Among dinitrogen (N2)-fixing some cyanobacteria can establish symbiosis with a broad range of host plants from all plant lineages including bryophytes, ferns, gymnosperms, and angiosperms. In the boreal forests, the symbiosis between epiphytic cyanobacteria and feathermosses Hylocomium splendens and Pleurozium schreberi is ecologically important. The main input of biological N to the boreal forests is through these cyanobacteria, and thus, they greatly contribute to the productivity of this ecosystem. Despite the ecological relevance of the feathermoss symbiosis, our knowledge about the establishment and maintenance of cyanobacterial-plant partnerships in general is limited, and particularly our understanding of the feathermoss symbiosis is rudimentary. The first aim of this thesis was to gain insight on the genomic rearrangements that enabled cyanobacteria to form a symbiosis with feathermosses, and their genomic diversity and similarities with other plant-symbiotic cyanobacteria partnerships. Genomic comparison of the feathermoss isolates with the genomes of free-living cyanobacteria highlighted that functions such as chemotaxis and motility, the transport and metabolism of organic sulfur, and the uptake of phosphate and amino acids were enriched in the genome of plant-symbiotic cyanobacteria. The second aim of this PhD study was to identify cyanobacterial molecular pathways involved in forming the feathermoss symbiosis and the regulatory rewiring needed to maintain it. Global transcriptional and post-transcriptional regulation in cyanobacteria during the early phase of establishment of the feathermoss symbiosis, and after colonization of the moss were investigated. The results revealed that the putative symbiotic gene repertoire includes pathways never before associated with cyanobacteria-plant symbioses, such as nitric-oxide sensing and regulation, and the transport and metabolism of aliphatic sulfonate. The third aim was to explore the role of the cyanobacterial community in contributing to the temporal variability of N2-fixation activity. Results from a field-study showed that temporal variation in N2-fixation rates could be explained to a high degree by changes in cyanobacterial community composition and activity. In particular, the cyanobacteria belonging to the genus Stigonema - although not dominating the community- appeared to be the main contributors to the N2-fixation activities. Based on this result, it is suggested that this genus is responsible for the main input of N in the boreal forest ecosystems. The last aim was to understand how the relationship between cyanobacterial community composition and N2-fixation activity will be affected by climatic changes such as, increased temperature (11oC compared to 19oC) and CO2 level (500 ppm compared to 1000 ppm). Laboratory experiments highlighted that 30 weeks of combined elevation of temperature and CO2 resulted in increased N2-fixation activity and moss growth rates. The observed increases were suggested to be allocated to reduced cyanobacterial diversity and changes in community composition, resulting in the dominance of cyanobacteria adapted to the future abiotic condition. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.</p>

Ce travail de thèse porte sur le devenir du N2 récemment fixé par les diazotrophes dans l’océan oligotrophe de surface.Il apparaît que le N2 récemment fixé est excrété dans le compartiment dissous par tous les diazotrophes marins étudiés et que l'amplitude de cette excrétion dépend d'abord des contraintes environnementales que des diazotrophes impliqués dans la fixation.Le transfert de N2 fixé vers le plancton non-diazotrophe a été quantifié en utilisant une méthodologie innovante (couplage de la spectrométrie de masse à ionisation secondaire à l’échelle nanoscopique (nanoSIMS) et du tri cellulaire par cytométrie en flux). En conditions naturelles, 5 à 20 % du N2 récemment fixé est transféré vers les communautés non diazotrophes, principalement via l’excrétion de NH4+. Ce transfert est deux fois plus efficace lorsque le N2 est fixé par le diazotrophe Trichodesmium que lorsqu’il est fixé par les diazotrophes unicellulaires Crocosphaera ou Cyanothece.L’export du N2 récemment fixé a été évalué en utilisant des larges mésocosmes équipés de pièges à sédiments, déployés dans le lagon de Nouvelle Calédonie, et enrichis en PO43- pour stimuler la fixation de N2. Lors de cette expérience, il a été démontré que la fixation de N2 a alimenté une grande partie de la production primaire nouvelle (>90 %) et que le N2 fixé par les diazotrophes a rapidement été exporté. Cet export a été direct, par la sédimentation des diazotrophes eux-mêmes (représentant ~20 % de la matière particulaire retrouvée dans les pièges au plus fort de l’efflorescence de diazotrophes), et indirect, par le transfert de ~20 % du N2 fixé vers les communautés non diazotrophes qui, à leur tour, ont sédimenté. / This PhD thesis, achieved within the framework of the VAHINE project, focuses on the fate of the recently fixed N2 by diazotrophes in the oligotrophic surface ocean.It appears that the release of the recently fixed N2 in the dissolved pool is a process shared between all diazotrophs tested and that the magnitude of this release depend on the environmental contrains rather than on diazotroph involved in fixation.The transfer of the N2 fixed toward non-diazotroph plankton has been investigated using an innovative methodology (coupling of nano-scale mass spectrometry (nanoSIMS) and cell sorting flow cytometry). It appeared that 5 to 20 % of the recently fixed N2 is transferred toward non-diazotroph plankton, mainly through NH4+ release. This transfer is twice more efficient when the N2 is fixed by the filamentous Trichodesmium compared to Crocosphaera and Cyanothece.Particulate export of the fixed N2 has been investigate in large in-situ mesocosms equipped with sediment traps, deployed in the New Caledonian lagoon and enriched with PO43- in order to stimulate N2 fixation. During this experiment, N2 fixation fueled a large part of the new primary production (>90 %) and that fixed N2 was quickly exported. The export has been direct, through the sedimentation of the diazotrophs themselves, and indirect, through the transfer of ~20 % of the recently fixed N2 toward non-diazotrophic plankton that have, in turn, sedimented.

Ce travail de thèse porte sur la quantification de la diazotrophie et son influence sur les cycles biogéochimiques dans l'océan de surface Pacifique tropical sud-ouest, une région particulièrement sous-échantillonnée à ce jour. Les objectifs de ce travail étaient (1) de quantifier la fixation de N2 et identifier les principaux acteurs de la diazotrophie dans cette région, (2) d’évaluer l'influence de la fixation de N2 sur la production primaire et sur l'export de carbone, (3) d’identifier les voies de transfert de l’azote fixé dans la chaine trophique planctonique.Il a été mis en évidence que la région du Pacifique tropical sud-ouest était un hot spot de fixation de N2. A l'ouest, les eaux oligotrophes des archipels Mélanésiens présentaient des taux de fixation de N2 élevés et la communauté diazotrophe était dominée par Trichodesmium. A l'est, les eaux ultra-oligotrophes de la gyre du Pacifique sud présentaient des taux de fixation de N2 plus faibles et la communauté diazotrophe était dominée par les UCYN-B.Des bilans d'azote montrent que la fixation de N2 contribuait à plus de 90 % des apports d'azote nouveau dans la couche euphotique, et soutenait donc la quasi intégralité de la production primaire nouvelle. L'étude des voies de transfert de l'azote fixé montre qu’entre 7 et 15 % de la fixation de N2 totale était transféré vers les organismes non-diazotrophes.Ces travaux de thèse démontrent que la diazotrophie soutient la pompe biologique dans l'océan Pacifique tropical sud-ouest, et qu'elle peut jouer un rôle déterminant dans la structure des communautés planctoniques et les cycles biogéochimiques du carbone et de l'azote dans les régions oligotrophes. / This PhD thesis focuses on the quantification of diazotrophy and its influence on biogeochemical cycles in the western tropical South Pacific Ocean, a critically under-sampled region so far. The aim of this work is to (1) quantify N2 fixation and identify the main contributors of diazotrophy in this region, (2) assess the influence of N2 fixation on primary production and carbon export, (3) identify transfer pathways of the fixed nitrogen in the planktonic food web.We have found that the western tropical South Pacific Ocean was a hotspot of N2 fixation. In the western part, the oligotrophic waters of the Melanesian archipelago presented high N2 fixation rates and diazotrophes were dominated by Trichodesmium. In the eastern part, the ultra-oligotrophic waters of the South Pacific gyre presented lower N2 fixation rates, and diazotrophs were dominated by UCYN-B.The nitrogen budgets show that N2 fixation contributed to more than 90 % of the of new nitrogen input in the photic layer. The study of the transfer pathways of the fixed nitrogen has shown that 7 to 15 % of total N2 fixation was transferred to non-diazotrophs.This PhD thesis indicates that diazotrophy sustains the biological pump in the western tropical South Pacific Ocean, and can have a critical influence in the planktonic community structure and in biogeochemical cycles of carbon and nitrogen in oligotrophic regions.

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