Research topics have been arranged within a conceptual framework that asserts that the shortgrass steppe ecological structure and function are governed by climate, natural disturbance, physiography, human use and biotic interactions. The shortgrass steppe is unique among North American grasslands for its long evolutionary history of intense selection by both drought and herbivory, resulting in an ecosystem that is well adapted to withstand grazing by livestock, the predominant land-use in a region where precipitation is both low and highly variable. Shortgrass steppe vegetation is dominated by two species of low-growing, warm-season perennial grasses (blue grama, Bouteloua gracilis, and buffalograss, Buchloe dactyloides) that are resistant to grazing and short-term drought. Small-scale disturbances caused by cattle fecal pats, harvester ants, small mammals and root-feeding invertebrates are the natural source of mortality for blue grama and create opportunities for the establishment and persistence of forbs and sub-shrubs. Prickly-pear cactus provides a refuge from grazing that increases local diversity. Biological activity is concentrated belowground, as reflected by the large allocation of plant production to roots and the high rates of energy flow through belowground food webs. Most biologically active elements in shortgrass steppe are protected from natural small-scale disturbances by being stored in soil organic matter. Shortgrass steppe is resistant to aboveground disturbances such as grazing, fire and invasive plants. In fact, removal of grazing results in plant communities which are more similar to disturbed areas than are heavily grazed pastures. The shortgrass steppe is, however, highly vulnerable to large-scale disturbances such as cultivation that disturb the soil, with recovery to native vegetation requiring many decades or more, as witnessed during the Dust Bowl years. It is predicted that changes in the magnitude and timing of precipitation or anthropogenic inputs of nutrients that modify the relative allocation of resources above- vs. belowground can dramatically alter ecosystem structure and function. Soil moisture, the driving abiotic determinant of productivity in shortgrass steppe, is dependent on the interactions between the biota and physiography, soil properties and the highly seasonal and pulsed nature of precipitation. Biological, geological and geochemical processes have interacted to shape the development and degradation of soils, topographic variation and the hydrological functioning of the ecosystem over tens to hundreds of thousands of years. Changes in the magnitude and timing of precipitation that will accompany anticipated climate change will alter the spatial distribution and temporal availability of soil moisture, and therefore net primary productivity, on the landscape. Low productivity and lawn-like physiognomy of shortgrass steppe vegetation are factors that shape the structure of the habitat and refuges for animals, and have a large influence on faunal populations and biodiversity. The shortgrass steppe fauna is dominated by omnivorous, seasonally-active generalists whose biogeographic affinities are closely aligned with adjacent prairie and montane provinces. In the harsh climate characteristic of shortgrass steppe, the presence of taller, cool-season grasses and shrubs provide critical cover, resources and habitat for many species, including some of regional conservation concern. Changes in climate, CO2 or land-use that alter the distribution of these plants will have profound effects across multiple trophic levels. Black-tailed prairie dogs behave as ecosystem engineers in the shortgrass steppe, constructing a network of burrows which are locally abundant and serve as a persistent source of refuge belowground for other animals, and in the shortgrass steppe, prairie dogs themselves are important prey for top-level predators. Plague (Yersinia pestis), a disease caused by an invasive pathogen, has altered the metapopulation dynamics of the black-tailed prairie dog, which has had ecosystem-wide effects via a climate-mediated trophic cascade. Plague wipes out entire colonies of black-tailed prairie dogs, eliminating for years an important disturbance agent and modifier of vegetation structure and plant species composition. Outbreaks of plague are influenced by regional climatic conditions that influence the abundance of prairie dogs, flea vectors and alternative rodent hosts, and by the spatial distribution of colonies on the landscape. Because black-tailed prairie dogs compete with livestock for forage, changes in the dynamics of plague that could accompany climate and land-use change will have important consequences for the management of public grasslands.