DOE Joint Genome Institute

Our Science
Home › Science Highlights

Effects of symbiosis on a fungal transcriptome

The soils of the boreal forests in the northern latitudes are estimated to store more than three times the amount of carbon contained in the atmosphere or in plant life on land. Recent studies suggest the relationship between fungi on the forest floor, plants and the microbial communities at the plant roots (or rhizosphere) plays… [Read More]

Analysis of a TCE-degrading metagenome

Groundwater sites contaminated with compounds such as trichloroethene (TCE), a pervasive organic groundwater pollutant often used by industry as cleansers or degreasers.Dehalococcoidesbacteria, often found in a community of other microorganisms at groundwater sites contaminated with these compounds, can break down TCE and convert it into ethene, a harmless chemical compound often used to help ripen… [Read More]

Searching for the basis of ligninolytic selectivity

Many fungal genome projects being carried out at the DOE JGI focus on understanding how enzymes can break down cellulose and lignin, the two most abundant biopolymers on Earth, in order to harness these capabilities for industrial applications such as biofuels production. Scanning electron micrograph of Ceriporiopsissubvermispora mycelium on wood.  (Robert Blanchette, University of Minnesota)… [Read More]

Bioinformatics challenges for metagenomic analyses

There are more microbes in, on and around the planet than there are stars in the sky. However, the vast majority of these microorganisms have not yet been studied, in part because many of them do not thrive when moved out of their natural environment. A spoonful of soil contains a complex and diverse microbial… [Read More]

Elucidating bacteria’s roles in ant fungal gardens

Leafcutter ants cultivate fungal gardens that serve as their primary food source. Working toward the goal of harnessing novel enzymes for breaking down plant biomass to produce cellulosic biofuels, Great Lakes Bioenergy Research Center (GLBRC) researchers have been studying the process by which the fungi break down the plant leaves harvested by the ants and… [Read More]

Analyzing enzymes for a PAH degradation pathway

Microbial activity is crucial for breaking down compounds, removing pollutants and chemically transforming organic compounds. Some of these pollutants are polycyclic aromatic hydrocarbons (PAHs) found in contaminated soils. The PAH phenanthrene, for example, can be broken down by the bacterium Arthobacterphenanthrenivorans, which was isolated from a creosote-polluted site in Greece, and used by the microbe… [Read More]

Dietary impacts on hoatzin crop microbial communities

Many DOE JGI metagenomic projects focus on microbial communities in the guts of the cow, termite and even the desert locust, all known to break down plant biomass for energy. In studying these and other gut microbial communities, researchers hope to identify and isolate genes involved in plant biomass degradation, and apply them to biofuel… [Read More]

A new approach for improve genome assembly

Assembling a genome from fragments of DNA sequence is often compared to assembling a puzzle. One of the problems researchers face with the increasing use of next-generation sequencing technologies is that the pieces of DNA sequence generated by the 454 or Illumina platforms are much smaller and far more numerous than those produced by the… [Read More]

The role of hydrophobins in plant-fungal mutualism

To get an idea of the importance of mutualistic relationships between plants and fungi, consider that a third of the carbon sequestered in the soil of boreal forests are composed of the wood residues after the fungi break down the cellulose. Maintaining the interface between the fungi and their hosts is the job of small… [Read More]

A toolkit for T. reesei

The availability of an organism’s genome sequence is useful for improving downstream applications such as large-scale biofuel production, but it is only the first step on this path. In the case of the fungus Trichoderma reesei, whose genome sequence was published by the DOE JGI in 2008, the cellulases in T. reesei have multiple industrial… [Read More]