Basidiomycete Genomics

Wood decay fungi play a pivotal role in forest carbon cycling. Certain basidiomycetes, collectively referred to as white rot fungi, efficiently degrade all the major components of wood, including the recalcitrant lignin. Brown rot fungi are phylogenetically related but unable to remove lignin. The precise mechanisms of lignocellulose conversion by these fungi are uncertain. However, laboratory studies have implicated oxidative systems in lignin and cellulose depolymerization by white rot and brown rot fungi, respectively. Relatively few investigations have examined complex microbial communities in natural environments. Addressing this issue, we have initiated metagenome, metatranscriptome and, most recently, metaproteome analyses of decaying Pinus contorta wood and associated litter collected from the Bitterroot National Forest. Mass spectroscopy-based identification of proteins was restrained by the paucity of reference fungal genomes. However, protein databases derived from de novo transcriptome assemblies substantially increased the number of proteins identified. Among the enzymes detected in these preliminary studies were manganese dependent lignin peroxidase and glycoside hydrolases, all consistent with lignocellulose degradation. Systematic studies along these lines will contribute to our understanding of microbial communities and physiological processes involved in carbon conversions in forest systems. The investigations may also identify novel enzymes of value in plant cell wall bioprocessing.