Although the earth's atmosphere is 78% nitrogen, free gaseous nitrogen cannot be utilized by animals or by higher plants. They depend instead on nitrogen that is present in the soil. To enter living systems, nitrogen must be "fixed" (combined with oxygen or hydrogen) into compounds that plants can utilize, such as nitrates or ammonia. A certain amount of atmospheric nitrogen is fixed by lightning and by some cyanobacteria (blue-green algae). But the great bulk of nitrogen fixation is performed by soil bacteria of two kinds: those that live free in the soil and those that live enclosed in nodules in the roots of certain leguminous plants (e.g., alfalfa, peas, beans, clover, soybeans, and peanuts). Among the free-living forms are species of Clostridium, discovered c.1893 by Sergei Winogradsky, and Azotobacter, discovered c.1901 by M. W. Beijerinck. Both Clostridium and Azotobacter are generally present in agricultural soils, and both are saprophytes, i.e., they use the energy from decaying organic matter in the soil to fuel soil processes, including nitrogen fixation.
Bacteria that live in the roots of legumes are of the genus Rhizobium, first isolated c.1888 by Beijerinck. These rod-shaped bacteria enter the roots chiefly through the root hairs and then work their way to the inner root tissues. There they stimulate the growth of tumorlike nodules. Within the nodules the bacteria develop into forms called bacteroids, which live in a symbiotic (mutually beneficial) relationship with the green plant. The bacteroids take carbohydrates from the plant for energy to fix nitrogen and synthesize amino acids; the plants take the amino acids elaborated in the nodule to build plant tissue. Animals in turn consume the plants and convert plant protein into animal protein. Rhizobia can be found free-living in the soil, but they cannot fix nitrogen in the free state, nor can the legume root fix nitrogen without Rhizobia.
The exact biochemistry of nitrogen fixation within the nodule is not yet understood. It is estimated that more than 300 lbs of nitrogen per acre (340 kg per hectare) can be fixed by fields of alfalfa and other legumes. After a harvest legume roots left in the soil decay, returning organic nitrogen compounds to the soil for uptake by the next generation of plants. For this reason crop rotation in which a leguminous crop is rotated with a nonleguminous one is a common practice for maintaining soil fertility.