The Aral Sea has lost >60% of its surface compared to 1960, due to increased water diversion in irrigation systems. The production of cotton in huge irrigation systems has brought about water misuse and land degradation, and due to the tough economic transformation process faced by the central Asian countries, the region is characterized by increasing poverty. Therefore, international development efforts today concentrate on improving ecological sustainability and economic efficiency of natural resource use in the region, as a contribution to combating poverty and desertification in the Basin, rather than on saving the Aral Sea as such. The Center for Development Research (ZEF) at the University of Bonn, together with its partners, has set up a research program aimed at providing options for a restructuring of land and water use that are based on sound, long-term, interdisciplinary integration of different disciplines of science, and that are aiming at strengthening local institutional and individual capacity building. The various elements of this program and first results are presented, and the steps undertaken towards integration of the results of the different research areas are outlined. This contribution relates the soil ecological studies carried out in the project from 2002-2005. It looks specifically at the effects of soil organisms under different environmental conditions, in natural forests, irrigated former drylands under different crops, and hedgerows between the fields, in order to determine the possible contribution soil organisms may have in the soils of the region.