La recherche en bactériologie et virologie est à la fois de nature cognitive et appliquée. Elle consiste à fédérer et mettre en place une capacité de recherche multidisciplinaire et pouvoir l'intégrer sur un champ très vaste de microorganismes et de maladies. Les nouvelles avancées conceptuelles et technologiques dans le domaine de la génomique, notamment les avancées dans les techniques à haut débit (séquençage, PCR...) permettent actuellement d’avoir rapidement des génomes bactériens et viraux entiers, ou seulement sur quelques gènes d’une grande population. Les progrès dans ce domaine permettent l’accès à ces informations en évitant une combinaison de plusieurs méthodologies, et à moindre coûts. Dans notre travail de thèse, nous avons été porté à analyser et traiter les données de deux études genomiques et métagenomiques, mettant en évidence avantages, limites et attentes liés à ces techniques. La première étude porte sur l'analyse génomique de nouveaux virus géants et chlamydia infectant Vermamoeba vermiformis. La deuxième étude concerne le pyroséquençage 16S de microbiote intestinal de nouveau-nés atteint de l'entérocolite nécrosante. Pour le premier projet du travail de thèse, nous avons analysé les génomes de trois nouvelles espèces de Chlamydiae et onze virus giants (premiers membres de deux probables nouvelles familles) qui se multiplient naturellement dans Vermamoeba vermiformis. L'objectif étant de mettre en évidence les caractéristiques génétiques spécifiques à ces micro-organismes. La deuxième partie a été consacrée à l'analyse des données de pyroséquençage 16S des selles de nouveau-nés atteints de l'entérocolite nécrosante. / Research in bacteriology and virology is both cognitive and applied. It involves federating and developing a multidisciplinary research capacity and being able to integrate it into a very broad field of microorganisms and diseases. New genomic and conceptual advances in genomics, including advances in high-throughput techniques, now permit rapid bacterial and viral genomes, or only a few genes of a large population. Progress in this area allows access to this information by avoiding a combination of several methodologies and at lower costs. In our thesis work, we were led to analyze and process the data of two genomic and metagenomic studies, highlighting advantages, limitations and expectations related to these techniques. The first study focuses on the genomic analysis of new giant viruses and chlamydia infecting Vermamoeba vermiformis. The second study concerns the 16S pyrosequencing of intestinal microbiota of neonates with necrotizing enterocolitis. The first project of the thesis work analyzed the genomes of three new species of Chlamydiae and eleven giant viruses (first members of two probable new families) which naturally multiply in Vermamoeba vermiformis. The objective is to highlight the genetic characteristics specific to these microorganisms. The second part was devoted to the analysis of 16S pyrosequencing data from neonatal enterocolitis neonatal stools. The goal was to identify an agent responsible for this disease.

An established host-parasitoid-hyperparasitoid system was used to investigate how the physiological and behavioural characteristics of parasitoids influence the outcomes of laboratory-based host specificity tests. The characteristics of the two pteromalid egg parasitoids, Enoggera nassaui (Girault) and Neopolycystus insectifurax Girault, were assessed and interpreted in regard to the particular host specificity testing methods used and the control of the eucalypt defoliating beetle Paropsis charybdis Stål (Chrysomelidae) in New Zealand. The physiology of N. insectifurax was examined to determine how to increase production of female parasitoids that were physiologically capable and motivated to parasitise P. charybdis eggs in laboratory trials. Neopolycystus insectifurax were found to be more synovigenic than E. nassaui. Provisioning them with honey and host stimuli for three days, and allowing females to parasitise hosts in isolation (i.e. in the absence of competition) was an effective means of achieving these goals. No-choice tests were conducted in Petri dish arenas with the four paropsine beetles established in New Zealand. All four were found to be within the physiological host ranges of E. nassaui and N. insectifurax, but their quality as hosts, as indicated by the percent parasitised and offspring sex ratios, varied. The results of paired choice tests between three of the four species agreed with those of no-choice tests in most instances. However, the host Trachymela catenata (Chapuis), which was parasitised at very low levels by E. nassaui in no-choice tests, was not accepted by that species in paired choice tests. A much stronger preference by N. insectifurax for P. charybdis over T. catenata was recorded in the paired choice test than expected considering the latter was parasitised at a high level in the no-choice test. The presence of the target host in paired choice tests reduced acceptance of lower ranked hosts. Both no-choice and choice tests failed to predict that eggs of the acacia feeding beetle Dicranosterna semipunctata (Chapuis) would not be within the ecological host range of E. nassaui and N. insectifurax. Behavioural observations were made of interspecific competition between E. nassaui and N. insectifurax for access to P. charybdis eggs. Two very different oviposition strategies were identified. Neopolycystus insectifurax were characterised by taking possession of, and aggressively guarding host eggs during and after oviposition. They also appeared to selectively oviposit into host eggs already parasitised by E. nassaui, but did not emerge from significantly more multi-parasitised hosts than E. nassaui. Enoggera nassaui did not engage in contests and fled when approached by N. insectifurax. Although often prohibited from ovipositing by N. insectifurax, E. nassaui were able to locate and begin ovipositing more quickly, and did not remain to guard eggs after oviposition. It is hypothesised that although N. insectifurax have a competitive advantage in a Petri dish arena, E. nassaui may be able to locate and parasitise more host eggs in the field in New Zealand, where competition for hosts in is relatively low. The biology of the newly established encyrtid Baeoanusia albifunicle Girault was assessed. It was confirmed to be a direct obligate hyperparasitoid able to exploit E. nassaui but not N. insectifurax. Field and database surveys found that all three parasitoids have become established in many climatically different parts of New Zealand. Physiological characteristics were identified that may allow B. albifunicle to reduced effective parasitism of P. charybdis by E. nassaui to below 10%. However, the fact that hyperparasitism still prevents P. charybdis larvae from emerging, and that B. albifunicle does not attack N. insectifurax, may preclude any significant impact on the biological control of P. charybdis. Overall, parasitoid ovigeny and behavioural interactions with other parasitoids were recognised as key characteristics having the potential to influence host acceptance in the laboratory and the successful biological control of P. charybdis in the field. It is recommended that such characteristics be considered in the design and implementation of host specificity tests and might best be assessed by conducting behavioural observations during parasitoid colony maintenance and the earliest stages of host specificity testing.