Militon C.,Clermont University |
Militon C.,CNRS Microorganisms Laboratory: Genome and Environment |
Boucher D.,Clermont University |
Boucher D.,CNRS Microorganisms Laboratory: Genome and Environment |
And 9 more authors.
FEMS Microbiology Ecology | Year: 2010
The microbial community response during the oxygen biostimulation process of aged oil-polluted soils is poorly documented and there is no reference for the long-term monitoring of the unsaturated zone. To assess the potential effect of air supply on hydrocarbon fate and microbial community structure, two treatments (0 and 0.056 mol h-1 molar flow rate of oxygen) were performed in fixed bed reactors containing oil-polluted soil. Microbial activity was monitored continuously over 2 years throughout the oxygen biostimulation process. Microbial community structure before and after treatment for 12 and 24 months was determined using a dual rRNA/rRNA gene approach, allowing us to characterize bacteria that were presumably metabolically active and therefore responsible for the functionality of the community in this polluted soil. Clone library analysis revealed that the microbial community contained many rare phylotypes. These have never been observed in other studied ecosystems. The bacterial community shifted from Gammaproteobacteria to Actinobacteria during the treatment. Without aeration, the samples were dominated by a phylotype linked to the Streptomyces. Members belonging to eight dominant phylotypes were well adapted to the aeration process. Aeration stimulated an Actinobacteria phylotype that might be involved in restoring the ecosystem studied. Phylogenetic analyses suggested that this phylotype is a novel, deep-branching member of the Actinobacteria related to the well-studied genus Acidimicrobium. FEMS Microbiology Ecology © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. No claim to original French government works.
Terrat S.,Clermont University |
Terrat S.,CNRS Microorganisms Laboratory: Genome and Environment |
Terrat S.,University Blaise Pascal |
Peyretaillade E.,Clermont University |
And 16 more authors.
BMC Bioinformatics | Year: 2010
Background: Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes.Results: First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently.Conclusions: We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license. © 2010 Terrat et al; licensee BioMed Central Ltd.
Singhania R.R.,University Blaise Pascal |
Christophe G.,University Blaise Pascal |
Perchet G.,Biobasic Environnement |
Troquet J.,Biobasic Environnement |
Larroche C.,University Blaise Pascal
Bioresource Technology | Year: 2012
Immersed membrane bioreactor (IMBR) has emerged as a novel potential technology which is considered globally as potent technology, primarily for wastewater treatment. It offers quality improvement in effluents treatment compared to other technological systems. It also offers potential benefits for the bioprocesses where product formation and separation is desired simultaneously in a compact container. This review gives insight for the wide range applications of IMBR focussing on anaerobiosis. It discusses the significance, advantages and drawbacks of IMBR against the conventional methods, highlighting the external membrane bioreactors. While the commercial significance of IMBR is obvious for industrial and municipal wastewater treatment, the current focus is shifting on other applications such as anaerobic bioprocesses. Though the IMBR technology is generally considered hand-in-hand as sustainable technology, the major bottleneck in its application at commercial scale for wastewater treatment seems its economic feasibility and compatibility. Among the technical issues, the membrane fouling is considered as a major problem for which several strategies have been developed to overcome the problem, though there is no complete or universal solution to this problem. © 2012 Elsevier Ltd.