title: Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw.
abstract: BACKGROUND
  New lignocellulolytic enzymes are needed that maintain optimal activity under the harsh conditions present during industrial enzymatic deconstruction of biomass, including high temperatures, the absence of free water, and the presence of inhibitors from the biomass. Enriching lignocellulolytic microbial communities under these conditions provides a source of microorganisms that may yield robust lignocellulolytic enzymes tolerant to the extreme conditions needed to improve the throughput and efficiency of biomass enzymatic deconstruction. Identification of promising enzymes from these systems is challenging due to complex substrate-enzyme interactions and requirements to assay for activity. In this study, metatranscriptomes from compost-derived microbial communities enriched on rice straw under thermophilic and mesophilic conditions were sequenced and analyzed to identify lignocellulolytic enzymes overexpressed under thermophilic conditions. To determine differential gene expression across mesophilic and thermophilic treatments, a method was developed which pooled gene expression by functional category, as indicated by Pfam annotations, since microbial communities performing similar tasks are likely to have overlapping functions even if they share no specific genes.
  
  
  RESULTS
  Differential expression analysis identified enzymes from glycoside hydrolase family 48, carbohydrate binding module family 2, and carbohydrate binding module family 33 domains as significantly overexpressed in the thermophilic community. Overexpression of these protein families in the thermophilic community resulted from expression of a small number of genes not currently represented in any protein database. Genes in overexpressed protein families were predominantly expressed by a single Actinobacteria genus, Micromonospora.
  
  
  CONCLUSIONS
  Coupling measurements of deconstructive activity with comparative analyses to identify overexpressed enzymes in lignocellulolytic communities provides a targeted approach for discovery of candidate enzymes for more efficient biomass deconstruction. Glycoside hydrolase family 48 cellulases and carbohydrate binding module family 33 polysaccharide monooxygenases with carbohydrate binding module family 2 domains may improve saccharification of lignocellulosic biomass under high-temperature and low moisture conditions relevant to industrial biofuel production.
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Department of Food Science and Technology, University of California, Davis, CA 95616 USA.
authors: Christopher W
authors: CW
authors: Simmons
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA.
authors: Amitha P
authors: AP
authors: Reddy
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA.
authors: Patrik
authors: P
authors: D'haeseleer
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA.
authors: Jane
authors: J
authors: Khudyakov
authors: Joint Genome Institute, Walnut Creek, CA 94598 USA.
authors: Konstantinos
authors: K
authors: Billis
authors: Joint Genome Institute, Walnut Creek, CA 94598 USA.
authors: Amrita
authors: A
authors: Pati
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA 94551 USA.
authors: Blake A
authors: BA
authors: Simmons
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA.
authors: Steven W
authors: SW
authors: Singer
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA.
authors: Michael P
authors: MP
authors: Thelen
authors: Joint BioEnergy Institute, Emeryville, CA 94608 USA ; Department of Biological and Agricultural Engineering, University of California, One Shields Ave, Davis, CA 95616 USA.
authors: Jean S
authors: JS
authors: VanderGheynst
keywords: Biofuels; Carbohydrate binding module family 2; Carbohydrate binding module family 33; Cellulase; Glycoside hydrolase family 48; Lignocellulose deconstruction; Microbial communities; Solid-state culture
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