the basis of all complex multicellular life on Earth. Their evolutionary histories, inferred from gene sequences, are part of the profound record of all life forms having evolved from a few common ancestors.
Metabolism is a universal feature of living systems. All organisms must acquire and transform energy into forms that they can use to make new cells and repair old ones. In the process, all organisms exchange gases with their environment. Gas exchange provides a mechanism to analyze metabolic pathways and fluxes on local and global scales. It is a crucial link between organisms and their environment. When organisms take up energy and resources and expel metabolic byproducts, they shape not only their local environment but ultimately the planetary environment (Frausto da Silva and Williams, 1996; Sterner and Elser, 2002). Although the environmental consequences of an individual organism’s metabolism can be small and localized, the metabolic effects of large collections of organisms are global. The planet is habitable for large, multicellular, air-breathing animals like humans only because other creatures have made it habitable. The atmosphere also dissipates heat and buffers temperature, which allows for relatively stable forms of life. Because the metabolisms of organisms are linked, to each other and to the atmosphere and climate, this is an area with potential for theoretical unification.
There are conserved metabolic pathways by which organisms capture, transform, and dissipate energy. This chapter considers the evolution of these pathways and the interaction of energy metabolism with pivotal materials such as carbon and nitrogen. An expansive view of metabolism is taken throughout the chapter. It is considered both at the level of cells and organisms and at the level of ecological systems and the entire biosphere. This multiscale approach is essential given that it is the combined effect of individual organisms’ metabolisms, which have the potential to affect regional and global environmental conditions.
An important challenge at the intersection of biology, geochemistry, and physics is to understand how the global metabolic network evolved, what the feedbacks were that led to the constrained variations in gas composition of the planetary atmosphere, and the limitations of these processes on organismal, ecological, and geological spatial and time scales. Understanding this vast global metabolic network requires developing a global “systems geobiology,” the root of which lies in the origins of life on Earth and which is deeply grounded in the fundamental physiological pathways of life.
“Systems geobiology,” in this report, is defined as the integrated study incorporating geochemistry, geophysics, and other environmental sciences with genomics, ecophysiology, and mathematics to understand the processes and feedback mechanisms influencing Earth’s overall metabolism. The further goal is to improve our ability to predict responses of the Earth’s systems to external and internal perturbations. This discipline is as new as