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In a cross-disciplinary project (LEGATO) combining inter- and transdisciplinary methods, we quantify the dependency of rice-dominated socio-ecological systems on ecosystem functions (ESF) and the ecosystem services (ESS) the integrated system provides. In the collaboration of a large team including geo- and bioscientists, economists, political and cultural scientists, the mutual influences of the biological, climate and soil conditions of the agricultural area and its surrounding natural landscape have been analysed. One focus was on sociocultural and economic backgrounds, another on local as well as regional land use intensity and biodiversity, and the potential impacts of future climate and land use change. LEGATO analysed characteristic elements of three service strands defined by the Millennium Ecosystem Assessment (MA): (a) provisioning services: nutrient cycling and crop production; (b) regulating services: biocontrol and pollination; and (c) cultural services: cultural identity and aesthetics. However, in line with much of the current ESS literature, what the MA called supporting services is treated as ESF within LEGATO. As a core output, LEGATO developed generally applicable principles of ecological engineering (EE), suitable for application in the context of future climate and land use change. EE is an emerging discipline, concerned with the design, monitoring and construction of ecosystems and aims at developing strategies to optimise ecosystem services through exploiting natural regulation mechanisms instead of suppressing them. Along these lines LEGATO also aims to create the knowledge base for decision-making for sustainable land management and livelihoods, including the provision of the corresponding governance and management strategies, technologies and system solutions.