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Avis de soutenance de thèse en microbiologie par Junwei Cao

Cette thèse intitulée "Isolement et caractérisation de microorganismes impliqués dans le cycle du soufre, provenant de sources hydrothermales sous-explorées" sera soutenue le mercredi 23 mars 2016 à 13h30 dans l'amphi A de l'IUEM.

Deep-sea hydrothermal vents are among the most biologically active regions, and support highly productive ecosystems fueled by chemosynthesis. Although our knowledge of the diversity and roles of hydrothermal vents isolates has remarkably expanded, extensive investigation of the microbiology and physiology remain imperative for several reasons, especially in the poorly-documented hydrothermal vents of the Indian Ocean. In this era of omics, the cultivation of microorganisms remains crucial in several respects. Estimations indicate that more than 99% of all existing prokaryotes have resisted cultivation in the laboratory, limiting the study of their physiology and ecological role. The cultivation makes it possible to perform a direct and easy study of the microbial morphology, physiology, genetics and pathogenicity. From an ecological point of view, it is very helpful to have isolates to integrate at the cell level ecological data got via top-down (meta-omics, rate measurements, etc.) and bottom-up (single-cell techniques, metabolomics, transcriptomics, etc.) approaches. Finally, microbial isolates allow testing hypotheses that arise from (meta-)genomic data. Sulfate/sulfur-reducing prokaryotes, ubiquitous in anoxic habitats, play an important role in both the sulfur and carbon cycles. These cycles are particularly important at deep-sea hydrothermal vents and our study focused aimed at cultivating novel taxa involved in these cycles from the poorly documented Indian Ocean.

Six anaerobic prokaryotes were isolated from deep-sea hydrothermal samples from the Indian Ocean. For taxonomic study of 3 novel strains, 16S rRNA gene phylogenetic analysis, phenotypic and chemotaxonomic characterizations were carried out. The genomes of these three isolates were sequenced and annotated.

The first characterized isolate was strain J2T, a novel sulfate-reducing bacterium. It was isolated from a serpentinized peridotite sample collected at a depth of 3173 m. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2T grouped with the genus of Desulfovibrio within the class Deltaproteobacteria, with highest sequence similarity of 98.05% to Desulfovibrio dechloracetivorans SF3T, but it showed low similarity (87.95%) to the type species D. desulfuricans DSM 642T. The combined genotypic and phenotypic data showed that strain J2T represents a novel species of a novel genus Pseudodesulfovibrio, for which the name Pseudodesulfovibrio indicus gen. nov., sp. nov. was proposed.

The second characterized isolate was a novel sulfur-reducing bacterium, strain K6013T. It was isolated from a sulfide sample collected at a depth of 2771 m from a high-temperature hydrothermal vent. Phylogenetic 16S rRNA gene sequence analyses showed that strain K6013T falls into the genus Desulfurobacterium within the class Aquificae, with highest sequence similarity of 96.93% to Desulfurobacterium atlanticum SL22T. On the basis of genotypic and phenotypic data, strain K6013T is considered to represent a novel species of the genus Desulfurobacterium, for which the name Desulfurobacterium indicum sp. nov. is proposed.

Another characterized isolate was a novel sulfate-reducing bacterium, strain S606T. It was isolated from a sulfide sample collected at a depth of 2764 m from a deep-sea chimney wall in the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S606T falls into the genus Thermodesulfatator within the class Thermodesulfobacteria, with highest sequence similarity of 98.15% to Thermodesulfatator indicus DSM 15286T. The combined genotypic and phenotypic data show that strain S606T represents a novel species of the genus Thermodesulfatator, for which the name Thermodesulfatator autotrophica sp. nov. is proposed.

Finally, experiments aimed at trying to design a genetic tool with the archaea Paleococcus pacificus and another part aimed at testing the response of a deep-sea microbial isolates to hydrostatic pressure.

 

Photo du mois

Geovide_PLherminier_0790.JPG

(C) Pascale Lherminier / Ifremer