The CLAVATA1 (CLV1), CLV2 and CORYNE (CRN) receptors egulate cell proliferation in shoot meristems through inhibition of WUSCHEL (WUS). Mutations in these receptors produce more floral organs. The prevailing model proposes that the extra organs are generated from enlarged floral meristems. Using forward and reverse genetics, I identified new alleles in clv1, clv2 and crn and found that most alleles only affect fruit organ number and not sepal, petal or stamen number. Analysis of inflorescence and floral meristems of clv1, clv2 and crn mutants revealed that most mutants do not have altered meristem size. I show that mutations in the ERECTA gene enhance the extra valve phenotype in crn mutants by increasing proliferation in floral meristems. Further data indicate that all mutants tested generate extra organs during fruit development and that CLV1, CLV2 and CRN expression in developing fruit overlaps with regions of increased cell division and extra organs formation. In addition, I provide evidence that CLV1 regulates the transcription factor SHOOTMERISTEMSLESS (STM) in these same regions, as mutations in STM suppress the fruit development phenotype in clv1 mutants.Analysis of the relationship between CLV pathway receptors in meristems and fruit revealed that during fruit development, all three are required to regulate fruit organ number. In meristems, I find that CLV1 appears to play a predominant role, based on evidence that the CLV1 homolog BARELY ANY MERISTEM1 (BAM1) compensates for the absence of CLV1 in the meristem but not in fruit. The fact that BAM1 does not interact genetically with CLV2 or CRN in meristems, further supports the hypothesis that BAM1/CLV1 receptor complexes play key roles in meristems. My analyses suggest that CLV3 acts specifically in the meristem pathway, and not in fruit. Also, I provide genetic data for a CLV3-related CLE gene as a ligand for the fruit-specific pathway. The work presented here provides evidence that a CLV/CRN-STM pathway acts in fruit to restrict cell division and consequently organ number via a mechanism analogous to the CLV/CRN-WUS pathway in shoot meristems, supporting the hypothesis that plants use conserved CLE/Receptor-like kinase/Homeodomain signaling module to maintain meristematic regions throughout the plant.

Les communautés du coralligène dominées par des gorgonaires ont été sévèrement affectées par des évènements de mortalités massives liés au réchauffement de la Méditerranée. Pour évaluer la contribution des bactéries associées à l’holobionte Paramuricea clavata à son fonctionnement et sa santé, il est apparu primordial de caractériser le compartiment microbien naturel de ce gorgonaire tempéré.Dans ce contexte, l’objectif général de cette thèse était de décrire les interactions existant entre la gorgone rouge P. clavata et ses bactéries associées en Méditerranée nord-occidentale. Les analyses entreprises par des techniques culture-indépendantes basées sur l’analyse des ADN ribosomiques 16S bactériens ont inclus (i) la caractérisation de la variation spatio-temporelle des communautés bactériennes, (ii) la localisation des bactéries dans les tissus de l’hôte, (iii) l’évaluation de la stabilité des associations gorgones-bactéries en conditions de stress et (iv) la détermination de la spécificité d’hôte des bactéries dominantes entre différentes espèces de gorgonaires sympatriques (Eunicella singularis, Eunicella cavolini et Corallium rubrum). Les résultats obtenus ont établi que P. clavata et son microbiote forment un holobionte au sein duquel hôte et bactéries vivent en étroite association, stable dans le temps et l’espace ou en conditions de stress. Les communautés bactériennes associées sont principalement endosymbiotiques et dominées par un ribotype bactérien appartenant à un genre nouveau de la famille des Hahellaceae qui semble présenter une forte spécificité d’hôte. Ces résultats suggèrent un rôle particulier de ce genre bactérien chez les holobiontes gorgonaires. / Coralligenous communities dominated by gorgonian species have been severely affected by diseases and mass mortality events linked to the current warming trends reported for the Mediterranean Sea. The characterization of the natural microbial compartment of this temperate gorgonian species becomes a crucial step in the evaluation of the bacterial contribution to health and functioning of the Paramuricea clavata holobiont.Under these circumstances, the global aim of this PhD work was to describe the interactions existing between the red gorgonian P. clavata and its associated bacteria in the Northwestern Mediterranean basin. The culture-independent analyses based on the bacterial 16S ribosomal DNA included (i) the characterization of spatiotemporal variation of the bacterial communities, (ii) the localization of the bacteria within host tissues, (iii) the evaluation of the stability of gorgonian-bacterial associations under stress conditions and (iv) the determination of the host-specificity of dominant bacteria in different sympatric gorgonian species (Eunicella singularis, Eunicella cavolini and Corallium rubrum).The results of this study highlighted that P. clavata and its microbiota form a holobiont in which host and bacteria live in close association. This association is spatiotemporally stable and maintained under stress conditions. Associated bacterial communities are mostly endosymbiotic and dominated by a bacterial ribotype belonging to a new genus within the Hahellaceae family that seems to be host-specific. These results suggest a particular role of this bacterial genus in the gorgonian holobionts.

Les arbres ont la capacité de percevoir des sollicitations mécaniques quotidiennes dues au vent et d’acclimater leur croissance et leur développement en conséquence. Ce stress mécanique se traduit essentiellement par des flexions des organes, en particulier des branches et de la tige. Des études antérieures ont montré que la croissance en diamètre du peuplier était stimulée en réponse aux flexions mimant l’effet du vent. Cette augmentation de la croissance s’accompagne d’une modification de la nature du bois mis en place, qui a pu être observé chez quelques conifères et angiospermes, et nommé « bois de flexion ». Mais la caractérisation anatomique de ce bois a été peu approfondie, et les acteurs moléculaires de sa formation n’ont jamais été recherchés. De plus, dans la plupart de ces études les sollicitations mécaniques appliquées à la tige sont des flexions multidirectionnelles et d’intensité non contrôlée. Or, la déformation étant la variable physique perçue par la plante, il est nécessaire de contrôler l’amplitude de la flexion appliquée à la tige. Grâce à un dispositif expérimental original, nous avons appliqué des flexions unidirectionnelles sur de jeunes tiges de peupliers tout en contrôlant l’intensité des déformations appliquées. Cette étude a montré que la perception des déformations s’effectuait à une échelle locale, conduisant à une ovalisation de la tige. Nous avons pu également différencier le bois formé sous des déformations en tension, que nous avons nommé Tensile Flexure Wood, du bois formé sous des déformations en compression, que nous avons nommé Compressive Flexure Wood. Les analyses anatomiques et moléculaires montrent que l’intensité des déformations en valeur absolue ne suffit pas à expliquer toutes les réponses et que le signe (tension ou compression) de ces déformations joue également un rôle. Chez des arbres stimulés par des flexions unidirectionnelles plus fréquentes, la croissance et la différenciation cellulaire sont modulés encore différemment, notamment dans la zone en compression, apportant à la tige un bénéfice adaptatif face aux sollicitations suivantes. Le gène CLE12.2 appartenant à la famille des gènes CLAVATA, gènes impliqués dans les régulations méristématiques, a été montré mécanosensible. Une approche de génomique fonctionnelle du gène CLE12.2 par l’utilisation de plants transgéniques présentant une sous- ou une surexpression du gène nous a permis d’émettre l’hypothèse d’une implication du peptide CLE12.2 dans la régulation des voies de biosynthèse de la paroi cellulaire. Cette étude a permis de mettre en avant la complexité des mécanismes moléculaires impliqués dans la formation du bois et apporte de nouvelles connaissances pour la poursuite des études sur l’acclimatation des arbres au vent. / Trees have the ability to perceive daily mechanical stresses related to wind and to acclimate their growth and development accordingly. Wind essentially results in organs bending, in particular in branches and stem. Previous studies have shown that growth diameter of poplar stem increased in response to bending; mimicking wind mechanical effect. This growth increment goes along with a change in the structure of the wood formed under bending stimulation. This type of reaction wood has been described for some conifers and angiosperms species, and was called "flexure wood". Until now, its anatomical characteristics have been poorly described, and the molecular actors of its formation have never been investigated. In addition, in most of these previous studies the mechanical stresses applied to the stem were bidirectional bendings with an uncontrolled intensity. Because mechanical strains constitute the physical variable perceived by the plant, it appeared necessary to carefully control the bending amplitude applied to the stem. Thanks to an original experimental setup, we applied unidirectional bendings on young poplar stems, while controlling its intensity. This study showed that the strains are perceived at a local scale and that the secondary growth response was also local, leading to stem ovalization. We also distinguished the wood formed under tension we named “Tensile Flexure Wood” from the wood formed under compression we named “Compressive Flexure Wood”. The anatomical and molecular analyzes show that the strain intensity in absolute value is not enough to explain all the answers and that the sign (tension or compression) of these strains also plays a role. In trees stimulated by more frequent unidirectional bendings, growth and cell differentiation are modulated even differently, especially in the area under compression, bringing to the stem an adaptive benefit to the following solicitations. The CLE12.2 gene, which belongs to the CLAVATA gene family involved in meristematic regulation, has been shown to be mechanosensitive. Functional analysis of the CLE12.2 gene in transgenic plants with under- or overexpression of the gene allowed us to hypothesize that the CLE12.2 peptide is involved in the regulation of the cell-wall biosynthesis pathways. This work highlighted the complexity of the molecular mechanisms involved in wood formation and brings new knowledge for further studies on trees acclimation to wind.

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Parasiten können den Energietransfer in Lebensgemeinschaften über trophische Kaskaden beeinflussen, indem sie Änderungen in den Konsumenten-Ressourcen-Interaktionen induzieren. In der vorliegenden Arbeit wurde die Rolle von Trematoden auf das Freßverhalten ihrer Wirte auf zwei trophischen Ebenen untersucht. Vier verschiedene Süßwasserschnecken-Trematoden-Systeme wurden verwendet, um zu testen, ob ein allgemeines Muster für die Auswirkung von Infektionen auf die Grazingaktivität von Schnecken auf das Periphyton nachgewiesen werden kann. Die Grazingraten auf Periphyton bei infizierten Schnecken entweder höher, niedriger oder ähnlich denen derjenigen von nicht infizierten Artgenossen. Augenparasiten können die Leistungsfähigkeit ihres Wirtes beeinträchtigen, was die Auswirkungen auf das Erkennen von Beutetieren, Raubtieren und Artgenossen hat. Mit Tylodelphys clavata experimentell infizierte Flussbarsche wurden mit zwei verschiedenen Beutetierarten eingesetzt, um das Fraßverhalten in Konkurrenz mit nicht infizierten Artgenossen zu untersuchen. Die Entfernung, aus der infizierte Fische die beiden Beutetierarten attackierten, war im Vergleich zu nicht infizierten Artgenossen signifikant kürzer. Die Tendenz war, dass nicht infizierte Fische mehr von den verfügbaren Beutetieren verzehrten. Um zu prüfen, ob der Fisch als Kompensation seine Beutepräferenz verändert, wurde die Beutezusammensetzung von Flussbarschen aus dem Müggelsees mittels Mageninhalts- und Stabilisotopenanalysen untersucht. Beide Methoden ergaben, dass sich die Fische mit zunehmender Intensität der Infektion selektiver ernährten, während sich geringer infizierte Fische Generalisten herausstellten. Die Ergebnisse dieser Studie bestätigen, dass Trematoden eine wichtige Rolle in Nahrungsnetzen spielen können, indem sie das Freßverhalten ihres Wirtes verändern. Darüber hinaus können Trematoden so die Stärke der Interaktion ihrer Wirte mit anderen Arten auf verschiedenen trophischen Ebenen beeinflussen. / Parasites can influence energy transfer through communities via trophic cascades by inducing alterations on consumer-resource interactions. This study evaluated the role of trematodes on their host’s feeding behaviour at two trophic levels. Four different freshwater snail–trematode systems were used to test whether a general pattern can be detected for the impact of infections on snail periphyton grazing activity. Mass-specific periphyton grazing rates of infected snails were higher, lower, or similar to rates of non-infected conspecifics. The variation across systems may result from differences on how the parasites use the resources of the snail and thus affect its energy budget. Eye parasites can impair their host’s sensory performance with important consequences for the detection of prey, predators and conspecifics. European perch experimentally infected with Tylodelphys clavata were used to evaluate their feeding behaviour under competition with non-infected conspecifics, for two different prey species (Asellus aquaticus and Daphnia magna). The distance at which infected fish attacked both prey species was significantly shorter in comparison to non-infected conspecifics. Additionally, infected fish had more unsuccessful attacks and there was a general tendency that non-infected fish consumed more of the available prey. To evaluate whether fish alter their prey preference as a compensatory mechanism, perch from Lake Müggelsee were sampled and their diet was evaluated using both stomach content and stable isotope analyses. Both methods indicated that with increasing infection intensity fish had a more selective diet, while less intensively infected fish appeared to be generalist feeders. The results from this study confirm that trematodes can play a relevant role within food webs by altering their hosts’ feeding behaviour. Furthermore, in this way trematodes can affect the interaction strengths of their hosts with other species at various trophic levels.

Plant form is a product of emergent processes of cell division, patterning and morphogenesis. These fundamental processes remain poorly characterised in plants. However, engineering approaches can provide new tools and frameworks for the study and manipulation of plant development. This dissertation describes the development of engineering frameworks for reprogramming of the early diverging land plant Marchantia polymorpha (Marchantia). I describe the generation of genomic and transcriptomic datasets for Marchantia, which has provided the basis for the compilation of a gene-centric registry of DNA parts for engineering (MarpoDB). I describe the development of Loop assembly, an efficient and standardised DNA assembly system based on Type IIS restriction enzymes for recursive fabrication of DNA circuits with high efficiency. MarpoDB was used to mine new DNA parts compatible with Loop assembly which were used to generate plant transformation vectors for labelling of cellular features to study aspects of growth and development. I performed image analysis of genetic markers for segmentation and quantification of cellular properties in germinating gemmae. I implemented high-efficiency Cas9-mediated mutagenesis in Marchantia for use in functional molecular genetics studies. Furthermore, I produced inducible systems for expression of heterologous elements by transactivation which showed negligible levels of basal activity. It was possible to use this system for induction of gene expression in single cells. Finally, these new frameworks were applied to study the gametophytic meristem in Marchantia gemmae. I mapped the expression of several putative candidate homologues for higher plant meristem regulators, performed overexpression and loss-of-function studies for homologues of WUSCHEL, CLAVATA3 and SHOOT MERISTEMLESS. A strategy for misregulation of endogenous genes was developed using inducible transactivation, and was used with cellular markers for WUSCHEL and CLAVATA3 homologues in Marchantia.