Researchers are using “experimental evolution” to develop bacteria that are more efficient at decomposing biomass. The Science: Clostridium phytofermentans is a soil-dwelling bacterium that helps decompose leaf litter. Researchers grew successive generations of bacteria on different woody material that make up plant cell walls (cellulose, cellobiose and xylan) and found that the bacteria adapted and became… [Read More]

A new system called ScanDrop could revolutionize how we identify pathogens in drinking water. The Science: Researchers from Lawrence Berkeley National Laboratory (the Joint BioEnergy Institute and the DOE Joint Genome Institute) and Northeastern University and the Massachusetts General Hospital/Harvard Medical School) have developed a portable, network-enabled system for testing drinking water contamination. The system, called ScanDrop, developed by… [Read More]

Capacities for DOE JGI’s twin genome analysis systems, IMG and IMG/M have both been expanded in the last two years. The Science: The DOE Joint Genome Institute maintains the Integrated Microbial Genomes (IMG) data warehouse, which contains a rich collection of genomes from all three domains of life. IMG/M provides a similar collection of microbial… [Read More]

Researchers assembled genomes from several single-cell isolates of the SAR11 group of Alphaproteobacteria and found that they form microclusters within the freshwater clade. [Read More]

New tool aims to help life science researchers formalize naming conventions for the environments they study. The Science: Biological and biomedical research is increasingly referencing and compiling data from environmental samples, leading to a growing need for a formal and standardized approach to describing those environments. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open-access… [Read More]

The newest iteration of the DOE Joint Genome Institute’s and analytical tools sports improved user interface and infrastructure. The Science: The DOE Joint Genome Institute’s massive genomic database and data management system, the Genome Portal (http://genome.jgi.doe.gov), has recently been upgraded with a more robust infrastructure to manage the torrent of genomic data available and a… [Read More]

Rare and ancient plant gobbles up entire mitochondria from other plants and holds onto them for eons. The Science: One of the oldest flowering plants, Amborella trichopoda, split off from the lineage of other flower plants about 200 million years ago. Analysis reveals that it has a record-setting amount of foreign DNA in its mitochondria,… [Read More]

Looking at a combination of whole genomes and gene databases suggests a new way to examine this fungus family tree. The Science: Researchers reviewed 10 currently available whole genomes, comparing them to known gene datasets. They reported family trees for several taxonomic subgroupings called clades. They also analyzed several single-copy genes to assess them for… [Read More]

A combination of time-lapse fluorescence and transmission electron microscopy reveals how cyanobacteria put together an essential component The Science Cyanobacteria use carboxysomes to make their own energy by “fixing” carbon from carbon dioxide from ocean waters and other aquatic and terrestrial habitats. After deleting the genes cyanobacteria need to build carboxysomes, researchers introduced fluorescent-tagged components… [Read More]