Ecosystems biology of microbial metabolism

The metabolic capabilities of many environmentally and medically important microbes can be quantitatively explored using systems biology approaches to metabolic networks. Yet, as we learn more about the complex microbe–microbe and microbe–environment interactions in microbial communities, it is important to understand whether and how system-level approaches can be extended to the ecosystem level. Here we summarize recent work that addresses these challenges at multiple scales, starting from two-species natural and synthetic ecology models, up to biosphere-level approaches. Among the many fascinating open challenges in this field is whether the integration of high throughput sequencing methods and mathematical models will help us capture emerging principles of ecosystem-level metabolic organization and evolution.

► Microbial ecosystems are ubiquitous on our planet and important for human life.
► We review efforts to extend cell-level models of metabolism to ecosystem-level.
► Some researchers are designing artificial ecosystems, in a ‘synthetic ecology’ approach.
► Integration of models and metagenomic data will help understand ecosystem evolution.