Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes

The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional...

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Bibliographic Details
Published in:Applied and environmental microbiology 2016-01, Vol.82 (2), p.528-537
Main Authors: Forsberg, Kevin J, Patel, Sanket, Witt, Evan, Wang, Bin, Ellison, Tyler D, Dantas, Gautam
Format: Article
Language:English
Subjects:
Bacteria - classification
Bacteria - genetics
Bacteria - isolation & purification
Bacteria - metabolism
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biotechnology
Catalysts
Deoxyribonucleic acid
DNA
Fermentation
Genes
Lignin
Lignin - metabolism
Lignocellulose
Metagenome
Soil - chemistry
Soil Microbiology
Toxicity
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Summary:The production of fuels or chemicals from lignocellulose currently requires thermochemical pretreatment to release fermentable sugars. These harsh conditions also generate numerous small-molecule inhibitors of microbial growth and fermentation, limiting production. We applied small-insert functional metagenomic selections to discover genes that confer microbial tolerance to these inhibitors, identifying both individual genes and general biological processes associated with tolerance to multiple inhibitory compounds. Having screened over 248 Gb of DNA cloned from 16 diverse soil metagenomes, we describe gain-of-function tolerance against acid, alcohol, and aldehyde inhibitors derived from hemicellulose and lignin, demonstrating that uncultured soil microbial communities hold tremendous genetic potential to address the toxicity of pretreated lignocellulose. We recovered genes previously known to confer tolerance to lignocellulosic inhibitors as well as novel genes that confer tolerance via unknown functions. For instance, we implicated galactose metabolism in overcoming the toxicity of lignin monomers and identified a decarboxylase that confers tolerance to ferulic acid; this enzyme has been shown to catalyze the production of 4-vinyl guaiacol, a valuable precursor to vanillin production. These metagenomic tolerance genes can enable the flexible design of hardy microbial catalysts, customized to withstand inhibitors abundant in specific bioprocessing applications.
ISSN:0099-2240
1098-5336
DOI:10.1128/AEM.02838-15