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The depiction of the phylogenetic structure of the genus Frankia is still troublesome and the evolutionary forces guiding the speciation, dispersion and diversity are not well documented. The current phylogeny has been defined on the basis of the comparative analysis of the 16S rRNA gene sequence while de genomospecies definition is still subjected to DNA-DNA hybridization trials. Aiming to bring to light the genomic variability of the genus and its translation into the ecological and specific diversity, our studies consisted in, firstly, evaluating the specific diversity within the genus and the ability of the Amplified Fragment Length Polymorphism technique (AFLP) to describe Frankia genomospecies and their phylogenetic liaisons. Moreover this technique was also tested for the study of the non isolated Frankia directly in the actinorhizal nodules. Secondly, we defined a MLSA (Multilocus Sequence analysis) scheme which allowed us to establish a phylogeny of the genus by using a hundred of strains and for the first time to describe the phylogenetic divergence of a group of non culturable strains exhibiting the particular ability (phenotype) of sporulating in planta (Sp+). The Sp+ strains are distributed into two divergent clades whose structure is highly correlated to the host genotype. The importance of genetic markers having impact over ecology of the strains has been revised. In this regard we have studied the phylogenetic analysis and the occurrence of the genetic components for the siderophore production and of the sodF gene in Frankia.

Bacterial taxonomy is the science of classifying, naming, and identifying bacteria. The scope and practice of taxonomy has evolved through history with our understanding of life and our growing and changing needs in research, medicine, and industry. As in animal and plant taxonomy, the species is the fundamental unit of taxonomy, but the genetic and phenotypic diversity that exists within a single bacterial species is substantially higher compared to animal or plant species. Therefore, the current "type"-centered classification scheme that describes a species based on a single type strain is not sufficient to classify bacterial diversity, in particular in regard to human, animal, and plant pathogens, for which it is necessary to trace disease outbreaks back to their source. Here we discuss the current needs and limitations of classic bacterial taxonomy and introduce LINbase, a Web service that not only implements current species-based bacterial taxonomy but complements its limitations by providing a new framework for genome sequence-based classification and identification independently of the type-centric species. LINbase uses a sequence similarity-based framework to cluster bacteria into hierarchical taxa, which we call LINgroups, at multiple levels of relatedness and crowdsources users' expertise by encouraging them to circumscribe these groups as taxa from the genus-level to the intraspecies-level. Circumscribing a group of bacteria as a LINgroup, adding a phenotypic description, and giving the LINgroup a name using the LINbase Web interface allows users to instantly share new taxa and complements the lengthy and laborious process of publishing a named species. Furthermore, unknown isolates can be identified immediately as members of a newly described LINgroup with fast and precise algorithms based on their genome sequences, allowing species- and intraspecies-level identification. The employed algorithms are based on a combination of the alignment-based algorithm BLASTN and the alignment-free method Sourmash, which is based on k-mers, and the MinHash algorithm. The potential of LINbase is shown by using examples of plant pathogenic bacteria. / Doctor of Philosophy / Life is always easier when people talk to each other in the same language. Taxonomy is the language that biologists use to communicate about life by 1. classifying organisms into groups, 2. giving names to these groups, and 3. identifying individuals as members of these named groups. When most scientists and the general public think of taxonomy, they think of the hierarchical structure of “Life”, “Domain”, “Kingdom”, “Phylum”, “Class”, “Order”, “Family”, “Genus” and “Species”. However, the basic goal of taxonomy is to allow the identification of an organism as a member of a group that is predictive of its characteristics and to provide a name to communicate about that group with other scientists and the public. In the world of micro-organism, taxonomy is extremely important since there are an estimated 10,000,000 to 1,000,000,000 different bacteria species. Moreover, microbiologists and pathologists need to consider differences among bacterial isolates even within the same species, a level, that the current taxonomic system does not even cover. Therefore, we developed a Web service, LINbase, which uses genome sequences to classify individual microbial isolates. The database at the backend of LINbase assigns Life Identification Numbers (LINs) that express how individual microbial isolates are related to each other above, at, and below the species level. The LINbase Web service is designed to be an interactive web-based encyclopedia of microorganisms where users can share everything they know about micro-organisms, be it individual isolates or groups of isolates, for professional and scientific purposes. To develop LINbase, efficient computer programs were developed and implemented. To show how LINbase can be used, several groups of bacteria that cause plant diseases were classified and described.

La définition de la structure phylogénétique du genre Frankia est encore problématique, les forces évolutives guidant son spéciation, dispersion et donc la génération de sa diversité ne sont pas complètement documentées. La phylogénie actuelle du genre a été définie par l’analyse comparative de la séquence du 16S rRNA. Par ailleurs, la définition des espèces génomiques a été gênée par la faible applicabilité de la technique d’hybridation ADN-ADN. Dans le cadre de cette thèse nos travaux ont consisté à étudier la variabilité génomique dans le genre et sa conséquente traduction en variabilité spécifique et écologique. Dans un premier temps, nous avons évalué la diversité spécifique du genre ainsi que l’utilité de la technique AFLP (Amplified Fragment Length Polymorphism) pour la définition des espèces génomiques. De plus, notre protocole fut aussi utilisé pour analyser souches non isolées en appliquant le protocole directement sur des nodosités actinorhiziennes. Dans un deuxième temps, un schéma MLSA (Multilocus Sequence Analysis) nous a permis de redéfinir la phylogénie du genre sur une centaine de souches, et pour la première fois de décrire la divergence phylogénétique d’un groupe de souches non-isolées présentant un phénotype unique de sporulation in planta (Sp+). Les souches Sp+ sont distribuées dans deux clades très divergents dont la structuration est fortement corrélée au génotype de la plante hôte et au phénotype Sp+/Sp- de la souche. L’intérêt de marqueurs génétiques présentant un intérêt pour l’écologie des souches a été révisé. Dans ce but nous avons étudié la présence, distribution et phylogénie de sodF et des différents composants génétiques impliquées dans la production des siderophores chez Frankia. / The depiction of the phylogenetic structure of the genus Frankia is still troublesome and the evolutionary forces guiding the speciation, dispersion and diversity are not well documented. The current phylogeny has been defined on the basis of the comparative analysis of the 16S rRNA gene sequence while de genomospecies definition is still subjected to DNA-DNA hybridization trials. Aiming to bring to light the genomic variability of the genus and its translation into the ecological and specific diversity, our studies consisted in, firstly, evaluating the specific diversity within the genus and the ability of the Amplified Fragment Length Polymorphism technique (AFLP) to describe Frankia genomospecies and their phylogenetic liaisons. Moreover this technique was also tested for the study of the non isolated Frankia directly in the actinorhizal nodules. Secondly, we defined a MLSA (Multilocus Sequence analysis) scheme which allowed us to establish a phylogeny of the genus by using a hundred of strains and for the first time to describe the phylogenetic divergence of a group of non culturable strains exhibiting the particular ability (phenotype) of sporulating in planta (Sp+). The Sp+ strains are distributed into two divergent clades whose structure is highly correlated to the host genotype. The importance of genetic markers having impact over ecology of the strains has been revised. In this regard we have studied the phylogenetic analysis and the occurrence of the genetic components for the siderophore production and of the sodF gene in Frankia.