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.
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.
Wood Decay by Soft Rot Fungi
This project seeks to ascertain the mechanisms of lignocellulose deconstruction employed by these soft rot fungi.
Scaling Microbial Traits From Genomes to Watersheds
Using remote sensing, metagenomics and machine learning, we are building new ways to predict of how plant and microbial metabolism interact to influence biogeochemistry across watersheds in the headwaters of the Colorado River.
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.
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.
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.
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.
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.
A Step Toward Controlling Soybean Rust
The United States is the world’s leading soybean producer, and soybeans are used to produce biodiesel. The fungus Phakopsora pachyrhizi causes Asian Soybean Rust (ASR) and is the major pathogen of soybean. Left uncontrolled, soybean rust could reduce crop yields by as much as 90 percent. As part of the DOE Joint Genome Institute’s 2016…