Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community

Allagier, Martin, Reddy, Amitha, Park, Joshua I., Ivanova, Natalia, D'haeseleer, Patrik, Lowry, Steve, Sapra, Rajat, Hazen, Terry C., Simmons, Blake A., VanderGheynst, Jean S. and Hugenholtz, Philip (2010) Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community. PLoS One, 5 1: e8812-1-e8812-9. doi:10.1371/journal.pone.0008812

Author Allagier, Martin
Reddy, Amitha
Park, Joshua I.
Ivanova, Natalia
D'haeseleer, Patrik
Lowry, Steve
Sapra, Rajat
Hazen, Terry C.
Simmons, Blake A.
VanderGheynst, Jean S.
Hugenholtz, Philip
Title Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2010-01-21
Sub-type Article (original research)
DOI 10.1371/journal.pone.0008812
Open Access Status DOI
Volume 5
Issue 1
Start page e8812-1
End page e8812-9
Total pages 9
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Collection year 2011
Language eng
Formatted abstract
Development of cellulosic biofuels from non-food crops is currently an area of intense research interest. Tailoring depolymerizing enzymes to particular feedstocks and pretreatment conditions is one promising avenue of research in this area. Here we added a green-waste compost inoculum to switchgrass (Panicum virgatum) and simulated thermophilic composting in a bioreactor to select for a switchgrass-adapted community and to facilitate targeted discovery of glycoside hydrolases. Small-subunit (SSU) rRNA-based community profiles revealed that the microbial community changed dramatically between the initial and switchgrass-adapted compost (SAC) with some bacterial populations being enriched over 20-fold. We obtained 225 Mbp of 454-titanium pyrosequence data from the SAC community and conservatively identified 800 genes encoding glycoside hydrolase domains that were biased toward depolymerizing grass cell wall components. Of these, ,10% were putative cellulases mostly belonging to families GH5 and GH9. We synthesized two SAC GH9 genes with codon optimization for heterologous expression in Escherichia coli and observed activity for one on carboxymethyl cellulose. The active GH9 enzyme has a temperature optimum of 50°C and pH range of 5.5 to 8 consistent with the composting conditions applied. We demonstrate that microbial communities adapt to switchgrass decomposition using simulated composting condition and that full-length genes can be identified from complex metagenomic sequence data, synthesized and expressed resulting in active enzyme.
Keyword Compost
Microbial community
Targeted discovery
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status Non-UQ
Additional Notes Article # e8812

Document type: Journal Article
Sub-type: Article (original research)
Collections: Non HERDC
School of Chemistry and Molecular Biosciences
Institute for Molecular Bioscience - Publications
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Created: Tue, 22 Mar 2011, 14:43:25 EST by Susan Allen on behalf of School of Chemistry & Molecular Biosciences