title: Specialized activities and expression differences for Clostridium thermocellum biofilm and planktonic cells.
abstract: Clostridium (Ruminiclostridium) thermocellum is a model organism for its ability to deconstruct plant biomass and convert the cellulose into ethanol. The bacterium forms biofilms adherent to lignocellulosic feedstocks in a continuous cell-monolayer in order to efficiently break down and uptake cellulose hydrolysates. We developed a novel bioreactor design to generate separate sessile and planktonic cell populations for omics studies. Sessile cells had significantly greater expression of genes involved in catabolism of carbohydrates by glycolysis and pyruvate fermentation, ATP generation by proton gradient, the anabolism of proteins and lipids and cellular functions critical for cell division consistent with substrate replete conditions. Planktonic cells had notably higher gene expression for flagellar motility and chemotaxis, cellulosomal cellulases and anchoring scaffoldins, and a range of stress induced homeostasis mechanisms such as oxidative stress protection by antioxidants and flavoprotein co-factors, methionine repair, Fe-S cluster assembly and repair in redox proteins, cell growth control through tRNA thiolation, recovery of damaged DNA by nucleotide excision repair and removal of terminal proteins by proteases. This study demonstrates that microbial attachment to cellulose substrate produces widespread gene expression changes for critical functions of this organism and provides physiological insights for two cells populations relevant for engineering of industrially-ready phenotypes.
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Alexandru
authors.initials: A
authors.lastname: Dumitrache
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Klingeman
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Jace
authors.initials: J
authors.lastname: Natzke
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rodriguez
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Giannone
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Brian H
authors.initials: BH
authors.lastname: Davison
authors.affiliation: BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, U.S.A.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
mesh_terms: D018441:Biofilms; D015415:Biomarkers; D018533:Biomass; D053898:Biosynthetic Pathways; D050260:Carbohydrate Metabolism; D048013:Acetivibrio thermocellus / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D004734:Energy Metabolism; D005285:Fermentation; D005786:Gene Expression Regulation; D015964:Gene Expression Regulation, Bacterial; D050356:Lipid Metabolism; D018384:Oxidative Stress; D010933:Plankton / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D013312:Stress, Physiological
chemical_list: D015415:Biomarkers