Enhancing microbial degradation of recalcitrant chlorinated compounds by microbial stimulation and metal addition

International audienc

Soil microbial community structure vs. function - Who's driving?

International audienc

Microbial Social Networks in Contaminated Soils

International audienc

Metagenomic and metagenic approaches applied to enhanced anaerobic reductive dechlorination of polychlorinated biphenyls: linking structure and function

International audienc

ASSESSING DEHALOGENASE ACTIVITIES UTILIZING INTEGRATING QUANTITATIVE PCR AND MICROARRAYS DURING PCE BIOREMEDIATION : THE CONTRUCTION OF A NEW DEGRADATION MODEL

International audienceThe bioremediation of groundwater contaminated by tetrachloroethylene (PCE), a widely used chlorinated solvent, can lead to toxic metabolites. In order to evaluate the entire degradation of PCE, we quantify the mRNA of the genes responsible for the degradation of each metabolite by using quantitative PCR and reverse transcriptase quantitative PCR, and correlated their expression levels to the bacterial community structure observed by phylogenic microarray hybridization. This approach was applied to 120 microcosms in which we added lactate, molasses, or soybean oil. These organic substrates are often used to induce reductive dechlorination during bioremediation in situ. These different organic substrates cause changes in the bacterial community structure, and the production of hazardous metabolites depends on the organic substrate added. In order to determine whether relevant biomarkers can signal the hazardous metabolite production, we correlated quantitative PCE results and phylogenic microarrays hybridizations under the different organic substrate conditions. In addition, we incorporated the qPCR and RTqPCR data in a PCE degradation kinetic model, which takes into account bacterial activity, hydrogeological and geochemical data

GENOME FLEXIBILITY ACROSS DIFFERENT STRAINS OF THE HEXACHLOROCYCLANE-DEGRADING BACTERIUM SPHINGOBIUM FRANCENSE SP+ IDENTIFIED BY A GLOBAL APPROACH OF GENOME SEQUENCING AND MICROARRAY COMPARATIVE GENOMIC HYBRIDIZATION

International audiencePhenotypic and genomic dynamics enable bacteria to adapt quickly to various ecological niches and environmental fluctuations such as the presence of xenobiotic compounds. We explored the different adaptive mechanisms in the bacterium Sphingobium francense, which is able to degrade lindane, a chlorinated xenobiotic compound historically used in agricultural and medicine. Previous studies demonstrated the association of mobile genetic elements with lin genes implicated in lindane catabolic pathways. We also observed that the wildtype, sp+, a lindane degrading strain, produces mutants (at a rate of 4 percent per replating) unable to degrade lindane. In order to study the role of mobile genetic elements in the adaptability of this bacterium, we developed an original strategy based on the pyrosequencing data obtained for the genome of Sphingobium francense sp+ and microarray comparative genomic hybridizations. This approach uses a two-color process to estimate the different types of genomic rearrangements that occurred in a mutant genome in comparison to the reference strain sp+ genome. For this study, five non-lindane degrading mutants and one revertant, which recovered the capacity to degrade lindane, were characterized. Analyzes of each microarray showed that the nonlindane degrading mutants underwent large genomic rearrangements and the selected mutants were genetically different. Moreover, we established the proximity between some environmental genes and mobile genetic elements. Some of these regions were deleted in the mutants reinforcing the observation that mobile genetic elements play an important role in bacterial adaptation to environmental perturbation. Thus, all the data obtained confirms the extraordinary plasticity of the Sphingobium genome linked to the presence of multiple mobile genetic elements, which are involved in the instability of lindane degradation capability and other environmental functional genes

CRISPRs based phage-host interactions in glacial ice

International audienc

FROM “OMICS” TO “OHMICS”: ELECTRICITYPRODUCING BACTERIAL COMMUNITY STRUCTURES IN MICROBIAL FUEL CELLS

International audienceMicrobial Fuel Cells (MFCs) are being developed as a novel biotechnology to harvest energy from dissolved organic matter with potential applications ranging from wastewater treatment to power sources for remote environmental sensors. To date, there is limited information about the structure of electro-active bacterial communities, and in order to optimize energy production in MFCs, a better understanding of these communities is essential. Our objective was to determine the taxonomic structure and spatial organization of the bacterial communities present at the surface of the electrodes during the formation and development of electro-active biofilms. Experiments were performed using single chamber MFCs fed with primary clarifier effluent from a municipal wastewater treatment plant. Community structure analyses were performed as a function of time and electrical performances using a combination of molecular tools (metagenomic DNA extraction, 16S-rRNA-based phylogenetic microarrays, pyrosequencing...). Analyses of the biofilm structure, distribution and physiological state of the bacterial cells at the surface of the electrodes were performed using a range of fluorochromes and epifluorescence microscopy equipped with a 3D imaging system. Metagenomic approaches helped us to identify putative bacterial species and genes involved in electricity production in MFCs. In combination with image analyses, data obtained strongly supports the possibility of increasing electrical performances by modifying electrode design, feeding and microbial growth conditions in MFCs

HOW MICROBIAL COMMUNITY STRUCTURE AND FUNCTION RELATE TO EACH OTHER WHEN CHLORINATED COMPOUNDS ARE INVOLVED

International audienceThe genetic resources available in an ecosystem are represented in part by the microbial community structure given that not all genes can be found in all prokaryotic species. The importance of the microbial community structure on the functional capacity to degrade chlorinated solvents in soil and groundwater was investigated. A combination of phylogenetic measurements using phylochip microarrays and 16S rDNA cloning and sequencing and functional gene quantification (both DNA and RNA) was used to evaluate the importance of structure on functional analyses. The quantitative PCR (qPCR) and Reverse Transcriptase-qPCR was applied to a range of genes implicated in chlorinated solvent degradation in the environment. The presence of chlorinated solvents induced a relative degree of stress on the microbial community, which was relieved by the chlorinated compound degradation. Certain members of the community were correlated to the degradation capacity while others were inversely correlated, probably due to inhibitory effect of the compounds. This work helps establish the relationship between structure and function at least within the narrow context of chlorinated solvent degradation. And improve the understanding of efficient community for the biodegradation of pollutant

The Dynamic Arctic Snowpack Microbial Habitat

International audienceHuman-­‐induced environmental changes are affecting cold ecosystems and predicted impacts include rapid warming, increased nitrogen and pollutant deposition, yet the effect of these on microbial communities and nutrient cycling is poorly understood. Much of the research concerning Arctic microbial community structure and function stems from soil and permafrost studies, however relatively little is known about the snowpack. Seasonal snow cover extends over a third of the Earth's land surface, covering up to 47 million km2 and is also an important feature of the Arctic. Snow cover can be considered as a dynamic habitat of limited duration that acts as a medium and a mediator by transmitting and modifying interactions among microorganisms, plants, animals, nutrients, the atmosphere and soil. A growing body of evidence suggests that microbial communities play key roles in biogeochemical cycling in the snowpack, but little is known about the processes controlling their biogeographic distributions. We used metagenomic tools such as phylogenetic microarrays and high throughput sequencing to explore microbial community structure in samples collected from various Arctic snowpacks (North Pole, Greenland and Ny-­‐Alesund) at different seasons (spring, summer, winter) and compared these to publicly available data from other ecosystems to evaluate the roles of niche-­‐based processes vs spatial processes in explaining variations in community structure. The biogeography of Arctic microbial communities appears to be influenced by environmental factors, such as snow physics and chemistry relative to geographic distance. The results from this study offer insights into the mechanisms that generate and maintain diversity, such as speciation, extinction, dispersal and species interactions