U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights

Genome Watch Highlights DOE JGI Explorations of Microbial “Dark Matter.”
Published: January 16, 2014
Posted: February 12, 2014

Adam Walker of the Wellcome Trust’s Sanger Institute has published an analysis of the Department of Energy’s Joint Genome Institute’s (DOE JGI) explorations of “microbial dark matter” metagenomics and single cell genomics. Four recent publications are highlighted, two directly from DOE JGI and two involving past and present collaborators. All used novel technologies to characterize microbes and microbial communities refractory to standard culture in the lab and involved in mission-relevant activities such as bioenergy and bioremediation. Most microbes cannot be readily grown in culture, so they are difficult to study with molecular and genetic approaches that require large amounts of starting genomic material. With the advent of single cell techniques, it is now possible to derive information about the genome of single isolated cells without a cultivation step. Furthermore, with the massive sequencing throughput available at DOE JGI, the DNA from bulk environmental samples can be characterized and a “fingerprint” of the sampled environment can be studied and compared, for example, both before and after perturbations. Even some whole microbial genomes can be assembled from the sequence fragments. These genomes, as noted by Walker, can provide new opportunities for biochemistries relevant to bioenergy, environmental remediation, and carbon and nutrient processing.

Reference: Walker, A. 2014. “Adding Genomic ‘Foilage’ to the Tree of Life,” Nature Reviews Microbiology 12, 78. DOI:10.1038/nrmicro3203. (Reference link)

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Research Technologies and Methodologies

Division: SC-23.2 Biological Systems Science Division, BER


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

May 10, 2019
Quantifying Decision Uncertainty in Water Management via a Coupled Agent-Based Model
Considering risk perception can improve the representation of human decision-making processes in age [more...]

May 09, 2019
Projecting Global Urban Area Growth Through 2100 Based on Historical Time Series Data and Future Scenarios
Study provides country-specific urban area growth models and the first dataset on country-level urba [more...]

May 05, 2019
Calibrating Building Energy Demand Models to Refine Long-Term Energy Planning
A new, flexible calibration approach improved model accuracy in capturing year-to-year changes in bu [more...]

May 03, 2019
Calibration and Uncertainty Analysis of Demeter for Better Downscaling of Global Land Use and Land Cover Projections
Researchers improved the Demeter model’s performance by calibrating key parameters and establi [more...]

Apr 22, 2019
Representation of U.S. Warm Temperature Extremes in Global Climate Model Ensembles
Representation of warm temperature events varies considerably among global climate models, which has [more...]

List all highlights (possible long download time)