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Understanding Biomass Conversion within Thermophilic Communities and Isolates


EMSL Project ID
40022

Abstract

Efficient deconstruction of lignocellulose into monomeric sugars is a key step in the development of renewable and sustainable liquid transportation fuels from biomass. The DOE Joint BioEnergy Institute (JBEI) is tasked with developing these advanced lignocellulosic biofuels. Part of this mission is to develop efficient methods to deconstruct biomass, by both gaining a more in-depth understanding of biomass degrading microbial communities, and identifying and charactering novel lignocellulolytic microorganisms and enzymes. Current deconstruction technologies typically rely on fungal glycosyl hydrolases that do not function effectively under the conditions required for enzymatic hydrolysis at an industrial scale. Enzymes derived from thermophilic bacteria are a potential resource for more robust enzymatic cocktails that can be used to deconstruct biomass at elevated temperatures or in the presence of residual chemicals and inhibitors from pre-treatment. Identifying glycosyl hydrolases expressed by thermophilic microbes that are grown on targeted biomass feedstocks is critical to developing these new cocktails.
To address this challenge, thermophilic bacterial communities derived from compost have been enriched on switchgrass at 55-60 degrees C in both liquid and solid state cultures. The composting process involves the synergistic decomposition of heterogeneous residues similar to feedstocks being considered for liquid fuel production. Therefore, compost microbial communities have evolved to decompose plant cell walls (lignocellulose). Furthermore, these communities can tolerate extremes in temperature, redox potential and water activity, and recover quickly from major environmental perturbations. Phylotype small subunit (SSU) rRNA gene analysis has demonstrated that the enriched microbial communities are simple microbial consortia consisting of 3-4 dominant species from the Firmicutes, Bacteriodetes, Chloroflexi and Gemmatimonadetes phyla in the liquid cultures and Firmicutes, Actinobacteria and Proteobacteria phyla in the solid-state cultures. From the liquid cultures, representative isolates for most of the dominant consortium members have been obtained. Secretome extracts obtained from both liquid and solid-state cultures have high levels of biomass-deconstructing hydrolytic activities when assayed with purified substrates and pre-treated biomass.
To understand the cellular responses of both the communities and isolates to growth on biomass, we will need to document the complement of proteins expressed on biomass substrates and understand whether post-translational modifications are important, especially for glycosyl hydrolases. In addition, proteomic measurements will be important in determining the differential responses of isolates to biomass substrates in comparison to closely related species living in a mixed microbial consortia. Coordinating the proteomics with detailed analysis of biomass deconstruction by these thermophilic enzymes deconstruct biomass, and how these enzymes can be utilized in a biorefinery setting.

Project Details

Project type
Large-Scale EMSL Research
Start Date
2010-10-01
End Date
2013-09-30
Status
Closed

Team

Principal Investigator

Steven Singer
Institution
Lawrence Berkeley National Laboratory

Team Members

Alyse Hawley
Institution
The University of British Columbia

Amitha Reddy
Institution
Joint BioEnergy Institute

Jean VanderGheynst
Institution
Joint BioEnergy Institute

John Gladden
Institution
Joint BioEnergy Institute

Blake Simmons
Institution
Lawrence Berkeley National Laboratory

Angela Norbeck
Institution
Environmental Molecular Sciences Laboratory

Samuel Purvine
Institution
Environmental Molecular Sciences Laboratory

David Brown
Institution
Environmental Molecular Sciences Laboratory

Related Publications

D'haeseleer P, JM Gladden, M Allgaier, P Chain, SG Tringe, S Malfatti, JT Aldrich, CD Nicora, EW Robinson, L Pasa-Tolic, P Hugenholtz, BA Simmons, and SW Singer. 2013. "Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass." PLoS One 8(7):e68465. doi:10.1371/journal.pone.0068465
Hiras J, YW Wu, K Deng, CD Nicora, JT Aldrich, D Frey, S Kolinko, EW Robinson, JM Jacobs, P Adams, TR Northen, BA Simmons, and SW Singer. 2016. "Comparative community proteomics demonstrates the unexpected importance of an actinobacterial glycoside hydrolase family 12 protein for crystalline cellulose hydrolysis." mBio 7(4):Article No. e01106-16. doi:10.1128/mBio.01106-16