DOE JGI Science Highlights: 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 community. Informatics capabilities are proving to be bottlenecks in metagenomic studies.  by  Chiot's Run 

DOE JGI Science Highlights: 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 convert them into nutrients.

New information about microbial activity in leafcutter ant gardens could improve biofuel production. 

 by  Alejandro Soffia Vega 

DOE JGI Science Highlights: 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 Arthobacter phenanthrenivorans, which was isolated from a creosote-polluted site in Greece, and used by the microbe as an energy source.

Scanning electron micrograph of the bacterial strain of A. phenanthrenivorans. 

 (Image from Kallimanis A et al, SIGS 2011 via CC 3.0 License)

DOE JGI Science Highlights: 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 production. 

Researchers compared the effects of diet on hoatzin gut microbial communities

  by  David Cook Wildlife Photography (kookr) 

2013 federal budget proposal in GenomeWeb Daily News

The Department of Energy's Office of Science, which funds the Joint Genome Institute and other biology research aimed at developing better renewable biofuels and energy-related technologies, would receive $5 billion, compared to $4.9 billion this fiscal year.

Read the full GenomeWeb News story on the Obama administration's 2013 budget proposal.

DOE JGI Science Highlights: 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 Sanger platform. Assembling these pieces into a genome for study is both costly and time-consuming.

DOE JGI researchers led by Deputy Director of Genomic Technologies Len Pennacchio and Advanced Sequencing Group head Feng Chen have developed a way to more efficiently assemble the short DNA segments.

DOE JGI researchers developed CLIP-PE for the de novo assembly of short reads. 

(Image by Mykl Roventine, Fotopedia/CC2.0)

DOE JGI Science Highlights: 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. 

Hydrophobins in Laccaria bicolor may be crucial to forming mutualistic relationships with plant hosts.    

  by  manual crank 

Permafrost study referenced in ScienceNews

In Nature in December, a team of researchers at the Department of Energy’s Joint Genome Institute in Walnut Creek, Calif., and colleagues reported one such microbe’s draft genome — put together from DNA acquired from the semifrozen dirt in an Alaskan black spruce forest. The Alaskan microbe carries genes tuned to transform organic matter into methane, a finding that may one day help provide a vivid picture of what will happen as soil conditions change. 

Read more on ScienceNews

DOE JGI Science Highlights: 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 applications, but fungal strains have traditionally been developed by random mutagenesis. 

             T. reesei (Image by Irma Salovuori, VTT Biotechnology)

1000 Fungal Genomes project in The Daily Barometer

Joey Spatafora, an associate professor at Oregon State University, is leading an international project to sequence the genomes of a thousand fungi, a project aptly named 1000 fungal genomes.    "It's a really, really exciting time in fungal biology because we can sequence fungal genomes more easily than we could ten years ago," Spatafora said.

Read more in The Daily Barometer