Bioprospecting metagenomes: glycosyl hydrolases for converting biomass

Luen-Luen Li,Daniel Van Der Lelie,Safiyh Taghavi,Sebastien Monchy,Sean R Mccorkle

doi:10.1186/1754-6834-2-10

Abstract

Throughout immeasurable time, microorganisms evolved and accumulated remarkable physiological and functional heterogeneity, and now constitute the major reserve for genetic diversity on earth. Using metagenomics, namely genetic material recovered directly from environmental samples, this biogenetic diversification can be accessed without the need to cultivate cells. Accordingly, microbial communities and their metagenomes, isolated from biotopes with high turnover rates of recalcitrant biomass, such as lignocellulosic plant cell walls, have become a major resource for bioprospecting; furthermore, this material is a major asset in the search for new biocatalytics (enzymes) for various industrial processes, including the production of biofuels from plant feedstocks. However, despite the contributions from metagenomics technologies consequent upon the discovery of novel enzymes, this relatively new enterprise requires major improvements. In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. We also describe the unusual enzymes discovered via metagenomics approaches, and discuss the future prospects for metagenome technologies.

Highlights

In recent years, biofuels have attracted great interest as an alternative, renewable source of energy in the face of the ongoing depletion of fossil fuels, our energy dependence on them, and our growing environmental awareness of the critical consequences of burning such fuels
We have an incomplete understanding of the plant cell wall and its deconstruction and conversion; considerable research will be needed to better appreciate the fundamental and applied aspects of enzymatic hydrolysis and microbial hydrolysis and/or fermentation of plant cell walls
Metagenome samples taken from environments that are characterized by a steady input and turnover of complex plant cell wall biomass have an increased abundance of putative glycosyl hydrolases (GHase): the metagenomes from microbial communities derived from termite, human, and mouse guts displayed more putative GHase homologues than those from other samples, such as human oral microflora, uranium-contaminated groundwater or Singapore air sample

Summary

Background

Biofuels have attracted great interest as an alternative, renewable source of energy in the face of the ongoing depletion of fossil fuels, our energy dependence on them, and our growing environmental awareness of the critical consequences of burning such fuels. Metagenome samples taken from environments that are characterized by a steady input and turnover of complex plant cell wall biomass have an increased abundance of putative GHases: the metagenomes from microbial communities derived from termite, human, and mouse guts displayed more putative GHase homologues (approximately 1.5% total gene count) than those from other samples, such as human oral microflora, uranium-contaminated groundwater or Singapore air sample (approximately 0.3% total gene count) More innovative and sophisticated bioinformatics tools must be devised to assure continued valuable progress in the field of metagenomics

Conclusion

Findings

Himmel ME