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…
Tracking Coniferous Tree Root-Associated Microbial Activity
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…
The First Sugarcane Genome Sequence
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…
Gene Function in Rumen Microbes
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…
Exploring the “Gymnosperm Giga Genomes”
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…
Gene Network Regulation of Plants and Algae
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…
Genomics of Pyrophilous Fungi
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
Molecular Basis of Ionizing Radiation Resistance
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…
Mapping the Global Methanome
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)…
Metatranscriptome Analysis of Pinus Contorta
Woody biomass makes up the major portion of terrestrial carbon, and forest ecosystems contain enormous reservoirs of lignocellulose belowground, in dead trees, and litter. Decomposition of this recalcitrant material and mobilization of nutrients are major components of the carbon cycle and essential for forest health. Whether releasing carbon dioxide (CO2) or transforming humic substances, the…