Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models

The Science

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.

The Impact

• 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.

Summary

Respiration by soil bacteria and fungi is one of the largest fluxes of carbon (C) from the land surface. Although this flux is a direct product of microbial metabolism, controls over metabolism and their responses to global change are a major uncertainty in the global C cycle. Here, researchers explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling.

References

Saifuddin, M., J. M. Bhatnagar, D. Segrè, A. C. Finzi. 2019. “Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models,” Nature Communications 10, 3568. DOI:10.1038/s41467-019-11488-z.