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Breaking the Petabit barrier, a Tweet at a time

Earlier this year, the DOE JGI teamed with the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory to scale up its computing infrastructure to meet increasing user needs and the rising amount of data being generated. ESnet traffic map by Jon Dugan, ESnet Network Engineering Group, LBNL On Dec. 14, the… [Read More]

Unpredictable MDA biases in metagenomic analyses

Genomic studies of low-biomass environments is often limited by the amount of DNA available, and one solution has been to use a whole genome amplification technique that uses phi29 DNA polymerase known as multiple displacement amplification (MDA). When used in single cell genomic studies, one noted drawback of the procedure has been amplification bias that… [Read More]

Methanotroph Methylosinus trichosporium

Considered the second most important greenhouse gas, methane is 21 times more potent than carbon dioxide. Methane-oxidizing bacteria called methanotrophs help reduce levels of atmospheric methane. To better understand the bacteria involved in the global methane cycle, the DOE JGI sequenced, assembled and annotated the genome of Methylosinus trichosporium OB3b. The project was led by… [Read More]

Clostridia bacterial genomes sequenced for biofuel production

Cellulose and hemicellulose are considered the largest components of plant biomass and researchers have been looking for ways to break down these materials efficiently and cost-effectively for commercial cellulosic biofuel production. Many microbes that can break down biomass do so with the help of enzyme complexes known as cellulosomes, and the DOE JGI has been… [Read More]

Chlorella for the carbon cycle and biodiesel production

Green algae are key components of the global carbon cycle and help sequester half of the carbon in the atmosphere. From a bioenergy perspective, algae are increasingly viewed as a viable feedstock for biofuel and biodiesel production because of their high lipid content. However, algal viruses can infect up to a fifth of all algae… [Read More]

Leaf-cutter ant microbiome breaks down plant biomass

Leaf-cutter ants are community gardeners on a very large scale. Living in colonies composed of several millions, the ants harvest hundreds of kilograms of leaves annually and use them to cultivate fungal gardens that serve as their primary food source. Leaf-cutter ant. (From the October 2010 issue of PLoS Genetics. Image by Jarrod J. Scott,… [Read More]

A bacterium for breaking down dioxins

Isolated from the River Elbe in Germany, Sphingomonas wittichii RW 1 belongs to a family of bacteria that play a role in breaking down complex aromatic compounds associated with decaying plant mater and chemical pollution. S. wittichii itself is capable of completely breaking down toxic dioxin pollutants, and was selected for sequencing by the DOE… [Read More]

New clues for understanding a novel cellulolytic process

Fibrobacter succinogenes is an anaerobic bacterium that breaks down plant cell wall biomass in ruminants and converts the cellulose into glucose. Sequenced at the DOE JGI for the Great Lakes Bioenergy Research Center (GLBRC), the 3.8 million base genome was completed and the information submitted to the National Center for Biotechnology Information in late 2009…. [Read More]

Bacterial lessons in rare metal recovery

One of the goals of the DOE’s Genomics:GTL Program is understanding how microbes and microbial communities perform the functions that have helped them thrive in a wide variety of environments and which have applications in the DOE mission areas of bioenergy, carbon cycling and biogeochemistry. British scientists applied information gleaned from Desulfovibrio genomes sequenced by… [Read More]

Standardizing metagenomic classifications

A five-tier metagenome classification system would  enable genomic researchers to better extract and understand data. (Image from Ivanova et al. Env Microbiol. 2010: 12(7):1803-1805.) Studying the genomes of microbial communities, or metagenomics, has been facilitated in the last few years by advances in sequencing technologies. However, as the DOE JGI’s Natalia Ivanova, Susannah Tringe, Dino… [Read More]