Single cell genomics reveals diversity of cyanobacteria subpopulations. The Science: Single cell genomics allowed researchers to examine the subpopulations of the marine microbe Prochlorococcus, affording a glimpse at “a new dimension of microdiversity.” The Impact: The cyanobacterial subpopulations were found to be distinct, comprised of “genomic backbones” made of highly conserved core gene alleles and… [Read More]

Detailed protocol outlines steps for extracting ample DNA from uncultured microbes. The Science: Characterizing uncultured microbes starts with isolating and sequencing enough DNA from an environmental sample that may be as small as a single cell. The Impact: The protocol has been successfully employed to amplify the genomes of 201 single cells from uncultured microbes… [Read More]

Researchers employ RNA-Seq techniques to improve annotations for analysis. The Science: A team of researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), the University of California, Berkeley, and the Great Lakes Bioenergy Research Center generated an ultra-deep, high quality transcriptome–the fraction of the genome that provides information about gene activity–of maize…. [Read More]

Recently sequenced microbes living in Deep Lake are mostly specialists, cornering different niches in the lake ecosystem The Science: Four microbes dominate in the Antarctica’s Deep Lake, making up 70% of the microbial community. They belong to a group called haloarchaea that require high salt concentrations to grow and are naturally adapted to extreme conditions… [Read More]

Medical compounds harvested from a marine sponge are actually produced by symbiotic bacteria living in the sponges. The Science: The research team used single-cell genome analysis, and metagenomic sequencing to find that just two bacterial tenants of a marine sponge, Theonella swinhoei, make medically important compounds called polyketides. Both bacteria belong an uncultivated genus, Enthotheonella. The research… [Read More]

The recently sequenced genome of Spirodela polyrhiza showcases why the plant makes an excellent raw source for biofuels. The Science: Duckweed is one of the smallest and fastest-growing flowering plants that can be a hard-to-control weed in ponds and small lakes. Sequencing the genome of Greater Duckweed (Spirodela polyrhiza) has provides clues about how the tiny… [Read More]

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]