Legumes like clover and soybeans have nitrogen fixing bacteria in their roots. These bacteria supply plants with a form of nitrogen that they can utilize. The surplus nitrogen-- not needed by these plants-- is added to the soil around these plants; this enriches the soil for other plants to use.
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Fertilizers also add nitrogen to the soil, but this nitrogen is often washed out/off the soil during heavy rainfalls. The accumulation of nitrogenous nutrients in aquatic habitats, produces undesirable overgrowth of plant species in swamps, lakes, ponds and slowly flowing rivers.