Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models

CABBI Theme: Sustainability

Keywords: Metabolomics, Modeling, Phylogenetic Relationship

Citation

Saifuddin, M., Bhatnagar, J.M., Segrè, D., Finzi, A.C. Aug. 8, 2019. “Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models.” Nature Communications 10, Article 3568. DOI: 10.1038/s41467019-11488-z.

Potential CUE versus genome size. Potential CUE regressed against genome size (bp). Blue lines show GLS fit. Points are colored by phylum.

Overview

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, we explore an in silico approach to predict bacterial C-use efficiency (CUE) for over 200 species using genome-specific constraint-based metabolic modeling. We find that potential CUE averages 0.62 ± 0.17 with a range of 0.22 to 0.98 across taxa and phylogenetic structuring at the subphylum levels. Potential CUE is negatively correlated with genome size, while taxa with larger genomes are able to access a wider variety of C substrates. Incorporating the range of CUE values reported here into a next-generation model of soil biogeochemistry suggests that these differences in physiology across microbial taxa can feed back on soil-C cycling.

Data

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Table S1: CUE for BiGG models across substrate types

Table S2: CUE under substrate limitation

Table S3: Contribution indices for variation in potential CUE by taxonomic level

Table S4: Regression summary for predictors of potential CUE

Table S5: Parameterization of CUE in the model