Plant substrate is defined as a substance on or in which plants grow. Thus, even soil can be viewed as a substrate. The main functions of the substrate are generally: providing plant anchorage, and delivering water, nutrients and oxygen to the roots. Moreover, root waste products such as CO2, excreted nutrient surplus, and several root exudates should not accumulate in the substrate. Therefore, ideally the substrate for horticultural plants is inert and airy. Although soil can be viewed as a substrate that provides the plant with its needs it should not be viewed as “dead material”. The soil contains many living organisms that should be managed with care as they have a big impact on nutrient retention time, water supply, pathogen suppression, plant disease resistance and root anchorage strengths.

For roots to grow optimally the substrate should not be too dense. That is, it should still allow a flow of water, nutrients and oxygen to the roots and provide enough anchorage if needed. In fully controlled cultivation systems with optimal oxygen, nutrient and water delivery, roots to shoot ratio can be smaller because there is less need for the plant to invest in its uptake organs. This is a situation to strive for in horticulture because this means there is relatively less carbon allocated to root growth and more to the product of economic interest. An ongoing discussion in horticulture is whether to grow sterile or not. Fact is that the inert substrate in almost all greenhouses is heavily populated with micro-organisms. This is not a bad thing, because it creates a natural buffer or barrier for pathogen invasion. However, fundamental scientific knowledge on such systems is lacking. In soil under open field conditions there is much more knowledge on plant-micro-organism interactions see §5.3.