Well, some plants require more nitrgen than others and thus deplete the soil of nitrogen more quickly. For example, corn consumes quite a bit of nitrogen, so it is important to rotate crops after planting corn, preferably with one that fixes nitrogen, such as beans or alfalfa.
Other plants are water hogs, so they will use water agressively, decreasing that which is available to other plants. Eucalyptus trees are an example of this type of plant.
Finally, some pants release chemical compounds into the rooting zone that are toxic to other plants or animals. They do this to minimize competition and herbivory. It is not harmful to the soil, per se, but it does impact some biology negatively. A good example of this is walnut trees which produce a compound called juglone that prevents many other plants from growing.
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