Rhizobia are soil bacteria that fix nitrogen (diazotrophs) after becoming established inside root nodules of legumes (Fabaceae). Rhizobia require a plant host; they cannot independently fix nitrogen. In general, they are Gram-negative, motile, non-sporulating rods.
The first species of rhizobia, Rhizobium leguminosarum, was identified in 1889, and all further species were initially placed in the Rhizobium genus. However, more advanced methods of analysis have revised this classification, and now there are many in other genera. Most research has been done on crop and forage legumes such as clover, alfalfa, beans, and soy; recently, more work is occurring on North American legumes.
The word rhizobia comes from the Ancient Greek ῥίζα, rhíza, meaning "root" and βίος, bios, meaning "life". The word rhizobium is still sometimes used as the singular form of rhizobiaThey are parasitic.
Rhizobia are a paraphyletic group that fall into two classes of the proteobacteria—the alpha- and beta-proteobacteria. As shown below, most belong to the order Rhizobiales, but several rhizobia occur in distinct bacterial orders of the proteobacteria.
These groups include a variety of non-symbiotic bacteria. For instance, the plant pathogen Agrobacterium is a closer relative of Rhizobium than the Bradyrhizobium that nodulate soybean (and may not really be a separate genus). The genes responsible for the symbiosis with plants, however, may be more closely related than the organisms themselves, acquired by horizontal transfer (via bacterial conjugation) rather than vertical gene transfer (from a common ancestor).
Importance in agriculture 
Although much of the nitrogen is removed when protein-rich grain or hay is harvested, significant amounts can remain in the soil for future crops. This is especially important when nitrogen fertilizer is not used, as in organic rotation schemes or some less-industrialized countries. Nitrogen is the most commonly deficient nutrient in many soils around the world and it is the most commonly supplied plant nutrient. Supply of nitrogen through fertilizers has severe environmental concerns.
Symbiotic relationship 
Rhizobia are unique in that they are the only nitrogen-fixing bacteria living in a symbiotic relationship with legumes. Common crop and forage legumes are peas, beans, clover, and soy.
Infection and signal exchange 
The symbiotic relationship implies a signal exchange between both partners that leads to mutual recognition and development of symbiotic structures. Rhizobia live in the soil where they are able to sense flavonoids secreted by the roots of their host legume plant. Flavonoids trigger the secretion of nod factors, which in turn are recognized by the host plant and can lead to root hair deformation and several cellular responses, such as ion fluxes. The best-known infection mechanism is called intracellular infection, in this case the rhizobia enter through a deformed root hair in a similar way to endocytosis, forming an intracellular tube called the infection thread. A second mechanism is called "crack entry"; in this case, no root hair deformation is observed and the bacteria penetrate between cells, through cracks produced by lateral root emergence. Later on, the bacteria become intracellular and an infection thread is formed like in intracellular infections.
Nodule formation and functioning 
Infection threads grow to the nodule, infect its central tissue and release the rhizobia in these cells, where they differentiate morphologically into bacteroids and fix nitrogen from the atmospheric, elemental N2 into a plant-usable form, ammonium (NH3 + H+ → NH4+), using the enzyme nitrogenase. The reaction for all nitrogen-fixing bacteria is:
- N2 + 8 H+ + 8 e− → 2 NH3 + H2
In return, the plant supplies the bacteria with carbohydrates, proteins, and sufficient oxygen so as not to interfere with the fixation process. Leghaemoglobins, plant proteins similar to human hemoglobins, help to provide oxygen for respiration while keeping the free oxygen concentration low enough not to inhibit nitrogenase activity. Recently, a Bradyrhizobium strain was discovered to form nodules in Aeschynomene without producing nod factors, suggesting the existence of alternative communication signals other than nod factors.
The legume–rhizobium symbiosis is a classic example of mutualism—rhizobia supply ammonia or amino acids to the plant and in return receive organic acids (principally as the dicarboxylic acids malate and succinate) as a carbon and energy source—but its evolutionary persistence is actually somewhat surprising. Because several unrelated strains infect each individual plant, any one strain could redirect resources from nitrogen fixation to its own reproduction without killing the host plant upon which they all depend. But this form of cheating should be equally tempting for all strains, a classic tragedy of the commons. There are two competing hypotheses for the mechanism that maintains legume-rhizobium symbiosis (though both may occur in nature). The sanctions hypothesis suggests the plants police cheating rhizobia. Sanctions could take the form of reduced nodule growth, early nodule death, decreased carbon supply to nodules, or reduced oxygen supply to nodules that fix less nitrogen. The partner choice hypothesis proposes that the plant uses prenodulation signals from the rhizobia to decide whether to allow nodulation, and chooses only noncheating rhizobia. There is evidence for sanctions in soybean plants, which reduce rhizobium reproduction (perhaps by limiting oxygen supply) in nodules that fix less nitrogen. Likewise, wild lupine plants allocate fewer resources to nodules containing less-beneficial rhizobia, limiting rhizobial reproduction inside. This is consistent with the definition of sanctions just given, although called "partner choice" by the authors. However, other studies have found no evidence of plant sanctions, and instead support the partner choice hypothesis.
Other diazotrophs 
Many other species of bacteria are able to fix nitrogen (diazotrophs), but few are able to associate intimately with plants and colonize specific structures like Legume nodules. Bacteria that do associate with plants include the actinobacteria Frankia, which form symbiotic root nodules in actinorhizal plants, and several cyanobacteria (Nostoc) associated with aquatic ferns, Cycas and Gunneras. Free-living diazotrophs are often found in the rhizosphere and in the intercellular spaces of several plants including rice and sugarcane, but in this case the lack of a specialized structure results in poor nutrient transfer efficiency compared to legume or actinorhizal nodules.
- "Current taxonomy of rhizobia". Retrieved 2006-08-07.
- "Taxonomy of legume nodule bacteria (rhizobia) and agrobacteria". Retrieved 2008-11-14.
- "What is Rhizobia". Retrieved 2008-07-01.
- The Nitrogen cycle and Nitrogen fixation, Jim Deacon, Institute of Cell and Molecular Biology, The University of Edinburgh http://www.biology.ed.ac.uk/archive/jdeacon/microbes/nitrogen.htm
- Giraud, Eric; et al., L; Vallenet, D; Barbe, V; Cytryn, E; Avarre, JC; Jaubert, M; Simon, D et al. (2007). "Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia". Science 316 (5829): 1307–12. doi:10.1126/science.1139548. PMID 17540897.
- Denison, R. F. (2000). "Legume sanctions and the evolution of symbiotic cooperation by rhizobia". American Naturalist 156: 567–576.
- Kiers ET, Rousseau RA, West SA, Denison RF 2003. Host sanctions and the legume–rhizobium mutualism. Nature 425 : 79-81
- Simms et al. 2006. An empirical test of partner choice mechanisms in a wild legume-rhizobium interaction. Proc. Roy. Soc. B 273:77-81.
- Heath, K. D.; Tiffin, P. (2009). "Stabilizing mechanisms in legume-rhizobium mutualism". Evolution 63: 652–662.
- Marco, D. E., R. Perez-Arnedo, A. Hidalgo-Perea, J. Olivares, J. E. Ruiz-Sainz, and J. Sanjuan. 2009. A mechanistic molecular test of the plant-sanction hypothesis in legume-rhizobia mutualism. Acta Oecologica-International Journal of Ecology 35:664-667
- Jones, KM; et al., H; Davies, BW; Taga, ME; Walker, GC (2007). "How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model". Nat Rev Microbiol. 5 (8): 619–33. doi:10.1038/nrmicro1705. PMC 2766523. PMID 17632573.