When we add excessive fertilizer, some of the fertilizer will diffuse directly to the roots and be taken up immediately, helping the plant. The rest of the fertilizer - the part the plant doesn't need right now - needs to be immobilized by soil organisms and retained in a soil "savings account" for later use by the plant. Without these organisms present, retention in the soil doesn't happen and the nutrients can be, and often are, leached into the groundwater.

The most leachable form of nitrogen is nitrate. Loss of N from soil by leaching can be minimized if nitrogen is present as organic N, instead of nitrate. Thus in the fall and winter, nitrogen should be stored in organic N forms, it's least leachable form, which are bacteria, fungi, and soil organic matter. Bacteria make extracellular slime layers that glue them to any surface, so they do not move as water washes past them. Fungi grow as long thread-like strands that tie soil particles together and prevent the fungi from being washed from the soil. In the spring, nitrogen immobilized in bacteria and fungi need to be converted to plant-available forms by being eaten by protozoa, nematodes and microarthropods.

In hydroponics, nutrients are added into the hydroponic fluid at the rate the roots are thought to take up those nutrients. The water moves nutrients to the roots, the place the plant needs the nutrients delivered. That doesn't happen easily in soil, as soil particles and organic matter prevent the soil solution from moving nutrients to the roots rapidly. Plants growing in soil need other soil organisms to transport nutrients for them. But even in hydroponics, we don't really understand the minute by minute needs of the plant, so we load the nutrient solution with excess nutrients, to the point that water quality is usually extremely poor in a hydroponics system. This leads to water pollution problems that could be avoided if the normal nutrient cycling processes were allowed to occur.