Rhizobia
Encyclopedia
Soil
Soil is a natural body consisting of layers of mineral constituents of variable thicknesses, which differ from the parent materials in their morphological, physical, chemical, and mineralogical characteristics...
bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
that fix
Nitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
(diazotrophs) after becoming established inside root nodule
Root nodule
Root nodules occur on the roots of plants that associate with symbiotic nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria known as rhizobia...
s of legumes (Fabaceae
Fabaceae
The Fabaceae or Leguminosae, commonly known as the legume, pea, or bean family, is a large and economically important family of flowering plants. The group is the third largest land plant family, behind only the Orchidaceae and Asteraceae, with 730 genera and over 19,400 species...
). Rhizobia require a plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
host
Host (biology)
In biology, a host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. In botany, a host plant is one that supplies food resources and substrate for certain insects or other fauna...
; they cannot independently fix nitrogen. Morphologically
Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....
, they are generally gram negative
Gram staining
Gram staining is a method of differentiating bacterial species into two large groups ....
, motile, non-sporulating
Sporogenesis
Sporogenesis is the production of spores in biology. The term is also used to refer to the process of reproduction via spores. Reproductive spores are formed in many eukaryotic organisms, such as plants, algae and fungi, during their normal reproductive life cycle...
rods.
History
The first speciesSpecies
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
of rhizobia, Rhizobium leguminosarum, was identified in 1889, and all further species were initially placed in the Rhizobium
Rhizobium
Rhizobium is a genus of Gram-negative soil bacteria that fix nitrogen. Rhizobium forms an endosymbiotic nitrogen fixing association with roots of legumes and Parasponia....
genus
Genus
In biology, a genus is a low-level taxonomic rank used in the biological classification of living and fossil organisms, which is an example of definition by genus and differentia...
. However, more advanced methods of analysis have revised this classification
Biological classification
Biological classification, or scientific classification in biology, is a method to group and categorize organisms by biological type, such as genus or species. Biological classification is part of scientific taxonomy....
, and now there are many in other genera. Most research has been done on crop
Crop (agriculture)
A crop is a non-animal species or variety that is grown to be harvested as food, livestock fodder, fuel or for any other economic purpose. Major world crops include maize , wheat, rice, soybeans, hay, potatoes and cotton. While the term "crop" most commonly refers to plants, it can also include...
and forage
Forage
Forage is plant material eaten by grazing livestock.Historically the term forage has meant only plants eaten by the animals directly as pasture, crop residue, or immature cereal crops, but it is also used more loosely to include similar plants cut for fodder and carried to the animals, especially...
legumes such as clover
Clover
Clover , or trefoil, is a genus of about 300 species of plants in the leguminous pea family Fabaceae. The genus has a cosmopolitan distribution; the highest diversity is found in the temperate Northern Hemisphere, but many species also occur in South America and Africa, including at high altitudes...
, alfalfa
Alfalfa
Alfalfa is a flowering plant in the pea family Fabaceae cultivated as an important forage crop in the US, Canada, Argentina, France, Australia, the Middle East, South Africa, and many other countries. It is known as lucerne in the UK, France, Australia, South Africa and New Zealand, and known as...
, bean
Bean
Bean is a common name for large plant seeds of several genera of the family Fabaceae used for human food or animal feed....
s, and soy; recently, more work is occurring on North American legumes.
The word rhizobia comes from the Ancient Greek
Ancient Greek
Ancient Greek is the stage of the Greek language in the periods spanning the times c. 9th–6th centuries BC, , c. 5th–4th centuries BC , and the c. 3rd century BC – 6th century AD of ancient Greece and the ancient world; being predated in the 2nd millennium BC by Mycenaean Greek...
, rhíza, meaning "root" and , bios, meaning "life". The word rhizobium is still sometimes used as the singular form of rhizobia
Taxonomy
Rhizobia are a paraphyletic group which fall into two classesClass (biology)
In biological classification, class is* a taxonomic rank. Other well-known ranks are life, domain, kingdom, phylum, order, family, genus, and species, with class fitting between phylum and order...
of the proteobacteria
Proteobacteria
The Proteobacteria are a major group of bacteria. They include a wide variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, and many other notable genera....
—the alpha- and beta-proteobacteria. As shown below, most belong to the order Rhizobiales
Rhizobiales
Rhizobiales is an order of alpha proteobacteria. They are gram-negative.The rhizobia, which fix nitrogen and are symbiotic with plant roots, appear in several different families here. The Bradyrhizobiaceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae are the four families that contain...
, but several rhizobia occur in distinct bacterial orders of the proteobacteria.
α-proteobacteria
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β-proteobacteria
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These groups include a variety of non-symbiotic
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
bacteria. For instance, the plant pathogen
Pathogen
A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...
Agrobacterium
Agrobacterium
Agrobacterium is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. Agrobacterium tumefaciens is the most commonly studied species in this genus...
is a closer relative of Rhizobium than the Bradyrhizobium that nodulate soybean (and may not really be a separate genus). The gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s responsible for the symbiosis
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
with plants, however, may be more closely related than the organisms themselves, acquired by horizontal transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...
(via bacterial conjugation
Bacterial conjugation
Bacterial conjugation is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells...
) rather than vertical gene transfer (from a common ancestor
Common descent
In evolutionary biology, a group of organisms share common descent if they have a common ancestor. There is strong quantitative support for the theory that all living organisms on Earth are descended from a common ancestor....
).
Importance in agriculture
Although much of the nitrogen is removed when proteinProtein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
-rich grain
Cereal
Cereals are grasses cultivated for the edible components of their grain , composed of the endosperm, germ, and bran...
or hay
Hay
Hay is grass, legumes or other herbaceous plants that have been cut, dried, and stored for use as animal fodder, particularly for grazing livestock such as cattle, horses, goats, and sheep. Hay is also fed to pets such as rabbits and guinea pigs...
is harvest
Harvest
Harvest is the process of gathering mature crops from the fields. Reaping is the cutting of grain or pulse for harvest, typically using a scythe, sickle, or reaper...
ed, significant amounts can remain in the soil for future crops. This is especially important when nitrogen fertilizer
Fertilizer
Fertilizer is any organic or inorganic material of natural or synthetic origin that is added to a soil to supply one or more plant nutrients essential to the growth of plants. A recent assessment found that about 40 to 60% of crop yields are attributable to commercial fertilizer use...
is not used, as in organic
Organic farming
Organic farming is the form of agriculture that relies on techniques such as crop rotation, green manure, compost and biological pest control to maintain soil productivity and control pests on a farm...
rotation schemes
Crop rotation
Crop rotation is the practice of growing a series of dissimilar types of crops in the same area in sequential seasons.Crop rotation confers various benefits to the soil. A traditional element of crop rotation is the replenishment of nitrogen through the use of green manure in sequence with cereals...
or some less-industrialized
Industrialisation
Industrialization is the process of social and economic change that transforms a human group from an agrarian society into an industrial one...
countries. Nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
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.
Symbiosis
Rhizobia are unique because they live 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 flavonoidFlavonoid
Flavonoids , are a class of plant secondary metabolites....
s secreted by the roots of their host legume plant. Flavonoids trigger the secretion of nod factor
Nod factor
Nodulation factors are signaling molecules produced by bacteria known as rhizobia during the initiation of nodules on the root of legumes. A symbiosis is formed when legumes take up the bacteria...
s, which in turn are recognized by the host plant and can lead to root hair deformation and several cellular responses, such as ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...
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
Endocytosis
Endocytosis is a process by which cells absorb molecules by engulfing them. It is used by all cells of the body because most substances important to them are large polar molecules that cannot pass through the hydrophobic plasma or cell membrane...
, 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.
The infection triggers cell division
Cell division
Cell division is the process by which a parent cell divides into two or more daughter cells . Cell division is usually a small segment of a larger cell cycle. This type of cell division in eukaryotes is known as mitosis, and leaves the daughter cell capable of dividing again. The corresponding sort...
in the cortex
Cortex (botany)
In botany, the cortex is the outer layer of the stem or root of a plant, bounded on the outside by the epidermis and on the inside by the endodermis. It is composed mostly of undifferentiated cells, usually large thin-walled parenchyma cells of the ground tissue system. The outer cortical cells...
of the root where a new organ, the nodule, appears as a result of successive processes.
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 atmosphereAtmosphere
An atmosphere is a layer of gases that may surround a material body of sufficient mass, and that is held in place by the gravity of the body. An atmosphere may be retained for a longer duration, if the gravity is high and the atmosphere's temperature is low...
into a plant-usable form, ammonium
Ammonium
The ammonium cation is a positively charged polyatomic cation with the chemical formula NH. It is formed by the protonation of ammonia...
(NH4+), using the enzyme nitrogenase
Nitrogenase
Nitrogenases are enzymes used by some organisms to fix atmospheric nitrogen gas . It is the only known family of enzymes that accomplish this process. Dinitrogen is quite inert because of the strength of its N-N triple bond...
. In return, the plant supplies the bacteria with carbohydrate
Carbohydrate
A carbohydrate is an organic compound with the empirical formula ; that is, consists only of carbon, hydrogen, and oxygen, with a hydrogen:oxygen atom ratio of 2:1 . However, there are exceptions to this. One common example would be deoxyribose, a component of DNA, which has the empirical...
s, protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
s, and sufficient oxygen
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
so as not to interfere with the fixation process. Leghaemoglobins
Leghemoglobin
Leghemoglobin is a nitrogen or oxygen carrier, because naturally occurring oxygen and nitrogen interact similarly with this protein; and a hemoprotein found in the nitrogen-fixing root nodules of leguminous plants. But nitrogen is necessary for the cycle to occur...
, plant proteins similar to human hemoglobin
Hemoglobin
Hemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates, with the exception of the fish family Channichthyidae, as well as the tissues of some invertebrates...
s, help to provide oxygen for respiration
Cellular respiration
Cellular respiration is the set of the metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate , and then release waste products. The reactions involved in respiration are catabolic reactions that involve...
while keeping the free oxygen concentration low enough not to inhibit nitrogenase
Nitrogenase
Nitrogenases are enzymes used by some organisms to fix atmospheric nitrogen gas . It is the only known family of enzymes that accomplish this process. Dinitrogen is quite inert because of the strength of its N-N triple bond...
activity. Recently, a Bradyrhizobium strain was discoveredd to form nodules in Aeschynomene
Aeschynomene
Aeschynomene is a genus of flowering plants in the family Fabaceae. They are known commonly as jointvetches. These legumes are most common in warm regions and many species are aquatic...
without producing nod factors, suggesting the existence of alternative communication signals other than nod factors.
The legume–rhizobium symbiosis
Symbiosis
Symbiosis is close and often long-term interaction between different biological species. In 1877 Bennett used the word symbiosis to describe the mutualistic relationship in lichens...
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 acid
Dicarboxylic acid
Dicarboxylic acids are organic compounds that contain two carboxylic acid functional groups. In molecular formulae for dicarboxylic acids, these groups are often written as HOOC-R-COOH, where R may be an alkyl, alkenyl, alkynyl, or aryl group...
s malate
Malic acid
Malic acid is an organic compound with the formula HO2CCH2CHOHCO2H. It is a dicarboxylic acid which is made by all living organisms, contributes to the pleasantly sour taste of fruits, and is used as a food additive. Malic acid has two stereoisomeric forms , though only the L-isomer exists...
and succinate
Succinic acid
Succinic acid is a dicarboxylic acid. Succinate plays a biochemical role in the citric acid cycle. The name derives from Latin succinum, meaning amber, from which the acid may be obtained....
) as a carbon and energy source—but its evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...
ary persistence is actually somewhat surprising. Because several unrelated strains infect each individual plant, any one strain could redirect resources from nitrogen fixation
Nitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
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
Tragedy of the commons
The tragedy of the commons is a dilemma arising from the situation in which multiple individuals, acting independently and rationally consulting their own self-interest, will ultimately deplete a shared limited resource, even when it is clear that it is not in anyone's long-term interest for this...
. 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
Oxygen
Oxygen is the element with atomic number 8 and represented by the symbol O. Its name derives from the Greek roots ὀξύς and -γενής , because at the time of naming, it was mistakenly thought that all acids required oxygen in their composition...
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. Similarly, 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 (diazotrophDiazotroph
Diazotrophs are bacteria and archaea that fix atmospheric nitrogen gas into a more usable form such as ammonia.A diazotroph is an organism that is able to grow without external sources of fixed nitrogen. Examples of organisms that do this are rhizobia and Frankia and Azospirillum. All diazotrophs...
s), 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
Actinobacteria
Actinobacteria are a group of Gram-positive bacteria with high guanine and cytosine content. They can be terrestrial or aquatic. Actinobacteria is one of the dominant phyla of the bacteria....
Frankia
Frankia
Frankia is a genus of nitrogen fixing, filamentous bacteria that live in symbiosis with actinorhizal plants, similar to the Rhizobia bacteria that are found in the root nodules of legumes in the Fabaceae family. Bacteria of this genus also form root nodules.The genus Frankia was originally named by...
, which form symbiotic root nodules in actinorhizal plant
Actinorhizal plant
Actinorhizal plants are a group of angiosperms characterized by their ability to form a symbiosis with the nitrogen fixing actinobacteria Frankia...
s, and several cyanobacteria (Nostoc) associated with aquatic ferns, Cycas
Cycas
Cycas is the type genus and the only genus currently recognised in the cycad family Cycadaceae. About 95 species are currently accepted. The best-known species is Cycas revoluta, widely cultivated under the name "Sago Palm" or "King Sago Palm" due to its palm-like appearance although it is not a...
and Gunnera
Gunnera
Gunnera is a genus of herbaceous flowering plants, some of them gigantic. The genus is the only member of the family Gunneraceae.The 40-50 species vary enormously in leaf size...
s. Free-living diazotrophs are often found in the rhizosphere
Rhizosphere
The rhizosphere is the narrow region of soil that is directly influenced by root secretions and associated soil microorganisms. Soil which is not part of the rhizosphere is known as bulk soil. The rhizosphere contains many bacteria that feed on sloughed-off plant cells, termed rhizodeposition, and...
and in the intercellular spaces of several plants including rice
Rice
Rice is the seed of the monocot plants Oryza sativa or Oryza glaberrima . As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies...
and sugarcane
Sugarcane
Sugarcane refers to any of six to 37 species of tall perennial grasses of the genus Saccharum . Native to the warm temperate to tropical regions of South Asia, they have stout, jointed, fibrous stalks that are rich in sugar, and measure two to six metres tall...
, but in this case the lack of a specialized structure results in poor nutrient transfer efficiency compared to legume or actinorhizal nodules.