Biomass Depolymerization projects
Thermophilic Filamentous Fungi and Yeasts from Compost and Sugarcane Bagasse
This project investigates cellulose degrading enzyme activity of mesophilic fungi that actively bioconvert plant cell wall material. Enzymes secreted by these fungi are being characterized using nucleotide sequence of their transcriptome and mass spectroscopy of their secreted proteins. To recover fungi, an approach is used that recovers one colony-forming unit (CFU) per micro-well, and this approach is being modified to work at high temperature throughout the process. Promising theromphilic fungi enzyme activity will be assayed and the secretomes of the thermophiles described. These fungi are not sought for their enzymes, but as thermophilic agents of biofuel production, and as thermophilic hosts for engineered biofuel production (started in 2012).
Sugarcane bagasse compost samples at 50°C were collected from Florida’s sugarcane refineries in October 2013 and January 2014, then processed to isolate thermotolerant and thermophillic fungi. Several samples of the thermotolerant yeast Kluyveromyces marxianus were successfully isolated. Preliminary yeast phenotype characterization suggested several distinct strains representative of a natural population. Genomic DNA was collected from 57 yeast samples and submitted for whole genome sequencing. The combination of genomes and growth phenotype data for thermotolerance, inhibitor and ethanol tolerance, and carbon preference will be used to conduct a genome-wide association study matching phenotypes with their genetic basis. More thermophilic filamentous fungi were collected from compost in Watsonville, CA and assessed for lignocellulose degradation abilities.
Our project has two parts. The first aims to find genes responsible for traits important to biofuels production for thermophilic yeasts. To match genes with traits, we will conduct a genome-wide association study to associate genetic variation in Kluyveromyces marxianus and Pichia occidentalis (Issatchenkia orientalis) with phenotypic variation. The second aims to find secreted proteins useful to the bioconversion of lignocellulosic feedstock from mesophilic fungi that decay Miscanthus or sugarcane in nature or from thermophilic fungi cultivated from straw compost or sugarcane bagasse.
Published in 2013
Fungal Systematics: Is a New Age of Enlightenment at Hand? David S. Hibbett, John W. Taylor, Nature Reviews Microbiology, doi: 10.1038/nrmicro2963, February 2013.