Data from Microbial Carbon Use Efficiency Predicted from Genome-Scale Metabolic Models

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.

土壤细菌与真菌的呼吸作用是陆地表面碳（C）通量的最大组成部分之一。尽管该通量是微生物代谢的直接产物，但代谢调控机制及其对全球变化的响应，仍是全球碳循环研究中尚未明确的核心不确定性之一。本研究采用计算机模拟（in silico）方法，借助基于基因组特异性约束的代谢模型，对200余种细菌的碳利用效率（C-use efficiency, CUE）进行预测。研究发现，不同微生物类群的潜在碳利用效率均值为0.62±0.17，取值范围为0.22至0.98，且在亚门级别存在显著的系统发育结构特征。潜在碳利用效率与基因组大小呈负相关关系，而拥有较大基因组的类群可利用更多样化的碳底物。将本研究报道的碳利用效率取值范围嵌入土壤生物地球化学新一代模型后，结果表明，微生物类群间的生理差异可对土壤碳循环产生反馈调控作用。