Strategies for enhancing the effectiveness of metagenomic-based enzyme discovery in lignocellulytic microbial communities

Journal Article · Mon Mar 01 04:00:00 EST 2010 · The BioEnergy Research Journal

DOI:https://doi.org/10.1007/s12155-010-9089-z· OSTI ID:983017

DeAngelis, K M; Gladden, J G; Allgaier, M; D'haeseleer, P; Fortney, J L; Reddy, A; Hugenholtz, P; Singer, S W; Vander Gheynst, J; Silver, W L; Simmons, B; Hazen, T C

Producing cellulosic biofuels from plant material has recently emerged as a key U.S. Department of Energy goal. For this technology to be commercially viable on a large scale, it is critical to make production cost efficient by streamlining both the deconstruction of lignocellulosic biomass and fuel production. Many natural ecosystems efficiently degrade lignocellulosic biomass and harbor enzymes that, when identified, could be used to increase the efficiency of commercial biomass deconstruction. However, ecosystems most likely to yield relevant enzymes, such as tropical rain forest soil in Puerto Rico, are often too complex for enzyme discovery using current metagenomic sequencing technologies. One potential strategy to overcome this problem is to selectively cultivate the microbial communities from these complex ecosystems on biomass under defined conditions, generating less complex biomass-degrading microbial populations. To test this premise, we cultivated microbes from Puerto Rican soil or green waste compost under precisely defined conditions in the presence dried ground switchgrass (Panicum virgatum L.) or lignin, respectively, as the sole carbon source. Phylogenetic profiling of the two feedstock-adapted communities using SSU rRNA gene amplicon pyrosequencing or phylogenetic microarray analysis revealed that the adapted communities were significantly simplified compared to the natural communities from which they were derived. Several members of the lignin-adapted and switchgrass-adapted consortia are related to organisms previously characterized as biomass degraders, while others were from less well-characterized phyla. The decrease in complexity of these communities make them good candidates for metagenomic sequencing and will likely enable the reconstruction of a greater number of full length genes, leading to the discovery of novel lignocellulose-degrading enzymes adapted to feedstocks and conditions of interest.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
• Sponsoring Organization: Earth Sciences Division
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 983017
• Report Number(s): LBNL-3158E
• Journal Information: The BioEnergy Research Journal, Journal Name: The BioEnergy Research Journal Journal Issue: 2 Vol. 3; ISSN 1939-1234; ISSN 1939-1242
• Country of Publication: United States
• Language: English

Related Subjects

54 ENVIRONMENTAL SCIENCES
58 GEOSCIENCES
BIOFUELS
BIOMASS
CARBON SOURCES
COMMUNITIES
COMPOST
ECOSYSTEMS
EFFICIENCY
ENZYMES
FORESTS
GENES
LIGNIN
PRODUCTION
PUERTO RICO
RAIN
SOILS
WASTES