title: Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures.
abstract: Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity.
authors.affiliation: Department of Biotechnology, IFP Energies nouvelles, Rueil-Malmaison, France.
authors.forename: Senta
authors.identifier: http://orcid.org/0000-0001-8533-3274
authors.initials: S
authors.lastname: Heiss-Blanquet
authors.affiliation: Department of Biotechnology, IFP Energies nouvelles, Rueil-Malmaison, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Fayolle-Guichard
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.|INRA, AFMB, Marseille, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Lombard
authors.affiliation: Department of Biotechnology, IFP Energies nouvelles, Rueil-Malmaison, France.
authors.forename: Agnès
authors.initials: A
authors.lastname: Hébert
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.|INRA, AFMB, Marseille, France.
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.affiliation: Centre de Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Groppi
authors.affiliation: Centre de Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Barre
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.|INRA, AFMB, Marseille, France.|Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D018533:Biomass; D002480:Cellulase / Q000378:metabolism*; D002482:Cellulose / Q000378:metabolism*; D017753:Ecosystem; D006868:Hydrolysis; D008031:Lignin / Q000378:metabolism*; D054892:Metagenome / Q000235:genetics; D006109:Poaceae / Q000378:metabolism; D011134:Polysaccharides / Q000378:metabolism*; D032107:Populus / Q000378:metabolism; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology; D013379:Substrate Specificity; D013696:Temperature; D014908:Triticum / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D011134:Polysaccharides; D012987:Soil; C036909:lignocellulose; C007916:hemicellulose; D002482:Cellulose; D008031:Lignin; D002480:Cellulase