Carbon fixation by marine ultra-small prokaryotes

Autotrophic carbon fixation is a crucial process for sustaining life on Earth. To date, six pathways, the Calvin-Benson-Bassham cycle, the reductive tricarboxylic acid cycle, the 3-hydroxypropionate bi-cycle, the Wood-Ljungdahl pathway, the dicarboxylate/4-hydroxybutyrate cycle, and the 4-hydroxybutyrate cycle have been described. Nanoorganisms, such as members of the Candidate Phyla Radiation (CPR) bacterial superphylum and the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohalorchaeota (DPANN) archaeal superphylum, could deeply impact carbon cycling and carbon fixation in ways that are still to be determined. CPR and DPANN are ubiquitous in the environment but understudied; their gene contents are not exhaustively described, and their metabolisms are not yet fully understood. Here, the completeness of each of the above pathways were quantified and tested for the presence of all key enzymes in a diversity of nanoorganisms across the World Ocean. The novel marine ultra-small prokaryotes was demonstrated to collectively harbor the genes required for carbon fixation, in particular the ‘energetically efficient’ DH pathway, and HBC pathways. This contrasted with the known carbon metabolic pathways associated with CPR memebers in aquifers, where they are described as degraders (Castelle 2015 et al., 2015, Castelle et al., 2018, Anantharaman et al., 2016). Our findings offer the possibility that nanoorganisms have a broader contribution to carbon fixation and cycling than currently assumed. Furthermore, CPR and DPANN are possibly not the only nanosized prokaryotes; therefore, the discovery of new autotrophic marine nanoorganisms, by future single cell genomics is anticipated

Recherche de séquences environnementales inconnues d’intérêt médical/biologique par l’utilisation de grands réseaux de similarité de séquences

The objective of this thesis was to identify as yet unknown microorganisms present in various environments and to characterize some of their metabolisms. This unidentified diversity, both taxonomic and functional, is commonly referred to as microbial dark matter. I have used and developed new network methods, including sequence similarity networks, to exploit very large sequence datasets from metagenomic projects. In particular, my work has highlighted the ecological role of ultra-small micro-organisms in some autotrophic metabolic pathways in the oceans. It also shows that CPR and DPANN, recently discovered ultra-small bacteria and archaea, participate in the dynamics of microbial communities through quorum sensing systems similar to those of better characterized organisms. An application of sequence similarity networks to meta-barcoding data also revealed a previously unknown diversity of Holozoans, which could allow us to better understand the transition to multicellularity of Metazoans. Finally, I have developed a method and software for searching for remote homologs of proteins of interest in very large datasets, such as those from metagenomics. This method, now validated, should make it possible to search for sequences belonging to still unknown and very divergent organisms, in the hope of discovering new deep branching phyla, or even new domains of life.L’objectif de cette thèse a été d’identifier des micro-organismes encore inconnus présents dans divers environnements et de caractériser certains de leurs métabolismes. Cette diversité non identifiée, à la fois taxonomique et fonctionnelle, est communément appelée matière noire microbienne. J’ai utilisé et développé de nouvelles méthodes de réseaux, et notamment des réseaux de similarité de séquences, afin d’exploiter de très grands jeux de données de séquences, issus de projets de métagénomique. En particulier, mon travail a mis en évidence le rôle écologique de micro-organismes ultra-petits dans certaines voies métaboliques autotrophes des océans. Il montre également que les CPR et DPANN, bactéries et archées ultra-petites récemment découvertes, participent à la dynamique des communautés microbiennes via des systèmes de quorum sensing homologues à ceux d’organismes mieux caractérisés. Une application des réseaux de similarité de séquences à des données de métabarcoding a également révélé une diversité jusque là inconnue d’Holozoa, qui pourrait nous permettre de mieux comprendre la transition vers la multicellularité des Metazoa. Enfin, j’ai développé une méthode et un logiciel destiné à la recherche d’homologues distants de protéines d’intérêt dans de très grands jeux de données, tels que ceux issus de la métagénomique. Cette méthode, maintenant validée, devrait permettre de rechercher des séquences appartenant à des organismes encore inconnus et très divergents, dans l’espoir de découvrir de nouveaux phylums profonds, voire même de nouveaux domaines du vivant

Search for unknown environmental sequences of medical/biological interest using large sequence similarity networks

L’objectif de cette thèse a été d’identifier des micro-organismes encore inconnus présents dans divers environnements et de caractériser certains de leurs métabolismes. Cette diversité non identifiée, à la fois taxonomique et fonctionnelle, est communément appelée matière noire microbienne. J’ai utilisé et développé de nouvelles méthodes de réseaux, et notamment des réseaux de similarité de séquences, afin d’exploiter de très grands jeux de données de séquences, issus de projets de métagénomique. En particulier, mon travail a mis en évidence le rôle écologique de micro-organismes ultra-petits dans certaines voies métaboliques autotrophes des océans. Il montre également que les CPR et DPANN, bactéries et archées ultra-petites récemment découvertes, participent à la dynamique des communautés microbiennes via des systèmes de quorum sensing homologues à ceux d’organismes mieux caractérisés. Une application des réseaux de similarité de séquences à des données de métabarcoding a également révélé une diversité jusque là inconnue d’Holozoa, qui pourrait nous permettre de mieux comprendre la transition vers la multicellularité des Metazoa. Enfin, j’ai développé une méthode et un logiciel destiné à la recherche d’homologues distants de protéines d’intérêt dans de très grands jeux de données, tels que ceux issus de la métagénomique. Cette méthode, maintenant validée, devrait permettre de rechercher des séquences appartenant à des organismes encore inconnus et très divergents, dans l’espoir de découvrir de nouveaux phylums profonds, voire même de nouveaux domaines du vivant.The objective of this thesis was to identify as yet unknown microorganisms present in various environments and to characterize some of their metabolisms. This unidentified diversity, both taxonomic and functional, is commonly referred to as microbial dark matter. I have used and developed new network methods, including sequence similarity networks, to exploit very large sequence datasets from metagenomic projects. In particular, my work has highlighted the ecological role of ultra-small micro-organisms in some autotrophic metabolic pathways in the oceans. It also shows that CPR and DPANN, recently discovered ultra-small bacteria and archaea, participate in the dynamics of microbial communities through quorum sensing systems similar to those of better characterized organisms. An application of sequence similarity networks to meta-barcoding data also revealed a previously unknown diversity of Holozoans, which could allow us to better understand the transition to multicellularity of Metazoans. Finally, I have developed a method and software for searching for remote homologs of proteins of interest in very large datasets, such as those from metagenomics. This method, now validated, should make it possible to search for sequences belonging to still unknown and very divergent organisms, in the hope of discovering new deep branching phyla, or even new domains of life

Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

International audienceEpigenetic modifications have an important role to explain part of the intra-and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential presence of TEs in the evolutionary divergence of duplicates through variation in the epigenetic landscape

Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur

International audienceRecently, we uncovered the genetic components from six carbon fixation autotrophic pathways in cleaned ultrasmall size fractions from marine samples (<0.22 mm) gathered worldwide by the Tara Oceans Expedition. This first finding suggested that prokaryotic nanoorganisms, phylogenetically distantly related to the known CPR and DPANN groups, could collectively impact carbon cycling and carbon fixation across the world's ocean. To extend our mining of the functional and taxonomic microbial dark matter from the ultrasmall size fraction from the Tara Oceans Expedition, we investigated the distribution of 28 metabolic pathways associated with the cycling of carbon, methane, nitrogen, and sulfur. For all of these pathways, we report the existence not only of novel metabolic homologs in the ultrasmall size fraction of the oceanic microbiome, associated with nanoorganisms belonging to the CPR and DPANN lineages, but also of metabolic homologs exclusively found in marine host taxa belonging to other (still unassigned) microbial lineages. Therefore, we conclude that marine nanoorganisms contribute to a greater diversity of key biogeochemical cycles than currently appreciated. In particular, we suggest that oceanic nanoorganisms may be involved in a metabolic loop around Acetyl-CoA, have an underappreciated genetic potential to degrade methane, contribute to sustaining redox-reactions by producing Coenzyme F420, and affect sulfur cycling, notably as they harbor a complete suite of homologs of enzymes of the SOX system

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

International audienceMicrobes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns

Network studies unveil new groups of highly divergent proteins in families as old as cellular life with important biological functions in the ocean

Abstract Metagenomics has considerably broadened our knowledge of microbial diversity, unravelling fascinating microbial adaptations and characterising multiple novel major taxonomic groups, e.g. CPR bacteria, DPANN and Asgard archaea, and novel viruses. Such findings profoundly reshaped the structure of the tree of life and emphasised the central role of investigating uncultured organisms. However, despite significant progresses, a large portion of proteins predicted from metagenomes remain today unannotated, both taxonomically and functionally, across many biomes and in particular in oceanic waters, including at relatively lenient clustering thresholds. Here, we used an iterative network-based approach to probe a dataset of 40 million ORFs, predicted in marine environments. We assessed the environmental diversity of a selection of 53 gene families as old as cellular life, broadly distributed across the Tree of Life. About half of them harboured clusters of environmental homologs that diverged significantly from the known diversity of published complete genomes, with representatives distributed across all the ocean. Network analyses also enabled the detection of environmental clades with new structural variants of essential genes (SMC), divergent polymerase subunits forming deep branching clades in the polymerase tree, and potentially deep taxonomic groups at the basis of Archaea or Bacteria, from ultra-small microorganisms distinct from CPR and DPANN. These diverse results provide a strong proof of concept for the capabilities of sequence network approaches to make better sense of microbial dark matter across taxonomical scales. Still, further methodological developments appear warranted in order to better comprehend the most divergent members of the oceanic microbial dark matter

J Clin Microbiol

Trichosporon mycotoxinivorans is a novel pathogen recently found in cystic fibrosis patients. We report the first case of a disseminated fatal infection with T. mycotoxinivorans associated with invasive Aspergillus fumigatus and Scedosporium apiospermum infection after lung and liver transplantation in a cystic fibrosis patient

Can histologically normal epileptogenic zone share common electrophysiological phenotypes with focal cortical dysplasia? SEEG-based study in MRI-negative epileptic patients

International audienc