We present a general model concept and a flexible software framework for the description of plant-scale soil-root interaction processes including the essential fluid mechanical processes in the vadose zone. The model is developed in the framework of non-isothermal, multi-phase, multi-component flow and transport in porous media. The software is an extension of the open-source porous media flow and transport simulator \dumux to embedded mixed-dimensional coupled schemes. Our coupling concept allows us to describe all processes in a strongly coupled form and adapt the complexity of the governing equations in favor of either accuracy or computational efficiency. We present the necessary numerical tools to solve the arising strongly coupled non-linear PDE systems with a locally mass conservative numerical scheme even in the context of evolving root architectures. We demonstrate the model concept and its features discussing a virtual hydraulic lift experiment including evaporation, root tracer uptake on a locally refined grid, the simultaneous simulation of root growth and root water uptake, and an irrigation scenario comparing different models for flow in unsaturated soil. We analyze the impact of evaporation from soil on the soil water distribution around a single plant's root system. Further, we show that locally refined grids around the root sytem increase computational efficiency while maintaining accuracy. Finally, we demonstrate that the assumptions behind Richards equation may be violated under certain conditions.
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