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

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)