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163 results on '"Bouchez, Théodore"'

25. Study of a Pilot Scale Microbial Electrosynthesis Reactor for Organic Waste Biorefinery.

Author

Tian, Jiang-Hao, Lacroix, Rémy, Yaqoob, Asim Ali, Bureau, Chrystelle, Midoux, Cédric, Desmond-Le Quéméner, Elie, and Bouchez, Théodore

Subjects
ELECTROSYNTHESIS, ELECTROLYTIC cells, CHEMICAL oxygen demand, STANDARD hydrogen electrode, WASTE products, ORGANIC wastes
Abstract

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 goals. However, the long-term viability of bioanode activity might become a major concern. In this work, a 15-L MES reactor was designed with specific electrode configurations. An electrochemical model was established to assess the feasibility and possible performance of the design, considering the aging of the bioanode. The reactor was then constructed and tested for performance as well as a bioanode regeneration assay. Biowaste from an industrial deconditioning platform was used as a substrate for bioanode. The chemical oxygen demand (COD) removal rate in the anodic chamber reached 0.83 g day−1 L−1 of anolyte. Acetate was produced with a rate of 0.53 g day−1 L−1 of catholyte, reaching a maximum concentration of 8.3 g L−1. A potential difference (from 0.6 to 1.2 V) was applied between the bioanode and biocathode independent of reference electrodes. The active biocathode was dominated by members of the genus Pseudomonas, rarely reported so far for MES activity. [ABSTRACT FROM AUTHOR]

Published
2023
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27. Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics.

Author

Ngo, Vuong Quoc Hoang, Enault, François, Midoux, Cédric, Mariadassou, Mahendra, Chapleur, Olivier, Mazéas, Laurent, Loux, Valentin, Bouchez, Théodore, Krupovic, Mart, and Bize, Ariane

Subjects
METHANOGENS, STABLE isotopes, METAGENOMICS, CARBON cycle, BIOCONVERSION, VIRAL genomes, VIRUS-like particles
Abstract

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 between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head‐tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near‐complete genomes of spindle‐shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head‐tailed virus‐like particles and the presence of spindle‐shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens. [ABSTRACT FROM AUTHOR]

Published
2022
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28. Comparison of conventional and new energy-based models for modeling activated sludge dynamics

Author

Katipoglu-Yazan, Tugce, Delattre, Hadrien, Bouchez, Théodore, Filali, Ahlem, Filali, Ahlem, Procédés biotechnologiques au service de l'environnement (UR PROSE), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, ComputingMilieux_MISCELLANEOUS, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract

International audience

Published
2021

37. Feedback on a c omparative metatranscriptomic analysis

Author

Midoux, Cédric, Delforno, Tiago P., Macedo, Thais Z., Lacerda, Gileno V., Rué, Olivier, Mariadassou, Mahendra, Varesche, Maria B.A., Bouchez, Théodore, Bize, Ariane, Oliveira, Valéria M., Loux, Valentin, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), University of Campinas, Universidade de São Paulo (USP), and Société Française de Bio-Informatique (SFBI). FRA.

Subjects
[SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math]
Abstract

National audience; The progress of next generation sequencing favors the development of more comprehensive ecosystem studies thanks to metatranscriptomic approaches. These latter can indeed provide access to functional information at a good analysis depth. Through a study of anaerobic digesters treating anionic surfactant contaminated wastewater [1] (namely the linear alkylbenzene sulfonate, LAS), we developed a bioinformatics pipeline to perform the RNAseq data analysis for shotgun metatranscriptomics data.In this pipe-line, the raw data are cleaned and pre-processed. Reads corresponding to rRNA are detected and discarded from the datasets. After a normalization step based on k-mer counts, the mRNA reads from the datasets are de novo co-assembled using the Trinity software. Coding regions of the metatranscriptomic assembly are subsequently predicted and annotated. For functional annotation, sequences with matches to the eggNOG and KEGG GENES databases are retrieved to establish functional categories and reconstruct the metabolic pathways. For taxonomic classification, the sequences are assigned by comparing them to a NCBI-nr database. For each dataset individually, reads are mapped back to the co-assembled contigs. Eventually, a count table is constructed; it contains, for each predicted gene, the counts obtained by samples, as well as the associated taxonomic and functional annotations.After aggregation and statistical analysis, this study enabled detecting active genes likely involved in each step of LAS biodegradation and exploring the microbial active core related to LAS degradation.We developed a bioinformatics pipeline to perform the RNAseq data analysis for shotgun metatranscriptomics data, through a study of anaerobic digesters treating anionic surfactant contaminated wastewater.In this pipeline, the raw data are cleaned and pre-processed. Reads corresponding to rRNA are detected and discarded from the datasets. After a normalization step based on k-mer counts, the mRNA reads from the datasets are de novo co-assembled. Coding regions of the metatranscriptomic assembly are subsequently predicted and annotated. Taxonomic and functional annotations are obtained by comparison to public reference databases. The latter are used to define functional categories and reconstruct metabolic pathways. For each dataset individually, reads are mapped back to the co-assembled contigs. Finally, a count table is constructed; it contains, for each predicted gene, the counts obtained by samples, as well as the associated taxonomic and functional annotations.After aggregation and statistical analysis, this study enabled detecting active genes likely involved in each step of the anionic surfactant degradation and exploring the associated microbial activse core.

Published
2019

38. Towards environmental biorefinery: upscaling of microbial electrosynthesis cell fueled with heterogeneous organic waste

Author

Tian, Jiang-Hao, Desmond-Le Quéméner, Elie, Bouchez, Théodore, Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), and International Water Association (IWA). INT.

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, anerobic process, micoribla electrosynthesis, ComputingMilieux_MISCELLANEOUS, environmental biorefinery
Abstract

International audience

Published
2019

39. Modeling an environmental biorefinery scenario with anaerobic digestion coupled to bioelectrosynthesis: analyzing the requirements for profitability

Author

Moscoviz, Roman, Huyard, Alain, Desmond-Le Quéméner, Elie, Tian, Jiang-Hao, Bouchez, Théodore, Crest, Marion, SUEZ, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), and International Water Association (IWA). INT.

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

42. Easy16S : a user-friendly Shiny interface for analysis and visualization of metagenomic data

Author

Midoux, Cedric, Rué, Olivier, Chapleur, Olivier, Mariadassou, Mahendra, Bouchez, Théodore, Loux, Valentin, Bize, Ariane, Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), and Société Française de Bio-Informatique (SFBI). FRA.

Subjects
[SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

44. Results from a French Inter‐laboratory Campaign on the Biological Methane Potential of Solid Substrates

Author

Cresson, Romain, Pommier, Sébastien, Beline, Fabrice, Bouchez, Théodore, Bougrier, Claire, Buffière, Pierre, Pauss, André, Pouech, Philippe, Preys, S., Ribeiro, Thierry, Rouez, Maxime, Torrijos, Michel, INRA Transfert Environnement, INRA Transfert, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Hydrosystèmes et bioprocédés (UR HBAN), Veolia Recherche et Innovation, Veolia France, Déchets Eaux Environnement Pollutions (DEEP), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Transformation Intégrée de la Matière Renouvelable (TIMR), Université de Technologie de Compiègne (UTC), APESA, Département R&D Ondalys, Ondalys, Institut Polytechnique LaSalle Beauvais, CIRSEE, Suez Environnement, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA), CRITT GENIE DES PROCEDES ET TECHNOLOGIES ENVIRONNEMENTALES TOULOUSE FRA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Gestion environnementale et traitement biologique des déchets (UR GERE), Hydrosystèmes et Bioprocédés (UR HBAN), Veolia Environnement (FRANCE), APESA PAU FRA, SUEZ ENVIRONNEMENT LE PECQ FRA, INRA Transfert Environnement [Narbonne], Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Centre International de Recherche Sur l'Eau et l'Environnement [Suez] (CIRSEE), SUEZ ENVIRONNEMENT (FRANCE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Veolia Recherche & Innovation (VeRI)

Subjects
[CHIM.GENI]Chemical Sciences/Chemical engineering, [SDE.IE]Environmental Sciences/Environmental Engineering, [SDE]Environmental Sciences, BMP, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, POTENTIEL METHANOGENE, ComputingMilieux_MISCELLANEOUS, SUBSTRAT SOLIDE
Abstract

International audience; A French inter-laboratory campaign on BMP assessment was realised in two phases: free protocol at first, then harmonized protocol. Results show good intra-laboratory repeatability and reproducibility, but in spite of an attempt in the harmonization of practices, the inter-laboratoryreproducibility could not be improved and ranges in the magnitude of 20% RSD.

Published
2015

47. How animals can help us on anaerobic digestion? The microbial and process engineering points of view

Author

Godon, Jean-Jacques, Arcemisbehere, Laure, Hamelin, Jérôme, Escudié, Renaud, Bouchez, Théodore, Guillot, Alain, Li, Tianlun, Miambi, Edouard, Robert, Alain, Steyer, Jean-Philippe, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Hydrosystèmes et bioprocédés (UR HBAN), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
anaerobic digestion, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, digestive system, methane, microbial diversity, organic matter
Abstract

Over the last decade, pre-treatment and even anaerobic co-digestion strategies have emerged in order to make organic matter more accessible. However, these technologies have been reached less than 60% degradation/conversion of organic matter to methane. In comparison, over millions of years, living organisms have explored and optimized the digestion of a wide variety of substrates with high yields (> 70%). The aim of the study is the analysis of natural innovation in animal digestive tracts in order to improve anaerobic digestion processes. The approach consists of a large descriptive inventory of animal digestive tracts. Animals (vertebrates, arthropods, molluscs, etc.) use all types of organic matter as food. Moreover over evolutionary time, organisms become more and more specialized and use only specific type of food (leaves, seed, meat, bones, faeces, etc.). In parallel, the digestive systems evolve to optimize the nutrient recovery. Each animal species domesticates its own microbe consortium and develops its own digestive tract structure. The digestive systems can be seen as a microbial reactor with abiotic pre- and/or post-treatments. When considering their functions, physiological compartments can be imagined as reactors. Thus, continuous stirred-tank reactors, continuous stirred-tank reactors in series, plug-flow reactors, and batch reactors can be used to model the function of these compartments. In this paper, we relate animal size, animal phylogeny and the feeding habit (carnivorous, omnivorous, granivorous, herbivorous) to the type and the position of microbial compartment with respect to the abiotic compartments within the digestive tract. We also relate the role of these parameters on the microbial diversity within the microbial compartment. The results show that (i) the feeding habit determines the type of microbial reactor and its position within the digestive tract; (ii) the phylogeny of the animal determines the type of abiotic pre- and/or post-treatment; (iii) finally, the size of the animal determines the level of diversity of the microbial communities.

Published
2011

48. Biomimicry in anaerobic digestion of biological sludge

Author

Godon, Jean-Jacques, Arcemisbehere, Laure, Escudie, Renaud, Bouchez, Théodore, Guillot, Alain, Li, T.T., Miambi, E., Robert, A., Steyer, Jean-Philippe, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biogéochimie et écologie des milieux continentaux (Bioemco), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Hydrosystèmes et bioprocédés (UR HBAN), and Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Paris (ENS Paris)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, ANAEROBIC DIGESTION, BIOMIMETISME, DIGESTIVE TRACT, BIOMIMICRY
Abstract

absent

Published
2011

49. Combined eukaryotic and bacterial community fingerprinting of natural freshwater biofilms using automated ribosomal intergenic spacer analysis

Author

Fechner, Lise, Vincent-Hubert, Françoise, Gaubert, Philippe, Bouchez, Théodore, Gourlay-Francé, Catherine, Tusseau-Vuillemin, Marie-Hélène, Hydrosystèmes et Bioprocédés (UR HBAN), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Hydrosystèmes et bioprocédés (UR HBAN), Sorbonne Université (SU)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Institut de Recherche pour le Développement (IRD)

Subjects
Diatoms, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, eukaryotic community, Bacteria, Population Dynamics, Fungi, Fresh Water, Sequence Analysis, DNA, freshwater periphyton, DNA Fingerprinting, bacterial community, RNA, Ribosomal, 5.8S, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biofilms, ARISA, DNA, Ribosomal Spacer, Ciliophora, Water Microbiology, Ecosystem, Phylogeny, DNA Primers
Abstract

[Departement_IRSTEA]Eaux [TR1_IRSTEA]BELCA; International audience; Biofilms are complex communities playing an important role in aquatic ecosystems. Automated ribosomal intergenic spacer analysis (ARISA) has been used successfully to explore biofilm bacterial diversity. However, a gap remains to be filled as regards its application to biofilm eukaryotic populations. The aim of this study is to use ARISA to detect eukaryotic population shifts in biofilm. We designed a new set of primers to focus specifically on the ITS1-5.8S-ITS2 region of diatoms and tested it on natural biofilms. Additionally, we tested universal primers, used previously to perform ARISA on fungal communities. Cloning and sequencing showed that the universal primer set amplified various eukaryotes, whereas the new set was diatom specific. The new set amplified a wider variety of diatoms. Therefore, the universal set is appropriate to study the general eukaryotic population shifts in biofilms, whereas the new set is more appropriate to study diatoms specifically. We used both primer sets, along with a bacterial set, to study the population shifts in natural river biofilms. Principal component analysis of the ARISA fingerprints revealed seasonal shifts that did not coincide for bacterial and eukaryotic communities. Therefore, the use of both eukaryotic and bacterial primers provides a useful insight to assess microbial succession in biofilms.

Published
2010

50. Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties.

Author

Badalato, Nelly, Guillot, Alain, Sabarly, Victor, Dubois, Marc, Pourette, Nina, Pontoire, Bruno, Robert, Paul, Bridier, Arnaud, Monnet, Véronique, Sousa, Diana Z., Durand, Sylvie, Mazéas, Laurent, Buléon, Alain, Bouchez, Théodore, Mortha, Gérard, and Bize, Ariane

Subjects
PROTEOMICS, CELLULOSE, SOLID waste, ANAEROBIC digestion, CELLULOLYTIC bacteria
Abstract

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 handkerchief, cotton discs and Whatman filter paper. Fermentation of paper handkerchief occurred the fastest and resulted in a specific metabolic profile: it resulted in the lowest acetate-to-lactate and acetate-to-ethanol ratios. By shotgun proteomic analyses of paper handkerchief and Whatman paper incubations, 151 proteins with significantly different levels were detected, including 20 of the 65 cellulosomal components, 8 non-cellulosomal CAZymes and 44 distinct extracytoplasmic proteins. Consistent with the specific metabolic profile observed, many enzymes from the central carbon catabolic pathways had higher levels in paper handkerchief incubations. Among the quantified CAZymes and cellulosomal components, 10 endoglucanases mainly from the GH9 families and 7 other cellulosomal subunits had lower levels in paper handkerchief incubations. An in-depth characterization of the materials used showed that the lower levels of endoglucanases in paper handkerchief incubations could hypothetically result from its lower crystallinity index (50%) and degree of polymerization (970). By contrast, the higher hemicellulose rate in paper handkerchief (13.87%) did not result in the enhanced expression of enzyme with xylanase as primary activity, including enzymes from the “xyl-doc” cluster. It suggests the absence, in this material, of molecular structures that specifically lead to xylanase induction. The integrated approach developed in this work shows that subtle differences among cellulosic materials regarding chemical and structural characteristics have significant effects on expressed bacterial functions, in particular the cellulolysis machinery, resulting in different metabolic patterns and degradation dynamics. [ABSTRACT FROM AUTHOR]

Published
2017
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