestrial ecosystems, Burkholderia spp. must negotiate favourable outcomes with both the primary producers and the primary decomposers, namely plants and fungi. It is these ongoing negotiations which govern many rhizosphere processes and lead to niche differentiation for Burkholderia spp. This research set out to design an in vitro model for investigating Burkholderiaeukaryote interactions. Surface and cellular interactions between Burkholderia spp. and both plants and fungi were then investigated. Specifically, mechanisms of adherence and invasion of plant and fungal cells were studied. The Burkholderia spp. B. vietnamiensis and B. pseudomallei were applied to mycorrhizal fungus spores as well as to several plant species. Bacterial inoculation had varying effects on germination of plant and fungal dormant forms. B. vietnamiensis-inoculation consistently increased Gigaspora decipiens spore germination, while B. pseudomallei produced no significant change. The effect of B. vietnamiensis on Acacia colei seed germination was density dependant, resulting in either increases or decreases in seed germination rates. ... Detection of B. pseudomallei in surface waters and soils was improved by the use of a rapid on-site molecular method. The related species B. thailandensis and B. ubonensis were also cultured from northern Western Australia. Mycorrhizal spores were isolated from soils of melioidosis-endemic regions. Burkholderia spp., including B. pseudomallei and B. vietnamiensis were detected in extracts of these mycorrhizal spores. Therefore, associations of Burkholderia spp. with mycorrhizal spores extend beyond the in vitro setting. These studies have increased our understanding of several specific interactions between Burkholderia spp. and eukaryotes of the rhizosphere. Common themes in adherence and invasion have emerged. Burkholderia spp. are able to closely associate with eukaryotes and to gain access to protected niches. Such access helps to explain the persistence of these bacteria in the environment during periods of desiccation and nutrient limitation.
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Yeates, G. "Microbial population dynamics of the rhizosphere." Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.334939.
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Macey, Michael. "Characterisation of methylotrophs in the rhizosphere." Thesis, University of East Anglia, 2017. https://ueaeprints.uea.ac.uk/66855/.
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Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority of this methanol being produced as a waste metabolic by-product of the growth and decay of plants. There is a large disparity between the amount of methanol estimated as being produced and that which enters the atmosphere. This disparity is believed to be due to the utilisation of methanol by plant associated methylotrophs. The diversity and activity of methylotrophs associated with the root and rhizosphere of pea and wheat plants was assessed through a range of cultivation independent and dependent approaches. Enrichments performed with a range of environmental samples supplemented with methanol resulted in the isolation of several strains of methylotrophic bacteria, including two novel species of methylotroph belonging to the family Methylophilaceae, whose genomes were sequenced and their physiological capabilities assessed. The diversity and abundance of methanol dehydrogenase encoding genes in bulk soil and the pea and wheat rhizosphere was assessed through 454 sequencing and qPCR respectively. Sequencing showed high levels of diversity of methylotrophic bacteria within the bulk soil and also showed a shift in this diversity between the bulk soil and the plant associated soils, in spite of no shift in the abundance of these genes occurring. Active methylotrophs present in the bulk and plant associated soils were identified by DNA stable isotope probing using 13C labelled methanol. Next generation sequencing of the 16S rRNA genes and construction of metagenomes from the 13C labelled DNA revealed members of the Methylophilaceae as highly abundant in all of the soils. A greater diversity of the Methylophilaceae and the genus Methylobacterium were identified as active in the plant associated soils relative to the bulk soil. A 13CO2 stable isotope probing experiment identified methylotrophs as utilising plant exudates in the pea and wheat root and rhizosphere communities. Several methylotrophic genera were identified as exudate utilising, in addition to heterotrophic genera and Actinomycetes. The specific 13C labelled genera were shown to vary between both the wheat and pea plants and between the rhizosphere and root communities.
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Deery, Sarah Jane. "Monitoring rhizosphere microbial communities of tomato." Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/12759/.
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Tomato is an economically important crop that can be devastated by many root infecting pathogens. The development of alternative and sustainable crop cultivation techniques and disease control methods is a must for the tomato industry, due to more strict government regulations and concerns over the sustainability of conventional chemical-intensive agriculture (Dixon and Margerison, 2009). In this thesis, the molecular fingerprinting method Terminal-Restriction Fragment Length Polymorphism (T-RFLP) and next generation sequencing method (pyrosequencing) were used, targeting ITS1, ITS2 and 23S ribosomal DNA to characterize and examine microbial community assemblages in the rhizosphere of tomato. These molecular techniques were employed alongside traditional cultivation, microscopy and plant health assessment techniques to determine the effects of growth media, plant age and disease control methods on rhizosphere microbial populations and tomato root health. Plant age and media were found to significantly affect microbial community assemblages; conversely, microbial populations were not altered by soil amendments or rootstock disease control measures used. These findings suggest that the factors influencing rhizosphere community structure can be ranked by importance. Furthermore, if the most influential factors are kept consistent then rhizosphere microbial structures are robust and difficult to perturb with changes in a factor contributing less control over microbial community composition. No direct link between crop health assessments and rhizosphere microbial community diversity or presence of root pathogens could be established. Furthermore, high abundance of potential pathogens and poor crop health assessments during the growing season did not always result in poor health or disease symptoms at the end of cropping assessment in our trials. These results imply that many factors control the rhizosphere competence and ecological role of different species, ultimately affecting the outcome of disease. As no known methods are capable of efficiently assessing the fate of total microorganisms in the rhizosphere over time and space, this study could be considered as part the ‘descriptive phase’ in this field (Kent and Triplett, 2002). Pyrosequencing increased the resolution and confidence of rDNA analysis compared to T-RFLP, identifying organism within samples to a genus and often species level. Advances in next generation sequencing and analytical tools and pipelines associated with this analysis are likely to develop as these methods become common practice. With this in mind, next generation sequencing represents the future approach for resolving complex microbial communities in environmental samples.
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Curnow, Philip Kenneth. "Influence of root exudates on rhizosphere pseudomonads." Thesis, Imperial College London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286230.
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Sheta, Omar T. "Phytoremediation and rhizosphere manipulation using different amendments." Thesis, University of Glasgow, 2006. http://theses.gla.ac.uk/2147/.
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In two pot experiments using two different crop ryegrass (Lolium perenne) and two flax (Linum usitatissimum) varieties Viola and Elise, ryegrass decreased in the pool of heavy metals compared with bare soil using EDTA as extractant. NH4+ decreased the soil pH, increased EDTA-extractable Zn and increased the Zn uptake. Lime addition increased the pH and depressed Zn uptake. The pool of extractable EDTA was not changed by growing both of the flax varieties. Lime increased EDTA-extractable Cu and Pb significantly, but decreased the Zn, and pH increased in this order NH4+
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Giles, Madeline E. "Where does denitrification occur in the rhizosphere?" Thesis, University of Aberdeen, 2012. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=192249.
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Denitrification is the sequential reduction of NO3- to N2, through a number of intermediary steps, one of which is N2O, a potent green house gas. N2O has a global warming potential over 300 times greater than that of CO2 over a 100 a year period (IPCC, 2007). Soils are a significant source of N2O through the microbially mediated process of denitrification. The rhizosphere is a potentially important source of N2O as rhizodeposited carbon from plant roots can support a larger and more active microbial biomass. Despite this little is known about the effects of low molecular weight carbon (LMWC) on the production of N2O or N2 or how the production of these gases can vary with the small scale variation in carbon quantity found in the rhizosphere. Studies using a soil microcosm revealed that not all LMWC compounds were able to stimulate the production of N2O. Of the three compounds studied the addition of glucose or glutamine to soil resulted in a greater production of N2O than occurred in the control, while the addition of citric acid did not. An experimental system was developed that would allow the creation of a carbon gradient over 6 cm and along which N2O and N2 could be quantified. This allowed an insight into the potential for small scale variation in denitrification. Similar spatial variation in N2O and N2 concentrations were found in both glucose and glutamine treated soil, while no spatial variation in these gasses was found in citric acid treated soil. Peak N2 concentrations occurred closer to the carbon source than peak N2O concentrations, potentially as a result of the higher C : N ratio. This was associated with a shift in the bacterial community, and in glucose treated soil with an increase in the proportion of bacteria containing nosZ or nirK. Despite this spatial patterns in N2O production remained similar even in experiments where the community did not change. The bacterial community did however exert an influence by affecting the magnitude of N2O and N2 produced. The results from this thesis suggest that denitrification has the potential to vary in the rhizosphere as a result of changes in carbon concentrations, carbon compounds and the associated changes in the microbial community.
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Pires, Ana Cecília da Cruz. "Mangrove rhizosphere effect on sediment Archael communities." Master's thesis, Universidade de Aveiro, 2010. http://hdl.handle.net/10773/3491.
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Mestrado em MicrobiologiaOs mangais são económica e biologicamente importantes. Sendo, contudo, cada vez mais ameaçados. Com o intuito de recuperar estes ecossistemas, têm sido desenvolvidos programas de reabilitação. Todavia, geralmente, estes programas não consideram a importância e os possíveis efeitos das interacções entre microrganismos e plantas no ecossistema dos mangais, devido ao número limitado de estudos em ecologia microbiana neste ecossistema. Sabe-se que as raízes de espécies de plantas terrestres influenciam a composição das comunidades bacterianas do solo. Por sua vez, os microrganismos podem contribuir no crescimento e saúde das plantas. Este estudo teve como objectivos desenvolver um sistema primers para reacção em cadeia da polimerase -electroforese em gel com gradiente desnaturante (PCRDGGE) para o domínio Archaea e o género Nanoarchaeum e determinar se as raízes de plantas de mangal (Rhizophora mangle e Laguncularia racemosa) afectam a composição das comunidades de Archaea e Nanoarchaeum que habitam o solo que está sob a influência das raízes de mangal (efeito “rizosfera”). As comunidades de Archaea e Nanoarchaeum foram analisadas por métodos moleculares, como a PCR e o DGGE. Foi desenvolvido um sistema de primers para PCR-DGGE adequado para o domínio Archaea e para o género Nanoarchaeum com base em novas sequências do gene 16S rRNA recentemente publicadas. Os perfis de DGGE foram analisados com a análise de similaridades (ANOSIM), o método de escalonamento multidimensional não paramétrico (MDS) e o índice de Shannon-Wiener. Os resultados de MDS e ANOSIM sugerem que existem diferenças significativas entre as amostras de sedimento e as amostras de rizosfera de R. mangle e L. racemosa. Por sua vez, a análise de MDS sugere que as raízes de L. racemosa afectam mais a composição da comunidade de Archaea do sedimento do que as raízes de R. mangle. Pelo contrário, os resultados de MDS e ANOSIM sugerem que as plantas de L. racemosa e R. mangle não exercem qualquer efeito na composição de Nanoarchaeum e que não existem diferenças entre as amostras de sedimento e as de rizosfera. A diversidade das populações de Archaea e Nanoarchaeum foi estimada pelo índice de Shannon-Wiener; e mostrou que a diversidade de Archaea era mais elevada do que anteriormente descrito em sedimentos marinhos. Com o propósito de completar este estudo algumas bandas dominantes das amostras de rizosfera vão ser clonados e sequenciados, vão ser criadas bibliotecas de clones para Nanoarchaeum e serão efectuadas análises de pirosequenciação às comunidades de Archaea.
Mangrove forests are economically and biologically important; however, they are also increasingly threatened. In order to recuperate these ecosystems, rehabilitation programs have been developed. However, in general these programs have no knowledge about the importance of plant-microbe interactions in mangrove ecosystem. This happens also because the limited numbers of studies on microbial ecology in this ecosystem. Therefore, they do not consider the possible effects of plant-microbe interactions in mangrove reforestation approaches. It is known that roots of terrestrial plant species influence the composition of soil bacterial communities. In turn, microorganisms can contribute to plant growth and health. In this study we aimed to develop a polymerase chain reaction -denaturing gradient gel electrophoresis (PCRDGGE) primer system suitable for Archaea domain and Nanoarchaeum genus and to determine if roots of mangrove plants (Rhizophora mangle and Laguncularia racemosa) affect the composition of Archaea and Nanoarchaeum communities inhabiting the sediment under influence of mangrove roots (rhizosphere effect). Archaea and Nanoarchaeum communities were analyzed using molecular methods, such as PCR and DGGE. A PCR-DGGE primer system suitable for Archaea domain and Nanoarchaeum genus was developed based on new 16S rRNA gene sequences recently published. DGGE profiles were analyzed with analysis of similarities (ANOSIM), non-metric multidimensional scaling (MDS) and Shannon-Wiener index. Both MDS and ANOSIM results suggest that there are significant differences between bulk and rhizosphere samples of R. mangle and L. racemosa. In turn, MDS analyses suggest that roots of L. racemosa affect more the composition of Archaea community from bulk sediment than roots of R. mangle. On the opposite, ANOSIM statistics and MDS analyses suggest that L. racemosa or R. mangle plants do not influence the nanoarchaeal composition and that there are no differences between bulk and rhizosphere samples. Diversity of Archaea and Nanoarchaeum populations was estimated by using the Shannon-Wiener index; and showed that diversity of Archaea was higher than previously reported in marine sediments. With the purpose to complete this study some dominant bands of rhizosphere samples will be cloned and sequenced, clone libraries for Nanoarchaeum will be generated and pyrosequencing analysis of archaeal communities will be performed.
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Obeidy, Carole. "Effet de la végétation sur la mobilité de l’arsenic dans la rhizosphère." Thesis, Saint-Etienne, EMSE, 2011. http://www.theses.fr/2011EMSE0608/document.
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La pollution des sols par l’Arsenic (As) est une préoccupation environnementale grandissante dans plusieurs pays du monde : États-Unis, Canada, Mexique, Chine, Vietnam et France. L’émergence des techniques écologiques dites « phytoremédiation » constitue à l’heure actuelle une des solutions aux problématiques de décontamination des sols pollués par l’As. Aussi, elle permet de rallier le respect de l’état écologique des sites d’une part et le coût financier de traitement d’autre part. Pour cela, l’appréhension des interactions entre le végétal et l’As à l’interface racine-sol est nécessaire afin d’accélerer la mise en place de la phytoremédiation et de tester son efficacité. D’où l’objectif général de ce travail est d’étudier l’effet de quatres espèces végétales Holcus lanatus, Dittrichia viscosa, Lotus corniculatus et Plantago lanceolata sur la mobilité de l’As dans un sol à contamination géochimique en As (2000 mg kg-1). Notre étude a permis au départ de comparer et de caractériser la tolérance et la capacité accumulatrice des espèces séléctionnées à l’égard de l’As en milieu de culture et en sol contaminé chimiquement par l’As. Ensuite, l’étude de la mobilisation de l’As dans la rhizosphère a été réalisée par deux approches d’étude complémentaires : l’approche « rhizopot-rhizons » et l’approche « tapis racinaire ». L’approche « rhizopot-rhizons » nous a permis d’identifier d’intéressantes corrélations entre l’As et les paramètres suivis (NO3-, SO42- , Ca, Mg, P, pH, COD) tout au long de la période de croissance. Nous avons identifié et caractérisé plusieurs processus ifluençant la mobilisation de l’As dans la rhizosphère (alcalinisation/acidification, compétition anionique…). L’avantage de l’approche « rhizopot-rhizons » réside dans le fait que les plantes se sont développées sans prétraitement du substrat de croissance (contamination artificielle, ajout de solutions nutritives…). Par ailleurs, l’approche « tapis racinaire » a permis d’identifier quelques anions organiques dans les racines de P. lanceolata et de mettre en évidence le rôle du Phosphore dans la mobilisation de l’As dans la rhizosphère. Elle permet d’amplifier l’effet du système racinaire sur la mobilité de l’As dans le sol d’une part, et de récupérer entièrement le système racinaire tout en limitant les artefacts liés à la contamination des racines par le sol d’autre partThe pollution of soils with Arsenic (As) is an increasing environmental concerns in several countries in the world: USA, Canada, Mexico, China, Vietnam and France. Recently, the emergence of green technologies sush as “phytoremediation” is considered an attractive soil remediation strategy due to its low cost and soil preservation. For this reason, the understanding of interactions between plants and As at the soil-root interface is necessary in order to accelerate phytoremediation implementation and to test its effectiveness. Hence the aim of this work was to study the effect of four plant species Holcus lanatus, Dittrichia viscosa, Plantago lanceolata and Lotus corniculatus on As mobility in a natural As contaminated soil (up to 2000 mg kg-1). First, we compared and characterized the tolerance behaviour of the four selected species to As and their accumulation capacity in hydroponic and in natural soil conditions. Then, the study of As mobilization in the rhizosphere was conducted by using two approaches "rhizopot-rhizons” and "root mat”. We identified by the “rhizopot-rhizons” approach, some interesting correlations between As and the monitored parameters (NO3-, SO42-, Ca, Mg, P, pH, COD) over the vegetative growing period. We observed several processes affecting As mobilization in the rhizosphere (alkalization / acidification, anionic competition ...). The advantage of this approach is that the plants have grown normally without growth substrate pretreatment (artificial contamination, addition of nutrient solutions ...).Whereas, the "root mat" approach allowed the identification of some organic anions in the root system of P. lanceolata and highlighted the role of phosphorus on As mobilization due mainly toto the easy roots collection at the end of experiment
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Lecomte, Solène. "Anaerobic respiration diversification in Agrobacterium fabrum C58." Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1231.
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La respiration anaérobie peut être un trait essentiel dans le mode de vie, la colonisation de l'environnement et la survie. Jusqu'à présent, la seule respiration anaérobie confirmée chez Agrobacterium spp. est la dénitrification. De façon intéressante, cette voie est inégalement répandue chez les agrobactéries. Ces observations m'ont amené à mon hypothèse, à savoir la respiration anaérobie et notamment la dénitrification pourraient expliquer la coexistence d'agrobactéries et leur distribution dans des niches spécifiques de la rhizosphère. Ma thèse visait à explorer les stratégies de respiration anaérobie d’Agrobacterium spp. et de les relier à l'adaptation de niche écologiques différentes. Les objectifs de ma thèse étaient (1) de caractériser tous les gènes impliqués dans la dénitrification chez A. fabrum C58 in vitro, (2) d'explorer les gènes de la dénitrification nécessaires à la colonisation des racines du maïs et (3) de découvrir de nouvelles respirations anaérobies pendant la colonisation racinaire du maïs (Figure 16). Réaliser des mutants et les tester dans des conditions particulières est le moyen classique de déterminer l'implication d'un gène dans une voie spécifique. Cependant, cette méthode implique une vision à priori et des connaissances solides sur les gènes cibles et ne peut pas être appliquée à toutes les situations. Nous avons alors dû développer une méthode plus adaptée pour identifier les gènes essentiels impliqués dans la croissance dans des conditions anaérobies spécifiques. - Gènes de dénitrification chez A. fabrum C58 in vitro. Pour compléter la voie de dénitrification chez A. fabrum C58 et identifier tous les gènes et régulateurs impliqués dans la dénitrification, nous avons adopté deux stratégies : Premièrement, une vision à priori pour (1) identifier la nitrate réductase impliquée dans la première étape de la dénitrification et (2) valider le rôle d'un ARN non codant dans le contrôle de la dénitrification. Pour ce faire, nous avons construit un mutant napA de A. fabrum C58 et un mutant de l'ARN non codant NopR et nous avons évalué leur croissance et leur capacité à produire du N2O dans des conditions anoxiques. Deuxièmement, pour identifier tous les gènes impliqués dans la dénitrification, nous avons construit une banque de transposons mutants de C58 et testé sa croissance dans des conditions de dénitrification in vitro en présence de nitrate ou de nitrite. - Rôle des gènes de la denitrification de A. fabrum C58 dans la colonisation racinaire du maïs. Il est bien connu que le séquençage de transposons (Tn-Seq) est une méthode très puissante pour déterminer les gènes nécessaires à la croissance bactérienne en présence de leur hôte. Pour déterminer les gènes de dénitrification impliqués dans la colonisation des racines en anoxie, nous avons utilisé la banque construite chez C58 et l’avons inoculée sur les plants de maï cultivées sur un sol fertile et cultivées dans des conditions inondées mimant des conditions anaérobies. Le séquençage des cellules d ‘A. fabrum C58 récupérées mettra en évidence les gènes impliqués dans la colonisation anaérobie de cette niche spécifique. - Découverte de nouvelles voies de respiration anaérobie chez A. fabrum C58. Pour découvrir de nouvelles voies de respiration anaérobie, nous avons mis en place des tests de croissance de C58 dans des conditions anoxiques en présence de sources de C et de N en tant qu'accepteurs terminaux d'électrons. De façon interéssante, en cultivant des souches WT et mutée dans le gène napA au contact de la racine de maïs dans des conditions anoxiques (chapitre 1), nous avons montré une croissance des deux souches. Ce résultats suggère que les exsudats de racine servent d'accepteurs d'électrons terminaux pour la croissance anaérobie de C58. Pour déterminer quels composés exsudés du maïs peuvent servir de TEA, les principaux métabolites ont été identifiés par HPLC et certains ont été testés en tant que TEA dans des conditions anoxiquesAnaerobic respiration may be an essential trait in lifestyle, environment colonization and survival. Until now, the only confirmed anaerobic respiration in Agrobacterium spp. is denitrification. Interestingly, this pathway is unequally widespread among Agrobacteria. These observations led me to my hypothesis which is anaerobic respiration and notably denitrification could explain the coexistence of Agrobacteria and their distribution in specific niches in the rhizosphere. My thesis was undertaken to explore the anaerobic respiration strategies of Agrobacterium spp. and to relate them to niche adaptation. The objectives of my thesis were to (1) characterize all the genes involved in denitrification in A. fabrum C58 in vitro, (2) explore the genes of denitrification that are needed during maize root colonization and (3) discover new anaerobic respirations that occur during maize root colonization (Figure 16). Mutational analysis is the classic way to determine the involvement of a gene in specific pathway. However, this method implies an a priori view and solid knowledge on target genes and cannot be applied for every situation. We have to develop a more adapted method to identify essential genes involved in growth in specific anaerobic conditions. - Denitrification genes in A. fabrum C58 in vitro. To complete denitrification pathway in A. fabrum C58 and identify all the genes and regulators involved in the denitrification function, we adopted two strategies: Firstly, an a priori view to (1) identify the nitrate reductase involved in the first step of denitrification and (2) validate the role of a non-coding RNA in denitrification control. To do so, we constructed a mutant of napA of A. fabrum C58 and a mutant of the non-coding RNA NopR and we evaluated their growth and capacity to produce N2O under anoxic conditions. Secondly, to identify all the genes involved in denitrification, we constructed a mutant transposon library of C58 and tested its growth under denitrification conditions in vitro in the presence of either nitrate or nitrite. - Role of A. fabrum C58 denitrifying genes in the root colonization of maize. It is well known that Transposon-sequencing (Tn-Seq) is a very powerful method to determine genes required for bacterial growth in the presence of their host. To determine denitrifying genes involved in root colonization under anaerobic conditions, we used the library constructed in C58 and performed in planta assays. The mutant library was inoculated on maize plants grown on fertile-ground and cultured under flooded conditions miming anaerobic conditions. Sequencing the recovered A. fabrum C58 cells will evidence the genes involved in this anaerobically specific niche colonization. - Discovery of new anaerobic respiration pathways in A. fabrum C58. To discover new anaerobic respiration pathways, we set-up growth assays of C58 under anoxic conditions in the presence C and N sources as terminal electrons acceptors. Interestingly, by culturing WT and NapA-deficient strains in contact with maize root under anoxic conditions (Chapter 1), we showed growth of both strains, suggesting that root exudates serve as terminal electrons acceptors for anaerobic growth of C58. To determine which maize exuded compounds can serve as TEAs, primary metabolites were identified by HPLC and some were tested as TEAs under the set-up conditions
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Goddard, Victoria Jane. "Population dynamics of fluorescent pseudomonads in the rhizosphere." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298609.
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Biran, Gemma Louisa. "Rhizosphere dynamics of Meloidogyne incognita and Verticillium chlamydosporium." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.619510.
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Meharg, Andrew Alexander. "Factors affecting rhizosphere carbon-flow in Lolium perenne." Thesis, University of Aberdeen, 1989. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU031803.
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The dynamics of root carbon have been studied on a limited number of plants under a limited range of environmental conditions. This is particularly true of temperate pasture grasses. It was proposed to investigate rhizosphere carbon flow within Lolium perenne, to determine environmental factors affecting root exudation and root respiration. A number of microcosms were designed in which ryegrass could be pulse labelled with 14C-CO2, and the fate of the label determined within a plant-soil system. A wide range of factors were found to affect the distribution of carbon within the plant and soil under laboratory conditions. These factors include plant stage of development, micro-organisms, temperature, soil pH, soil water stress and soil anaerobism. A field experiment was carried out to estimate rhizosphere carbon flow under 'natural' conditions and to determine if the laboratory studies could be related to field conditions. Results showed that rhizosphere carbon flow varied greatly depending on environmental conditions. It was proposed that the major loss of newly photoassimilated carbon was dominated by root respiration rather than by root exudation. Inoculation with micro-organisms affected carbon loss from plant roots as exudates. The pattern of carbon distribution within the plant and rhizosphere varied greatly depending on the inoculant.
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Rogers, Michael. "PCR-SSCP analysis of microbial communities in a model system." Thesis, University of Kent, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270818.
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George, Tim. "Enhanced phosphorus acquisition by Tithonia diversifolia and other potential agroforestry species." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326188.
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Naseby, David Craig. "Soil enzymes as indicators of perturbations in the rhizosphere." Thesis, University of Surrey, 1996. http://epubs.surrey.ac.uk/844143/.
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Most attempts to monitor the effects of introductions of Genetically Modified Micro-organisms (GMMs) have centred on the enumeration of specific populations. However for a significant perturbation to be measured, changes of between 100% and 300% (0.3 and 0.5 on a log scale) are necessary for the impact to be significant. Standard population measurements, assessing the survival, dissemination and effect on total indigenous populations do not give an indication of the functioning of the ecosystem. A range of soil enzyme assays have been developed as alternatives to population measurements. Assays for determining chitobiosidase, N-acetyl glucosaminidase, beta-glucosidase, beta-galactosidase, acid phosphatase, alkaline phosphatase, phosphodiesterase, aryl sulphatase and urease activities from small soil samples were developed. These assays were employed to assess the impact of microbial inoculation into the rhizosphere of crop plants and compared to traditional microbial population measurements. The impact of a chromosomally modified Pseudomonas fluorescens (SBW25) in the wheat rhizosphere using a large intact core microcosm was studied with a combined substrate addition of urea, colloidal chitin and glycerophosphate. The substrate addition caused an increase in the soil chitobiosidase, N-acetyl glucosaminidase aryl sulphatase and urease activities but did not affect acid and alkaline phosphatase and phosphodiesterase activity. Seed inoculated with P. fluorescens caused significant increases in rhizosphere chitobiosidase and urease activities and a significant decrease in alkaline phosphatase activity. Inoculation with the bacteria in the presence of substrate gave opposing effects to those treatments without substrate addition. Using these enzyme assays perturbations of less than 20% could be detected. Two strains of Pseudomonas fluorescens were compared in microcosm experiments one with a functional modification of strain F113 with repressed production of the antibiotic 2,4-diacetylphloroglucinol (DAPG), to create the DAPG negative strain F113 G22. The other, SBW25 EeZY 6KX, with nonfunctional modifications consisting of marker genes (LacZY, xylE and kan') only. Both were assessed, along with the corresponding wild types (F113 and SBW25), for their effects upon the indigenous microflora, plant growth and rhizosphere soil enzyme activities. Significant perturbations were found in the indigenous bacterial population structure, with the F113 (DAPG+) strain causing a shift towards slower growing colonies (K strategists). The DAPG+ strain also significantly reduced, in comparison with the other inocula, the total Pseudomonas populations. The survival of the F113 strains were an order of magnitude lower than the SBW25 strains. The DAPG+ strain caused a significant decrease in the shoot to root ratio in comparison to the control and other inoculants. The F113 (DAPG+) inocula resulted in higher alkaline phosphatase, phosphodiesterase and aryl sulphatase activities than the other inoculants and lower beta glucosidase, beta galactosidase and N-acetyl glucosaminidase activities. These results indicate that the soil enzymes are extremely sensitive to perturbations in the rhizosphere ecosystem and are sensitive enough to measure the impact of GMM inoculation.
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Osborne, Meave Catherine. "The spatial ecology of phytopathogenic zoospores in the rhizosphere." Thesis, University of Aberdeen, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369560.
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This thesis is concerned with an analysis of swimming of oomycete zoospores, particularly in relation to the hypothesis that electrotaxis mediated host root colonisation. A correlation was found between the electrotactic behaviour of zoospores of Phytophthora palmivora and Pythium aphanidermatum and their localisation relative to anodic or cathodic regions of the majority of non-host roots. Cathodotropic P. aphanidermatum zoospores were found to be attracted to the cathode generated at the wound site on monocotyledonous and dicotyledonous plant roots studied. Zoospores of P. aphanidermatum were also found to become gradually less attracted to these wound sites as they dissipated over time. Anodotropic P. palmivora zoospores were found to be repelled by the cathodic wound sites on roots of all plants investigated, with the exception of Petunia hybrida. In addition to this zoospores of P. aphanidermatum were found not exhibit chemotaxis or encystment in gradients of the wound-specific metabolite acetosyringone. This suggests that electrotaxis and chemotaxis both operate in directing zoospore accumulation around roots. This reduction of the conductivity of the bathing medium by the addition of different concentrations of sodium chloride salts did not appear to affect the accumulation of both zoospore species around roots of rye grass. The results of this study supports the hypothesis that zoospores use electrotaxis as one means to locate new plant hosts in the rhizosphere. However, chemotaxis may still augment the regulation of zoospore colonisation and encystment.
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Hale, Christopher Charles. "Characterisation of plant (Brassica spp.) and microbial rhizosphere functions." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/102344/.
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The rhizosphere is defined as the area of soil surrounding plant roots, which is influenced by plant exudates. The rhizosphere hosts a diverse and dynamic microbiome, which is shaped by both plant and environmental factors. The plant-microbe and microbe-microbe functional interactions which occur in the rhizosphere can have significant impacts on plant growth. Developing understanding of the composition, functions and interactions of the rhizosphere microbiome and the factors which shape it, may prove valuable to improve agricultural sustainability. The rhizosphere and bulk soil microbiomes of contrasting Brassica napus genotypes growing in the field under high and low N inputs were characterised using amplicon sequencing. Taxonomic identification, functional prediction tools and network analysis were used to gauge how nutrient availability and plant genotype influenced the microbiome. N availability was seen to have a greater influence on composition, function and connectivity of the microbiome than crop genotype, with varying effects on microbes from different Kingdoms. Metatranscriptome analysis enables analysis of the functioning of the microbiome. The effectiveness of different methods for the separation of root and rhizosphere soil for metatranscriptome analysis was compared. Washing roots in water to separate roots and rhizosphere soil followed by freeze drying prior to RNA extraction was shown to be the best method to avoid distorting the metatranscriptome profile. Metatranscriptome analysis of field grown B. napus revealed increases in the rhizosphere relative to soil for protein metabolism functions, and the root compartment contained a high proportion of transcripts related to phage activity. Plant rhizosphere functions were investigated using transcriptomic analysis of a diverse range of cultivated and wild Brassica oleracea plants. Uptake of PO4 is a vital plant process but the identity of PO4 transporters is unknown in B. oleracea. A number of putative PHT1 PO4 transporter genes were identified. Significant differences in expression of the putative PHT1 genes were found between cultivated and wild lines, which may inform future plant breeding strategies.
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Pacheco, Adriana. "Contribution of methanotrophic groundwater and rhizosphere bacteria to phytoremediation." [Gainesville, Fla.] : University of Florida, 2006. http://purl.fcla.edu/fcla/etd/UFE0013836.
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Randima, Livhuwani Priscilla. "Rhizosphere microbial diversity in PAH's contaminated and uncontaminated soil." Pretoria : [s.n.], 2009. http://upetd.up.ac.za/thesis/available/etd-11302009-195201/.
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Zamberlin, Mary Frances. "Rhizosphere : Gilles Deleuze and minor American literature and thought /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/6622.
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Maboreke, Hazel Ruvimbo. "Effect of plant-parasitic nematodes on rhizosphere interactions in oaks." Doctoral thesis, Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, 2017. http://dx.doi.org/10.18452/17783.
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Diese Arbeit untersucht die Reaktion der Stieleiche auf pflanzenparasitären Nematoden mittels RNA-Sequenzierung und Analyse von stabilen Isotopen und Fettsäuren. Einblicke in Rhizosphäreninteraktionen wurden über mutualistische Partner (Ektomykorrhizapilze, Rhizosphärenhelferbakterien), fungivore Collembolen und multitrophische Gemeinschaften gewonnen. Die Struktur und Biomasse der Mikroorganismen sowie die Fitness der Eichen wurden erfasst. Die Effekte wurzelfressender Nematoden auf die Eiche wurden durch das endogene rhythmische Wachstum des Baumes reguliert. Die Nematoden lösten eine stärkere Reaktion während des Sprosswachstumsschubs aus, u.a. Aktivierung von Abwehrmechanismen und Hemmung der Photosynthese, wohingegen beim Wurzelwachstumsschub pathogen bezogene Signale unterdrückt waren. Die Anwesenheit des Pilzsymbionten schwächte die Pflanzenabwehr und verbesserte die Stresstoleranz, was indirekt das Wachstum der Mikroorganismen förderte. Die Helferbakterien begünstigten den Mykorrhizapilz, was wiederum das Pflanzenwachstum stimulierte und dem negativen Effekt der Nematoden entgegenwirkte. Parasitäre Nematoden und fungivore Collembolen beeinflussten die Verteilung des pflanzlichen Kohlenstoffes unabhängig voneinander; Nematoden verringerten und Collembolen verbesserten die Allokation von Photoassimilaten in Gram-postiven Bakterien. Zudem war steigende trophische Diversität der Bodenfauna in der Rhizosphäre entscheidend für die Balance innerhalb der mikrobiellen Gemeinschaft, welche das Pflanzenwachstum fördert. Diese Arbeit stellt die Bedeutung der endogenen Ressourcenzuteilung von Pflanzen für unterirdische biotische Wechselbeziehungen heraus. Diese Pflanzenstrategie als bedeutender Faktor für Rhizosphärenprozesse sollte in zukünftige Studien Berücksichtigung finden. Die Einbeziehung der Hauptakteure in der Rhizosphäre ermöglicht zudem ein realistischeres Bild von Nematoden-Pflanzen Interaktionen und damit ein effektiveres Management.This thesis investigated the response of Pedunculate oak to the plant-parasitic nematode Pratylenchus penetrans, using RNA-sequencing, stable isotope labelling and fatty acid analyses. Insight into rhizosphere interactions was gained by employing beneficial biotic partners (ectomycorrhizal fungi, rhizosphere helper bacteria), fungal grazers (Collembola) and multitrophic environments. Microbial biomass and community structure as well as oak fitness were assessed. The effects of root-feeding nematodes on oak were largely governed by the endogenous rhythmic growth of the tree. The nematodes triggered a stronger response during shoot flush, e.g. activation of multi-layered defence mechanisms and repression of photosynthesis, as compared to root flush where pathogen-related signalling was repressed. With the presence of the mycorrhizal symbiont plant defence was attenuated and stress tolerance enhanced, indirectly promoting the growth of rhizosphere microorganisms. The helper bacteria fostered the ectomycorrhizal fungus, which in turn stimulated plant growth, counteracting the negative effects of nematodes. Plant-parasitic nematodes and Collembola grazers had independent roles in plant carbon allocation patterns, with nematodes hampering whilst Collembola enhancing the flux of recent photoassimilates to Gram-positive bacteria. Lastly, increasing trophic diversity of the soil fauna in the rhizosphere of oaks was crucial for the maintenances of a microbial community equilibrium that promotes plant growth. In sum, this study highlights the importance of endogenous resource allocation pattern of plants in determining the outcome of belowground biotic interactions. Therefore such plant traits should be considered as important drivers for rhizosphere processes in future studies. Moreover, taking into account the rhizosphere main players in studies on parasitic nematode-plant interactions will result in a more realistic picture and thus more effective nematode management.
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Münch, Christiane. "Die Bedeutung der wurzelassoziierten Mikroorganismen für die Stickstoffumsetzungen in Pflanzenkläranlagen." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2003. http://nbn-resolving.de/urn:nbn:de:swb:14-1067340834875-91707.
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Plants in constructed wetlands serve as carriers for attached microbial growth. They mainly transfer oxygen and release exudates into the root zone. As a result, an area exists around the roots (rhizosphere) in which bacteria are stimulated by root growth. Our goals were to ascertain whether stimulating the microbial community only has a local effect on the rhizoplane, and to establish the importance of this stimulation for wastewater purification in the root zone. Observations were carried out in a planted and an unplanted laboratory batch reactor incubated with an artificial wastewater with a high concentration of ammonia. Samples were taken at intervals of 10 mm away from the roots. The chemical and physical conditions and enzyme activities in soil sections at various distances from the roots affecting the efficiency of microbial nitrogen removal were characterized. An influence on the nitrification and denitrification process was detected via several parameters up to a range of different root distances: microbial parameters such as the total bacterial number, respiratory activity, protein and DNA amount seem to be affected by roots up to a distance of 50 mm from the roots, whereas the oxygen concentration, DOC and redox potential are unaffected at a distance exceeding 20-30 mm. This indicates that improved nitrogen removal is also possible in the wider root surroundings. Given the average root-to-root distance of 35 mm, the root-influenced area could therefore be expanded to the whole rooted zone in a constructed wetland.
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Stevens, Daryl Philip. "Uptake of fluorides by the plant root." Title page, contents and abstract only, 1996. http://web4.library.adelaide.edu.au/theses/09PH/09phs8442.pdf.
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Copies of author's previously published articles in pocket. Bibliography: leaves 203-219. Main objectives of the thesis are: i. to verify a sealed chamber acid digestion technique for dissolution of plant material for total F analysis by a F ion selective electrode.--ii. to improve this technique for routine, rapid F analysis of plant material.--iii. to identify the inorganic ionic species of F which could be present in the soil solution.--iv. to determine which of these species are taken up by the plant root and those which are toxic to the plant.
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Zysko, Agnieszka. "Bacterial responses to changes in phosphorus supply in Ryegrass Rhizosphere." Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518478.
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Keeble, Alison. "Interaction between mycorrhiza, rhizosphere bacteria and take-all on wheat." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342050.
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Avery, Lisa Marie. "The influence of UV-B radiation on rhizosphere microbial communities." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247141.
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Alegria, Terrazas Rodrigo. "Defining the host genetic control of the barley rhizosphere microbiota." Thesis, University of Dundee, 2019. https://discovery.dundee.ac.uk/en/studentTheses/4ca9658f-c69d-4c23-b1b2-46d0ef40339d.
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Limiting environmentally harmful consequences of crop production while increasing productivity amid climatic modifications is one of the major challenges facing agriculture in the XXIst century. Crucially, over the course of the next 30 years, innovative strategies are required to tackle this challenge and ensure a sustainable and safe access to food resources to a global population of over 9 billion people in 2050. One of these strategies proposes to exploit the microbial communities thriving in association with plant roots, collectively referred to as the rhizosphere microbiota, to uncouple profitable crop yield from the input of synthetic compounds in the agroecosystem. In the last decade technical advances have allowed scientists to gain unprecedented insights into plant-microbiota interactions in the rhizosphere. However, a precise understanding of how plants can shape these communities is still missing. This is information will be crucial to assist breeders in developing crops capable of maximising the mutualistic relationships with soil microbes. To fill this knowledge gap, in this thesis I use Barley (Hordeum vulgare), a global crop and an excellent experimental model, and will capitalise on state-of-the art sequencing and computational approaches to gain fundamentally novel insights into the host genetic control of the rhizosphere microbiota. The overarching hypothesis of my work is that the host genotype has the capacity to shape the rhizosphere microbiota to sustain plant growth in given soil conditions. I further hypothesize that this capacity impacts both the taxonomic and functional compositions of the rhizosphere microbiota and can be ultimately traced to loci in the barley genome. To test these hypotheses, I developed three major experimental lines aimed at a) characterising the microbiota of wild and cultivated barley genotypes grown in agricultural soils and how this impacts on plant growth; b) assessing the modulation of structure and function of the rhizosphere microbiota by the plant host under different nitrogen regimes and c) identifying the barley genetic region(s) responsible for the microbiota recruitment using experimental segregating populations between wild and modern barley genotypes. These experiments will contribute to decipher the genetic relationships between a plant genome and its associated microbiota and, in the long term, they will be key to devise novel strategies to enhance nutrient uptake efficiency in cereals.
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Tkacz, Andrzej. "Plant genotype, immunity and soil composition control the rhizosphere microbiome." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/48113/.
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Three model plant and three crop plant species were grown for three generations in sand and compost. Pots were inoculated with 10 % soil initially, and with 10% of growth medium from the previous generation in generations 2 and 3, keeping replicates separate for all three generations. The microbiome community structure of the plant rhizosphere in each generation was characterised using ARISA DNA fingerprinting and 454 sequencing. Rhizosphere bacterial and fungal communities are different from those in bulk soil and there are also differences in the microbial community between different plant species. Plants both select and suppress specific bacteria and fungi in the rhizosphere microbiome, presumably via composition of their root exudates. Two out of three most abundant bacteria selected in the rhizosphere were isolated. These isolates proved to possess plant growth promotion properties. Plants are able to “farm” the soil in order to enrich it with plant growth promoting rhizobacteria (PGPR) species. However, in some plant species rhizospheres, invasions of opportunists and pathogens take place, mimicking events in plant monocultures. Other experiments using this multi-replicate system allowed for statistical analysis of the influence of Arabidopsis and Medicago mutants on the rhizosphere microbiome. Three groups of Arabidopsis mutants were tested: plants unable to produce aliphatic glucosinolates, plants impaired in the PAMP-triggered immune response and plants unable and over-expressed in methyl halides production and one group of Medicago mutants which are impaired in the mycorrhization ability. All these plant genotypes, except those for methyl-halide production and one genotype involved in PAMP response, significantly altered the rhizosphere microbiome.
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Wakeford, Tom. "The molecular ecology of a legume rhizosphere : patterns and mechanisms." Thesis, University of York, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.273883.
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Lee, Nathan Robert William. "Long Term Glyphosate Effects on Roundup Ready Soybean Rhizosphere Microorganisms." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1525689141453883.
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Porteous, Fiona. "Use of lux-marked rhizobacteria to investigate rhizosphere C-flow." Thesis, University of Aberdeen, 1998. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU112116.
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The aim of this study was to develop a protocol for the use of a lux-marked pseudomonad for the investigation of rhizosphere C-fluxes, and then use this to examine a system experiencing change in C flow due to pollutant pressure. In this study a typical rhizobacterium, Pseudomonas fluorescens, was marked by the insertion of the lux gene cassette of Vibrio fischeri. Two constructs were produced, P. fluorescens pUCD607 (marked with the full lux gene cassette of CDABE) and P. fluorescens FAC510 (chromosomally marked with the lux AB genes), both with bioluminescence directly linked to metabolic activity. The bioluminescence response of C-starved suspensions of these constructs to typical rhizosphere C substrates, was determined by exposure of the cells to substrate over a 30 minute period. It was shown that P. fluorescens pUCD607 can distinguish between substrate type and concentration, in terms of bioluminescence. In terms of Michaelis-Menten kinetics, glucose had a Km of 30.4mMC, and a Vmax of 200 RLU's/mMC. However, an amino acid (glutamic acid) produced a Vmax of 23316 RLU's/mMC, and a Km of 1mMC. Succinic acid, an organic acid, caused a much lower Vmax in P. fluorescens pUCD607 of 240 RLU's/mMC, and a Km of 2.5mMC. Clearly, this reporter construct offers great potential for modelling rhizosphere C-flow, as indicated by the data shown. Following this, P. fluorescens pUCD607 was used to investigate the effects of pollutant stress on rhizosphere C-flow. Plantago lanceolata was treated with paraquat and sodium arsenate, two common soil pollutants. Both caused an increase in root exudate C from 20-350%, depending on application time and concentration. P. fluorescens pUCD607 was able to detect this change, with bioluminescence directly correlated to actual C concentration. This study demonstrates that P. fluorescens pUCD607 offers a valuable tool for the reliable investigation of rhizosphere C-flow, and that lux gene technology offers the potential to further model the rhizosphere. This novel technique opens up many possibilities for applications in monitoring of ecosystem health, organic agriculture and bioremediation.
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Moritsuka, Naoki. "STUDIES ON THE DYNAMICS OF SOIL NUTRIENTS IN THE RHIZOSPHERE." Kyoto University, 2001. http://hdl.handle.net/2433/150333.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第9148号
農博第1209号
新制||農||831(附属図書館)
学位論文||H13||N3579(農学部図書室)
UT51-2001-K355
京都大学大学院農学研究科地域環境科学専攻
(主査)教授 小﨑 隆, 教授 櫻谷 哲夫, 教授 關谷 次郎
学位規則第4条第1項該当
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Devau, Nicolas. "Processus rhizosphériques déterminant la disponibilité en phosphore : apport de la modélisation mécaniste géochimique." Thesis, Montpellier, SupAgro, 2010. http://www.theses.fr/2010NSAM0019.
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Les processus rhizosphériques sont reconnus comme une des stratégies majeures élaborées par les plantes afin d'augmenter la disponibilité en phosphore (P) et ainsi améliorer leur nutrition phosphatée. Pourtant, l'effet exact de ces processus est encore mal caractérisé et quantifié. L'objectif de ces travaux a été d e déterminer le rôle exercé par les modifications chimiques induites par les racines, particulièrement la modification de pH, dans les changements de disponibilité en P dans la rhizosphère. Pour ce faire, nous avons utilisé des modèles mécanistes géochimiques (« triple plane », échange d'ion et Nica-Donnan) en considérant une approche additive pour simuler l'effet de l'activité racinaire sur la disponibilité en P. Dans une première étape, nous avons caractérisé l'effet du pH sur la disponibilité en P dans plusieurs sols, un Cambisol et un Luvisol. Le Luvisol présentait deux concentrations en P inorganique contrastées en raison d'un essai de fertilisation phosphatée longue durée. Dans la rhizosphère du blé dur (Triticum turgidum durum L.) cultivé sur les mêmes sols, nous avons caractérisé qu'en plus de l'alcalinisation, le prélèvement en P et surtout en calcium (Ca) sont les processus rhizosphériques responsables du changement de disponibilit é en P observé. Le prélèvement du Ca favorise l'augmentation de la disponibilité en P dans la rhizosphère, en diminuant l'effet promoteur du processus d'adsorption-désorption du Ca sur celui du P. L'influence relative de ces trois processus rhizosphériques dépend toutefois de la composition chimique de la solution du sol (concentration en Ca et pH en particulier). Nos simulations mettent également en évidence la relation entre les changements de disponibilité en P est la distribution du P adsorbé sur les différentes phases minérales. La minéralogie du sol, spécialement l'abondance relative d'illite vs. les oxydes de fer, contrôle l'influence des processus rhizosphériques en déterminant les minéraux impliqués dans l'adsorption du P. A travers l'identification d'un nouveau processus rhizosphérique découlant du prélèvement en Ca et de ses effets sur la disponibilité en P, nos résultats démontrent la validité des modèles géochimiques pour prédire l'influence des processus rhizosphériques déterminant la disponibilité en PRoot-induced chemical processes are recognized as a major strategy developed by plants to enhance phosphorus (P) availability and thus to promote P acquisition. However, the exact influence of these root-induced chemical processes is still poorly understood and quantified. The present study aimed at investigating the influence of root-induced chemical processes, especially root-induced pH changes, on P availability in the rhizosphere. In this work, we used a set of mechanistic adsorption models (« 1-pK triple plane », ion-exchange and Nica-Donnan) within the framework of the component additive approach in order to simulate the effects of root activity on P availability. First, we described the effects of pH on P availability in several soils unaffected by roots, a Chromic Cambisol and a Luvisol. The Luvisol showed different concentrations in inorganic P because of a long-term fertilisation trial. In the rhizosphere of durum wheat (Triticum tu rgidum durum L.) grown on these two soils, we found that calcium (Ca) uptake, in addition to P uptake and root-induced alkalisation, controlled to various extents the changes of soil P availability. Calcium uptake markedly increased P availability by decreasing the promoting effect of Ca adsorption on P adsorption. The relative influence of these three root processes depended on the solution composition (especially concentration of Ca and pH). Our simulations showed the relationship between changes in P availability and the speciation of adsorbed P onto the different soil minerals. Soil mineralogy, especially the relative abundance of illite vs. Fe oxides, controlled the influence of root processes by regulating the contribution of soil minerals to P adsorption. By identifying a novel root-induced processes, namely the Ca uptake, and describing its influence on P availability, our results demonstrate the ability of surface complexation models to predict the effects of root-i nduced processes on P availability in soils
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Ndanga, Mbakop Éliane. "Effet de la végétation dans le processus d'oxydation passive du méthane par les biosystèmes des sites d'enfouissement." Thèse, Université de Sherbrooke, 2015. http://hdl.handle.net/11143/7547.
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Résumé : Les biosystèmes d’oxydation passive du CH[indice inférieur 4] constituent une alternative techniquement et économiquement viable pour la réduction des émissions fugitives de CH[indice inférieur 4] dans l’atmosphère par les sites d’enfouissement. Directement intégrés au recouvrement final, ils sont constitués d’une succession de couche de matériaux au sein desquelles se développent les bactéries méthanotrophes capable d’oxyder le CH[indice inférieur 4] en CO[indice inférieur 2] de façon passive, en présence de l’oxygène moléculaire. La capacité des BOPMs à réduire les émissions de CH[indice inférieur 4] a été associée à plusieurs paramètres météorologiques et environnementaux, entre autres la végétation. L’objectif de ce projet est de déterminer l’effet de la végétation dans l’oxydation du CH[indice inférieur 4] par les biosystèmes. Pour atteindre cet objectif, des études de l’efficacité d’oxydation du CH[indice inférieur 4] dans des bacs pourvus de végétation, dans des conditions contrôlées de laboratoire et partiellement contrôlées de terrain, suivie d’une étude de la cinétique d’oxydation des sols de rhizosphère pré-conditionnés au CH[indice inférieur 4], ont été effectuées. Quatre bacs ont été testés, comprenant : le trèfle blanc (Trifolium repens L.), la fléole des prés (Phleum pratense L.), un mélange des deux espèces végétales (mélange) et le sol nu (dépourvu de végétation). Les résultats des bacs d’oxydation ont montré que, jusqu’à un débit de 100 g CH[indice inférieur 4]/m[indice supérieur 2]/jr, les espèces végétales n’avaient pas d’influence sur les résultats, et les efficacités d’oxydation étaient de l’ordre de ~100%. Au-delà de cette valeur, les efficacités étaient toujours élevées, et une différence statistiquement significative a été observée entre les espèces végétales. Le sol nu était le plus efficace, tandis que le mélange et le trèfle étaient les moins efficaces au laboratoire et sur le terrain respectivement. Néanmoins, les différences d’efficacités entre les bacs n’étaient pas très grandes et les taux d’oxydation dans les bacs n’ont pas cessé de croitre tout au long des essais, suggérant que la capacité d’oxydation maximale des bacs n’a pas été atteinte. L’étude de la cinétique d’oxydation a également montré que la végétation n’avait pas d’effet significatif sur les taux d’oxydation. Ces observations ne corroborent pas ce qui est rapporté dans la littérature concernant l’effet positif de la végétation. Néanmoins, les conclusions de cette étude ont été en adéquation par l’analyse des profils d’efficacité, de la biomasse racinaire et des caractéristiques physico-chimiques des sols du BOPM. Par ailleurs, un effet significatif de la végétation sur le degré de saturation en eau dans les BOPMs a également été observé. Cette dernière observation a été associée au mécanisme de régulation de la teneur en eau par les racines des plantes. Les principales limitations de cette étude concernaient la durée des essais et le nombre d’espèces végétales. En résumé, pour les espèces végétales testées, il a été démontré que la végétation ne constitue pas un facteur clé stimulant l’oxydation du CH[indice inférieur 4] dans les BOPMs. De plus, l’étude de la cinétique d’oxydation a montré que de meilleur taux d’oxydation étaient obtenus dans un sol de rhizosphère modérément pré-exposé au CH[indice inférieur 4] comparativement à un sol sans végétation, ou à une rhizosphère non pré-exposée ou très pré-exposée au CH[indice inférieur 4].Abstract : The passive CH[subscript 4] oxidation Biosystems are a cost-effective technology for the reduction of landfills fugitive CH[subscript 4] emissions in the atmosphere. As part of the final cover, they are made up of a sequence of soil layers capable to develop methanotrophic bacteria for passive CH[subscript 4] oxidation into CO[subscript 2], in the presence of molecular oxygen. The ability of biosystems to reduce CH[subscript 4] emissions was related to several meteorological and environmental parameters, including vegetation. The main objective of this project is to determine the effect of vegetation on CH[subscript 4] oxidation by biosystems. Studies of the CH[subscript 4] oxidation efficiencies of vegetated column under controlled conditions prevailing in the laboratory and under the partially controlled conditions in the field, followed by the study of the CH[subscript 4] oxidation kinetics of the preconditioned rhizospheric soil, were carried out. Four columns were tested, including: white clover (Trifolium repens L.), timothy grass (Phleum pratense L.), a mixture of both (mixture) and bare soil (control biosystem). The results of the column study showed that up to a loading of 100 g CH[subscript 4]/m[superscript 2]/d, plant species did not influence the results, and the CH[subscript 4] oxidation efficiencies were in the vicinity of ~ 100%. Beyond this value, the efficiencies were still high, and a statistically significant difference was observed between plant species. Bare soil was the most efficient while the mixture and white clover were the least in the laboratory and the field respectively. However, differences in efficiencies between the columns were not high and the oxidation rates continued to increase throughout the test, suggesting that the maximum oxidation capacity of the biosystems tested may have never been fully attained. The kinetics study also showed that vegetation did not have significant effect on CH[subscript 4] oxidation rate. These observations do not corroborate what is reported in technical literature on the positive effect of vegetation. Nevertheless, the findings of this study were adequacy with the analysis of the profiles of efficiencies, root biomass and physico-chemical characteristics of soils. Moreover, a significant effect of vegetation on the degree of water saturation in Biosystems was also observed. The latter was associated with the mechanism of water content regulation through plant roots. The main limitations of this study concerned the duration of the tests and the number of plant species. In summary, for the plant species studied herein, it was shown that the vegetation is not a key factor for enhancing CH[subscript 4] oxidation in biosystems. Moreover, the study of the kinetics of CH[subscript 4] oxidation showed that better oxidation rate were obtained in a moderately pre-exposed rhizospheric soil compared to bare soils, to never before pre-exposed or very pre-exposed rhizospheric soils to CH[subscript 4].
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Bressan, Mélanie. "Effets des exsudats racinaires d'une plante Brassicaceae sur les microorganismes rhizophériques : influence de la production d'un glucosinolate exogène chez Arabidopsis thaliana : utilisation d'une approche par traçafe de l'ADN (DAN-SIP)." Aix-Marseille 2, 2009. http://theses.univ-amu.fr.lama.univ-amu.fr/2009AIX22057.pdf.
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Une caractéristique des Brassicaceae est la production de métabolites secondaires soufrés appelés les glucosinolates, hydrolysés en divers dérivés bioactifs. Ces produits d’hydrolyse présentent des effets toxiques sur de nombreux microorganismes du sol. L’objectif de cette étude est d’examiner le rôle des glucosinolates et de leurs produits d’hydrolyse en tant que facteur de sélection et de structuration des communautés microbiennes de la rhizosphère des Brassicaceae. Pour cela, nous avons développé une approche de traçage isotopique de l’ADN (DNA-SIP) pour cibler les populations microbiennes impliquées dans l’assimilation des exsudats racinaires dans la rhizosphère. Après vérification de sa construction génétique et de son phénotype, une lignée transgénique d’Arabidopsis thaliana (lignée CYP79A1) produisant un glucosinolate exogène est cultivée sur un sol naturel, sous une atmosphère enrichie en 13CO2, avec la lignée sauvage associée. Dans nos conditions de culture, les racines des plantes transgéniques présentent les modifications attendues de leur contenu en glucosinolates ainsi que d’autres modifications mineures. Au niveau du sol rhizosphérique, les produits d’hydrolyse des glucosinolates n’ont pas pu être détectés, vraisemblablement à cause de quantités trop faibles et d’une dégradation rapide de ces composés. Cependant, il existe probablement un gradient de concentration de ces métabolites depuis la racine vers le sol. Pour analyser la structure et la composition des communautés microbiennes, l’ADN total extrait du sol rhizosphérique est séparé sur gradient de densité. La structure des communautés bactérienne (alphaprotéobactéries, métaprotéobactéries, gammaprotéobactéries et acidobactéries), Archaea et fongique est analysée par PCR-DGGE. Les populations spécifiques sont caractérisées par séquençage des fragments DGGE. Dans la rhizosphère, nous avons pu mettre en évidence dans tous les taxa testés des populations microbiennes actives, utilisant spécifiquement les exsudats racinaires d’A. Thaliana comme source de carbone. La comparaison des communautés microbiennes entre les 2 types de plantes montre que la modification du contenu en glucosinolates des plantes transgéniques influence significativement les communautés microbiennes associées aux racines et des populations actives dans la rhizosphère. Les lphaprotéobactéries, en particulier les Rhizobiaceae, et la communauté fongique apparaissent comme les plus influencés par ces métabolites. Différents mécanismes, directs ou indirects, peuvent expliquer cet impact : toxicité des composés, relation de trophisme, compétition, signal spécifique. Nos résultats montrent que même une modification mineure au niveau des racines peut avoir des répercussions importantes sur les communautés microbiennes du sol. Des conséquences possibles sur des fonctions microbiennes importantes pour l’équilibre de l’écosystème restent encore à évaluerA specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolyzed into glucose and biocidal products. These metabolites are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated to living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere is achieved. After checking its genetic construction and its phenotype, the transgenic Arabidopsis thaliana line CYP79A1, producing an exogenous glucosinolate, were grown under enriched 13CO2 atmosphere on natural soil with the wild type plant associated. In our conditions, roots of the transgenic plant line presented the expected altered profile of glucosinolates as well as other minor additional modifications compared to the wild type. In rhizospheric soil, hydrolysis products of these metabolites could not be successfully detected, probably because of very small quantities and rapid degradation. We hypothesized that a gradient of concentration of all these compounds set up from plant roots to rhizospheric soil. After harvest, to analyze the structure and composition of soil microbial community, DNA from rhizospheric soil was separated by density gradient centrifugation. Bacterial (alphaproteobacteria, betaproteobacteria, gammaproteobacteria and acidobacteria), archaeal and fungal community structure were analyzed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. In rhizosphere, we pointed out for the first time several active microbial populations, in all tested taxa, which specifically used A. Thaliana root exudates as carbon source. The comparison of the structure and composition of microbial community between the 2 plant types showed that the modifications of glucosinolate content in transgenic plant significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Different mechanisms, direct or indirect, could be promoted to explain this impact: compounds toxicity, trophism interaction, competition, specific signal. Our results showed that even a minor modification in plant root could have important repercussions on soil microbial communities. Possible consequences on specific microbial functions implicated in ecosystems equilibrium should be then evaluated
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Wouterlood, Madeleine. "Carboxylates in the rhizosphere of chickpea (Cicer arietinum) in relation to P acquisition." University of Western Australia. School of Plant Biology, 2005. http://theses.library.uwa.edu.au/adt-WU2005.0029.
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[Truncated abstract] The highly weathered, phosphorus-fixing soils of Western Australia require large amounts of P fertiliser to produce acceptable crop yields. Chickpea (Cicer arietinum L.) is an important leguminous crop that is increasingly used in rotations with wheat (Triticum aestivum L.), Western Australia’s major crop. Chickpea and a range of other species exude P-mobilising carboxylates into the rhizosphere. Plants that exude carboxylates may need less P fertiliser or may use P in the soil that is unavailable to other plants. There is a wealth of information about P mobilisation and carboxylate exudation by white lupin; in contrast, research on carboxylate exudation by chickpea is fairly limited. The major aim of this PhD research project was to investigate the relationships between exudation of carboxylates and soil and plant P status for chickpea ... In conclusion, whereas carboxylate exudation of plants such as white lupin is clearly targeted at P acquisition, chickpea showed constitutive carboxylate exudation mainly of malonate into the rhizosphere in a series of experiments, each with a different design. Unlike white lupin, chickpea forms associations with mycorrhizal fungi that may improve plant P status. Some of the functions of constitutive carboxylate exudation by chickpea may include P acquisition and deterring microorganisms, but the exact reasons and mechanisms remain unresolved.
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Delafuente, Leonardo. "Characterization of the ecological and physiological basis of superior rhizosphere colonization by 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas genotypes." Online access for everyone, 2005. http://www.dissertations.wsu.edu/Dissertations/Fall2005/l%5Fdelafuente%5F1082405.pdf.
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Hart, Timothy David. "Diffusion of ions and water through microbial polysaccharides in the rhizosphere." Thesis, University of Surrey, 1997. http://epubs.surrey.ac.uk/842747/.
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It is proposed that microbial polysaccharides behave anion-exclusively, permitting the transport of cations, but excluding the diffusion of anions. This hypothesis has been investigated in the context of polysaccharides produced by microorganisms in the rhizosphere. The anion-exclusive behaviour of exopolysaccharides, extracted from broth cultures of a range of rhizosphere microorganisms together with several commercial polysaccharides (i.e., xanthan, scleroglucan, dextran, guar gum) was investigated by measuring the electrochemical potential which developed as a result of the diffusion of KC1 across a polymer layer. Considering xanthan as a 'model' microbial polysaccharide, polymer concentration, layer thickness and the presence of either O-acetyl or pyruvyl groups were found to positively affect the degree of anion exclusion. The anion-exclusive behaviour of xanthan was verified by direct ion analysis of solutions either side of the polymer layer. It was found that in a range of ionic environments, the diffusion of anions was reduced by ~70% by the presence of a 3% w/w xanthan layer. The influence of xanthan on the diffusion of cations was studied using magnetic resonance imaging. In contrast to the proposed theory of anion exclusion, the rate of cation (Mn2+) diffusion through a 3% w/w xanthan layer was found not to be greater than that through free aqueous solution. The possible occurrence of anion exclusion and consequences thereof in the rhizosphere were assessed by studying the effect of substitution of the water films in soil with a layer of 3% xanthan on the growth of wheat seedlings. The phosphate, but not potassium content of those plants grown in soil with xanthan was ~20% lower than in the control plants. Those plants grown in xanthan-amended soil produced ~30% more biomass by dry weight. The anion-exclusive properties of polysaccharides produced naturally in bulk soil, the rhizosphere and root surface of pea was studied by the measurement of diffusion potentials. All three were found to show a high level of anion exclusion. The influence of O-acetyl groups in xanthan on the rate of water transport and degree of water binding was studied using stray field NMR methods. It was found that removal of O-acetyl groups reduces the rate of water transport and increases the rate of water binding at any given xanthan concentration. It is proposed that microoganisms produce anion-exclusive polysaccharides in the rhizosphere to protect themselves against the potentially lethal effects of water stress.
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Devine, Gary J. "Detecting pathogens and beneficial microorganisms in the tomato rhizosphere using microarrays." Thesis, University of Nottingham, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.665477.
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The cultivation of tomato (Solanum lycopersicum) plants for their edible fruits is a worldwide industry that was valued at over $58.7B in 2011. Traditional breeding has predominantly focused on increasing fruit yield or the accumulated concentrations of health-promoting phytochemicals, such as the antioxidant Iycopene. As a result, tomato crops remain susceptible to a large number of potentially devastating diseases which cause significant economic losses to commercial producers. These diseases are incited by a diverse group of microorganisms including bacteria, fungi, nematodes and oomycetes. DNA microarrays are a rapid, sensitive and relatively low cost molecular tool. They can be used to simultaneously detect a large number of PCR-amplified target DNA fragments based on their hybridisation to pre-designed short (~30 bp) complementary oligonucleotide capture probes. Capture probes are commonly designed using barcode regions in the genome and rely on the presence of heterogeneous sequence. Several applications of microarrays have been proposed, including their use for detecting pathogen occurrence and monitoring environmental microbial populations. The ArrayTube platform consists of a 3 x 3 mm glass microprobe array biochip embedded within a modified 1.5 ml Eppendorf-style tube. It provides a discrete environment in which the entire hybridisation and enzyme-catalysed precipitation staining reactions can occur. Detection of hybridised probes is achieved by the acquisition of grey-value transmission data using a specialised ArrayTube Reader device.
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Turner, Thomas. "Metatranscriptomic analysis of community structure and metabolism of the rhizosphere microbiome." Thesis, University of East Anglia, 2013. https://ueaeprints.uea.ac.uk/49600/.
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Plant-microbe interactions in the rhizosphere, the region of soil influenced by plant roots, are integral to biogeochemical cycling, and maintenance of plant health and productivity. Interactions between model plants and microbes are well understood, but relatively little is about the plant microbiome. Here, comparative metatranscriptomics was used to determine taxonomic compositions and metabolic responses of microbes in soil and the rhizospheres of wheat, oat and pea. Additionally a wild-type oat was compared to a mutant (sad1) deficient in production of antifungal avenacins. Analyses of taxonomic compositions and functions based on rRNA and protein coding genes agreed that rhizosphere microbiomes differed from soil and between plant species. Pea had a stronger effect than wheat and oat, suggesting distinct cereal and legume microbiomes. Proportions of eukaryotic rRNA in the oat and pea rhizospheres were more than fivefold higher than in the wheat rhizosphere or soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, while the pea rhizosphere was highly enriched for fungi. Only the eukaryotic community was distinct from wild-type oat in the sad1 mutant, suggesting avenacins have a broader role than protecting from fungal pathogens. The addition of an internal RNA standard allowed quantitative determination of global transcriptional activity in each environment. This was generally higher in the rhizospheres, particularly pea, than in soil. Taxa known to possess metabolic traits potentially important for rhizosphere colonisation, plant growth promotion and pathogenesis were selected by plants. Such traits included cellulose and other plant polymer degradation, nitrogen fixation, hydrogen oxidation, methylotrophy and antibiotic production. These functions were also more highly expressed in rhizospheres than soil. Microbes also induced functions involved in chemotaxis, motility, attachment, pathogenesis, responses to oxidative stress, cycling of nitrogen and sulphur, acquisition of phosphorous, iron and other metals, as well as metabolism of a variety of sugars, aromatics, organic and amino acids, many plant species specific. Profiling microbial communities with metatranscriptomics allowed comparison of relative and quantitative abundance of microbes and their metabolism, from multiple samples, across all domains of life, without PCR bias. This revealed profound differences in the taxonomic composition and metabolic functions of rhizosphere microbiomes between crop plants and soil.
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Braga, Lucas Palma Perez. "Disentangling the influence of earthworms on microbial communities in sugarcane rhizosphere." Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-26052017-100757/.
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For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, it was performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW-, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In the second chapter of this thesis it was demonstrate that in EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW- treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW- rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated. Considering that earthworms contributed to with extra resources, it was evaluated in chapter three response of the soil resistome of sugarcane macrocosms under the influence of earthworms. Mechanisms of resistance against antimicrobial compounds appear to be an obligatory feature for the ecology and evolution of prokaryotic forms of life. However, most studies on resistance dynamics have been conducted in artificial conditions of anthropogenic inputs of antibiotics into very specific communities such as animal microbiomes. To resolve why and how resistance evolves, it is important to track antibiotics resistance genes (ARGs) (i.e., the resistome) in their natural hosts and understand their ecophysiological role in the environment. The results demonstrated that earthworms influenced changes of ARGs in bulk soil and rhizosphere. Negative correlations between ARGs and taxonomical changes were increased in EW+. Differential betweenness centrality (DBC=nBCEW+ - nBCEW-) values comparing the network models with and without earthworms showed earthworm presence changed the composition and the importance of the keystone members from the models. Redundancy analysis suggested that ARGs may be associated with microbial fitness, as the variance of relative abundance of members of the group Rhizobiales could be significantly explained by the variance of a specific gene responsible for one mechanism of tetracycline detoxificationAo longo dos últimos 150 anos muitos estudos têm demonstrado a importância das minhocas para o crescimento de plantas. Porém o exato mecanismo envolvido neste processo ainda é muito pouco compreendido. Muitas funções importantes necessárias para o crescimento de plantas podem ser realizadas pela comunidade microbiana da rizosfera. Para investigar a influência das minhocas na comunidade microbiana da rizosfera, foi desenvolvido um experimento de macrocosmo com cana-de-açúcar com e sem Pontoscolex corethrurus (EW+ e EW-, respectivamente) seguindo diversos procedimentos por 217 dias. No Segundo capítulo da tese é demonstrado que no tratamento EW+, as concentrações de N2O dentro do solo (15 cm profundidade) e a abundância relativa dos genes óxido nitroso redutase (nosZ) foram elevadas no solo e na rizosfera, sugerindo que microrganismos do solo foram capazes de consumir a emissão de N2O induzida pelas minhocas. O sequenciamento do DNA total revelou que aproximadamente 70 funções microbianas no solo e na rizosfera apresentaram diferenças entre os tratamentos EW+ e EW-. No geral, genes associados a biossíntese e proliferação de células foram enriquecidos em EW+, sugerindo uma influencia positiva por parte das minhocas. Na rizosfera EW+, funções associadas a simbiose entre planta e microrganismos foram relativamente enriquecidas comparado com rizosfera EW-. Modelos de rede de interação ecológica revelam menor número de diversificação de nichos e aumento de funções importantes como um efeito derivado da influência das minhocas. A biomassa das plantas foi aumentada no tratamento EW+ e a população de minhocas proliferou. Considerando que as minhocas contribuíram com o aumento de nutrientes, foi avaliado no capítulo três a resposta do resistoma presente nas comunidades microbianas dos solos do experimento. Mecanismos de resistência contra compostos antimicrobianos parecem ser características obrigatórias para a ecologia e evolução de procariotos. Entretanto, a maior parte dos estudos sobre genes de resistência tem sido conduzida em condições artificiais utilizando fontes antropogênicas de antibióticos em comunidades microbianas muito específicas como por exemplo o microbioma animal. Para resolver por que e como a resistência evolui, é importante estudar genes de resistência a antibióticos (GRA) (i.e., resistoma) no seu ambiente natural e entender seu papel ecofisiologico no ambiente. Os resultados demonstraram que minhocas influenciaram a mudança na composição de GRA no solo e na rizosfera. Tratamentos EW+ apresentaram maior número de correlações negativas entre ARG e grupos taxonômicos. A medida de centralidade diferencial (DBC=nBCEW+ - nBCEW-) comparando os modelos de rede de interações obtidos mostrou que a composição e o nível de importância dos indivíduos mais influentes é alterado nos tratamentos EW+ comparado com EW-. Além disso, por meio de uma análise de redundância (RDA) foi demonstrado que as alterações na abundancia relativa de GRA podem ser explicadas pelas alterações verificadas em grupos taxonômicos
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Murphy, Conor. "Investigation of rhizosphere priming effects for N mineralisation in contrasting soils." Thesis, University of Aberdeen, 2015. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=228575.
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In the context of nutrient cycling in soil, plant-mediated mineralisation of carbon (C) and nitrogen (N) is poorly understood. The broad focus of this thesis was to investigate the potential importance of plant-mediated mineralisation (i.e.priming) on C and N mineralisation in soils with contrasting crop productivities. The studies focus on two soils, which had similar chemical and physical properties but contrasting plant productivities relating to their N supply capacity. These soils were used to investigate the potential importance of priming processes in contributing to the contrasting capacities of these soils to supply N for plant growth. 13C and 15N stable isotopes were used to measure specific gross C and N fluxes. Sole C or N and combined C with N treatments were established to disentangle the effect of carbon and nitrogen availability on plant-mediated mineralisation. The addition of labile C increased gross carbon and nitrogen fluxes from native soil organic matter (SOM) but the effect was soil specific. The addition of nitrogen did not affect SOM mineralisation in either soil. The much lower C-to-N ratio of the 'primed' flux compared to the 'basal' flux indicated that the primed flux utilises different OM pools highlighting that primed and basal mineralisation may be distinct processes. The priming response (i.e. positive or negative and associated mechanisms) was different depending on carbon and nitrogen supply to the microbial community. Overall, the studies in this thesis places the microbial community as the focal point of soil N supply. This data strongly supports the concept that the release of labile carbon from plant roots functions as a nutrient acquisition response, increasing mineralisation of SOM. From the data a conceptual model of priming mechanisms, based on nutrient availability to the microbial community, was established. This could be used as the foundation to develop key concepts for sustainable agricultural practice.
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Lloyd, Davidson A. "Effects of rhizosphere priming and microbial functions on soil carbon turnover." Thesis, Cranfield University, 2015. http://dspace.lib.cranfield.ac.uk/handle/1826/9278.
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A major uncertainty in soil carbon studies is how inputs of fresh plant-derived carbon affect the turnover of existing soil organic matter (SOM) by so-called priming effects. Priming may occur directly as a result of nutrient mining by existing microbial communities, or indirectly via microbial population adjustments. Soil type and conditions may also influence the intensity and direction of priming effects. However the mechanisms are poorly understood. The objectives of this study were (1) to investigate how additions of labile C4 substrate affected SOM turnover in two contrasting unplanted C3 soils (clayey fertile from Temple Balsall, Warwickshire (TB) and sandy acid from Shuttleworth, Bedfordshire (SH) using13 C isotope shifts; (2) to investigate the influence of rhizodeposition from plant roots on SOM turnover in the same two soils planted with a C4 grass; (3) to assess an automated field system for measuring soil temperature, moisture and photosynthesis sensitivities of SOM turnover in the same two soils over diurnal to seasonal time scales. I used a combination of laboratory incubation, glasshouse and field experiments. In the soil incubation experiment, I made daily applications of either a maize root extract or sucrose to soil microcosms at rates simulating grassland rhizodeposition, and followed soil respiration (Rs) and its δ13 C over 19 days. I inferred the extent of priming from the δ13 C of Rs and the δ13 C of substrate and soil end-members. There were positive priming effects in both soils in response to the two substrates. In the SH soil there were no differences in priming effects between the substrates. However in the TB soil, sucrose produced greater priming effects than maize root extract, and priming effects with sucrose increased over time whereas with maize root extract declined after the first week. I explain these effects in terms of the greater fertility of the TB soil and resulting greater microbial nitrogen mineralization induced by priming. Because the maize root extract contained some nitrogen, over time microbial nitrogen requirements were satisfied without priming whereas with sucrose the nitrogen demand increased over time. In the glasshouse experiment, I planted C4 Kikuyu grass (Pennisetum clandestinum) in pots with the same two soils. The extent of rhizodeposition by the plants was altered by intermittently clipping the grass in half the pots (there were also unplanted controls) and priming effects were inferred from the δ13 C of Rs and the δ13 C of plant and soil end-members. Unclipped plants in both soils generated positive priming effects, while clipping reduced priming in TB soil and produced negligible PEs in SH soil. Microbial nutrient mining of SOM again explained the observed PEs in this experiment. Photosynthesis was a major driver of priming effects in the planted systems. In the third experiment, I found that the tested automated chamber system provided reliable measurements of Rs and net ecosystem exchange (NEE), and it was possible to draw relations for the dependency of Rs and NEE on key environmental drivers. Collectively, the results contribute to a better understanding of the mechanisms of priming effects and highlight possibilities for further research. The methods developed here will allow high temporal and spatial resolution measurements of Rs and NEE under field conditions, using stable isotope methods to separate fluxes into plant- and soil-derived components. Keywords: Soil respiration, soil moisture, soil temperature, Isotope ratio, maize root, flux chamber, climate change, organic matter, rhizodeposition.
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Colocho, Hurtarte Luis Carlos. "Plant Nitrogen status driving soil organic matter mineralization in the rhizosphere." Universidade Federal de Viçosa, 2016. http://www.locus.ufv.br/handle/123456789/10440.
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Os fatores que regulam a dinâmica do Carbono (C) e Nitrogênio (N) do solo na rizosfera são ainda pouco compreendidos. A mineralização de C na rizosfera pode ser fortemente influenciada pelo estado nutricional da planta, a concentração de CO2 na atmosfera e a temperatura do ambiente, entre outros. Em este estudo, avaliamos o status nutricional de N em plantas de Eucalyptus spp. e sua influência na dinâmica do C e do N n a rizosfera. Realizamos um experimento usando um rhizobox dividido em dois compartimentos. No compartimento de cima plantas foram cultivadas e areia lavada e supridas com uma solução nutritiva contendo todos o nutrientes e a mesma solução porém sem N . No compartimento inferior o contato das raízes com o solo foi limitado usando uma membrana de nylon com abertura de 5 μm. Observamos uma maior razão raiz:parte aérea e maiores concentrações de CO2 no solo das plantas com deficiência de N. As raízes das plantas deficientes em N, apresentaram maiores concentrações em relação as plantas não deficientes em N, de citrato e tallose, e menores concentrações de sucrose e aminoácidos. A análise de C e N da fração de matéria orgânica ligada aos minerais , junto com os dados obtidos pela termoquimolise indicam um aumento na mineralização de C e uma modificação na dinâmica do N. Devido a impossibilidade de contato físico direto com o solo, pela presença da membrana de nylon, a única forma de modificar o solo seria então pela exsudação de compostos pelas raízes. O contrastante conteúdo de aminoácidos e açúcares na raiz, junto com os dados do extrato da solução do solo e de mineralização de C, indica que a composição destes exsudatos diferiu em razão da deficiência de N. Enquanto as plantas deficientes em N exsudaram mais ácidos orgânicos, as plantas com ótimo status nutricional foram capazes de exsudar compostos energeticamente ricos. Os dados de δ13C da matéria orgânica ligada aos minerais indica que as plantas deficientes em N afetaram um maior volume de solo que as plantas supridas de N. Tudo isto mostra que, diferentes mecanismos de efeito priming foram dominantes, dependendo do status nutricional da planta. Em plantas deficiente de N, a mineralização de C no solo foi dominada pelo mecanismo chamado de “mineração de N”, enquanto no solo das plantas supridas de N o mecanismo dominante foi a “estequiometria microbiana”. Este trabalho demostra pela primeira vez, ao nosso saber, a atuação de diferentes mecanismos de efeito priming n a mesma planta, sobre diferente status de N . Assim ressaltando, a importância do manejo de nutrientes na dinâmica do C da rizosfera.
The factors that regulate the dynamics of soil Carbon (C) and Nitrogen (N) in the rhizosphere are still poorl y understood. The soil C mineralization in the rhizosphere ca n be heavil y influenced by plant’s nutritional status, atmospheric CO2 concentration and temperature, among others. In this study, we assess the influence of Eucalyptus spp. N status on the C and N dynamics in the rhizosphere. We performed an experiment us ing two compartment rhizobox. In the upper compartment, plants were cultivated in washed sand and supplied with a solution containing all nutrients or all nutrients but N. The lower compartment limited the contact of the roots with the soil using a 5 μm mesh nylon membrane. We observed a higher root-shoot ratio for the N deficient plants and an increase in its soil CO2 concentration. The roots of the –N planted treatment had higher concentrations of citrate and tallose and lower concentration of sucrose and aminoacids, when compared to the +N planted treatment. The C and N anal ysis of the mineral associated organic matter fraction, together with the thermochemol ysis data showed an increase in C mineralization in both planted treatments and changes in N dynamics. As the roots had no physical contact with the soil due to the nylon membrane, the changes in the soil must have been consequence of root exudation. The contrasting sugar and aminoacid root content, together with the citrate concentration in soil solut ion extract and the C mineralization data, indicate that exudate composition changed due to the plants N status. The data indicates that the plants in the –N treatment exudated more organic acids than the plants of the +N treatment. Still the exudate comp osition of the plants with the +N treatment may had a higher energetic content and thus affected differentl y the soil microbial communities. The δ13C data indicate that the N deficient plants affected a higher volume of soil than the plants of the +N treatment. All this together shows different priming mechanisms were dominant due to the plants N status. As the plants were N deficient, the mineralization of soil C was driven by the “N-mining” mechanism while in the soil of the +N planted treatment the dominant mechanism was “microbial stoichiometry”. This work demonstrates, to our knowledge, by the first time using the same plants, different priming mechanisms due to the plants N status. Thus highlighting, the importance of plants nutrient management in the rhizosphere C dynamics.
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Betencourt, Elodie. "Interactions entre céréale et légumineuse en association et acquisition de phosphore du sol : processus rhizosphériques sous-jacents." Thesis, Montpellier, SupAgro, 2012. http://www.theses.fr/2012NSAM0018/document.
Full textAbstract:
L'objectif de cette étude a été de préciser l'implication des processus rhizosphériques dans lesinteractions pour l'acquisition de phosphore (P) entre une céréale et une légumineuse enassociation. Nous avons proposé comme mécanisme de facilitation l'acidification de la rhizosphèredes espèces en association induite par la fixation de N2 de la légumineuse dans le cas de sol neutres àalcalins. Ainsi, l'étude s'est focalisée sur l'influence des changements de pH induits par les racines.Les effets de la disponibilité initiale en P du sol ainsi que de la distance entre les racines des espècesassociées ont également été testés. Les expérimentations ont été menées au champ ainsi qu'enconditions contrôlées. Le blé dur et différentes légumineuses ont été cultivés en culturemonospécifique ou en association sur un même sol pour toutes les expérimentations. Le sol neutreutilisé (Luvisol) présentait trois niveaux contrastés de fertilisation phosphatée et provenait desparcelles d'un essai de longue durée. Nous avons pu démontrer que la manipulation des interactionsrhizosphériques entre une céréale et une légumineuse en association pouvait être optimisée pourpermettre l'augmentation de la disponibilité en P dans la rhizosphère des espèces associées, etencore plus dans le cas de sols présentant une faible valeur initiale de disponibilité. Lescaractéristiques du sol ont eu un rôle clé dans la détermination des processus rhizosphériquesimpliqués. Dans notre cas, les changements de pH induits par les racines ont permis d'augmenter defaçon substantielle la disponibilité en P suite à une acidification, mais aussi à une alcalinisation de larhizosphère. Ainsi la légumineuse, mais aussi la céréale sont susceptibles de faciliter l'acquisition del'espèce associée. Les interactions relatives au pH peuvent influencer la disponibilité en P sur unedistance de plusieurs millimètres et ainsi améliorer l'acquisition de P des plantes à proximité del'espèce facilitatrice.Mots clés : culture associée, facilitation, rhizosphère, disponibilité, phosphore, pH, racineThe aim of the study was to elucidate the implication of rhizospheric processes on plant speciesinteractions for phosphorus (P) acquisition between a cereal and a legume, when intercropped. Weproposed that root-induced acidification of the rhizosphere by the intercropped legume due to N2-fixation as a mechanism of facilitation in neutral to alkaline soils. Thus, the study focused on rootinducedchanges of pH. The effects of initial soil P availability and distance between roots ofintercropped species were also tested. In order to achieve our goals, experiments in the field and incontrolled condition for several cropping devices were conducted. Durum wheat and differentlegumes were grown as sole crops and intercropped on the same soil for all the experiments. Weused a neutral soil (Luvisol) presenting three contrasted fertilization rates from the field of a longtermP fertilizer trial. We demonstrated that cereal-legume can be used to enhance P availability, andeven more so in low P soils, through managing rhizospheric interactions to optimize P acquisition ofintercropped species. Soil characteristics are also a key factor determining the influence of thoserhizospheric processes. In our studied soil root-induced changes of pH substantially enhanced Pavailability in the rhizosphere either through acidification or alkalization. Thus the legume but alsothe cereal may facilitate the acquisition of the intercropped species. Interactions involving pH canaffect P availability over distance of several millimeters and ultimately enhance P acquisition ofplants in the surrounding of the facilitative species.Key words: intercrop, facilitation, rhizosphere, availability, phosphorus, pH, root
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Gautier, Antoine. "Rôles du porte-greffe et du greffon dans la réponse à la disponibilité en phosphore chez la Vigne." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0257/document.
Full textAbstract:
La Vigne est cultivée en système greffé, combinant les qualités de production fruitière des Vignes Européennes (Vitis vinifera) et la tolérance phylloxérique des Vignes Américaines (Vitis spp.). Cependant l’utilisation de porte-greffes américains modifie le développement, la physiologie, et l’alimentation hydrique et minérale du greffon. Plus particulièrement, le fond génétique des porte-greffes de la Vigne semble impliqué dans la régulation de la nutrition en phosphore (P) du greffon. Le phosphore est un élément nutritif essentiel pour la croissance des plantes, impliqué dans la composition de nombreux composants cellulaires, ainsi que dans le contrôle des voies métaboliques via son apport énergétique et la régulation de l’activité enzymatique. Malgré son importance, P un est des éléments minéraux les plus limitants pour la croissance des plantes en raison de sa faible disponibilité assimilable dans le sol. L’objectif de ce travail est de déterminer les mécanismes impliqués dans le contrôle de la nutrition en P de la Vigne, en comparant deux porte-greffes V. riparia cv. Riparia Gloire de Montpellier (RGM) et V. rupestris x V. berlandieri cv. 1103 Paulsen (1103P) connus pour conférer respectivement de faibles ou fortes concentrations en P à leur greffon. Les résultats montrent que 1103P est plus adapté à acquérir le P que RGM, en partie grâce à un système racinaire plus développé permettant une meilleure exploration du sol ainsi qu’une meilleure efficience d’acquisition du P disponible. Ce porte-greffe montre également meilleure utilisation de ses réserves en P dans les parties pérennes afin d’optimiser la croissance des parties aériennes. En revanche la capacité des génotypes à augmenter le P assimilable dans la rhizosphère ne semble pas être différente. Enfin l’effet du greffage et plus particulièrement du greffon a été étudié, révélant le rôle de V. vinifera sur le développement et le fonctionnement racinaire du porte-greffe. Ces résultats contribuent à la compréhension des mécanismes régulant l’alimentation minérale de la Vigne, mettant ainsi en évidence le rôle du fond génétique du porte-greffe sélectionné, ainsi que la régulation de ce dernier par son greffonGrapevine is grown in a grafted system, combining the fruit production qualities of the European species (Vitis vinifera) and the phylloxera tolerance of American species (Vitis spp.). However, the use of American rootstocks affects the development, the physiology, and the water and mineral status of the scion. Particularly, the genetic background of grapevine rootstocks appears to be involved in the regulation of phosphorus (P) content of the scion. Phosphorus is an essential nutrient for plant growth, involved in the composition of many cellular components, as well as in the control of metabolic pathways via its role in energy transfer and the regulation of enzymatic activity. Despite its importance, P is one of the most limiting mineral elements for plant growth because of its poor availability in the soil. The objective of this work is to determine mechanisms involved in the control of P nutrition in grapevine, by comparing two rootstocks V. riparia cv. Riparia Gloire de Montpellier (RGM) and V. rupestris x V. berlandieri cv. 1103 Paulsen (1103P) known to confer low and high concentrations of P to their scion respectively. The results show that 1103P is more efficient at acquiring P than RGM, with a higher developed root system allowing greater soil exploration as well as a higher efficiency of P acquisition. In addition, this rootstock shows better use of its reserves of P in perennial parts to optimize the growth of the shoot. However, the ability of genotypes to increase the assimilable P in the rhizosphere does not seem to be different. Finally, the effect of grafting, and more particularly of the scion genotype, has been studied, demonstrating the capacity of V. vinifera to alter the development and root functioning of the rootstock. These results contribute to our understanding of the mechanisms regulating the mineral nutrition in grapevine and highlight the role of the genetic background of the rootstock, as well as its regulation by the scion