BER launches Environmental System Science Program. Visit our new website under construction!

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

BER Research Highlights

Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models
Published: August 08, 2018
Posted: August 03, 2021


Characterizing variation in microbial carbon use efficiency (CUE) across taxa and substrate types in soils.


  • Generated theoretical predictions of CUE for more than 200 taxa using genome-scale constraint-based metabolic modeling.
  • Used genome-scale metabolic models to predict microbial physiology based on genes.
  • Developed hypotheses on CUE structure across taxa and substrate types.


  • A wide range in average potential CUE (0.62 ± 0.17) across taxa with structuring at subphylum levels.
  • CUE declines with increasing genome size, while larger genomes are able to access a wider range of C substrate types.
  • These findings provide a framework for predicting CUE from genomic traits and for inferring potential impacts of shifts in bacterial community composition on C cycling.
  • Phylogenetic variation in microbial CUE can dramatically alter patterns in soil C cycling over time.

Saifuddin, M. et al. “Microbial carbon use efficiency predicted from genome-scale metabolic models.” Nature Communications 10, 3568 (2019). [DOI:10.1038/s41467-019-11488-z]

Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: DOE Bioenergy Research Centers (BRC)

Division: SC-33.2 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

Mar 23, 2021
Molecular Connections from Plants to Fungi to Ants
Lipids transfer energy and serve as an inter-kingdom communication tool in leaf-cutter ants&rsqu [more...]

Mar 19, 2021
Microbes Use Ancient Metabolism to Cycle Phosphorus
Microbial cycling of phosphorus through reduction-oxidation reactions is older and more widespre [more...]

Feb 22, 2021
Warming Soil Means Stronger Microbe Networks
Soil warming leads to more complex, larger, and more connected networks of microbes in those soi [more...]

Jan 27, 2021
Labeling the Thale Cress Metabolites
New data pipeline identifies metabolites following heavy isotope labeling.

Analysis [more...]

Aug 31, 2020
Novel Bacterial Clade Reveals Origin of Form I Rubisco

  • All plant biomass is sourced from the carbon-fixing enzyme Rub [more...]

List all highlights (possible long download time)