Soil Science integrates specific contributions from physics, chemistry, biology, and the human sciences. During the last 2 decades, these approaches, which had primarily developed separately and at different speeds, have been progressively integrated. Ecology has contributed a significant number of integrative concepts and questions, some, such as nutrient cycling and energy budgets, that are rather old, and others, such as soil engineering by macroinvertebrates, the relationship between biodiversity and soil function, and the impact of landscape fractionation, that are more recent. An important issue common to all disciplines in Soil Science is that of scales. Ecological studies have shown that similar activities, e.g., the building of solid structures by invertebrates for their sheltering or gut transit of soil for digestion, may affect soil function at different scales, affecting the rates of processes in sometimes opposite directions. The concept of functional domains in soil, derived from soil ecological research, defines a scale at which physical, chemical, and biological processes can be studied efficiently in a true multidisciplinary approach. Functional domains are specific sites in soils defined by a main organic resource (leaf litter or soil organic matter), a major regulator, biotic (i.e., an invertebrate 'engineer' or roots) or abiotic (like freezing/thawing or drying/rewetting alternates), a set of structures created by the regulator (for example, fecal pellets, galleries, or cracks), and a community of dependent invertebrates of smaller size and microorganisms that live in these structures. Functional domains may be physically identified in soils and specifically studied using the different disciplinary approaches. Specific micromorphologic, isotopic, and other techniques allow us to address issues at this scale adequately. Ecological research also provides a theoretical background for management of soils at the larger integrative scales of landscape and regions. Essential issues for the near future should use this interdisciplinary approach. Sustainability of cropping systems and maintenance of soil ecosystem services depend more on an integrated approach than do the extreme developments in single disciplines in isolation that originated the series of problems we now face: large scale soil erosion, nutrient transfers to neighboring ecosystems, threats of genetically modified organisms, or biodiversity accidents.