Investigation of anaerobic lignocellulose decomposition in Puerto Rico tropical forest soils
EMSL Project ID
40102
Abstract
As one of the primary objectives of the DOE Joint BioEnergy Institute (JBEI), our project aims to identify and characterize unique microorganisms, enzymes and pathways with novel lignocellulolytic activities from tropical rain forest soil. Our proposal includes use of EMSL resources including NMR-based metabolomics, transcriptomics, MS proteomics, flow cytometry and cell sorting, and will integrate these sophisticated analyses to comprehensively understand the molecular basis for lignin and lignocellulose deconstruction by microbial communities. Our studies focus on Puerto Rico soils at the El Yunque Experimental Forest (US Forest Service), an NSF-sponsored long-term ecological research (LTER) site, where we are able to take advantage of a long history of research in decomposition and forest ecology, as well as tropical forest ecology experts at University of California, Berkeley and at the US Forest Service in Puerto Rico. Our current research projects entail three main research thrusts: 1: anaerobic microbial isolates able to grow on lignin as a sole carbon source; 2: feedstock-adapted consortia selected for mesophilic, anaerobic growth on extracted switchgrass (twice extracted with water and ethanol to remove labile sugars) as a sole carbon source; and 3: a large-scale field decomposition experiment, where we are following a time course of switchgrass (Panicum virgatum) decomposition in Puerto Rico along an elevational and rainfall gradient that spans soils that are mostly aerobic, to fluctuating redox potential, to mostly anaerobic.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2010-10-01
End Date
2013-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
DeAngelis KM, D Sharma, R Varney, BA Simmons, NG Isern, LM Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, and EW Robinson. 2013. "Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1." Frontiers in Microbiology 4:Article No. 280.
DeAngelis KM, JL Fortney, S Borglin, W Silver, BA Simmons, and TC Hazen. 2012. "Anaerobic Decomposition of Switchgrass by Tropical Soil-Derived Feedstock-Adapted Consortia." mBio 3(1):, doi:10.1128/?mBio.00249-11
DeAngelis KM, M Allgaier, Y Chavarria, JL Fortney, P Hugenholtz, BA Simmons, K Sublette, W Silver, and TC Hazen. 2011. "Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil." PLoS One 6(4):e19306. doi:10.1371/journal.pone.0019306
DeAngelis KM, P D'Haeseleer, D Chivian, JL Fortney, JI Khudyakov, BA Simmons, H Woo, AP Arkin, KW Davenport, LA Goodwin, A Chen, N Ivanova, NC Kyrpides, K Mavromatis, T Woyke, and TC Hazen. 2011. "Complete genome sequence of “Enterobacter lignolyticus” SCF1." Standards in Genomic Sciences 5(1):69-85. doi:10.4056/sigs.2104875
DeAngelis KM, W Silver, A Thompson, and MK Firestone. 2010. "Microbial communities acclimate to recurring changes in soil redox potential status." Environmental Microbiology 12(12):3137-3149. doi:10.1111/j.1462-2920.2010.02286.x
Orellana, Roberto, Gina Chaput, Lye Meng Markillie, Hugh Mitchell, Matt Gaffrey, Galya Orr, and Kristen M. DeAngelis. "Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium." PloS one 12, no. 10 (2017): e0186440.