DOE Joint Genome Institute

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Fungal-bacterial symbioses with Populus

Bacteria and fungi are known to interact with plants and contribute to ecosystem health and productivity, defining the plant microbiome. Recent studies indicate that some fungal-bacterial symbioses may date back over 400 million years and may be important in driving the formation of soil and rhizosphere communities. This project focuses on a diversity of fungi… [Read More]

Gene expression analyses of Populus crosses

Populus is one of DOE JGI’s Flagship Plant Genome species and is of special interest as a biofuels feedstock. It was selected as the model forest species for genome sequencing due to its modest genome size, rapid growth, relative ease of experimental manipulation and range of available genetic tools. As such, Populus trichocarpa was the… [Read More]

Carbon studies in Northern California

The global terrestrial carbon reservoir is primarily distributed among grasslands, forests   and cultivated farms. While the majority of fixed carbon is stored in vegetation in forests, most fixed carbon in grasslands is stored in soil. Thus, it is critical to understand the carbon cycling in grassland soil. One challenge climate researchers face is making accurate… [Read More]

Salt-tolerant trees and their symbionts

Over 800 million hectares of land throughout the world are salt-affected and a common method for dealing with salt stress problems is to reclaim affected soils with fast-growing salt- tolerant tree species such as Casuarina trees. Fast growing trees from the Casuarinaceae family have been successfully introduced in several tropical and subtropical countries to prevent… [Read More]

Pilot phase of the Thousand Microbial Genomes project

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the DOE JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. At the time the major project goals were to provide evidence to support the use of the phylogenetic diversity of organisms in the tree… [Read More]

Carboxysomes and the carbon cycle

Cyanobacteria thrive in a diverse range of habitats. In the oceans they are estimated to fix 40 percent of total carbon globally. Long used as a simple model organism to study plant photosynthesis, they are becoming a platform for production of biofuels and industrially important compounds. All cyanobacteria carry out the key step of carbon… [Read More]

Reducing methane with rumen microbiome studies

The rumen microbiome is comprised primarily of microbes such as bacteria, methanogenic archaea, fungi, ciliate protozoa and viruses that have evolved to act together to rapidly breakdown of complex plant sugars, and ferment the released sugars to produce short-chain fatty acids. Methane is a potent greenhouse gas (GHG) with a global warming potential 25 times… [Read More]

Fungal enzymes in the cow rumen

The genes and genomes of microbes in the cow rumen represent a valuable source for new biomass-degrading enzymes that might enable processes to more efficiently convert biomass into biofuels. Fungi make up less than 10 percent of the microbial biomass in the rumen and fungal enzymes appear to have higher specific activities towards plant cell… [Read More]

Founding a grass transcription factor library

Sequenced at the DOE JGI, Brachypodium distachyon is a small temperate grass that is being used as a model for potential energy crops such as switchgrass, sorghum, and Miscanthus. One of the goals in cultivating bioenergy crops is producing enough biomass to convert and use for biofuel production to meet the nation’s needs. This project… [Read More]

Focusing on the Agave microbiome

Deserts and drylands currently encompass 40 percent of the Earth’s land surface and a further increase in such areas due to climate change and other processes is expected. There are approximately 200 species of Agave, most native to deserts and drylands in central Mexico and the Southwestern United States. Recently identified as candidate bioenergy feedstocks,… [Read More]