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11	Étude de l'évolution réductive des génomes bactériens par expériences d'évolution in silico et analyses bioinformatiques / Study of reductive genome evolution by in silico evolution experiments and bioinformatics analysis Batut, Bérénice 21 November 2014 (has links) Selon une vision populaire, l’évolution serait un processus de « progrès » qui s’accompagnerait d’un accroissement de la complexité moléculaire des êtres vivants. Cependant, les programmes de séquençage des génomes ont révélé l’existence d’espèces dont les lignées ont, au contraire, subi une réduction massive de leur génome. Ainsi, chez les cyanobactéries Prochlorococcus et Pelagibacter ubique, certaines lignées ont subi une réduction de 30% de leur génome. Une telle évolution « à rebours », dite évolution réductive, avait déjà été observée pour des bactéries endosymbiotiques, pour lesquelles la sélection naturelle n’est pas assez efficace pour éliminer les mutations délétères comme les pertes de gènes. Cela vient notamment du fait que ces bactéries endosymbiotiques subissent, à chaque reproduction de leur hôte, une réduction drastique de leur taille de population. Cette explication semble peu plausible pour des cyanobactéries marines comme Prochlorococcus et Pelagibacter, qui ont un mode de vie libre et qui font partie des bactéries les plus abondantes des océans. D’autres hypothèses ont ainsi été proposées pour expliquer l’évolution réductive comme l’adaptation à un environnement stable et pauvre en nutriments, des forts taux de mutation, mais aucun de ces hypothèses ne semble capable d’expliquer toutes les caractéristiques génomiques observées. Dans cette thèse, nous nous intéressons au cas de l’évolution réductive chez Prochlorococcus, pour laquelle de nombreuses séquences et données sont disponibles. Deux approches sont utilisées pour cette étude : une analyse phylogénétique des génomes de Prochlorococcus, et une approche théorique de simulation où nous testons différents scénarios évolutifs pouvant conduire à une évolution réductive. La combinaison de ces deux approches permet finalement de proposer un scénario plausible pour expliquer l'évolution réductive chez Prochlorococcus. / Given a popular view, evolution is an incremental process based on an increase of molecular complexity of organisms. However, some organisms have undergo massive genome reduction like the endosymbionts. In this case the reduction can be explained by the Muller’s ratchet due to the endosymbiont lifestyle with small population and lack of recombination. However, in some marine bacteria, like Prochlorococcus et Pelagibacter, lineage have undergo up to 30% of genome reduction. Their lifestyle is almost the opposite to the one of the endosymbionts and reductive genome evolution can not be easily explicable by the Muller’s ratchet. Some other hypothesis has been proposed but none can explain all the observed genomic characteristics. In the thesis, I am interested in the reductive evolution of Prochlorococcus. I used two approaches: a theoretical one using simulation where different scenarios are tested and an analysis of Prochlorococcus genomes in a phylogenetic framework to determine the causes and characteristics of genome reduction. The combination of these two approaches allows to propose an hypothetical evolutive history for the reductive genome evolution of Prochlorococcus. Biosciences Bioinformatique Evolution des génomes Evolution réductive Experience d'évolution in silico Génomique comparative Prochlorococcus Biosciences Bioinformatics Genome evolution Reductive evolution In silico evolution experiments Comparative genomics Prochlorococcus 570.285 072
12	Pico- and nanoplankton abundance and biomass in the Southwest Atlantic Ocean off Brazil / Abundância e biomassa pico- e nanoplanctônica no sudoeste do Oceano Atlântico ao largo da costa do Brasil Ribeiro, Catherine Gerikas 23 March 2016 (has links) Flow cytometry (FCM) is a well established technique used for enumeration and characterization of marine biological particles, which fulfills the scientific demands of rapid cell counting automation. FCM allows the discrimination of pico- and nanoplankton populations regarding its abundance, cell size, and pigment content both by natural or induced fluorescence. The cyanobacterium Prochlorococcus is widespread in the euphotic zone of the tropical and subtropical oceans, and is considered the smallest and most abundant photosynthetic organism in the planet. Synechococcus, other important cyanobacterium genus present in the picoplankton, is highly diverse and is widely distributed in marine ecosystems from cold and mesotrophic, to warm, open ocean oligotrophic waters. Photosynthetic pico- and nanoeukaryotes display a range of physiologies and life strategies. Although its abundance is generally lower, the larger cell size leads to a significant contribution to the epipelagic community biomass. In this thesis I aimed to investigate the abundance and carbon biomass distribution of heterotrophic bacteria, Prochlorococcus, Synechococcus, autotrophic pico- and nanoeukaryotes in the Southwest Atlantic Ocean off Brazil, their relation to the different water masses and the influence of hydrodynamic (South Atlantic Central Water intrusion) and biological processes (Trichodesmium spp. and Mesodinium rubrum blooms) on such distributions. / A citometria de fluxo (FCM, sigla em inglês) é uma técnica bem estabelecida, usada para enumeração e caracterização de partículas biológicas marinhas, a qual supre a demanda científica por automação rápida de contagem de células. A FCM permite a discriminação de populações pico- e nanoplanctônicas no que concerne à sua abundância, tamanho de célula e pigmentação, tanto por fluorescência natural ou induzida. A cianobactéria Prochlorococcus é amplamente disseminada pela zona eufótica dos oceanos tropicais e subtropicais, sendo considerada o menor e mais abundante organismo fotossintético do planeta. Synechococcus, outro importante gênero de cianobactérias presente no picoplâncton, é diverso e amplamente distribuído em ecossistemas marinhos, de águas frias e mesotróficas à regiões oceânicas quentes e de águas oligotróficas. Pico- e nanoeucariotos fotossintéticos apresentam uma grande variedade de fisiologias e estratégias de vida. Embora a abundância destes grupos seja geralmente menor, o maior tamanho de suas células resulta numa contribuição significante dos mesmos para a biomassa da comunidade epipelágica. Na presente tese eu objetivei investigar a abundância e a distribuição da biomassa de carbono de bactérias heterotróficas, Prochlorococcus, Synechococcus, pico- e nanoeucariotos autotróficos no sudoeste do Oceano Atlântico ao largo do Brasil, sua relação com as diferentes massas d\'água e a influência de processos hidrodinâmicos (como a intrusão da Água Central do Atlântico Sul) e biológicos (florações de Trichodesmium spp. e Mesodinium rubrum) em tais distribuições. Bactérias heterotróficas Citometria de fluxo Flow cytometry Heterotrophic bacteria Nanoeucariotos Nanoeukaryotes Picoeucariotos Picoeukaryotes Prochlorococcus Prochlorococcus Southwest Atlantic Ocean Sudoeste do Oceano Atlântico Synechococcus Synechococcus
13	Pico- and nanoplankton abundance and biomass in the Southwest Atlantic Ocean off Brazil / Abundância e biomassa pico- e nanoplanctônica no sudoeste do Oceano Atlântico ao largo da costa do Brasil Catherine Gerikas Ribeiro 23 March 2016 (has links) Flow cytometry (FCM) is a well established technique used for enumeration and characterization of marine biological particles, which fulfills the scientific demands of rapid cell counting automation. FCM allows the discrimination of pico- and nanoplankton populations regarding its abundance, cell size, and pigment content both by natural or induced fluorescence. The cyanobacterium Prochlorococcus is widespread in the euphotic zone of the tropical and subtropical oceans, and is considered the smallest and most abundant photosynthetic organism in the planet. Synechococcus, other important cyanobacterium genus present in the picoplankton, is highly diverse and is widely distributed in marine ecosystems from cold and mesotrophic, to warm, open ocean oligotrophic waters. Photosynthetic pico- and nanoeukaryotes display a range of physiologies and life strategies. Although its abundance is generally lower, the larger cell size leads to a significant contribution to the epipelagic community biomass. In this thesis I aimed to investigate the abundance and carbon biomass distribution of heterotrophic bacteria, Prochlorococcus, Synechococcus, autotrophic pico- and nanoeukaryotes in the Southwest Atlantic Ocean off Brazil, their relation to the different water masses and the influence of hydrodynamic (South Atlantic Central Water intrusion) and biological processes (Trichodesmium spp. and Mesodinium rubrum blooms) on such distributions. / A citometria de fluxo (FCM, sigla em inglês) é uma técnica bem estabelecida, usada para enumeração e caracterização de partículas biológicas marinhas, a qual supre a demanda científica por automação rápida de contagem de células. A FCM permite a discriminação de populações pico- e nanoplanctônicas no que concerne à sua abundância, tamanho de célula e pigmentação, tanto por fluorescência natural ou induzida. A cianobactéria Prochlorococcus é amplamente disseminada pela zona eufótica dos oceanos tropicais e subtropicais, sendo considerada o menor e mais abundante organismo fotossintético do planeta. Synechococcus, outro importante gênero de cianobactérias presente no picoplâncton, é diverso e amplamente distribuído em ecossistemas marinhos, de águas frias e mesotróficas à regiões oceânicas quentes e de águas oligotróficas. Pico- e nanoeucariotos fotossintéticos apresentam uma grande variedade de fisiologias e estratégias de vida. Embora a abundância destes grupos seja geralmente menor, o maior tamanho de suas células resulta numa contribuição significante dos mesmos para a biomassa da comunidade epipelágica. Na presente tese eu objetivei investigar a abundância e a distribuição da biomassa de carbono de bactérias heterotróficas, Prochlorococcus, Synechococcus, pico- e nanoeucariotos autotróficos no sudoeste do Oceano Atlântico ao largo do Brasil, sua relação com as diferentes massas d\'água e a influência de processos hidrodinâmicos (como a intrusão da Água Central do Atlântico Sul) e biológicos (florações de Trichodesmium spp. e Mesodinium rubrum) em tais distribuições. Bactérias heterotróficas Citometria de fluxo Nanoeucariotos Picoeucariotos Prochlorococcus Sudoeste do Oceano Atlântico Synechococcus Flow cytometry Heterotrophic bacteria Nanoeukaryotes Picoeukaryotes Prochlorococcus Southwest Atlantic Ocean Synechococcus
14	Ecological Controls on Prochlorococcus sp. Diversity, Composition, and Activity at High Taxonomic Resolution Larkin-Swartout, Alyse Anne January 2016 (has links) <p>Although there are many examples of microbial biogeography, few microbes have been studied at high taxonomic resolution over large spatial scales. As a result, the environmental and ecological processes that drive niche partitioning, diversity, composition, and activity of microbial taxa are often poorly understood. To address this gap, I examine the most abundant phytoplankton in the global ocean, Prochlorococcus sp., a marine cyanobacterium. Using amplicon libraries of the Prochlorococcus internal transcribed spacer (ITS) region and 23S rRNA gene as markers, I demonstrate several key differences between the two major high light (HL) clades of Prochlorococcus. First, by examining ITS amplicon libraries at high taxonomic resolution it is revealed that “sub-ecotype” clades have unique, cohesive responses to environmental variables and distinct biogeographies, suggesting that presently defined ecotypes can be further partitioned into ecologically meaningful units. Whereas unique combinations of environmental traits drive the distribution of the HL-I sub-ecotype clades, the HL-II sub-ecotype clades appear ecologically coherent. Second, using 23S rRNA and rDNA libraries I show that activity (rRNA) and abundance (rDNA) are highly correlated for Prochlorococcus across all sites and operational taxonomic units (OTUs) in the surface ocean, demonstrating a tight coupling between activity and abundance. Finally, I investigate the associations between Prochlorococcus and the rest of the microbial community in the North Pacific and find region-specific trends in both strength and sign. Associations with other microbes are strongest for HL-I in the temperate region and strongest for HL-II in the sub-tropical gyre. This dissertation clarifies the relative importance of the environment, geography, community, and taxonomy in terms of their role in creating complex assemblages of Prochlorococcus and helps improve our understanding of how marine microbial communities are assembled in situ.</p> / Dissertation Biological oceanography Ecology Microbiology Bacterioplankton Microbial activity Microbial diversity Microbial ecology Microbial interactions Prochlorococcus
15	Regulace fotosyntézy a primární produkce fytoplanktonu za podmínek nutričního a světelného stresu. FELCMANOVÁ, Kristina January 2018 (has links) Regulation of photosynthesis and primary production in globally important cyanobacterium Prochlorococcus marinus under nitrogen and light stress were examined. The study investigated the model describing relationship between photosynthetic activity and primary production. The photosynthetic energy budget and the efficiency of converting the photosynthetic energy into biomass were described. Molecular and physiological approaches were applied to analyse the utilization of photosynthetic energy and regulation of metabolism to investigate the influence of streamlined oxygen-evolving cluster on the photosynthetic activities.
16	Etude génomique et métagénomique de la diversité génétique, la distribution écologique et l'évolution des picocyanobactéries marines / Genomic and metagenomic study of the genetic diversity, ecological distribution and evolution of marine picocyanobacteria Farrant, Gregory 27 April 2015 (has links) Les picocyanobactéries marines des genres Prochlorococcus et Synechococcus sont les organismes photosynthétiques les plus abondants de la planète et ils contribuent de façon substantielle à la production primaire mondiale. Alors que le genre Prochlorococcus se caractérise par sa forte abondance dans les régions oligotrophes et son génome réduit, le genre Synechococcus se distingue par sa grande diversité génétique et pigmentaire ainsi qu'une aire de distribution plus étendue.Le principal objectif de ce travail a été de mettre en relation la diversité génétique de ces organismes avec leur niche écologique par des approches de génomique comparative et de métagénomique. Tout d'abord, le développement d'une méthode de scaffolding (WiseScaffolder) a permis de clore 32 nouveaux génomes de Synechococcus, lesquels ont été intégrés au système d'information Cyanorak, dédié à l'annotation de gènes orthologues. Ces nouveaux génomes, complétant les 65 génomes disponibles pour ces deux genres, ont fait l'objet d'analyses comparatives afin de mieux comprendre la diversité et l'évolution de ce phylum et de définir les gènes spécifiques de différents groupes phylogénétiques, potentiellement liés à leur adaptation à des niches écologiques distinctes.Ces génomes ont ensuite été utilisés comme référence, en conjonction avec le gène marqueur petB, pour analyser les données de métagénomique issues de l'expédition TARA-Océans. Ces analyses ont notamment mis en lumière la diversité génétique, la distribution et l'importance écologique de certains clades phylogénétiques. Ce travail soulève de nouvelles hypothèses quant au rôle des picocyanobactéries dans le fonctionnement global des océans. / Marine picocyanobacteria Prochlorococcus and Synechococcus genera are the most abundant photosynthetic organisms and contribute substantially to global primary production. While the genus Prochlorococcus is characterized by its high abundance in oligotrophic regions and its reduced genome, Synechococcus is characterized by a larger genetic and pigment diversity and a wider area of distribution.The main objective of this PhD thesis was to link the genetic diversity of these organisms to the environmental conditions of their ecological niche by comparative genomics and metagenomics approaches. Firstly, the development of a scaffolding method (WiseScaffolder) has allowed us to close 32 new genomes of Synechococcus which were integrated into the Cyanorak information system dedicated to the annotation of orthologous genes. These new genomes, supplementing the 65 genomes previously available for these two genera, allowed us to perform comparative analyses which led to a better understanding of the diversity and evolution of this phylum and to the definition of genes sets specific to different phylogenetic groups and thus potentially related to their adaptation to different ecological niches.These genomes were then used as reference, in conjunction with the marker gene petB gene, to analyze metagenomic data produced in the frame of the Tara-Oceans Expedition. In particular, these analyzes highlighted the genetic diversity, distribution and ecological importance of some phylogenetic clades. This work raises new hypotheses about the role of picocyanobacteria in the overall functioning of the oceans. Prochlorococcus Synechococcus Génomique comparative Métagénomique Tara-Océans Assemblage Comparative genomics Metagenomic 639.9
17	New Genomic Approaches Reveal the Process of Genome Reduction in Prochlorococcus Sun, Zhiyi 01 February 2011 (has links) Small bacterial genomes are believed to be evolutionarily derived from larger genomes through massive loss of genes and are usually associated with symbiotic or pathogenic lifestyles. It is therefore intriguing that a similar phenomenon of genome reduction has been reported within a group of free-living phototrophic marine cyanobacteria Prochlorococcus. Here I have investigated the roles of natural selection and mutation rate in the process of Prochlorococcus genome size reduction. Using a data set of complete cyanobacterial genomes including 12 Prochlorococcus and a sister group of 5 marine Synechococcus, I first reconstructed the steps leading to Prochlorococcus genome reduction in a phylogenetic context. The result reveals that small genome sizes within Prochlorococcus were largely determined by massive gene loss shortly after the split of Prochlorococcus and Synechococcus (a process we refer to as early genome reduction). A maximum likelihood approach was then used to estimate changes in both selection effect and mutation rate in the evolutionary history of Prochlorococcus. I also examined the effect of selection and functional importance of a subset of ancestor-derived genes those are lost in Prochlorococcus but are still retained in the genomes of its sister Synechococcus group. It appears that purifying selection was strongest when a large number of small effect genes were deleted from nearly all functional categories. And during this period, mutation rate also accelerated. Based on these results, I propose that shortly after Prochlorococcus diverged from its common ancestor with marine Synechococcus, its population size increased quickly and thus the efficacy of selection became very high. Due to limited nutrients and relatively constant environment, selection favored a streamlined genome for maximum economies in material and energy, causing subsequent reduction in genome size and possibly also contributing to the observed higher mutation rate. comparative genomics genome reduction marine cyanobacteria mutation rate natural selection Prochlorococcus Biology Ecology and Evolutionary Biology
18	The ‘Helper’ Phenotype: A Symbiotic Interaction Between Prochlorococcus and Hydrogen Peroxide Scavenging Microorganisms Morris, James Jeffrey 01 May 2011 (has links) The unicellular cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism throughout the temperate and tropical open oceans, but it is difficult to grow in pure cultures. We developed a system for rendering spontaneous streptomycin-resistant mutants of Prochlorococcus axenic by diluting them to extinction in the presence of “helper” heterotrophic bacteria, allowing them to grow to high cell concentrations, and then killing the helpers with streptomycin. Using axenic strains obtained in this fashion, we demonstrated that Prochlorococcus experiences a number of growth defects in dilute axenic culture, including reduced growth rate, inability to form colonies on solid media, and higher incidence of mortality (i.e., catastrophic failure of liquid cultures). These defects were eliminated when Prochlorococcus was grown in co-culture with a phylogenetically diverse array of helper bacteria. The primary mechanism of helping was enzymatic removal of hydrogen peroxide (HOOH) from the culture medium. Axenic Prochlorococcus cultures were profoundly sensitive to HOOH additions in comparison with reported tolerance levels for all other wild-type aerobic bacteria, but in co-culture their resistance was similar to that of the helpers. Neither is dependence on helpers limited to the laboratory. Sterile-filtered seawater exposed to sunlight accumulated enough HOOH in 24h to kill ecologically relevant cell concentrations of Prochlorococcus. We also refined a method for delivering HOOH at a defined, steady rate using the buffer HEPES to more accurately simulate the steady accumulation of HOOH in natural waters. Even at the lowest production rates that could sustain the in situ HOOH concentration in the ocean, HEPES-generated HOOH was lethal to Prochlorococcus; again, co-culture with helpers prevented this effect. We speculate on the ecological consequences of Prochlorococcus’ dependency on other organisms for survival, as well as the evolutionary forces that have led to this lack of self-sufficiency. prochlorococcus H2O2 oxidative stress helper HEPES cross protection Cellular and Molecular Physiology Microbial Physiology Oceanography
19	Putting marine microbes on the map : determining the global distribution of marine picophytoplankton using a combination of satellite and field data Lange, Priscila Kienteca January 2017 (has links) Picophytoplanktonic cells (0.2-2 μm) are the dominant phytoplankters in the largest marine biomes on Earth: the subtropical gyres. The overaching aim of this thesis is to develop algorithms that use remote-sensing observables to map the distribution of the smallest and most abundant member of picophytoplankton, Prochlorococcus, and assess its contribution to the marine carbon cycle. To understand how the photoacclimatory status and growth of Prochlorococcus and its sister genera Synechococcus are influenced by light and nutrients, experiments were conducted in the South Atlantic Gyre (SAG). Results from the manipulation experiments show that, in the central region of the SAG, nutrient addition can induce marked changes in the optical properties of Prochlorococcus cells when subjected to saturating light levels, leading to a decrease in cell abundance, whereas at the gyre periphery no substantive changes in cell growth or optical characteristics were observed. Since light plays a central role in shaping the distribution of cyanobacteria, an empirical algorithm based on relationships between Prochlorococcus abundance and remotely-sensed observables was developed. The outputs were then used in a modified primary production model to predict the vertical distribution of carbon fixation by Prochlorococcus. The models estimate that &Tilde; 3.4 x 10<sup>27</sup> Prochlorococcus cells in the global ocean fix 4.7 Gt C year<sup>-1</sup>. Most of the cell biomass and primary productivity is concentrated in the subtropical gyres and areas near the Equatorial Convergence, and 61&percnt; of the carbon fixation occurs in the upper water column (0-45 metres), where only 43&percnt; of the cells reside. However, in the gyres, carbon fixation is highest (62&percnt;) in deeper layers (45-200m), and both cell abundance and carbon fixation show marked seasonal patterns. The models developed in this study provide an unprecedented view of the vertical distribution of Prochlorococcus cells and their corresponding rates of carbon fixation in the global ocean.
20	Phytoplankton cell death induced by solar ultraviolet radiation Llabrés Comamala, Maria Moira 02 June 2008 (has links) En esta tesis se ha demostrado que la radiación ultravioleta induce mortalidad en comunidades de fitoplancton de diferentes áreas del Océano Atlántico, del Mar Mediterráneo y del Océano Antártico. El fitoplancton más pequeño (pico-fitoplancton) muestra mayor sensibilidad a la radiación UV respecto al fitoplancton de mayor tamaño. Este estudio identifica que el crecimiento de las poblaciones del fitoplancton antártico está controlado por la radiación ultravioleta con inhibiciones de biomasas por encima del 80-90%. Se demuestra también que la transferencia de radicales OH, generados por la radiación ultravioleta, desde la atmósfera hacia la superficie del Océano causa mortalidad en comunidades de fitoplancton de aguas tropicales, templadas y antárticas. El trabajo presentado en esta tesis muestra la importancia de la radiación ultravioleta como factor que induce mortalidad en el fitoplancton, su influencia en el balance del crecimiento neto de estas poblaciones, así como las consecuencias que se derivan en la cadena trófica. lethal radiation dose half-life Hydroxyl radical pico-eukaryots flagelates diatoms Synechococcus CDA Prochlorococcus Antarctic Ocean Oligotrophic Ocean ultraviolet radiation cell death phytoplankton dosi letal vides mitjanes pico-eucariotes Radical hidroxil diatomees flagelats Oceà Antàrtic CDA Prochlorococcus Synechococcus Oceà Oligotròfic radiació ultraviolada mortalitat Fitoplàncton dosis letales vidas medias Radical hidroxilo pico-eucariotas flagelados diatomeas Synechococcus Océano Antártico CDA Prochlorococcus Océano oligotrófico Radiación ultravioleta mortalidad Fitoplancton Ecologia de fitoplancton 57 574

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