A mature rainforest is an association of many different types of flora and fauna, and is composed of innumerable communities which act together to form an incredibly complex entity. The communities which comprise the rainforest can vary in many ways: temperature, moisture, species present, available habitats, soil type, and topography. The number and kinds of organisms present will influence the form of the ecosystem, and, conversely, the environment in which these organisms find themselves will influence their functioning. Certain species, known as keystone species, are thought to have dominant roles in an ecosystem, although this is still somewhat controversial. The idea is that, if a keystone species is absent, the ecosystem will change dramatically or damaged irreparably. Thus it is not necessarily the number of species per se which is vital to an ecosystem, but the presence of certain essential species, such as seed-dispersing mammals or the canopy trees of rainforests.

The functioning of an ecosystem, at base, depends upon the ways in which energy is used by organisms in the system. These processes consist of the capture, transfer, and loss of energy. Rainforest organisms acquire nutrients by obtaining moisture from clouds, intercepting rainfall, and directly fixing substances, especially carbon and nitrogen, from the atmosphere. Epiphytes, which have no roots, are vital in the rainforest ecosystem, as they obtain most of their nutrients from the atmosphere and so act as a major pathway for transferring nutrients from the atmosphere to other vegetation. They do this by intercepting and storing water, concentrating nutrients in their tissues, and eventually transferring nutrients to the soil through their stems or by dying. This is extremely important since the nutrient content of tropical soils is often so low. Plants store nutrients in their tissues; in fact, most nutrients in tropical forests are contained within the organisms, not in the soil. Most nutrients in tropical rainforest soils therefore come from dead and decaying organisms – plant, animal, fungal and microbial.

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