Éditeur(s) : HAL CCSD
Résumé : Evolution of organisms, genomes and genes does not strictly follow a tree-like process; symbiosis, horizontal gene transfers and gene fusions build high level composite objects with components of phylogenetically distinct origins. Such processes have been called introgressive events and are significant in evolution. They are involved in some major evolutionary transitions such as eukaryogenesis, photosynthesis acquisition in eukaryotes and the origins of major archaeal clades. Eukaryogenesis would have involved (at least) two kinds of partners: an archaeon and an alpha-proteobacterium. Photosynthetic eukaryotes arose from the integration of a cyanobacterium into a eukaryotic cell and recent findings suggested that most archaeal lineages emerged after massive acquisitions of bacterial genes. These composite lineages carry highly chimeric genomes where genes from symbiotic partners co-localize into the same genome. During my PhD thesis, I used sequence similarity networks and phylogenetic methods in order to study reticulate evolution. My research specifically focused on a previously hidden component of composite genomes: symbiogenetic genes (S genes). These chimeric genes are found in genetic mergers, and originate from the association of genes of symbiotic partners. Some association rules have been discovered. In a broad perspective, the discovery of S-genes extends the concept of genome chimerism to the within-gene level.
L'évolution des organismes, des génomes et des gènes n'est pas strictement arborescente; les symbioses, les transferts horizontaux de gènes ou encore la fusion de gènes créent des objets composites formés de parties dont les histoires évolutives sont différentes. Ces processus non arborescents sont appelés introgressifs et ont un impact non négligeable en évolution. Ils sont à l'origine de transitions évolutives majeures comme l'émergence des eucaryotes, des eucaryotes photosynthétiques ou encore de nombreux groupes d'Archaea. Dans le cas des eucaryotes, l'association et la stabilisation d'une Archaea et d'une alpha-protéobactérie a permis l'émergence d'un nouveau groupe d'organismes composites aux propriétés émergentes. L'acquisition de la photosynthèse chez les eucaryotes s'est faite via l'endosymbiose d'une cyanobactérie et, bien que débattue, l'apparition des grands groupes d'Archaea semble être concomitante avec l'acquisition de nombreux gènes d'origine bactérienne. Ces superorganismes ont la particularité d'avoir des génomes composés de gènes de différents partenaires symbiotiques. L'objectif de mon travail de thèse a constitué à étudier l'aspect introgressif de l'évolution par des méthodes de réseaux de similarité de séquence et des méthodes phylogénétiques. Je me suis particulièrement focalisé sur la détection de nouveaux gènes chimériques nommés gènes symbiogénétiques (S-gènes) car composés de parties originaires des différents partenaires symbiotiques. De tels gènes existent dans les génomes et plusieurs règles d'association ont pu être mises en évidence. Plus généralement, la présence de S-gènes étend la notion de mosaïcisme génomique au niveau infra-génique.
https://tel.archives-ouvertes.fr/tel-01536344

NNT : 2016PA066534
tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344
https://tel.archives-ouvertes.fr/tel-01536344/document
https://tel.archives-ouvertes.fr/tel-01536344/file/2016PA066534.pdf

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Functional aspects of biodiversity were investigated in a lowland tropical rainforest in French Guyana (5°2'N, annual precipitation 2200 mm). We assessed leaf '15N as a presumptive indicator of symbiotic N2 fixation, and leaf and wood cellulose '13C as an indicator of leaf intrinsic water-use efficiency (CO2 assimilation rate/leaf conductance for water vapour) in dominant trees of 21 species selected for their representativeness in the forest cover, their ecological strategy (pioneers or late successional stage species, shade tolerance) or their potential ability for N2 fixation. Similar measurements were made in trees of native species growing in a nearby plantation after severe perturbation (clear cutting, mechanical soil disturbance). Bulk soil '15N was spatially quite uniform in the forest (range 3-5‰), whereas average leaf '15N ranged from m0.3‰ to 3.5‰ in the different species. Three species only, Diplotropis purpurea, Recordoxylon speciosum (Fabaceae), and Sclerolobium melinonii (Caesalpiniaceae), had root bacterial nodules, which was also associated with leaf N concentrations higher than 20 mg gm1. Although nodulated trees displayed significantly lower leaf '15N values than non-nodulated trees, leaf '15N did not prove a straightforward indicator of symbiotic fixation, since there was a clear overlap of '15N values for nodulated and non-nodulated species at the lower end of the '15N range. Perturbation did not markedly affect the difference '15Nsoil m '15Nleaf, and thus the isotopic data provide no evidence of an alteration in the different N acquisition patterns. Extremely large interspecific differences in sunlit leaf '13C were observed in the forest (average values from m31.4 to m26.7‰), corresponding to intrinsic water-use efficiencies (ratio CO2 assimilation rate/leaf conductance for water vapour) varying over a threefold range. Wood cellulose '13C was positively related to total leaf '13C, the former values being 2-3‰ higher than the latter ones. Leaf '13C was not related to leaf '15N at either intraspecific or interspecific levels. '13C of sunlit leaves was highest in shade hemitolerant emergent species and was lower in heliophilic, but also in shade-tolerant species. For a given species, leaf '13C did not differ between the pristine forest and the disturbed plantation conditions. Our results are not in accord with the concept of existence of functional types of species characterized by common suites of traits underlying niche differentiation; rather, they support the hypothesis that each trait leads to a separate grouping of species.
ISSN: 0029-8549

hal-01032378
https://hal.archives-ouvertes.fr/hal-01032378
DOI : 10.1007/s004420050593

Résumé : La zone latérale des filaments branchiaux des bivalves Codakia orbiculata et Lucina pensylvanica est le lieu d'une symbiose chimioautotrophe avec des bactéries sulfo-oxydantes hébergées dans des cellules spécialisées, appelées bactériocytes. Dans cette étude, nous nous sommes proposés de déterminer les mécanismes qui sous-tendent la plasticité cellulaire et tissulaire observée au cours des processus de décolonisation et de recolonisation bactérienne. Pour ce faire, des individus collectés dans leur milieu naturel, ont été maintenus au laboratoire dans des bacs d'eau de mer filtrée en absence de nourriture et de soufre réduit, afin de provoquer la décolonisation bactérienne des filaments branchiaux. Lorsque la branchie apparaissait purgée de ses symbiotes, les individus ont été remis dans leur habitat naturel afin de provoquer sa recolonisation. L'analyse des branchies au cours de ces processus a fait appel à des techniques variées (histologie, immunohistochimie, hybridation in situ, cytométrie en flux, dosage des protéines et spectrométrie de fluorescence X). Les résultats obtenus ont permis de montrer que l'acquisition environnementale mise en évidence chez les juvéniles des Codakia se poursuivait tout au long de la vie des adultes. Cette étude a également permis une meilleure compréhension des mécanismes tissulaires sous-jacents à la plasticité du filament branchial en mettant en évidence les processus d'apoptose et de prolifération cellulaire qui ont lieu au cours des processus de décolonisation et de recolonisation. Ces processus s'accompagnent d'une variation de la teneur en soufre élémentaire, ainsi que de la taille relative et du contenu génomique des symbiotes
The lateral zone of gills filaments of coastal bivalves Codakia orbiculata and Lucina pensylvanica is the site of chemoautotrophic symbiosis with sulfur-oxidizing bacteria, housed in specialized cells called bacteriocytes. The objective of this thesis is to determine the mechanisms underlying cel1 plasticity and tissue plasticity observed in the lateral zone of gills filaments during the processes of bacterial decolonization and recolonization. In order to do this, the individuals collected in their natural habitat were maintained at the laboratory in seawater filtered tanks, without food and reduced sulfur, to cause bacterial decolonization. When the gills seemed to be purged, the individuals were returned to their natural habitat in order to cause the bacterial recolonization of gills filaments. The analysis of the gills during these processes involves several techniques (histology, immunohistochemistry, molecular hybridization, flow cytometry, total protein assays, protein sulfur assays, X-ray fluorescence spectrometry).This study shows that symbiont acquisition can occur during the entire life of Codakia bivalves. It also allows a better understanding of gills filaments plasticity by highlighting apoptosis and cell proliferation during decolonization and recolonization processes.Theses processes are accompanied with of elemental sufur, relative size and genomic content of symbiontes.

http://www.theses.fr/2011AGUY0461/document

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
In marine invertebrates that acquire their symbionts from the environment, these are generally only taken up during early developmental stages. In the symbiosis between lucinid clams and their intracellular sulfur-oxidizing bacteria, it has been shown that the juveniles acquire their symbionts from an environmental stock of free-living symbiont forms, but it is not known if adult clams are still competent to take up symbiotic bacteria from the environment. In this study, we investigated symbiont acquisition in adult specimens of the lucinid clam Codakia orbiculata, using transmission electron microscopy, fluorescence in situ hybridization, immunohistochemistry and PCR. We show here that adults that had no detectable symbionts after starvation in aquaria for 6 months, rapidly reacquired symbionts within days after being returned to their natural environments in the field. Control specimens that were starved and then exposed to seawater aquaria with sulfide did not reacquire symbionts. This indicates that the reacquisition of symbionts in the starved clams returned to the field was not caused by high division rates of a small pool of remaining symbionts that we were not able to detect with the methods used here. Immunohistochemistry with an antibody against actin, a protein involved in the phagocytosis of intracellular bacteria, showed that actin was expressed at the apical ends of the gill cells that took up symbionts, providing further evidence that the symbionts were acquired from the environment. Interestingly, actin expression was also observed in symbiontcontaining cells of untreated lucinids freshly collected from the environment, indicating that symbiont acquisition from the environment occurs continuously in these clams throughout their lifetime.
ISSN: 1462-2912

hal-00743019
https://hal.univ-antilles.fr/hal-00743019
DOI : 10.1111/j.1462-2920.2012.02748.x

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
In chemoautotrophic associations, sequence comparison of 16S rRNA has been the method of choice to study bacterial diversity in the context of host/symbiont coevolution. However, the relative low rate of evolution of 16S rRNA has been shown to result in a diminished capacity to discriminate between closely related bacterial strains or species. Within chemoautotrophic associations, as described in several studies, the use of other genetic markers may reveal previously unobserved strain diversity among gill endosymbionts. Herein, we conducted a survey of symbionts harbored by six species within the Lucinidae family using five genetic markers (dnaE, gyrB, aprA, cbbL genes and the 16S-23S internal transcribed spacer). Thus, within the already described SoLuc₁ bacterial species shared by six host species we observed an obvious bacterial strain diversity. This diversity is structured in function of the geographic location of the hosts and not in function of ecological parameters or host phylogeny. Interestingly at the local level (same seagrass bed environment), we observed an unexpected specificity in host species/bacterial strain association (i.e., all individuals of the same host species harbor the same symbiotic sequence type). This specificity of association implied that there was a control of symbiont strain acquisition by the host, which was confirmed by a cross-infection experiment of starved adults performed in our study. Based upon our results and other evidence from the literature, we hypothesize that this pattern may be due to a ``capture/escape'' type antagonist evolution of the two partners.
ISSN: 0025-3162

hal-01544753
https://hal.archives-ouvertes.fr/hal-01544753
DOI : 10.1007/s00227-016-2949-0