Unlike carbon, water, and nitrogen, phosphorus is not present in the atmosphere as a gas. Instead, most phosphorus in the ecosystem exists as compounds, such as phosphate ions (PO43-), found in soil, water, sediment and rocks. Phosphorus is often a limiting nutrient (i.e., in short supply). Consequently, phosphorus is added to most agricultural fertilizers, which can cause environmental problems related to runoff in aquatic ecosystems.

Bioremediation is the use of prokaryotes, fungi, or plants to remove pollutants from the environment. This process has been used to remove harmful toxins in groundwater as a byproduct of agricultural run-off and also to clean up oil spills.

Plants obtain inorganic minerals and water from the soil, which acts as a natural medium for land plants. The composition and quality of soil depend not only on the chemical constituents but also on the presence of living organisms. In general, soils contain three major components:

Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.