About
213
Publications
31,166
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,210
Citations
Introduction
The PROSE unit is conducting research on environmental biotechnologies, through scales spanning from the microbial community up to the whole process (wastewater treatment plants, anaerobic digesters, bioelectrochemical processes for biorefinery, …), addressing key societal issues of sustainable development, circular economy and bioeconomy. Our unit performs a transdisciplinary approach based on microbial ecology, biogeochemistry, process engineering, physical measurement and modelling.
Current institution
Additional affiliations
January 2001 - present
January 1997 - December 2000
Position
- PhD-Bioaugmentation into activated sludge
Description
- PhD
Education
June 2015 - June 2016
February 1997 - October 2000
Field of study
- Environmental Biotechnology
September 1993 - September 1996
Publications
Publications (213)
Microbial communities are key engines that drive earth’s biogeochemical cycles. However, existing ecosystem models have only limited ability to predict microbial dynamics and require the calibration of multiple population-specific empirical equations. In contrast, we build on a new kinetic “Microbial Transition State” (MTS) theory of growth derived...
Our ability to model the growth of microbes only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. In particular, the link between energy balances and growth dynamics is still not understood. Here we demonstrate a microbial growth equation relying on an explicit theoretical...
Identifying the function of uncultured microbes in their environments today remains one of the main challenges for microbial ecologists. In this article, we describe a new method allowing simultaneous analysis of microbial identity and function. This method is based on the visualization of oligonucleotide probe-conferred hybridization signal in sin...
Cellulose is the most abundant biopolymer on Earth. Optimising energy recovery from this renewable but recalcitrant material is a key issue. The metaproteome expressed by thermophilic communities during cellulose anaerobic digestion was investigated in microcosms. By multiplying the analytical replicates (65 protein fractions analysed by MS/MS) and...
A nitrifying sequencing batch reactor was inoculated twice with the aerobic denitrifying bacterium Microvirgula aerodenitrificans and fed with acetate. No improvement was obtained on nitrogen removal. The second more massive inoculation was even followed by a nitrification breakdown, while at the same time, nitrification remained stable in a second...
The biodegradable and renewable nature of lignocellulosic biomass (LCB) has gained significant interest in recent years. This study explores the lignocellulolytic and electrogenic potential of Shewanella oneidensis MR-1, Cellulomonas fimi ATCC 484, and Cellulomonas biazotea NBRC 12680 on LCB. Two strategies were tested: assessing strains LCB degrad...
Temperature is a key factor influencing microbial growth rates and yields. In literature, the influence of temperature on growth is studied either on yields or rates but not both at the same time. Moreover, studies often report the influence of a specific set of temperatures using rich culture media containing complex ingredients (such as yeast ext...
Microbial electrochemical technologies now enable microbial electrosynthesis (MES) of organic compounds using microbial electrolysis cells handling waste organic materials. An electrolytic cell with an MES cathode may generate soluble organic molecules at a higher market price than biomethane, thereby satisfying both economic and environmental goal...
Diversity of viruses infecting non‐extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling be...
Wastewater treatment is generally performed using energy-intensive processes, such as activated sludge. Improving energy efficiency has become one of the main challenges for next-generation wastewater treatment plants. Bioelectrochemical systems (BES) have been attracting attention because they take advantage of the chemical energy contained in was...
To move today’s agricultural and urban systems towards tomorrow’s circular economy and respond to climate change, it is imperative to turn organic residues and wastewater into resourceful assets. This article discusses the changes that are needed in research to drive this paradigm shift and to go from a “losses and waste” situation to a “resource a...
Insights into microbiota adaptation to increased ammonia stress, and identification of indicator microorganisms can help to optimize the operation of anaerobic digesters. To identify microbial indicators and investigate their metabolic contribution to acetoclastic methanogenesis (AM), syntrophic acetate oxidation (SAO) or hydrogenotrophic methanoge...
Microbial electrochemical snorkel (MES) is a short-circuited microbial fuel cell applicable to water treatment that does not produce energy but requires lower cost for its implementation. Few reports have already described its water treatment capabilities but no deeper electrochemical analysis were yet performed. We tested various materials (iron,...
To limit the nitrate contamination of ground and surface water, stimulation of denitrification by electrochemical approach is an innovative way to be explored. Two nitrate reducing bio-cathodes were developed under constant polarization (-0.5 V vs SCE) using sediments and water from a constructed wetland (Rampillon, Seine-et-Marne, France). The bio...
The present study deals with the possible pre-treatment of municipal solid wastes (MSW) in anaerobic conditions and their co-disposal with bottom ash. In this objective, the effect of the addition of bottom ash on organic matter degradation was checked using different analyses. The obtained results showed a great reduction of organic matter in the...
Biochemical methane potential (BMP) is essential to determine the production of methane for various substrates; literature shows important discrepancies for the same substrates. In this paper, a harmonized BMP protocol was developed and tested with two phases of BMP tests carried out by eleven French laboratories. Surprisingly, for the three same s...
Genetic diversification through the emergence of variants is one of the known mechanisms enabling the adaptation of bacterial communities. We focused in this work on the adaptation of the model strain Pseudomonas putida KT2440 in association with another P. putida strain (PCL1480) recently isolated from soil to investigate the potential role of bac...
Microbial transition state theory (MTS) offers a theoretically explicit mathematical model for substrate limited microbial growth. By considering a first order approximation of the MTS equation one recovers the well-known Monod’s expression for growth, which was regarded as a purely empirical function. The harvest volume of a cell as defined in MTS...
Environmental biorefineries aim to produce biofuels and platform biomolecules from organic waste. To this end, microbial electrochemical technologies theoretically allow controlled microbial electrosynthesis (MES) of organic molecules to be coupled to oxidation of waste. Here, we provide a first proof of concept and a robust operation strategy for...
Recent development of microbial electrochemical technologies has allowed microbial electrosynthesis (MES) of organic molecules with microbial electrolysis cell treating waste organic matter. An electrolytic cell with a MES cathode (ME-ME cell) can produce soluble organic molecules with higher market price than biomethane, and thus satisfy both econ...
To face up abiotic resource depletion and other environmental issues as climate change due to usual fossil-based chemical production technologies, some alternative strategies have been developed using renewable resources. To produce such bio-based chemicals, renewable raw materials such as cereal crops or vegetables are currently used. To promote a...
Waste management is a key environmental and socio-economic issue. Environmental concerns are encouraging the use of alternative resources and lower emissions to air, water and soil. Innovative technologies to deal with waste recovery that produce marketable bioproducts are emerging. Bioelectrochemical synthesis systems (BESs) are based on the prima...
Three distinct biological reactors fed with synthetic medium (UASB_Control), synthetic medium and linear alkylbenzene sulfonate (LAS; UASB_SL), and real laundry wastewater (UASB_LW) were compared using a metatranscriptomic approach to determine putative bioindicator genes and taxonomies associated to all steps of anaerobic LAS biodegradation pathwa...
La présente invention se rapporte à un procédé de synthèse de molécules organiques à partir de sources carbonées et de dihydrogène ainsi qu'à un dispositif apte à mettre en oeuvre ledit procédé. Le procédé selon l'invention peut utiliser des sources carbonées et/ou du dihydrogène issus de ressources renouvelables.
This study aimed at providing a better understanding of the influence of support media (10 g/L of zeolites, 10 g/L of activated carbons, and 1 g/L of chitosan) on key phylotypes steering anaerobic digestion (AD) performance in presence of 19 g/L of Total Ammonia Nitrogen (TAN) within batch digesters. Support media did not influence TAN concentratio...
In order to understand the correlation between ammonia and methanogenesis metabolism, methane production pathways and their specific rates were studied at total ammonium nitrogen (TAN) concentrations of 0.14 ∼ 9 g/L in three methanogenic sludges fed with acetate, at both mesophilic and thermophilic conditions. Results showed, high levels of TAN had...
Lignocellulosic materials from municipal solid waste emerge as attractive resources for anaerobic digestion biorefinery. To increase the knowledge required for establishing efficient bioprocesses, dynamics of batch fermentation by the cellulolytic bacterium Ruminiclostridium cellulolyticum were compared using three cellulosic materials, paper handk...
Data on fermentation of Tissue (black symbols), Whatman Paper (grey symbols) and Cotton (light grey symbols) by R. cellulolyticum.
(A) Evolution over time of the total Dissolved Organic Content (DOC). (B) Evolution over time of pH. (C) Cumulated gas production at the final incubation time point. Error bars indicate standard deviations calculated fr...
Mid-infrared absorption spectra obtained for Tissue, Whatman Paper and Cotton.
W. Paper: Whatman Paper. The 5 peaks annotated with arrows on the spectra are related to the presence of cellulose. Details on the method are available in S1 File.
(TIFF)
Molar mass distribution curves of the cellulose and hemicellulose chains from Tissue (black lines), Whatman Paper (grey lines) and Cotton (light grey lines).
M stands for Molar Mass. Vertical colored lines indicate the positions of the M values corresponding to the peak of individual (i.e. non-aggregated) cellulose chains (see Table 1). Grey area A...
Quantification of total extracted proteins and principal component analyses of the proteomes based on the individual protein quantification data.
A) Total amounts of proteins extracted from the Tissue (black) and Whatman Paper (grey) incubations, after 46h and 70h of incubation, from the pellets and supernatants respectively. B) Principal component...
Carbon mass distributions in the microcosms at the initial and final incubation time points.
The carbon masses are in mg. The average values (± one standard deviation where relevant) are shown. Cellulosic material: carbon mass in the substrate (contained either in Tissue, Whatman Paper or Cotton)–DOC: organic carbon mass in the liquid phase (Dissol...
Functional profiles for all proteins encoded in R. cellulolyticum genome and for proteins showing significantly different levels in the presence of Tissue compared to Whatman Paper.
a) BP: Biological Process—CC: Cellular Component—MF: Molecular Function. b) For each GO term, percentage of the GO term annotations among the significant proteins. c) F...
Average carbon mass distributions in the microcosms at the initial and final incubation time points.
The carbon masses are in mg. Sampled: carbon mass removed from the microcosms through sampling of the liquid phase—CO2 gas: carbon mass in CO2 in the headspace—DIC: inorganic carbon mass in the liquid phase (Dissolved Inorganic Carbon)–DOC: organic...
Illustrative microscopy images of substrate colonization by R. cellulolyticum during growth in microplates on Tissue (left column), Whatman Paper (middle column) and Cotton (right column) at a final concentration of 5 g/l.
Confocal Laser Scanning Microscopy images were acquired from Tissue (A-D), Whatman Paper (F-I) and Cotton (K-N) incubations, on...
Illustrative examples of statistically significant substrate and substrate-by-time interaction effects on the protein levels.
The illustrative examples are selected from the dataset of the pellet proteins. On each dot plot, the values are shown for the incubation times 46h, 70h and for the blank. The shown values correspond to the log-transformed a...
Summary of the quantitative results obtained for each protein of R. cellulolyticum.
(XLSX)
Supplementary Materials and Methods and References.
(PDF)
Functional profiles for all proteins encoded in R. cellulolyticum genome and for the proteins showing significantly different levels in the presence of Tissue compared to Whatman Paper.
A selection of 32 Gene Ontology (GO) terms is shown, corresponding to the categories with highest percentages of annotations and to the most enriched or depleted ca...
Extracytoplasmic proteins with at least one statistically significant effect when comparing incubations on Tissue and Whatman Paper.
The proteins are listed according to the observed effects, to the subcellular localization predicted by SurfG+ and according to their function. a) The Gene IDs (Ccel_) are given according to UniprotKB database. b) The...
To reduce the environmental footprint of human activities, the quality of environmental media such as water, soil and the atmosphere should be first assessed. Microorganisms are well suited for a such assessment because they respond fast to environmental changes, they have a huge taxonomic and genetic diversity, and they are actively involved in bi...
Performance stability is a key operational issue for anaerobic digestion (AD) and phenolic compounds are regularly mentioned as a major cause of digester failures. To get more insights into AD microbiota response to a wide range of inhibition levels, anaerobic batch toxicity assays were conducted with ten phenol concentrations up to 5.00 g/L. Final...
Analyses on bacterial, archaeal communities at family level and methane-production metabolism were conducted in thirteen full-scale and pilot-scale anaerobic sludge digesters. These digesters were operated at different conditions regarding solids concentration, sludge retention time, organic loading rate and feedstock composition, seeking to optimi...
In this study, the specific reduction of CO2 to acetate in presence of methanogenesis inhibitor 2-bromoethanesulfonate (BES) was studied in a bio-electrochemical system (BES) via a two stage experimental design. During first stage using untreated mixed anaerobic consortia, the methanogenesis was dominated and the CO2 reduction yielded methane at th...
Biocathodes polarized at high potential are promising for enhancing Microbial Fuel Cell performances but the microbes and genes involved remain poorly documented. Here, two sets of five oxygen-reducing biocathodes were formed at two potentials (-0.4V and +0.1V vs. saturated calomel electrode) and analyzed combining electrochemical and metagenomic a...
In natural settings, anaerobic digestion can take place in a wide temperature range, but industrial digesters are usually operated under either mesophilic (~35 °C) or thermophilic (~55 °C) conditions. The ability of anaerobic digestion microbiota to switch from one operating temperature to the other remains poorly documented. We therefore studied t...
Although mathematical modelling has reached a degree of maturity in the last decades, microbial ecology is still developing, albeit at a rapid pace thanks to new insights provided by modern molecular tools. However, whilst microbiologists have long enjoyed the perspectives that particular mathematical frameworks can provide, there remains a relucta...
Performance stability is a key issue when managing anaerobic digesters. However it can be affected by external disturbances caused by micropollutants. In this study the influence of phenol on the methanization of cellulose was evaluated through batch toxicity assays. Special attention was given to the dynamics of microbial communities by means of a...
Ammonia inhibition represents a major operational issue for anaerobic digestion (AD). In order to get more insights into AD microbiota resistance, anaerobic batch reactors performances were investigated under a wide range of Total Ammonia Nitrogen (TAN) concentrations up to 50.0 g/L at 35 °C. The half maximal inhibitory concentration (IC50) value w...
To get insights into selection criteria for feed efficiency, 2 rabbit lines have been created: the ConsoResidual line was selected for residual feed intake (RFI) with ad libitum feeding and the ADGrestrict line was selected for ADG under restricted feeding (-20% of voluntary intake). The first objective of this study was to evaluate, after 9 genera...
N° de la demande internationale : PCT/FR2015/052585
Procédé de régulation de l'activité d'un dispositif électrochimique comportant une bioanode et une biocathode plongées dans un électrolyte (10A, 10C) contenant des microorganismes, les compartiments anodique et cathodique étant séparés par au moins une membrane, éventuellement une électrode de référence, une différence de potentiel étant appliquée...
Two parallel anaerobic digestion lines were designed to match a "bovid-like" digestive structure. Each of the lines consisted of two Continuous Stirred Tank Reactors placed in series and separated by an acidic treatment step. The first line was inoculated with industrial inocula whereas the second was seeded with cow digestive tract contents. After...
The better understanding of the functioning of microbial communities is a challenging and crucial issue in the field of food microbiology, as it constitutes a prerequisite to the optimization of positive and technological microbial population functioning, as well as for the better control of pathogen contamination of food. Heterogeneity appears now...
Bioanodes were formed under constant polarization at -0.2V/SCE from fermented sewage sludge. Current densities reached were 9.3±1.2Am(-2) with the whole fermented sludge and 6.2±0.9Am(-2) with the fermented sludge supernatant. The bioanode kinetics was analysed by differentiating among the contributions of the three redox systems identified by volt...
The long-term operation of efficient bioanodes supplied with waste‑derived organics is a key challenge for using bioelectrochemical systems as a waste valorization technology. Here, we describe a simple procedure that allowed maintaining highly efficient bioanodes supplied with biowaste. Current densities up to 14.8 A/m2 were obtained with more tha...
Oxygen reducing biocathodes were formed from sludge under constant polarization at -0.2 and +0.4V/SCE. Under chronoamperometry at pH10.3±0.3, current densities of 0.21±0.03 and 0.12±0.01Am(-2) were displayed at -0.2V/SCE by the biocathodes formed at -0.2 and 0.4V/SCE, respectively. Voltammetry revealed similar general characteristics for all biocat...
Ammonia inhibition represents a major operational issue for anaerobic digestion. In order to refine our understanding of the terminal catabolic steps in thermophilic anaerobic digestion under ammonia stress, we studied batch thermophilic acetate fed experiments at low (0.26 g L(-1)) and high (7.00 g L(-1)) Total Ammonia Nitrogen concentrations (TAN...
A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolat...
Bioelectrochemical systems (BES) have gained a lot of attention in recent years as a promising technology to convert organic matters to electricity, to hydrogen or to transform CO2 to platform molecules. All these applications rely on the use of electrochemically active microorganisms (EAM) growing on the anode surface and able to oxidize organic m...
Genomes of two nondomesticated strains of Bacillus subtilis subspecies subtilis, NDmed and NDfood, have been sequenced. Both strains form very thick and spatially complex biofilms on submerged surfaces.
Moreover, biofilms of the NDmed isolate were shown to be highly resistant to antimicrobials action.
Bioelectrochemical systems (BES) as microbial fuel cells take advantages of microorganisms to convert the chemical energy of organic waste into electricity. Recently, the discovery that BES can also be used for the synthesis of biocommodities via microbial electrosynthesis (MES) has greatly expanded the horizons for their applications. Indeed, some...
The removal of the total organic load (COD) from urban wastewater was studied in different bio-electrochemical systems (BES): microbial electrolysis, microbial fuel cell (MFC), and microbial electrochemical snorkel (MES). Here is presented the concept of MES [1], a simplified design of a “short-circuited” MFC.
The MES cannot provide current but it...
A model-based approach was developed to detect interspecific interactions during biofilm development. This approach relied on the comparison of experimental data with a simple null model of biofilm growth dynamics where individual species grew independently of one another, except that they competed for space. Such a model was directly parameterized...
Clones of the WWE1 (Waste Water of Evry 1) candidate division were retrieved during the exploration of the bacterial diversity of an anaerobic mesophilic (35 ± 0.5°C) digester. In order to investigate the metabolic function of WWE1 members, a 16S rRNA gene -based stable isotope probing (SIP) method was used. Eighty-seven percent of 16S r rRNA gene...
Procédé de production d'éthanol à partir de déchets organiques renfermant des matières biodégradables, telles que des matières fermentescibles et des matières lignocellulosiques caractérisé en ce qu'il comporte les étapes successives suivantes : - placement une quantité de déchets organiques renfermant des matières biodégradables, telles que des ma...
Cellulose hydrolysis often limits the kinetics and efficiency of anaerobic degradation in industrial digesters. In animal digestive systems, specialized microorganisms enable cellulose biodegradation at significantly higher rates. This study aims to assess the potential of ruminal microbial communities to settle and to express their cellulolytic pr...
In order to identify the function of uncultured microorganisms in their environment, the SIMSISH method, combining in situ hybridization (ISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) imaging, has been proposed to determine the quantitative uptake of specific labelled substrates by uncultured microbes at the single cell level. This...
Municipal solid waste (MSW) biodegradable fraction is mainly composed of lignocellulosic materials in more developed countries, which can be exploited during anaerobic treatment processes. This renewable energetic material is however recalcitrant to degradation due to its insolubility and a highly complex and heterogeneous structure. Existing MSW m...
Biodegradation of 13C6-phenol until mineralisation was observed under mesophilic and thermophilic conditions during the degradation of municipal solid waste. In Mesophilic conditions, as well as in thermophilic, two types of degradation kinetics were obtained. One follows a first order kinetic and the other follows a lag-phase model. The pyrosequen...
13th World Congress on Anaerobic Digestion : Recovering (bio) Ressources for the World, Santiago de Compostella, ESP, 25-/06/2013 - 28/06/2013
Microbes are the most abundant living forms on earth and major contributors to the biogeochemical cycles. However, our ability to model their dynamics only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. Preeminent physicists such as Schrödinger and Prigogine have introduc...
Use of fluorescence excitation–emission spectroscopy as a complementary tool to evaluate the biological stability of municipal solid waste (MSW) during anaerobic degradation was investigated, and whether correlation between the stability of MSW and fluorescence spectroscopic analysis of leachate can be established. In this study, excitation–emissio...
Microbes are the most abundant living forms on earth and major contributors to the biogeochemical cycles. However, our ability to model their dynamics only relies on empirical laws, fundamentally restricting our understanding and predictive capacity in many environmental systems. Preeminent physicists such as Schrödinger and Prigogine have introduc...
Depuis le début du XXe siècle, l’homme exploite l’extraordinaire machinerie biogéochimique des biofilms microbiens pour intensifier l’épuration et le recyclage de la matière organique dans les stations d’épuration et les digesteurs de déchets. Les chercheurs utilisent désormais de nouveaux outils pour comprendre l’écologie de ces précieux alliés mi...
Le stockage de déchets en Installation de stockage de déchets ultimes non dangereux (ISDUND) est un maillon indispensable de la gestion de nos flux de déchets. Dans ces déchets, bien que les filières de valorisation de la matière organique et les filières de recyclage se développent, il reste toujours une part importante de déchets biodégradables....
Oxygen reducing microbial cathodes were made from garden compost leachate, under polarization at two different potentials, -0.4 V and +0.1 V versus SCE and characterized by chronoamperometry and cyclic voltammetry. Two redox systems were identified in the biofilms formed at +0.1 V but only one in the biofilms formed at -0.4 V. Analysis of the bacte...
Depuis le début du XXe siècle, l’homme exploite l’extraordinaire machinerie biogéochimique des biofilms microbiens pour intensifier l’épuration et le recyclage de la matière organique dans les stations d’épuration et les digesteurs de déchets. Les chercheurs utilisent désormais de nouveaux outils pour comprendre l’écologie de ces précieux alliés mi...
In this paper, the isotopic tracing using (13)C-labeled phenol and bisphenol A was used to study their biodegradation during anaerobic digestion of municipal solid waste. Microcosms were incubated anaerobically at 35°C (mesophilic conditions) and 55°C (thermophilic conditions) without steering. A continuous follow-up of the production of biogas (CH...
The goal of this study is to evaluate the impact of the inoculum to substrate ratio (I/S) on the anaerobic degradation potential of municipal solid waste (MSW). Reconstituted MSW samples were thus incubated under batch anaerobic conditions and inoculated with an increasing amount of inoculum originating from a mesophilic sludge digester. I/S tested...
Les géosynthétiques sont de plus en plus utilisés pour renforcer les barrières d'étanchéité des installations de stockage des déchets non dangereux. Afin de réduire l'impact environnemental des installations, les utilisateurs de ces matériaux ont donc besoin de guides et de recommandations sur leur mise en ½uvre délicate, mais également d'estimatio...
In a model study, polyethylene was preoxidized and incubated for a period of 7 months at 40°C in two different municipal solid waste leachates. During the postexperimental analyses, specific attention was paid to the carbonyl species and carboxylic acid depletion during the environmental exposure because it is well known that carboxylic acids are b...
Municipal solid waste (MSW) methanization is promising as it enables mass reduction of waste and methane recovery. Methanization has been implemented at the industrial level for decades, in particular on liquid effluents. However, solid waste substrates raise specific issues; process and performance optimization is still required. In the present wo...
