This study will explore the genetics of obligately symbiotic interactions between conifers (Pinaceae) and their host-specific ectomycorrhizal fungi in the mushroom genus Suillus, and their effects on ecological cycling of forest carbon. Using conifer seedlings experimentally inoculated with different Suillus species, we will employ integrated metatranscriptomic / metaproteomic/metabolomic approaches identify key fungal in EMF-Pinaceae roots… [Read More]

Climate change in the Arctic is progressing rapidly, and much of the focus, thus far, has been on permafrost thaw and the rapid mineralization of soil organic carbon (C) by soil microorganisms. However, climate change is also increasing the abundance of woody deciduous shrubs in the Arctic, altering the vegetative biochemical landscape, which could profoundly… [Read More]

Coniferous forests are widely distributed in temperate and boreal biomes and the fact that they efficiently store large stocks of carbon makes them globally important. Decomposer and mycorrhizal fungi are key players in the carbon and nitrogen cycles in this environment. Despite the recognition of potential effects of N availability on C cycle-related processes, detailed… [Read More]

This project aims to produce the first genome assembly of a cultivated sugarcane plant. To date no Saccharum species have been sequenced due to their large complex  polyploid genomes.  Cultivated sugarcane is grown throughout the tropics and sub tropic regions of the world and it produces 80% of the world’s sugar. Sugarcane is a C4 plant… [Read More]

This project aims to define gene function in rumen microbes to improve our knowledge of carbon (C) flow in the rumen, including the breakdown of lignocellulose, through the metabolism of substrates to volatile fatty acids (VFAs) and fermentation end products, to the final step of methane (CH4) formation. The project builds on the datasets and… [Read More]

This project would increase the sequence depth across a broader phylogenetic diversity of gymnosperms compared to previous focus on the Pinaceae. The specific transcriptomes and the genome targeted in this project would greatly accelerate our understanding of the functional and structural genomic underpinnings of the diverse secondary metabolic biosynthetic systems of these conifers, and facilitate… [Read More]

Bacteria and fungi that are intimately associated with plants comprise the plant microbiome . Interest in the role of these organisms in plant health and defense grows as research reveals the importance in modulating responses to defense and abiotic stress. Determining key and conserved nodes within the gene networks underlying these effects in a diverse… [Read More]

We will dissect the effects of fungi on post-fire soil carbon dynamics by using a systems biology approach that couples small experimental “pyrocosms”, genomics, amplicon metagenomics, transcriptomics, metatranscriptomics, and mass spectrometry. Proposer: Thomas Bruns, University of California, Berkeley [Read More]

The work continues and expands a previous effort carried out in collaboration with JGI. In the new efforts, we are taking both old and new populations through a total of at least 60 cycles of irradiation and outgrowth to achieve a level of radiation resistance that is the same or greater than that observed in… [Read More]

Here we propose to expand the search for new lineages of methanotrophs and methanogens by conducting multi-omic (DNA and RNA) sequencing in methane-rich environments enriched in uncultivated microbial “dark matter” (MDM). Specifically, we will focus on: 1) the distribution of methane metabolism in microbial dark matter; 2) capacity for facultative respiration in methanogenic archaea; 3)… [Read More]