DOE Joint Genome Institute

Our Projects
Home › CSP Plans

Genomic Variation in Mustard Family Metabolism

Studies of genomic variation are critical to developing a synthetic, systems and quantitative understanding of how to improve crops. However, modern short-read methodologies may actually miss the very genes that are critical to adapting crops to new environments or making them healthier. This project will create high-quality genomes of multiple crops and species from the mustard family to test new methods and technologies to ensure that these genes essential for adaptation and improvement are identified. [Read More]

Fungal Root Endophytes of Soybean

This project investigates fungal root endophytes of the oilseed crop soybean for their potential to deter biotic stresses from root pathogen such as the soybean cyst nematode and the sudden death syndrome fungal root-rot pathogen. [Read More]

Expanding Metabolic Understanding of C- and S- Cycling Microbes

Is there more biochemistry to be discovered in the microbial world? How universal is biochemistry between distantly related bacteria? A massive amount of microbial genome data exists, yet every new sequence finds genes for which we cannot predict a concrete function. This proposal seeks to combine genomic information with direct detection of metabolites to answer these questions and provide a path for assigning gene functions in two distantly related microbial groups that play key roles in carbon and sulfur cycling in multiple ecosystems across the planet. [Read More]

Microbial Roles in Plant Drought Tolerance in the Sahel

The Sahel region in West Africa is highly vulnerable to drought, endangering the livelihood of millions of millet subsistence farmers in the region. However, a solution has been revealed; when farmers grown millet in close proximity with native woody shrub gueira, the millet has greater biomass and yields. We predict that the millet-associated microbial community is influenced by the shrub such that the microbes are able to confer better drought resistance to their host millet in the presence of the shrub. We will characterize the metagenomes of millet to test this hypothesis. [Read More]

Plant-Microbe Interactions of a Wood Decay Fungus

This research project focuses on elucidating the plant-microbe interactions of the wood decay fungus Perenniporia fraxinea, a serious pathogen of hardwood trees. Multi-omics analyses will reveal the comprehensive mechanisms and key fungal genes involved in the wood infection and degradation processes will be identified. Furthermore, key fungal proteins involved in the processes will be biochemically characterized and subjected to chemical screening in our efforts to identify specific inhibitors with potential as novel wood-protective agents against P. fraxinea and related wood-decay fungi. [Read More]

How Black Fungi Adapt to Extremes

Black fungi spread in diverse extreme environments playing a crucial role by recycling organic matter, enabling nutrient uptake. They are also involved in biogeochemical processes, including rock transformations, bioweathering, mineral formation. The STRES project aims to dig into the genome diversity and metabolites involved in stress response to: i) gain insights into the evolutionary processes allowing black fungi to successfully adapt to extremes; ii) clarify their role in the functioning and balance in extreme-ecosystems; iii) explore the role of melanin in energy processes. [Read More]

Grass Genes Regulating Bioenergy Relevant Traits

Grass species have a tremendous potential to be engineered to generate biofuels that can feed our economy. A major challenge has been accessing the energy stored in plants. Purple false brome (Brachypodium distachyon), a wild grass species from the Mediterranean region, is a perfect model for testing novel ways of changing plants to help produce biofuels. In this study, researchers are accessing variation in this species to identify genes that could transform bioenergy crops. These resources are openly shared with the scientific community in order to speed up research and transform society. [Read More]

Mapping Methanogenic Metabolic Networks

Anaerobic digestion (AD) systems produce methane-rich biogas, which can be upgraded and distributed within the existing energy grid. Despite the widespread adoption of AD for waste management and bioenergy generation, the microbial networks driving methane production from organic matter remain poorly constrained, limiting our capacity to predict impacts of process perturbations. Here, we will combine stable isotope and amino acid tracers with genomic sequencing to determine “who is doing what” in AD, with the overall aim of improving biofuel production efficiency from renewable biomass. [Read More]