Symbioses are associations between individuals of two different species and are very widespread in nature. Parasitism is a form of symbiosis where one of the partners in the association is harmed, and mutualism is an association where both partners benefit. The association between root systems and microbes are often of the mutualistic type.

      Nitrogen is the most abundant element in the earth's atmosphere (roughly 80%) but cannot be taken up directly by plants because plants lack the enzymes needed to break up the triple bond in N₂. Nitrogen fixation is the conversion of this diatomic nitrogen to compounds that can be assimilated by plants and is accomplished only by certain bacteria. While some nitrogen-fixing bacteria live freely in the soil, others form mutualistic symbioses with plant roots. The bacteria in such symbioses receive photosynthates from the plant while the plant gets a usable form of nitrogen from the bacteria. These mutualistic bacteria live in nodules on the roots of 10 different angiosperm families including legumes.

      The presence of these nitrogen-fixing nodules on crops minimizes the use of commercial fertilizers, and thus they are environmentally beneficial. A great deal of genetic research is being done in hopes of transferring the capacity to form nodules, or the capacity to fix nitrogen or both to other crops.

      Certain plants release flavenoids into the soil that attract nitrogen-fixing bacteria. In response to the flavenoids the bacteria produce factors coded on nod genes. The nodule-forming plant responds to the nod factors by curling of root hairs and formation of infection threads by which the bacteria enter the host root. The bacteria take up residence in enlarged cells in the root cortex.

      Root nodules may be indeterminate in nature, growing as long as the plant grows. This type of nodule is found in association with alfalfa and peas. Determinate nodules are found in association with soybeans.

Coralloid Roots of Cycads

      Cycads produce specialized roots in response to mutualistic nitrogen-fixing cyanobacteria. Such roots are apogeotropic (uninfluenced in their growth by the force of gravity) and termed "coralloid" because they resemble dichotomously branched coral. Coralloid roots are occupied by the cyanobacterial (bluegreen algal) genera Anabaena or Nostoc. Since the algae require light for photosynthesis, the coralloid roots are commonly found near the soil surface.

Mycorrhizae

      The root systems of many plants are associated with mycorrhizal fungi that are involved in the uptake of phosphorus and other essential nutrients including zinc, manganese, and copper. The fungal hyphae extend outward from the root, increasing the surface area for water and nutrient uptake. The hyphae that penetrate into the root's interior deposit the nutrients inside root. Mycorrhizae may be ectotrophic, forming a mantle of hyphae around the root periphery. The hyphae also penetrate the cortical intercellular spaces but not the protoplast of the host cells. In contrast, endotrophic mycorrhizae invade the cells of the host. Suberin in the Casparian strip of the root's endodermis prevents fungal hyphae from entering the root's vascular tissue.

      Mycorrhizae can have an enormous impact on a plant's ability to grow. Without the essential nutrients provided by these root symbionts a plant will struggle to survive. Plants with mycorrhizal associations often have less extensive root systems than plants without such associations.