On viewing the lush plant growth of a tropical rain forest, most people would conclude that the soil beneath it is rich in nutrients. However, although rain forest soils are highly variable, they have in common the fact that abundant rainfall washes mineral nutrients out of them and into streams. This process is known as leaching. Because of rain leaching, most tropical rain forest soils have low to very low mineral nutrient content, in dramatic contrast to mineral-rich grassland soils. Tropical forest soils also often contain particular types of clays that, unlike the mineral-binding clays of temperate forest soils, do not bind mineral ions well. Aluminum is the dominant cation (positively charged ion) present in tropical soils; but plants do not require this element, and it is moderately toxic to a wide range of plants. Aluminum also reduces the availability of phosphorus, an element in high demand by plants.

High moisture and temperatures speed the growth of soil microbes that decompose organic compounds, so tropical soils typically contain far lower amounts of organic materials (humus) than do other forest or grassland soils. Because organic compounds help loosen compact clay soils, hold water, and bind mineral nutrients, the relative lack of organic materials in tropical soils is deleterious to plants. Plant roots cannot penetrate far into hard clay soils, and during dry periods, the soil cannot hold enough water to supply plant needs. Because the concentration of dark-colored organic materials is low in tropical soils, they are often colored red or yellow by the presence of iron, aluminum: and manganese oxides; when dry, these soils become rock hard. The famous Cambodian temples of Angkor Wat, which have survived for many centuries, were constructed from blocks of such hard rain forest soils.

Given such poor soils, how can lush tropical forests exist? The answer is that the forest's minerals are held in its living biomass—the trees and other plants and the animals. In contrast to grasslands, where a large proportion of plant biomass is produced underground, that of tropical forests is nearly all aboveground. Dead leaves, branches, and other plant parts, as well as the wastes and bodies of rain forest animals, barely reach the forest floor before they are rapidly decayed by abundant decomposers—bacterial and fungal. Minerals released by decay are quickly absorbed by multitudinous shallow, fine tree feeder roots and stored in plant tissues. Many tropical rain forest plants (like those in other forests) have mycorrhizal (fungus-root) partners whose delicate hyphae spread through great volumes of soil, from which they release and absorb minerals and ferry them back to the host plant in exchange for needed organic compounds. The fungal hyphae are able to absorb phosphorus that plant roots could not themselves obtain from the very dilute soil solutions, and fungal hyphae can transfer mineral nutrients from one forest plant to another. Consequently, tropical rain forests typically have what are known as closed nutrient systems, in which minerals are handed off from one organism to another with little leaking through to the soil. When mineral nutrients do not spend much time in the soil, they cannot be leached into streams. Closed nutrient systems have evolved in response to the leaching effects of heavy tropical rainfall. Evidence for this conclusion is that nutrient systems are more open in the richest tropical soils and tightest in the poorest soils.

The growth of organisms is dependent on the availability of nutrients, none of which is more important than nitrogen. Although there is an abundant supply of nitrogen in Earth’s atmosphere, it cannot be absorbed by plants unless it is “fixed,” or combined chemically with other elements to form nitrogen compounds. Nitrogen-fixing bacteria help tropical rain forest plants cope with the poor soils there by supplying them with needed nitrogen. Many species of tropical rain forest trees belong to the legume family, which is known for associations of nitrogen-fixing bacteria within root nodules. Also, cycads (a type of tropical plant that resembles a palm tree) produce special aboveground roots that harbor nitrogen-fixing cyanobacteria. By growing above the ground, the roots are exposed to sunlight, which the cyanobacteria require for growth. Nitrogen fixation by free-living bacteria in tropical soils is also beneficial.