京都大学 / 新制・課程博士 / 博士(理学) / 甲第23741号 / 理博第4831号 / 新制||理||1691(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 酒井 章子, 教授 髙林 純示, 教授 松下 智直 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Pseudomonas syringae is an important bacterial plant pathogen that, as a species, is known to cause disease on hundreds of different plant species. However, any individual pathovar of P. syringae typically only causes disease on one or a few plant species, which constitute the host range of the pathovar. Plants are generally resistant to most pathogens primarily because the plant innate immune system is capable of recognizing conserved microbial-associated molecular patterns (MAMPs). Adapted pathovars of P. syringae secrete effector proteins through a Type Three Secretion System (T3SS) to suppress the immune response elicited by their MAMPs. However, secretion of effectors can also trigger a strong plant immune response if the plant harbors resistance proteins capable of recognizing the secreted effectors. Successful pathovars, therefore, must secrete a combination of effectors capable of suppressing MAMP/Pattern-Triggered Immunity (PTI) without eliciting Effector-Triggered Immunity. Here we identify several novel strategies employed by P. syringae to overcome the plant immune system and cause disease. First, we demonstrate that, in place of the canonical T3SS used by all known pathogens of P. syringae, several apparently nonpathogenic isolates of P. syringae employ a novel T3SS that is functional but not necessary for colonization of plants. Despite being closely related to pathogenic isolates of P. syringae, the isolates employing the noncanonical T3SS do not cause disease on any tested plants and instead appear to act more as commensal organisms. Second, we advance the understanding of PTI by identifying a second region of bacterial flagellin that triggers PTI in addition to the archetypical MAMP flg22, which is recognized by the archetypical plant receptor FLS2. This new elicitor, termed flgII-28, is also detected by FLS2 and appears to be under selection in very closely related lineages of P. syringae. Alleles of flagellin present in one recently expanded and agriculturally problematic lineage of P. syringae appear to trigger less PTI on their host plant, tomato, than the ancestral allele suggesting that avoidance of PTI through allelic diversity in MAMPs is an effective alternative strategy to suppression of PTI through delivery of effectors. Finally, we start to elucidate a role for chemotaxis (chemical-directed movement) in P. syringae pathogenicity. Not only is chemotaxis required for pathogenicity of P. syringae on plants, but it also appears to contribute to delimiting the host range of several P. syringae pathovars. These results highlight that additional aspects of P. syringae pathogenicity, such as chemotaxis, can directly contribute to defining the host range of individual P. syringae pathovars. The current paradigm of P. syringae pathogenicity posits that MAMPS and the repertoire of effector proteins are the primary determinant of the host range of any P. syringae pathovar; in contrast these results inspire a more nuanced view of pathogenicity that considers multiple aspects of the infection process. / Ph. D.

Most plant pathogens are specialists where only few plant species are susceptible, while all other plants are resistant. Unraveling the mechanisms behind this can thus provide valuable information for breeding or engineering crops with durable disease resistance. A group of Pseudomonas syringae strains with different host ranges while still closely related were thus chosen for comparative study. We confirmed their close phylogenetic relationship. We found evidence supporting that these strains recombined during evolution. The Arabidopsis thaliana and tomato pathogen P. syringae pv. tomato (Pto) DC3000 was found to be an atypical tomato strain, distinct from the typical Pto strains commonly isolated in the field that do not cause disease in A. thaliana, such as Pto T1. Comparing A. thaliana defense responses to DC3000 and T1, we found that T1 is eliciting stronger responses than DC3000. T1 is likely lacking Type III effector genes necessary to suppress plant defense. To test this, we sequenced the genomes of strains that cause and do not cause disease in A. thaliana. Comparative genomics revealed candidate effector genes responsible for this host range difference. Effector genes conserved in strains pathogenic in A. thaliana were expressed in T1 to test whether they would allow T1 to growth better in A. thaliana. Surprisingly, most of them reduced T1 growth. One of the effectors, HopM1, was of particular interest because it is disrupted in typical Pto strains. Although HopM1 has known virulence function in A. thaliana, HopM1 reduced T1 growth in both A. thaliana and tomato. HopM1 also increased the number of bacterial specks but reduced their average size in tomato. Our data suggest that HopM1 can trigger defenses in these plants. Additionally, transgenic detritivore Pseudomonas fluorescens that can secrete HopM1 shows dramatically increased growth in planta. The importance of genetic background of the pathogen for the functions of individual effectors is discussed. T1 cannot be manipulated to become an A. thaliana pathogen by deleting or adding individual genes. We now have a list of genes that can be studied in the future for the molecular basis of host range determination. / Ph. D.

Plants and animals are characterized by intimate, enduring, often indispensable, and always complex associations with microbes. Therefore, it should come as no surprise that when the genome of a eukaryote is sequenced, a medley of bacterial sequences are produced as well. These sequences can be highly informative about the interactions between the eukaryote and its bacterial cohorts; unfortunately, they often comprise a vanishingly small constituent within a heterogeneous mixture of microbial and host sequences. Genomic analyses typically avoid the bacterial sequences in order to obtain a genome sequence for the host. Metagenomic analysis typically avoid the host sequences in order to analyze community composition and functional diversity of the bacterial component. This dissertation describes the development of a novel approach at the intersection of genomics and metagenomics, aimed at the extraction and characterization of bacterial sequences from heterogeneous sequence data using phylogenomic and bioinformatic tools. To achieve this objective, three interoperable workflows were constructed as modular computational pipelines, with built-in checkpoints for periodic interpretation and refinement. The MetaMiner workflow uses 16S small subunit rDNA analysis to enable the systematic discovery and classification of bacteria associated with a host genome sequencing project. Using this information, the ReadMiner workflow comprehensively extracts, assembles, and characterizes sequences that belong to a target microbe. Finally, AssemblySifter examines the genes and scaffolds of the eukaryotic genome for sequences associated with the target microbe. The combined information from these three workflows is used to systemically characterize a bacterial target of interest, including robust estimation of its phylogeny, assessment of its signature profile, and determination of its relationship to the associated eukaryote. This dissertation presents the development of the described methodology and its application to three eukaryotic genome projects. In the first study, the genomic sequences of a single, known endosymbiont was extracted from the genome sequencing data of its host. In the second study, a highly divergent endosymbiont was characterized from the assembled genome of its host. In the third study, genome sequences from a novel bacterium were extracted from both the raw sequencing data and assembled genome of a eukaryote that contained significant amounts of sequence from multiple competing bacteria. Taken together, these results demonstrate the usefulness of the described approach in singularly disparate situations, and strongly argue for a sophisticated, multifaceted, supervised approach to the characterization of host-associated microbes and their interactions. / Ph. D.

African tropical soils play an essential role in global biogeochemical cycles due to carbon (C) they store and the ecosystems they support. Rapid population growth is accelerat- ing land-use changes, particularly the conversion of forest to cropland, which can profoundly affect soil geochemical and microbial properties. How microbial properties relate to geochemical properties in these soils is poorly understood, thus limiting our ability to predict C and nutrient cycling. Our knowledge of the relationships between microbial and geochemical properties comes primarily from temperate regions and tropical regions of America and Asia. However, because of differences in climate, landform, and soil development, this knowledge is not readily transferable to tropical Africa. The objective of this research was to investigate the relationships between microbial and geochemical properties in African tropical forest and cropland soils developed from varying parent material to gain better insight into microbial strategies of nutrient acquisition and investment. Tropical montane forest and cropland soils developed from geochemically different parent ma- terials (mafic, mixed sedimentary rocks, and felsic) were collected in tropical Africa. These samples were analyzed under standardized moisture and temperature conditions to determine microbial properties, including microbial biomass C, potential extracellular enzyme activity, mi- crobial communities, and extracellular polymeric substances (EPS). The standardization was designed to minimize site-specific differences in climatic conditions and thus better assess how geochemical soil properties may influence microbial properties. Despite their long history of chemical weathering, tropical soils developed from different parent materials exhibit geochemical differences that subsequently influence microbial properties to varying degrees. In this study, the chemical index of alteration (CIA) was identified as a useful indicator of a range of geochemical properties. This index, often used to indicate the degree of silicate weathering, was innovatively used in this study to correlate geochemical properties with microbial properties. The role of geochemical properties in controlling microbial properties is particularly pronounced in organic matter (OM)-depleted soils, where geochemical properties likely determine the availability of essential nutrients for microbial life. The influence of OM on patterns of microbial properties is not only a matter of quantity, but also of quality. It has also been found that land-use conversion of forest to cropland does not necessarily reduce microbial diversity as long as soil fertility is maintained at a higher level. Nevertheless, land-use change causes a shift in microbial communities towards microbes that have different resource demand and allocation strategies. Overall, microbial communities in deeply weathered tropical soils are highly adaptive, particu- larly concerning their nutrient acquisition strategies. These strategies provide valuable insights into microbial resource demand and allocation, and potential impacts on C and nutrient cycling in tropical soils. Observed microbial nutrient acquisition strategies suggest that managing mi- crobial communities could potentially be leveraged to maintain or even improve soil fertility and C storage.:Summary Zusammenfassung List of Figures List of Tables List of abbreviations Thesis at a glance 1 General introduction 1.1 Why tropical soils? 1.2 Organic matter cycling: why do controls of soil microbial properties matter? 1.3 Geochemical properties of tropical soils: to what extent do they affect microbial properties? 1.4 Land-use change and its influence on soil properties 1.5 Research objective, questions, and hypotheses 1.5.1 Objective 1.5.2 Research questions and hypotheses 1.6 Outline 2 Materials and methods 2.1 Study area 2.2 Soilsampling 2.3 Incubation experiment 3 Microbial properties in tropical montane forest soils developed from contrast- ing parent material – an incubation experiment 3.1 Abstract 3.2 Introduction 3.3 Laboratory analyses 3.3.1 Soil enzyme assays 3.3.2 Microbial biomass 3.3.3 Soil properties 3.3.4 Data analysis 3.3.5 Statistics 3.4 Results 3.4.1 Soil properties of the different geochemical regions 3.4.2 Patterns of microbial biomass and salt-extractable DOC 3.4.3 Patterns of potential extracellular enzyme activity 3.4.4 Patterns of microbial investment in C and nutrient acquisition 3.4.5 Rotated principal components and mechanistic interpretation 3.4.6 Controls on microbial biomass and nutrient acquisition 3.4.7 Controls on microbial properties after statistical removal of soil depth effects 3.5 Discussion 3.5.1 Patterns of microbial properties in relation to resource availability and geochemical soil properties 3.5.2 Microbial investment in C and nutrient acquisition 3.6 Conclusion and outlook 4 Relationships between geochemical properties and microbial nutrient acquisition in tropical forest and cropland soils. 4.1 Abstract 4.2 Introduction 4.3 Laboratory analyzes 4.3.1 Microbial biomass and enzyme activity 4.3.2 DNA extraction and Quantitative Real-Time PCR (qPCR) 4.3.3 Soil properties 4.4 Data analysis. 4.4.1 An index to describe variation in geochemical soil properties 4.4.2 Statistics 4.5 Results 4.5.1 Variation in geochemical soil properties 4.5.2 Relationship between geochemical soil properties and microbial properties 4.6 Discussion 4.6.1 The CIA is a useful proxy for geochemical variation in tropical soils 4.6.2 Land use-dependent effects of geochemical changes on microbial C and P acquisition 4.6.3 Shifts in bacteria versus fungi abundance affecting C dynamics along the gradients 4.7 Conclusion 5 Extracellular polymeric substances are closely related to land use, microbial communities, and enzyme activity in tropical soils 5.1 Abstract 5.2 Introduction 5.3 Laboratory analyzes 5.3.1 Microbial biomass C, enzyme activity, and nutrient acquisition 5.3.2 Extracellular polymeric substances 5.3.3 DNA extraction 5.3.4 Illumina sequencing and sequence processing 5.3.5 Geochemical soil properties 5.4 Data analysis and statistics 5.4.1 K-means clustering of geochemical soil properties 5.4.2 Variance analysis of nutrient acquisition and EPS 5.4.3 Microbial communities 5.5 Results 5.5.1 EPS concentration and production efficiency 5.5.2 Microbial investment in nutrient acquisition 5.5.3 Patterns and drivers of microbial communities 5.5.4 Differential abundance of microbial taxa between forest and cropland soils 5.5.5 Drivers of EPS concentration and production efficiency 5.6 Discussion 5.6.1 Patterns of EPS concentration and production efficiency depend more on land use than on geochemical soil properties 5.6.2 Land use shapes microbial community assemblages 5.6.3 EPS concentration and production efficiency are related to fungal and bacterial taxa 5.6.4 EPS concentration and production efficiency is related to microbial nutrient acquisition 5.6.5 EPS production efficiency is negatively related to C availability 5.7 Conclusion 6 General discussion and conclusions 6.1 Controls of microbial properties in deeply weathered tropical soil 6.1.1 Organic matter: it is not just a matter of quantity 6.1.2 Geochemical soil properties: a single proxy can be reliable 6.1.3 The unexpected influence of land use 6.2 Microbial nutrient acquisition strategies in deeply weathered tropical soils: implications for C and nutrient cycling 6.3 Final remarks–limitations and perspectives Acknowledgments Bibliography A Appendix to Microbial properties in tropical montane forest soils developed from contrasting parent material – an incubation experiment A.1 Effects of site elevation on microbial properties A.2 Use of vector analysis in assessing microbial resource acquisition B Appendix to Relationships between geochemical properties and microbial nutrient acquisition in tropical forest and cropland soils C Appendix to Extracellular polymeric substances are closely related to land use, microbial communities, and enzyme activity in tropical soils List of publications in peer-reviewed journals Curriculum Vitae Declarations

付記する学位プログラム名: 社会を駆動するプラットフォーム学卓越大学院プログラム / 京都大学 / 新制・課程博士 / 博士(農学) / 甲第25317号 / 農博第2583号 / 新制||農||1104(附属図書館) / 京都大学大学院農学研究科森林科学専攻 / (主査)教授 北島 薫, 教授 小野田 雄介, 教授 井鷺 裕司 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Symbioses between microbes and multicellular eukaryotes are found in all biomes, and encompass a spectrum of symbiotic lifestyles that includes parasitism and disease, commensalism, and mutually beneficial interdependent host-microbe relationships. Regardless of outcome, these symbiotic lifestyles are governed by a complex molecular "courtship" between microbe and potential host. This courtship is the primary determinant of the host range of a given microsymbiont. Host immunity poses a formidable barrier to the establishment of host-microbe relationships, and the majority of microbial suitors will be thwarted by it. Only by successfully "wooing" the host cell's immune defenses with the appropriate molecular signals can a microsymbiont successfully colonize its host. A strategy common to microsymbionts across the spectrum of symbiotic lifestyles and host organisms is the delivery of microbial-encoded effector proteins into the cytoplasm of host cells to manipulate the host cell's molecular machinery for the purposes of subverting host immunity. Bacteria, in particular, have adapted a number of secretion systems for this purpose. The most well-characterized of these is the type III secretion system (T3SS), a molecular apparatus that specializes in injecting type III effector (T3Es) proteins directly into host cells. The work in this thesis focuses on T3Es of plant-associated bacteria, with particular emphasis on mutualistic bacteria. We present evidence that collections of T3Es from Sinorhizobium fredii and Bradyrhizobium japonicum are, in stark contrast to those of phytopathogenic bacteria, in a co-evolutionary equilibrium with their hosts. This equilibrium is characterized by highly conserved T3E collections consisting of many "core" T3Es with little variation in nucleotide sequence. The T3Es of Mesorhizobium loti MAFF303099 suggest a completely different picture of the evolution of T3Es. MAFF303099 recently acquired its T3SS locus, and the work in this thesis provides an evolutionary snapshot of a mutualist that is innovating a T3E collection primarily through horizontal gene transfer. Collectively, this work represents the first comprehensive catalog of T3Es of rhizobia and, in the case of Sinorhizobium and Bradyrhizobium, the first evidence of purifying selection for T3Es. / Graduation date: 2012

Virtuellement toutes les plantes hébergent des champignons et des bactéries endosymbiontes (endophytes). Ces microorganismes façonnent le développement de leur hôte et peuvent inhiber des phytopathogènes. Au niveau moléculaire, les interactions plante-endophyte sont médiées par des molécules secrétées y compris des protéines et métabolites secondaires. Au cours des dernières années, la recherche d’endophytes a augmenté chez nombreux plantes, cependant chez les Ericaceae les endophytes ne sont pas bien connus. Alors, on s’est mis à investiguer les endophytes racinaires de la canneberge, une plante membre d’Ericaceae native de l’Amérique du Nord. On a échantillonné quatre plants provenant d’une ferme commerciale organique. Au total, 30 souches fongiques et 25 bactériens ont été isolés. Les bactéries Pseudomonas sp. EB212, Bacillus sp. EB213 et EB214; et les champignons Hyaloscypha sp. EC200, Pezicula sp. EC205 et Phialocephala sp. EC208 ont supprimé la croissance de cinq pathogènes de la canneberge, incluant Godronia cassandrae, un champignon causant la pourriture des fruits de la canneberge au Québec. EB213 a été capable de promouvoir légèrement la croissance de plantules de la canneberge. En performant des techniques microscopiques, on a constaté l’habileté de EC200, EC205 et EC208 à coloniser internement les racines des plantules de la canneberge. De plus, les génomes de ces champignons ont été séquencés, assemblés et annotés. Les analyses génomiques se sont concentrées sur les protéines secrétées et les groupes des gènes impliqués dans la biosynthèse (GGB). On a trouvé un large répertoire de gènes codant pour des enzymes qui métabolisent les carbohydrates et d’autres codant pour des protéases. Les deux groupes d’enzymes seraient utiles à dégrader de la matière organique pour libérer des nutriments. Aussi bien, ces enzymes pourraient faciliter la colonisation des racines de la plante hôte. De plus, on a prédit des nombreuses protéines effectrices qui assisteraient les endophytes à éviter l’activation du système immunitaire des plants. A noter que parmi les GGB inférés dans les génomes de EC200, EC205 et EC208, environ 90% ne sont pas caractérisés. Finalement, on a performé des analyses transcriptomiques pour élucider la réponse de EC200, EC205 et EC208 envers la présence de leur hôte, simulée par l’addition d’un extrait de canneberge au milieu de culture. Les conclusions majeures sont que les racines des plantes de la canneberge qui ont été échantillonnées sont dominées par des microorganismes avec l’habileté d’inhiber des phytopathogènes ; et que les génomes de EC200, EC205 et EC208 codent pour un grand répertoire de protéines qui pourraient être liées aux interactions plante-endophyte. / Virtually all plants host fungal and bacterial endosymbionts (endophytes). These microbes shape plant development and may inhibit phytopathogens. At the molecular level, plant-endophyte interactions are mediated by secreted compounds, including proteins and secondary metabolites. While endophytes are increasingly studied in diverse plants, little is known about their presence in Ericaceae. Therefore, we set out to investigate the root endophytes of cranberry, an ericacean member native to North America. We sampled endophytes from four plants grown on an organic farm. In total, 30 fungal and 25 bacterial strains were isolated and identified. A subset of these, notably Pseudomonas sp. EB212, Bacillus sp. EB213 and EB214; and fungi Hyaloscypha sp. EC200, Pezicula sp. EC205, and Phialocephala sp. EC208, were tested for their ability to suppress phytopathogens. Altogether, they inhibited five cranberry pathogens, including Godronia cassandrae, an important cranberry fruit-rot agent in Quebec. EB213 was the only endophyte that increased the biomass of cranberry seedlings. Using microscopy techniques, we confirmed the ability of EC200, EC205, and EC208 to colonize cranberry roots internally. The genomes of these fungi were sequenced, assembled and annotated. Genomic analyses focused on secreted proteins and biosynthetic gene clusters (BGCs). We found an extensive repertoire of carbohydrate-active enzymes and proteases that could assist in recycling organic nutrients, rendering them accessible to plants; these enzymes may also facilitate root colonization. In addition, effector proteins were predicted; these molecules may assist endophytes to escape the plant immune system and favour colonization. We inferred 139 biosynthetic gene clusters (BGCs) across the three examined fungi. Remarkably, the product of around 90% of BGCs are unknown. Finally, transcriptomic analyses were performed to determine how EC200, EC205 and EC208 respond to the presence of cranberry, simulated by the addition of cranberry extract in the culture medium. The two major conclusions of this work are that the roots of the sampled cranberry plants are dominated by endophytes with biocontrol abilities, and that EC200, EC205 and EC208 encode a broad repertoire of proteins that could be involved in plant-endophyte interactions.

Os microrganismos endofíticos são aqueles, cultiváveis ou não, que habitam o interior da planta hospedeira sem causar danos aparentes ou estruturas externas visíveis. Essa interação microrganismos-planta é intrínseca a determinadas espécies de plantas e/ou bactérias. Nas últimas décadas os estudos de microrganismos endofíticos têm sido realizados em diversas plantas hospedeiras, sendo esses estudos direcionados principalmente para a diversidade e características benéficas induzidas, inclusive o controle biológico de doenças. A doença causada pelo fungo Ceratocystis fimbriata é considerada emergente no setor florestal. O Brasil está entre os maiores produtores mundiais de eucalipto e a expansão do setor juntamente com o cultivo clonal tem acarretado o aumento da incidência de patógenos. O surgimento de novas doenças exige estudos relacionados tanto a interação do agente patogênico com hospedeiro quanto de todos os componentes do patossistema. Neste contexto, os microrganismos endofíticos têm sido descritos como potenciais controladores biológicos de doenças. Dessa forma, o presente trabalho teve por objetivos avaliar a interação de C. fimbriata com a comunidade bacteriana associada à Eucalyptus sp. Adicionalmente, foi estudada a possível transferência desses endófitos via sementes e o padrão de colonização de Pantoea agglomerans em plântulas. Foi observado que plantas não infestadas por C. fimbriata apresentaram maior densidade bacteriana no rizoplano (20,66 x 104 UFC.cm2 -1 de raiz), enquanto que para a comunidade endofítica, a maior densidade foi observada em plantas infectadas pelo fungo (25,13 x 104 UFC.g-1 de raiz). As análises por ARDRA possibilitaram a obtenção de 8 e 13 ribotipos nas comunidades endofítica de raiz e do rizoplano, respectivamente. Os ribotipos mais freqüentes foram identificados como Bacillus cereus. As análises de diversidade por meio de DGGE das comunidades do rizoplano e endofítica de raiz mostraram que a infestação pelo fungo interfere na colonização de Eucalyptus. Foi observado também que bactérias endofíticas estão presentes no interior de sementes de Eucalyptus spp. em uma densidade de 0,33 a 1,83 X 102 UFC.g-1, para as espécies E. camandulensis e E. urophylla, respectivamente. A densidade bacteriana endofítica de plântulas obtidas de sementes desinfectadas superficialmente variaram entre 0,27 X 102 a 0,87 X 102 UFC.g-1, para E. citriodora e o híbrido E. robusta x E. grandis, respectivamente. Em algumas espécies de Eucalyptus não foram isoladas bactérias endofíticas das sementes e plântulas. Os resultados mostraram que algumas espécies de bactérias endofíticas podem ser transmitidas verticalmente por sementes. P. agglomerans inoculada nas sementes foi capaz de colonizar as plântulas após a germinação da semente, indicando que esta pode ser uma das formas utilizadas pelos microrganismos para colonizar e se estabelecer na planta hospedeira. Assim, os resultados obtidos neste trabalho mostram ainda que possa existir interação entre a presença de C. fimbriata e a comunidade bacteriana endofítica e do rizoplano de Eucalyptus. Foi possível observar também que estas bactérias endofíticas que são transmitidas por meio de sementes, permitindo que plântulas previamente inoculadas com bactérias benéficas possam ser produzidas antes de serem levadas a campo. / The endophytic microorganisms are those, cultivated or not, that inhabit the interior of the plant host without causing apparent damages or visible external structures. This interaction microorganisms-plant is specific to certain species of plants and/or bacteria. In the last few years studies of endophytic microorganisms have been carried out in several plant hosts, being these studies focused mainly to diversity and biotechnological potential, such as biological control of disease. The disease caused by the phytopathogenic fungi Ceratocystis fimbriata is considered emerging by the reforestation companies. Brazil is one of the largest world eucalyptus producers and the increasing of the eucalyptus production associated to clonal reproduction has allowed the increase in pathogen incidence. Studies that evaluate the interaction between pathogens and the microbial community associated to the host plant may allow understanding how disease symptoms come up. Endophytic microorganisms have been described as potential biological control of diseases and therefore, the aims of the present work were to i) study the interaction between C. fimbriata and the bacterial community associated to the Eucalyptus sp.; ii) evaluate the bacterial dissemination by seeds; iii) evaluate the colonization profile of Pantoea agglomerans in seedlings after seed inoculation. It was observed that the highest bacterial density on the rhizoplane (20.66 x 104 CFU.cm2 -1 of root) was observed in C. fimbriata uninfectedplants, while for endophytic community the highest density was observed in C. fimbriata infected plants (25.13 x 104 CFU.g-1 of root). The ARDRA analyses showed that the bacterial community of eucalyptus is composed by 8 and 13 ribotypes on rhizoplane and inside the roots (endophytic), respectively. The most frequent ribotypes were identified as Bacillus cereus. The DGGE analyses of diversity of endophytic and rhizoplane community showed that fungi infection shift the colonization of Eucalyptus associated bacteria. The bacterial community inside Eucalyptus spp. seeds ranged from 0.33 to 1.83 X 102 CFU.g-1, for E. camandulensis and E. urophylla, respectively. After seed germination the endophytic bacterial density in seedlings ranged from 0,27 X 102 to 0,87 X 102 CFU.g-1, for E. citriodora and the hybrid E. robusta x E. grandis, respectively. Although, endophytic bacteria have been isolated from seeds, for some plant species, bacteria were not isolated from seedlings. Also, some bacteria may be vertically transmitted from seed to seedlings, but some is specific for seeds. Seed inoculation of P. agglomerans resulted in seedlings colonized by these bacteria, suggesting that these bacteria could be seed transmitted. The results obtained in the present study show that the fungi C. fimbriata inside the Eucalyptus host can shift the endophytic and rhizoplane bacterial diversity. Also, these endophytic bacteria could be transmitted vertically by seeds, allowing that seeds previously inoculated with beneficial bacteria may result in protected plants before planting in the field.

Les principaux objectifs étaient d'évaluer la stabilité de l'environnement des scories métallurgiques de Cu résultant de différentes périodes d'activités industrielles et de différentes technologies de fusion. Parmi les scories étudiées, on retrouve: les scories historiques cristallines (SH) ainsi que modernes: les scories de four vertical (SFS), les scories granulées (GS) et les scories de plomb (LS). Les différentes approches adoptées dans ce travail de thèse ont tenu compte de: i) la composition chimique et la phase minérale des scories, ii) la sensibilité à la lixiviation des scories sous l’exposition à différentes conditions de pH en mode statique, iii) l’altération des scories sous exposition aux acides organiques couramment trouvés dans l'environnement du sol, iv ) la bio-altération des scories par les bactéries (Pseudomonas aeruginosa) et v) l’application future de la récupération des métaux provenant des scories étudiées en mettant en œuvre la méthode de lixiviation biologique. Résultats cruciaux: Les résultats des tests de lixiviation dépendant du pH ont montré une libération de métal plus élevée dans des conditions fortement acides (pH 2 et 4), alors que la lixiviation dans des conditions alcalines (pH 10.5) était moins importante pour toutes les scories analysées. L'effet de l’altération par le sol a été démontré, la dissolution des scories est notamment sensible à la présence d'exsudats racinaires artificiels (ARE), d’acides humiques (HA) et d’acides fulviques (FA), la contribution des ARE étant la plus forte. Selon les données recueillies, la dissolution relative des scories est strictement liée à leurs caractéristiques (composition chimique et minéralogique) en fonction des différentes conditions étudiées. L'étude concernant l’effet de l’altération biologique a révélé que Pseudomonas aeruginosa améliore considérablement la libération des éléments majeurs (Si et Fe) et métalliques (Cu, Zn, Pb) par rapport aux effets des facteurs abiotiques, indépendamment de la chimie et de la structure des scories. En outre, une récupération élevée (jusqu'à 90%) des métaux (Cu, Zn, Fe) pourrait être obtenue grâce à la lixiviation avec Acidithiobacillus thiooxidans dans des conditions de laboratoire. Conclusions générales : La stabilité des scories dans l'environnement dépend à la fois des caractéristiques chimiques et de la minéralogie. Cependant, les phases minérales hébergeant les métaux sont les facteurs les plus déterminants concernant l'intensité de la lixiviation des métaux. Pour cette raison, l'examen individuel du comportement des scories est important pour empêcher la contamination de l'environnement et devrait être considéré comme une priorité pour la gestion durable des scories. L’optimisation des paramètres de fonctionnement pour le biolessivage et le développement de la technologie à l'échelle industrielle pourrait permettre une bien meilleure gestion (voir l’exploitation) des scories métallurgiques de Cu / Problem statement: Copper pyrometallurgical slags are inevitable waste by-products of Cu smelting operations. These waste are considered to be important due to their production volume and high residual metal content that are inefficiently recovered during industrial process. Due to the lack of sustainable practices in the past, tremendous volumes of Cu-slags have been disposed in many industrial districts, regardless of the weathering and associated environmental risk. Consequently, there are many areas where slags have been proven to be a source of metallic pollution for the surrounding environment. At the present time, the outstanding contradiction between the sustainable development and environmental pollution encourages to undertake the action regarding this aspect. For this reason, slags are currently being used as supplementary materials for civil engineering purposes (e.g. cement and concrete additives, road bed filling materials, hydraulic construction materials) rather than disposed. Additionally, modern-day management strategies require slags to be thoroughly evaluated with respect to their environmental stability prior undertaking any reuse action. Main objectives were to evaluate environmental stability of Cu-metallurgical slags resulting from different periods of industrial activities and different smelting technologies. Those included: historical crystalline slag (HS) as well as modern: shaft furnace slag (SFS), granulated slag (GS) and lead slag (LS). Different approaches undertaken in this PhD work considered: i) chemical and mineral phase compositions of slags, ii) leaching susceptibility of slags under exposure to different pH-stat conditions, iii) slags weathering under exposure to organic acids commonly found in soil environment, iv) bacterially (Pseudomonas aeruginosa) mediated weathering of slags and v) future application of studied slags for metal recovery by implementing the bioleaching method. Crucial results: The results of the pH-dependent leaching tests showed a higher metal release in strong acidic conditions (pH 2 and 4), whereas leachability at alkaline conditions (pH 10.5) revealed a lower importance for all the slags analyzed. The study considering soil weathering scenario demonstrated that Cu-slags are susceptible to dissolution in the presence of artificial root exudates (ARE), humic (HA) and fulvic acids (FA), whereby ARE were found to have stronger contribution than HA and FA. According to data collected, the different behavior of individual slags is strictly related to their characteristics (chemical and phase composition) reflecting various susceptibilities to dissolution under the investigated conditions. The study considering bio-weathering scenario revealed that Pseudomonas aeruginosa considerably enhances the release of major (Si and Fe) and metallic (Cu, Zn, Pb) elements compared to the effects of abiotic factors, regardless of the slags chemistry and structure. Furthermore, a high gain (up to 90%) of metals (Cu, Zn, Fe) could be credited to bioleaching with Acidithiobacillus thiooxidans under laboratory conditions. General conclusions: The environmental stability of slags depends on both, their bulk chemistry and mineralogy. However, mineral phases harbouring the metals are the key players in metal leachability intensity. For, this reason consideration of individual slags behaviour is important for preventing environmental contamination and should be regarded as priority branch of sustainable slag management. Optimization of operating parameters for bioleaching following development of industrial scale technology is an incentive scheme for future management of Cu-metallurgical slags