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Root nodules are found on the of , primarily , that form a symbiosis with nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria known as rhizobia. This process has evolved multiple times within the legumes, as well as in other species found within the Rosid clade. Legume crops include , , and .
Within legume root nodules, nitrogen gas (N2) from the atmosphere is converted into ammonia (NH3), which is then assimilated into amino acids (the building blocks of proteins), nucleotides (the building blocks of DNA and RNA as well as the important energy molecule ATP), and other cellular constituents such as , , and plant hormones. Their ability to fix gaseous nitrogen makes legumes an ideal agricultural organism as their requirement for nitrogen fertilizer is reduced. Indeed, high nitrogen content blocks nodule development as there is no benefit for the plant of forming the symbiosis. The energy for splitting the nitrogen gas in the nodule comes from sugar that is translocated from the leaf (a product of photosynthesis). Malate as a breakdown product of sucrose is the direct carbon source for the bacteroid. Nitrogen fixation in the nodule is very oxygen sensitive. Legume nodules harbor an iron containing protein called leghaemoglobin, closely related to animal myoglobin, to facilitate the diffusion of oxygen gas used in respiration.
The ability to fix nitrogen is far from universally present in these families. For instance, of 122 genera in the Rosaceae, only 4 genera are capable of fixing nitrogen. All these families belong to the orders Cucurbitales, Fagales, and Rosales, which together with the Fabales form a nitrogen-fixing clade (NFC) of . In this clade, Fabales were the first lineage to branch off; thus, the ability to fix nitrogen may be plesiomorphic and subsequently lost in most descendants of the original nitrogen-fixing plant; however, it may be that the basic genetics and physiological requirements were present in an incipient state in the last common ancestors of all these plants, but only evolved to full function in some of them:
| Family: Genera
Betulaceae: Alnus (alders) Cannabaceae: Trema | ...... | Coriariaceae: Coriaria
| ...... | Myricaceae:
| ...... | Rhamnaceae: | ...... | Rosaceae:
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Determinate nodules are found on certain tribes of tropical legume such as those of the genera Glycine (soybean), Phaseolus (common bean), and Vigna. and on some temperate legumes such as Lotus. These determinate nodules lose meristematic activity shortly after initiation, thus growth is due to cell expansion resulting in mature nodules which are spherical in shape. Another type of determinate nodule is found in a wide range of herbs, shrubs and trees, such as Arachis (peanut). These are always associated with the axils of lateral or adventitious roots and are formed following infection via cracks where these roots emerge and not using . Their internal structure is quite different from those of the soybean type of nodule.
Indeterminate nodules are found in the majority of legumes from all three sub-families, whether in temperate regions or in the tropics. They can be seen in Faboideae legumes such as Pisum (pea), Medicago (alfalfa), Trifolium (clover), and Vicia (vetch) and all mimosoid legumes such as acacias, the few nodulated Caesalpinioideae legumes such as partridge pea. They earned the name "indeterminate" because they maintain an active apical meristem that produces new cells for growth over the life of the nodule. This results in the nodule having a generally cylindrical shape, which may be extensively branched. Because they are actively growing, indeterminate nodules manifest zones which demarcate different stages of development/symbiosis:
This is the most widely studied type of nodule, but the details are quite different in nodules of peanut and relatives and some other important crops such as lupins where the nodule is formed following direct infection of rhizobia through the epidermis and where infection threads are never formed. Nodules grow around the root, forming a collar-like structure. In these nodules and in the peanut type the central infected tissue is uniform, lacking the uninfected ells seen in nodules of soybean and many indeterminate types such as peas and clovers.
Actinorhizal-type nodules are markedly different structures found in non-legumes. In this type, cells derived from the root cortex form the infected tissue, and the prenodule becomes part of the mature nodule. Despite this seemingly major difference, it is possible to produce such nodules in legumes by a single homeotic mutation.
Partial curling can even be achieved by nod factor alone. This was demonstrated by the isolation of nod factors and their application to parts of the root hair. The root hairs curled in the direction of the application, demonstrating the action of a root hair attempting to curl around a bacterium. Even application on lateral roots caused curling. This demonstrated that it is the nod factor itself, not the bacterium that causes the stimulation of the curling.
When the nod factor is sensed by the root, a number of biochemical and morphological changes happen: cell division is triggered in the root to create the nodule, and the root hair growth is redirected to curl around the bacteria multiple times until it fully encapsulates one or more bacteria. The bacteria encapsulated divide multiple times, forming a microcolony. From this microcolony, the bacteria enter the developing nodule through the infection thread, which grows through the root hair into the basal part of the epidermis cell, and onwards into the root cortex; they are then surrounded by a plant-derived symbiosome and differentiate into bacteroids that fix nitrogen.
Effective nodulation takes place approximately four weeks after crop, with the size, and shape of the nodules dependent on the crop. Crops such as soybeans, or peanuts will have larger nodules than forage legumes such as red clover, or alfalfa, since their nitrogen needs are higher. The number of nodules, and their internal color, will indicate the status of nitrogen fixation in the plant.
Nodulation is controlled by a variety of processes, both external (heat, acidic soils, drought, nitrate) and internal (autoregulation of nodulation, ethylene). Autoregulation of nodulation controls nodule numbers per plant through a systemic process involving the leaf. Leaf tissue senses the early nodulation events in the root through an unknown chemical signal, then restricts further nodule development in newly developing root tissue. The Leucine rich repeat (LRR) receptor kinases (NARK in soybean ( Glycine max); HAR1 in Lotus japonicus, SUNN in Medicago truncatula) are essential for autoregulation of nodulation (AON). Mutation leading to loss of function in these AON receptor kinases leads to supernodulation or hypernodulation. Often root growth abnormalities accompany the loss of AON receptor kinase activity, suggesting that nodule growth and root development are functionally linked. Investigations into the mechanisms of nodule formation showed that the ENOD40 gene, coding for a 12–13 amino acid protein 41, is up-regulated during nodule formation 3.
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