Browsing by Author "Siegel, Anne"

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    Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae
    (2014) Dittami, Simon M.; Barbeyron, Tristan; Boyen, Catherine; Cambefort, Jeanne; Collet, Guillaume; Delage, Ludovic; Gobet, Angelique; Groisillier, Agnes; Leblanc, Catherine; Michel, Gurvan; Scornet, Delphine; Siegel, Anne; Tapia, Javier E.; Tonon, Thierry
    Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The "Ca. P. ectocarpi" genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, "Ca. P. ectocarpi" has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (>= 97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus "Phaeomarinobacter" may comprise several species, which may colonize different niches.
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    Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment
    (2020) Mandakovic, Dinka; Cintolesi, Angela; Maldonado, Jonathan; Mendoza, Sebastian N.; Aite, Meziane; Gaete, Alexis; Saitua, Francisco; Allende, Miguel; Cambiazo, Veronica; Siegel, Anne; Maass, Alejandro; Gonzalez, Mauricio; Latorre, Mauricio
    The Atacama Desert is the most arid desert on Earth, focus of important research activities related to microbial biodiversity studies. In this context, metabolic characterization of arid soil bacteria is crucial to understand their survival strategies under extreme environmental stress. We investigated whether strain-specific features of two Microbacterium species were involved in the metabolic ability to tolerate/adapt to local variations within an extreme desert environment. Using an integrative systems biology approach we have carried out construction and comparison of genome-scale metabolic models (GEMs) of two Microbacterium sp., CGR1 and CGR2, previously isolated from physicochemically contrasting soil sites in the Atacama Desert. Despite CGR1 and CGR2 belong to different phylogenetic clades, metabolic pathways and attributes are highly conserved in both strains. However, comparison of the GEMs showed significant differences in the connectivity of specific metabolites related to pH tolerance and CO2 production. The latter is most likely required to handle acidic stress through decarboxylation reactions. We observed greater GEM connectivity within Microbacterium sp. CGR1 compared to CGR2, which is correlated with the capacity of CGR1 to tolerate a wider pH tolerance range. Both metabolic models predict the synthesis of pigment metabolites (beta -carotene), observation validated by HPLC experiments. Our study provides a valuable resource to further investigate global metabolic adaptations of bacterial species to grow in soils with different abiotic factors within an extreme environment.