Title: Metatranscriptomic analysis of lignocellulolytic microbial communities involved in high-solids decomposition of rice straw

Abstract

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. 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 themore » 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. In conclusion, 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. Furthermore, 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.« less

Authors:

Simmons, Christopher W. ^[1]; Reddy, Amitha P. ^[1]; D’haeseleer, Patrik ^[2]; Khudyakov, Jane ^[2]; Billis, Konstantinos ^[3]; Pati, Amrita ^[3]; Simmons, Blake A. ^[4]; Singer, Steven W. ^[5]; Thelen, Michael P. ^[2]; VanderGheynst, Jean S. ^[1]

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+ Show Author Affiliations

1. Joint BioEnergy Institute, Emeryville, CA (United States); Univ. of California, Davis, CA (United States)
2. Joint BioEnergy Institute, Emeryville, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
3. Joint Genome Institute, Walnut Creek, CA (United States)
4. Joint BioEnergy Institute, Emeryville, CA (United States); Sandia National Lab. (SNL-CA), Livermore, CA (United States)
5. Joint BioEnergy Institute, Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Publication Date:

Wed Dec 31 00:00:00 EST 2014

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER); UC Office of the President; USDOE National Nuclear Security Administration (NNSA)

OSTI Identifier:

1257270

Alternate Identifier(s):

OSTI ID: 1860859

Report Number(s):

LLNL-JRNL-831202
Journal ID: ISSN 1754-6834; PII: 180

Grant/Contract Number:  

AC02-05CH11231; 237496; AC52-07NA27344

Resource Type:

Accepted Manuscript

Journal Name:

Biotechnology for Biofuels

Additional Journal Information:

Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 1754-6834

Publisher:

BioMed Central

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; lignocellulose deconstruction; solid-state culture; microbial communities; biofuels; cellulase; glycoside hydrolase family 48; carbohydrate binding module family 2; carbohydrate binding module family 33