Étude de la plasticité génomique des algues vertes de l'ordre Chlamydomonadales

Les récents progrès en génomique ont conforté la complexité de l’origine des algues; d’un point de vue de la phylogénie des hôtes de l’endosymbiose, les algues forment un groupe évolutif polyphylétique. Les algues vertes forment deux embranchements majeurs : les Streptophyta et les Chlorophyta. Les chlorophytes comprennent la majorité des algues vertes connues et se regroupent en quatre classes. La première, les Prasinophyceae, occupe la position la plus basale, tandis que l’ordre d’embranchement des trois autres classes (Ulvophyceae, Trebouxiophyceae et Chlorophyceae) demeure encore incertain. Pour clarifier les relations évolutives chez les Clorophyceae, huit génomes chloroplastiques appartenant à la lignée des Chlamydomonadales, lignée majeure des Chlorophyceae, ont été séquencés et analysés. Des études phylogénétiques ont confirmé les classifications préétablies et de nouveaux clades se sont vus formés. Les génomes de ces algues chlorophycéennes ont révélé une architecture conservée avec un certain nombre de caractères spécifiques à la classe des Chlamydomonadales. L’analyse de leurs caractères moléculaires a révélé des génomes marqués par la réduction ou le réarrangement de leur répertoire génomique comparativement aux génomes chloroplastiques des algues vertes plus ancestrales.Recent advances in genome sequencing and analysis have reinforced the complexity of the origin of the green algae. From the point of view of a host endosymbiotic phylogeny, green algae form a polyphyletic evolutionary group. Green algae form two major branches : the Streptophyta and Chlorophyta. Chlorophytes include the majority of green algae known and they are grouped into four classes. The first, that of Prasinophyceae, occupies the most basal position, while the branching order of the other three classes (Ulvophyceae, Trebouxiophycea and Chlorophyceae) remain uncertain. To clarify the evolutionary relationships amongst Chlorophyceae, eight chloroplast genomes belonging to the lineage of Chlamydomonadales, a major clade of Chlorophyceae were sequenced and analyzed. Phylogenetic studies have confirmed the pre-established classifications and new clades were seen to be formed. The genomes of these chlorophyll algae were revealed to be conserved with a number of specific architectural characters of the Chlamydomonadales class. Analysis of their molecular characteristics revealed a genome marked by the reduction or rearrangement of their genomic repertory compared to chloroplast genomes of the ancestral green algae

Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides

Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides. Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups

Genome basis for functional differentiation in uncultured lineages of marine bacterivores

Tesi per compendi de publicacionsIn the vast network of the ocean, microbes are abundant and unevenly distributed. As an important microbial component, the protists play a key role in global biogeochemical cycles and contribute to the recycling of nutrients necessary to sustain life on Earth. These unicellular eukaryotes exist and function as primary producers (drivers of photosynthesis), decomposers, parasites or as trophic linkers in aquatic food webs. Phagotrophic species, which acquire nutrition through feeding on other organisms, are commonly understudied due to the difficulty in culturing them. The recent characterization of their genomic and metabolic diversity starts to unveil their great ecological relevance in the oceans. In this dissertation, we focused on heterotrophic flagellates, the main bacterial grazers in marine systems, and especially on the MArine STramenopile (MAST) lineages that display numerous uncultured and, therefore, undefined species. The aim was to elucidate their ecological importance in marine food webs by understanding their presumed trophic strategy: phagocytosis, a process only well characterized in animals as an immune system response. We first attempted to provide new reference genomes of MAST species using single cell genomic sequencing and a co-assembly approach. Thus, we assembled 15 draft genomes from different MAST lineages, and predicted their gene repertoire with the objective to characterize specific genes related to their trophic strategy. Our comparative genomics analysis indicated that all MAST species were phagotrophs. We then targeted peptidases involved in prey digestion as well as proton pumps for vacuole acidification, but we did not find preferential genes specific for phagocytosis. In addition, this study revealed the relevant presence of rhodopsin proteins that may contribute in the acidification of the phagolysosome. In the second paper, we did a functional study of MASTs using metatranscriptomics in order to gain access to their gene expression within the natural environment. To do so, we started a grazing experiment with a natural sample from the Mediterranean Sea: in a controlled microcosm in the dark, we followed the cell growth of a natural community where we aimed to enrich for heterotrophic flagellates and therefore phagocytosis. We showed an increase in the relative abundance of heterotrophs, as compared with phototrophs, when phagocytosis occurred. Using the previously established reference genome collection of a few MASTs, we were able to target the MAST reads in the metatranscriptome and analyze the expression profile of genes involved in phagocytosis for a couple of MAST-4 species. Cathepsins and other digestive enzymes were highly expressed when bacterial consumption was observed. Finally, a similar experiment was conducted with a cultured organism, Cafeteria burkhardae, a cosmopolitan heterotrophic flagellate that proved to be a good model to study bacterivory within the Stramenopiles. Results demonstrated distinct expression profiles depending on the growth phase of this species. Upregulated genes at the Exponential phase were related to DNA duplication, transcription, translation, and phagocytosis, whereas upregulated genes in the Stationary phase were involved in signal transduction, cell adhesion and lipid metabolism. Phagocytosis genes, like peptidases and proton pumps, were highly expressed and could be used to target this ecologically relevant process in marine ecosystems. This thesis contributes to the understanding of the community of marine bacterial grazers, which include the smallest phagotrophs in the ocean, with a focus on their functional behavior within the natural and complex protistan assemblage.América Latina es una región heterogénea, tanto desde el punto de vista geográfico, demográfico como económico. Específicamente desde una perspectiva económica, el Banco Mundial clasifica a algunos países de la región como de altos ingresos según su PIB per cápita, mientras que a otros como de ingresos medios bajos. Igualmente, el Programa de las Naciones Unidas para el Desarrollo (PNUD) clasifica a algunos países de la zona dentro del grupo de muy alto desarrollo humano, así como también clasifica a otros como de desarrollo humano medio. Sin embargo, todos tienen una característica en común: una desigualdad en los ingresos, superior al promedio mundial. Dado el escenario anterior, se hace necesario fomentar el desarrollo y competitividad de las naciones latinoamericanas. Para ello, las universidades serían instituciones claves, ya que en su quehacer son responsables de la formación del capital humano, producen y difunden conocimiento científico, promueven el progreso tecnológico y las artes. Sin embargo, sólo un escaso número de universidades de América Latina es competitivo a nivel global. Lo anterior, dado que mayoritariamente son instituciones enfocadas a la docencia, siendo pocas las que se pueden considerar como universidades investigadoras. Por lo tanto, se hace necesario mejorar la competitividad de estas instituciones y uno de los factores que influyen en ello, y es necesario analizar, es su gobenanza. De acuerdo a lo anterior, esta tesis se planteó como objetivo determinar si los atributos propios de la estructura de gobierno, como el tamaño del consejo universitario, independencia del consejo universitario, método de nombramiento del rector, presencia e independencia de un comité o departamento de auditoría, son variables determinantes en el rendimiento de las universidades de América Latina. Para efectos de este estudio se consideró que el rendimiento de las universidades se mediría por medio de la posición que ellas obtienen en los rankings universitarios, específicamente el ranking QS para América Latina, versión 2019. Para el logro de los objetivos se plantearon seis hipótesis, cada una relacionada a los atributos de gobierno universitario mencionados en el párrafo anterior. Para contrastar las hipótesis se utilizó una muestra de 129 universidades que se clasificaron en el año 2019 en las primeras 150 posiciones del ranking QS para América Latina. Además, estadísticamente se aplicaron dos tipos de regresiones: mínimos cuadrados ordinarios y regresión TOBIT. Entre los resultados más destacados se evidenció que atributos de gobemanza como la composición del consejo universitario, método de nombramiento del rector y presencia de un departamento o comité de auditoría independiente serian variables estratégicas que deberían ser consideradas en la gestión universitaria. Igualmente, se comprobó que la incidencia de estas variables en el rendimiento de las universidades depende del tipo de institución, es decir, si es una institución pública o privada.Postprint (published version

Genome basis for functional differentiation in uncultured lineages of marine bacterivores

Tesi per compendi de publicacionsIn the vast network of the ocean, microbes are abundant and unevenly distributed. As an important microbial component, the protists play a key role in global biogeochemical cycles and contribute to the recycling of nutrients necessary to sustain life on Earth. These unicellular eukaryotes exist and function as primary producers (drivers of photosynthesis), decomposers, parasites or as trophic linkers in aquatic food webs. Phagotrophic species, which acquire nutrition through feeding on other organisms, are commonly understudied due to the difficulty in culturing them. The recent characterization of their genomic and metabolic diversity starts to unveil their great ecological relevance in the oceans. In this dissertation, we focused on heterotrophic flagellates, the main bacterial grazers in marine systems, and especially on the MArine STramenopile (MAST) lineages that display numerous uncultured and, therefore, undefined species. The aim was to elucidate their ecological importance in marine food webs by understanding their presumed trophic strategy: phagocytosis, a process only well characterized in animals as an immune system response. We first attempted to provide new reference genomes of MAST species using single cell genomic sequencing and a co-assembly approach. Thus, we assembled 15 draft genomes from different MAST lineages, and predicted their gene repertoire with the objective to characterize specific genes related to their trophic strategy. Our comparative genomics analysis indicated that all MAST species were phagotrophs. We then targeted peptidases involved in prey digestion as well as proton pumps for vacuole acidification, but we did not find preferential genes specific for phagocytosis. In addition, this study revealed the relevant presence of rhodopsin proteins that may contribute in the acidification of the phagolysosome. In the second paper, we did a functional study of MASTs using metatranscriptomics in order to gain access to their gene expression within the natural environment. To do so, we started a grazing experiment with a natural sample from the Mediterranean Sea: in a controlled microcosm in the dark, we followed the cell growth of a natural community where we aimed to enrich for heterotrophic flagellates and therefore phagocytosis. We showed an increase in the relative abundance of heterotrophs, as compared with phototrophs, when phagocytosis occurred. Using the previously established reference genome collection of a few MASTs, we were able to target the MAST reads in the metatranscriptome and analyze the expression profile of genes involved in phagocytosis for a couple of MAST-4 species. Cathepsins and other digestive enzymes were highly expressed when bacterial consumption was observed. Finally, a similar experiment was conducted with a cultured organism, Cafeteria burkhardae, a cosmopolitan heterotrophic flagellate that proved to be a good model to study bacterivory within the Stramenopiles. Results demonstrated distinct expression profiles depending on the growth phase of this species. Upregulated genes at the Exponential phase were related to DNA duplication, transcription, translation, and phagocytosis, whereas upregulated genes in the Stationary phase were involved in signal transduction, cell adhesion and lipid metabolism. Phagocytosis genes, like peptidases and proton pumps, were highly expressed and could be used to target this ecologically relevant process in marine ecosystems. This thesis contributes to the understanding of the community of marine bacterial grazers, which include the smallest phagotrophs in the ocean, with a focus on their functional behavior within the natural and complex protistan assemblage.América Latina es una región heterogénea, tanto desde el punto de vista geográfico, demográfico como económico. Específicamente desde una perspectiva económica, el Banco Mundial clasifica a algunos países de la región como de altos ingresos según su PIB per cápita, mientras que a otros como de ingresos medios bajos. Igualmente, el Programa de las Naciones Unidas para el Desarrollo (PNUD) clasifica a algunos países de la zona dentro del grupo de muy alto desarrollo humano, así como también clasifica a otros como de desarrollo humano medio. Sin embargo, todos tienen una característica en común: una desigualdad en los ingresos, superior al promedio mundial. Dado el escenario anterior, se hace necesario fomentar el desarrollo y competitividad de las naciones latinoamericanas. Para ello, las universidades serían instituciones claves, ya que en su quehacer son responsables de la formación del capital humano, producen y difunden conocimiento científico, promueven el progreso tecnológico y las artes. Sin embargo, sólo un escaso número de universidades de América Latina es competitivo a nivel global. Lo anterior, dado que mayoritariamente son instituciones enfocadas a la docencia, siendo pocas las que se pueden considerar como universidades investigadoras. Por lo tanto, se hace necesario mejorar la competitividad de estas instituciones y uno de los factores que influyen en ello, y es necesario analizar, es su gobenanza. De acuerdo a lo anterior, esta tesis se planteó como objetivo determinar si los atributos propios de la estructura de gobierno, como el tamaño del consejo universitario, independencia del consejo universitario, método de nombramiento del rector, presencia e independencia de un comité o departamento de auditoría, son variables determinantes en el rendimiento de las universidades de América Latina. Para efectos de este estudio se consideró que el rendimiento de las universidades se mediría por medio de la posición que ellas obtienen en los rankings universitarios, específicamente el ranking QS para América Latina, versión 2019. Para el logro de los objetivos se plantearon seis hipótesis, cada una relacionada a los atributos de gobierno universitario mencionados en el párrafo anterior. Para contrastar las hipótesis se utilizó una muestra de 129 universidades que se clasificaron en el año 2019 en las primeras 150 posiciones del ranking QS para América Latina. Además, estadísticamente se aplicaron dos tipos de regresiones: mínimos cuadrados ordinarios y regresión TOBIT. Entre los resultados más destacados se evidenció que atributos de gobemanza como la composición del consejo universitario, método de nombramiento del rector y presencia de un departamento o comité de auditoría independiente serian variables estratégicas que deberían ser consideradas en la gestión universitaria. Igualmente, se comprobó que la incidencia de estas variables en el rendimiento de las universidades depende del tipo de institución, es decir, si es una institución pública o privada.Postprint (published version

Expression of genes involved in phagocytosis in uncultured heterotrophic flagellates

Special issue Linking Metagenomics to Aquatic Microbial Ecology and Biogeochemical Cycles.-- 12 pages, 4 figures, 1 table, supporting information https://doi.org/10.1002/lno.11379Environmental molecular sequencing has revealed an abundance of microorganisms that were previously unknown, mainly because most had not been cultured in the laboratory. Within this novel diversity, there are the uncultured MAST clades (MArine STramenopiles), which are major components of marine heterotrophic flagellates (HFs) thought to be active bacterial grazers. In this study, we investigated the gene expression of natural HFs in a mixed community where bacterivory was promoted. Using fluorescence in situ hybridization and 18S rDNA derived from metatranscriptomics, we followed the taxonomic dynamics during the incubation, and confirmed the increase in relative abundance of different MAST lineages. We then used single cell genomes of several MAST species to gain an insight into their most expressed genes, with a particular focus on genes related to phagocytosis. The genomes of MAST‐4A and MAST‐4B were the most represented in the metatranscriptomes, and we identified highly expressed genes of these two species involved in motility and cytoskeleton remodeling, as well as many lysosomal enzymes. Particularly relevant were the cathepsins, which are characteristic digestive enzymes of the phagolysosome and the rhodopsins, perhaps used for vacuole acidification. The combination of single cell genomics and metatranscriptomics gives insights on the phagocytic capacity of uncultured and ecologically relevant HF speciesThis project was supported by the EU project SINGEK (H2020‐MSCA‐ITN‐2015‐675752) and the Spanish project ALLFLAGS (CTM2016‐75083‐R, MINECO). S.W. was supported by a Postdoctoral Fellowship from the European Union's Seventh Framework Program under Marie Sklodowska‐Currie grant agreement 6261882With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI

Assessment of the diversity and bacterivory-related genes of marine heterotrophic flagellates using multiomics

Association for the Sciences of Limnology and Oceanography (ASLO) Summer meeting, Water connects!, 10-15 June 2018, Victoria, CanadaThe smallest unpigmented eukaryotes in the marine plankton, known as heterotrophic flagellates (HFs), form a diverse collection of predominantly uncultured flagellated cells that are important grazers of bacteria, with crucial roles in nutrient remineralization. Here we explore the biodiversity of HF assemblages and their genetic repertoire, specifically those functions concerning bacterivory, using multiomics. First, we developed a pipeline to extract the taxonomic composition of HF cells in natural assemblages by retrieving and annotating V4 18S rDNA reads from metagenomes. Then, we promoted an enrichment of HFs by incubating natural communities in the dark, a setting where bacterivory was the main carbon metabolism process. Metatranscriptomic analyses of corresponding HF enriched samples pointed to the specific set of genes actively transcribed under this particular condition. Combining these bacterivory-related genes with a set of genomes from uncultured HFs obtained by single cell genomics allowed linking these functional genes to given taxa. Finally, we applied both the biodiversity and functional pipelines to a set of metagenomes obtained during the circumglobal Malaspina expedition and a seasonal study at the Blanes Bay Microbial Observatory. This study enabled the identification of the dominant heterotrophic flagellates in both systems together with their genetic repertoire associated to bacterivoryPeer Reviewe

Data from: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

Background: The class Chlorophyceae (Chlorophyta) includes morphologically and ecologically diverse green algae. Most of the documented species belong to the clade formed by the Chlamydomonadales (also called Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S rRNA gene or a few combined genes have shed light on the diversity and phylogenetic structure of the Chlamydomonadales, the positions of many of the monophyletic groups identified remain uncertain. Here, we used a chloroplast phylogenomic approach to delineate the relationships among these lineages. Results: To generate the analyzed amino acid and nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24 chlorophycean taxa; these included representatives from 16 of the 21 primary clades previously recognized in the Chlamydomonadales, two taxa from a coccoid lineage (Jenufa) that was suspected to be sister to the Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum likelihood inference methods, we analyzed an amino acid data set that was assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including 33 chlorophyceans), as well as two nucleotide data sets that were generated from the 69 genes coding for these proteins and 29 RNA-coding genes. The protein and gene phylogenies were congruent and robustly resolved the branching order of most of the investigated lineages. Within the Chlamydomonadales, 22 taxa formed an assemblage of five major clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis and the Crucicarteria, and was followed by the Radicarteria and then by the Chloromonadinia. The latter lineage was sister to two superclades, one consisting of the Oogamochlamydinia and Reinhardtinia and the other of the Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the two spine-bearing green algae belonging to the Golenkinia and Treubaria genera were recovered in a highly supported monophyletic group that also included three taxa representing distinct families of the Sphaeropleales (Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Conclusions: Our phylogenomic study advances our knowledge regarding the circumscription and internal structure of the Chlamydomonadales, suggesting that a previously unrecognized lineage is sister to the Sphaeropleales. In addition, it offers new insights into the flagellar structures of the founding members of both the Chlamydomonadales and Sphaeropleales

Comparative genomics of unculturable marine flagellates (MAST-4) using Single-Amplified Genomes

European Molecular Biology Organization (EMBO) Workshop, Comparative genomics of eukaryotic microbes: Dissecting sources of evolutionary diversity, 14 - 19 October 2017, Sant Feliu de Guíxols, Spain.-- 1 page, 3 figures, 2 tablesMarine heterotrophic flagellates (HF) have major importance in the organic carbon transfer to upper trophic levels thanks to their grazing activities on bacteria. Among the HF, Marine Stramenopiles (MASTs) are a highly represented group of organisms constituted by 18 different subgroups. Within the MASTs, there is one group, MAST-4, that due to its small size (2-3 μm), high relative abundance within both MASTs and HFs as well as worldwide distribution, is considered a good model to study marine HF1Peer Reviewe

Conduites (ou pratiques) alimentaires et nutrition

Ouvrage sous la direction de GUIHARD-COSTA Anne-Marie, BOETSCH Gilles, Froment Alain, GUERCI Antonio et ROBERT-LAMBLIN JoëlleL'étude du fait alimentaire, qui a la particularité de se situer à l'interface de la biologie et de la culture, est un terrain privilégié de rencontre entre les sciences biologiques et les sciences humaines et sociales. Selon que l'on privilégie l'une ou l'autre de ces orientations on parlera d'anthropologie alimentaire ou d'anthropologie nutritionnell