A methodology for coupling DGGE and mathematical modelling : application in bio-hydrogen production

Molecular biology techniques provide valuable information in terms of microbial dynamic and evolution. DGGE analysis is one of the most popular methods, which has been used in bioprocess assessment. A novel procedure that combines common experimental measurements, DGGE and image analysis is presented as a new methodology for preliminary assessment. In this study, the methodology was applied as an example to the start up of a hydrogen bioreactor, in order to have a preliminary estimation of the actual concentration of the different microbial species. The obtained results are used for determining the kinetic parameter by using a simple mathematical model focusing on species dynamic

A methodology for a quantitative interpretation of DGGE with the help of mathematical modelling: application in bio-hydrogen production

Molecular biology techniques provide valuable insights in the investigation of microbial dynamics and evolution. Denaturing gradient gel electrophoresis (DGGE) analysis is one of the most popular methods which have been used in bioprocess assessment. Most of the anaerobic digestion models consider several microbial populations as state variables. However, the difficulty to measure individual species concentrations may cause inaccurate model predictions. The integration of microbial data and ecosystem modelling is currently a challenging issue for improved system control. A novel procedure that combines common experimental measurements, DGGE, and image analysis is presented in this study in order to provide a preliminary estimation of the actual concentration of the dominant bacterial ribotypes in a bioreactor, for further use as variable in mathematical modelling of the bioprocess. This approach was applied during the start-up of a continuous anaerobic bioreactor for hydrogen production. The experimental concentration data were used for determining the kinetic parameters of each species, by using a multi-species chemostat-model. The model was able to reproduce the global trend of substrate and biomass concentrations during the reactor start-up, and predicted in an acceptable way the evolution of each ribotype concentration, depicting properly specific ribotype selection and extinction

Development of a reliable extraction method for the recovery of total genomic DNA from woodchip colonizing biofilm involved in gas biofiltration

[Abstract] This preliminary study focused on a critical step for the characterization of microbial ecosystem involved in biofiltration. Two aspects of nucleic acid recovery were explored: (i) cell dispersion (three methods tested) and (ii) total DNA extraction (four methods tested). The objective is to select the optimal combination of desorption/extraction methods, allowing subsequent molecular investigations to be reliable. Three relevant criteria are used to assess extraction efficiency: DNA amount and purity, and subsequent amplification feasibility

Effect of Acidic Industrial Effluent Release on Microbial Diversity and Trace Metal Dynamics During Resuspension of Coastal Sediment

Both industrial effluent discharge and the resuspension of contaminated marine sediments are important sources of trace metals in seawater which potentially affect marine ecosystems. The aim of this study was to evaluate the impact of the industrial wastewaters having acidic pH (2–3) and containing trace metals on microbial diversity in the coastal ecosystem of the Gulf of Gabès (Tunisia, southern Mediterranean Sea) subjected to resuspension events of marine sediments. Four trace elements (As, Cd, U, and V) were monitored during 10-day sediment resuspension experiments. The highest enrichment in the seawater dissolved phase was observed for Cd followed by U, V, and As. Cd remobilization was improved by indigenous microbial community, while U release was mainly abiotic. Acidic effluent addition impacted both trace metal distribution and microbial diversity, particularly that of the abundant phylum Bacteroidetes. Members of the order Saprospirales were enriched from sediment in natural seawater (initial pH > 8), while the family Flavobacteriaceae was favored by acidified seawater (initial pH < 8). Some Flavobacteriaceae members were identified as dominant species in both initial sediment and experiments with acidic wastewater, in which their relative abundance increased with increasing dissolved Cd levels. It could be therefore possible to consider them as bioindicators of metal pollution and/or acidification in marine ecosystems

Evaluation of the robustness of a biofiltration system for composting gas : structural and functional approach

Dans un contexte interdisciplinaire, l'étude a consisté à évaluer le niveau de robustesse de procédés pilotes de biofiltration appliqués au traitement d'un effluent caractéristique des émissions de compostage de boues d'épuration, soumis à des fluctuations de charge transitoires, répétées, et d'intensité croissante. L'impact de ces perturbations a été examiné à deux niveaux, par la mesure de la résultante fonctionnelle de dégradation d'une part, et par la caractérisation de la structure génétique de la communauté bactérienne totale d'autre part. La mise en relation de ces deux composantes a fait l'objet d'une attention particulière.The study aimed to evaluate the robustness capacity of pilot-scale biofilters applied to the treatment of sludge-composting emissions. The biofilters were submitted to repeated periodic fluctuations (shock loads) of increasing intensity. Their response was evaluated at two levels: functional resistance and resilience in terms of removal efficiency, and molecular characterization of the bacterial community structure. The objective was to establish the potential links between these two components

Étude de la variabilité de l'échelle de Sunnybrook dans l'évaluation des paralysies faciales périphériques

L’évaluation clinique de la paralysie faciale périphérique (PFP) nécessite un outil objectif, fiable et reproductible afin d’évaluer la sévérité de la paralysie et de suivre son évolution dans le temps. Le grading de Sunnybrook est l’échelle la plus utilisée en littérature scientifique, cependant elle est évaluateur-dépendant et non objective. Elle est donc sujette à différents degrés de variabilité.Notre travail a eu pour finalité la rédaction d’un article original « Sunnybrook Facial Grading System: Intra-rater and inter-rater variabilities » soumis à une revue anglophone Otology & Neurotology.Les objectifs de notre étude étaient d’évaluer les variabilités intra et inter-évaluateurs du grading de Sunnybrook et d’identifier d’éventuels facteurs de variabilité.Les enregistrements vidéo de 20 patients présentant des degrés variables de PFP ont été anonymisés puis présentés au hasard à 31 évaluateurs indépendants lors de 2 sessions. Les évaluateurs étaient des professionnels seniors et juniors impliqués dans la prise en charge des patients atteints de PFP (ORL, kinésithérapeutes, orthophonistes). Le grading de Sunnybrook a été utilisé pour coter les paralysies. Les variabilités intra-évaluateur et inter-évaluateurs ont été mesurées par le coefficient de corrélation intra-classe (ICC) pour le score composite et les trois sous-scores de l’échelle.Selon nos résultats, le grading de Sunnybrook présente une reproductibilité importante à presque parfaite dans le temps. Il est aussi reproductible d’un évaluateur à l’autre, avec un accord presque parfait pour le score global et le mouvement volontaire, et modéré pour la symétrie au repos et les syncinésies. Malgré des différences observées entre les groupes d’évaluateurs, la reproductibilité reste bonne pour tous les évaluateurs. Ainsi, le grading de Sunnybrook peut être utilisé avec une bonne reproductibilité par les seniors et les juniors, et par les tous les professionnels impliqués dans la prise en charge des patients atteints de PFP

Inhibitory effects of sodium azide on microbial growth in experimental resuspension of marine sediment

International audienc

Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii

International audienc

Correlations between microbial population dynamics, bamA gene abundance and performance of anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol

The relevant microorganims driving efficiency changes in anaerobic digestion of phenol remains uncertain. In this study correlations were established between microbial population and the process performance in an anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol (from 120 to 1200 mg L-1). Sludge samples were taken at different operational stages and microbial community dynamics was analyzed by 16S rRNA sequencing. In addition, bamA gene was quantified in order to evaluate the dynamics of anaerobic aromatic degraders. The microbial community was dominated by Anaerolineae, Bacteroidia, Clostridia, and Methanobacteria classes. Correlation analysis between bamA gene copy number and phenol concentration were highly significant, suggesting that the increase of aromatic degraders targeted by bamA assay was due to an increase in the amount of phenol degraded over time. The incremental phenol concentration affected hydrogenotrophic archaea triggering a linear decrease of Methanobacterium and the growth of Methanobrevibacter. The best performance in the reactor was at 800 mg L-1 of phenol. At this stage, the highest relative abundances of Syntrophorhabdus, Chloroflexus, Smithella, Methanolinea and Methanosaeta were observed and correlated positively with initial degradation rate, suggesting that these microorganisms are relevant players to maintain a good performance in the ASBR

Widespread microbial mercury methylation genes in the global ocean

International audienceMethylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, yet only anaerobic microorganisms have been identified so far as efficient methylmercury producers in anoxic environments. The microaerophilic nitrite oxidizing bacteria Nitrospina has been previously suggested as a possible mercury methylator in Antarctic sea ice. However, the microorganisms processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here we show metagenomic evidence from open ocean for widespread microbial methylmercury production in oxic subsurface waters. We find high abundances of the key mercury methylating genes hgcAB across all oceans corresponding to taxonomic relatives of known mercury methylators from Deltaproteobacteria, Firmicutes and Chloroflexi. Our result