''Bradyrhizobium'' is a genus of

Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wa ...

soil bacteria, many of which fix nitrogen.

Nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...

is an important part of the nitrogen cycle. Plants cannot use atmospheric nitrogen (N₂); they must use nitrogen compounds such as nitrates.

Characteristics

''Bradyrhizobium'' species are Gram-negative bacilli (rod-shaped) with a single subpolar or polar

flagellum A flagellum (; ) is a hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility. Many protists with flagella are termed as flagellates. A microorganism may have f ...

. They are common soil-dwelling micro-organisms that can form symbiotic relationships with

leguminous A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock for ...

plant species where they fix nitrogen in exchange for

carbohydrate In organic chemistry, a carbohydrate () is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water) and thus with the empirical formula (where ''m'' may or m ...

s from the plant. Like other rhizobia, many members of this genus have the ability to fix atmospheric nitrogen into forms readily available for other organisms to use. Bradyrhizobia are also major components of forest soil microbial communities, where strains isolated from these soils are not typically capable of nitrogen fixation or nodulation. They are slow-growing in contrast to ''

Rhizobium ''Rhizobium'' is a genus of Gram-negative soil bacteria that fix nitrogen. ''Rhizobium'' species form an endosymbiotic nitrogen-fixing association with roots of (primarily) legumes and other flowering plants. The bacteria colonize plant cells ...

'' species, which are considered fast-growing rhizobia. In a liquid medium, ''Bradyrhizobium'' species take 3–5 days to create a moderate turbidity and 6–8 hours to double in population size. They tend to grow best with

pentose In chemistry, a pentose is a monosaccharide (simple sugar) with five carbon atoms. The chemical formula of many pentoses is , and their molecular weight is 150.13 g/mol. Some strains (for example, USDA 6 and CPP) are capable of oxidizing carbon monoxide aerobically.

Taxonomy

Accepted Species

''Bradyrhizobium'' comprises the following species: * '' B. agreste'' Klepa ''et al''. 2021 * '' B. algeriense'' Ahnia ''et al''. 2019 * '' B. americanum'' Ramírez-Bahena ''et al''. 2017 * '' B. amphicarpaeae'' Bromfield ''et al''. 2019 * '' B. arachidis'' Wang ''et al''. 2013 * '' B. archetypum'' Helene ''et al''. 2020 * '' B. australiense'' Helene ''et al''. 2020 * '' B. betae'' Rivas ''et al''. 2004 * '' B. cajani'' Araújo ''et al''. 2017 * '' B. canariense'' Vinuesa ''et al''. 2005 * '' B. centrosematis'' corrig. Ramírez-Bahena ''et al''. 2017 * '' B. cosmicum'' Wasai-Hara ''et al''. 2020 * '' B. cytisi'' Chahbourne ''et al''. 2011 * '' B. daqingense'' Wang JY ''et al''. 2012 * '' B. denitrificans'' (Hirsch and Müller 1986) van Berkum ''et al''. 2011 * '' B. diazoefficiens'' Delamuta ''et al'' 2013 * '' B. diversitatis'' Serenato Klepa ''et al''. 2021 * '' B. elkanii'' Kuykendall ''et al''. 1993 * '' B. embrapense'' Delamuta ''et al.''2015 * '' B. erythrophlei'' Yao ''et al''. 2015 * '' B. ferriligni'' Yao ''et al''. 2015 * '' B. frederickii'' de Oliveira Urquiaga ''et al''. 2019 * '' B. ganzhouense'' Lu ''et al''. 2014 * '' B. glycinis'' Serenato Klepa ''et al''. 2021 * '' B. guangdongense'' Li ''et al''. 2015 * '' B. guangxiense'' Li ''et al''. 2015 * '' B. hipponense'' Rejili ''et al''. 2020 * '' B. huanghuaihaiense'' Zhang ''et al''. 2012 * '' B. icense'' Durán ''et al''. 2014 * '' B. ingae'' da Silva ''et al''. 2014 * '' B. iriomotense'' Islam ''et al''. 2010 * '' B. ivorense'' Fossou ''et al''. 2020 * '' B. japonicum'' (Kirchner 1896) Jordan 1982 ** symbiovar ''genistearum'' ** symbiovar ''glycinearum'' * '' B. jicamae'' Ramírez-Bahena ''et al''. 2009 * '' B. kavangense'' Lasse gronemeyer et al. 2015 * '' B. lablabi'' Chang ''et al''. 2011 * '' B. liaoningense'' Xu ''et al''. 1995 * '' B. lupini'' Peix ''et al''. 2015 * '' B. manausense'' Silva ''et al''. 2014 * '' B. mercantei'' Helene ''et al''. 2017 * '' B. murdochi'' Helene ''et al''. 2020 * '' B. namibiense'' Grönemeyer ''et al''. 2017 * '' B. nanningense'' Li ''et al''. 2020 * '' B. neotropicale'' Zilli ''et al''. 2014 * '' B. niftali'' Klepa ''et al''. 2019 * '' B. nitroreducens'' Jang ''et al''. 2020 * '' B. oligotrophicum'' (Ohta and Hattori 1985) Ramírez-Bahena ''et al''. 2013 * '' B. ottawaense'' Yu ''et al''. 2014 * '' B. pachyrhizi'' Ramírez-Bahena ''et al''. 2009 * '' B. paxllaeri'' Durán ''et al''. 2014 * '' B. retamae'' Guerrouj ''et al''. 2013 * '' B. rifense'' Chahboune ''et al''. 2012 * '' B. ripae'' Bünger ''et al''. 2018 * '' B. shewense'' Aserse ''et al''. 2018 * '' B. stylosanthis'' Marçon Delamuta ''et al''. 2016 * '' B. subterraneum'' Gronemeyer ''et al''. 2015 * '' B. symbiodeficiens'' Bromfield ''et al''. 2020 * '' B. tropiciagri'' Delamuta et al. 2015 * '' B. vignae'' Grönemeyer ''et al''. 2016 * '' B. viridifuturi'' Helene et al. 2015 * '' B. yuanmingense'' Yao ''et al''. 2002

Provisional Species

The following species have been published, but not validated according to the

Bacteriological Code The International Code of Nomenclature of Prokaryotes (ICNP) formerly the International Code of Nomenclature of Bacteria (ICNB) or Bacteriological Code (BC) governs the scientific names for Bacteria and Archaea.P. H. A. Sneath, 2003. A short histor ...

. * "''B. brasilense''" Martins da Costa ''et al''. 2017 * "''B. campsiandrae''" Cabral Michel ''et al''. 2021 * "''B. centrolobii''" Michel ''et al''. 2017 * "''B. forestalis''" Martins da Costa ''et al''. 2018 * "''B. guangzhouense''" Li ''et al''. 2019 * "''B. macuxiense''" Michel ''et al''. 2017 * "''B. sacchari''" de Matos ''et al''. 2017 * "'' Photorhizobium thompsonianum''" Eaglesham ''et al''. 1990 * "''B. uaiense''" Cabral Michel ''et al''. 2020 * "'' B. valentinum''" Durán ''et al''. 2014 * "''B. zhanjiangense''" Li ''et al''. 2019

Phylogeny

The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the nomenclature, naming and Taxonomy (biology), taxonomy of prokaryotes, following the taxonomy requirements and rulings of the In ...

(LPSN). The phylogeny is based on whole-genome analysis.

Nodulation

Nodule formation

Nodules are growths on the roots of leguminous plants where the bacteria reside. The plant roots secrete

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha a ...

s and sugars into the

rhizosphere The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microo ...

. The rhizobia move toward the roots and attach to the root hairs. The plant then releases flavonoids, which induce the expression of ''nod'' genes within the bacteria. The expression of these genes results in the production of enzymes called

Nod factor Nod factors (nodulation factors or NF), are signaling molecules produced by soil bacteria known as rhizobia in response to flavonoid exudation from plants under nitrogen limited conditions. Nod factors initiate the establishment of a symbiotic rel ...

s that initiate

root hair curling Root nodules are found on the roots of plants, primarily legumes, 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 a ...

. During this process, the rhizobia are curled up with the root hair. The rhizobia penetrate the root hair cells with an infection thread that grows through the root hair into the main root. This causes the infected cells to divide and form a nodule. The rhizobia can now begin nitrogen fixation.

''Nod'' genes

Over 55 genes are known to be associated with nodulation. ''NodD'' is essential for the expression of the other ''nod'' genes. The two different ''nodD'' genes are: ''nodD₁'' and ''nodD₂''. Only ''nodD₁'' is needed for successful nodulation.

Nitrogen fixation

''Bradyrhizobium'' and other rhizobia take atmospheric nitrogen and fix it into ammonia (NH₃) or ammonium (NH₄⁺). Plants cannot use atmospheric nitrogen; they must use a combined or fixed form of the element. After

photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...

nitrogen fixation Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...

(or uptake) is the most important process for the growth and development of plants. The levels of ureide nitrogen in a plant correlate with the amount of fixed nitrogen the plant takes up.

Genes

''Nif'' and ''fix'' are important genes involved in nitrogen fixation among ''Bradyrhizobium'' species. ''Nif'' genes are very similar to genes found in ''

Klebsiella pneumoniae ''Klebsiella pneumoniae'' is a Gram-negative, non-motile, encapsulated, lactose- fermenting, facultative anaerobic, rod-shaped bacterium. It appears as a mucoid lactose fermenter on MacConkey agar. Although found in the normal flora of the mo ...

'', a free-living

diazotroph Diazotrophs are bacteria and archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia. A diazotroph is a microorganism that is able to grow without external sources of fixed nitrogen. Examples of organisms that ...

. The genes found in bradyrhizobia have similar function and structure to the genes found in ''K. pneumoniae''. ''Fix'' genes are important for symbiotic nitrogen fixation and were first discovered in rhizobia species. The ''nif'' and ''fix'' genes are found in at least two different clusters on the

chromosome A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...

. Cluster I contains most of the nitrogen fixation genes. Cluster II contains three ''fix'' genes located near ''nod'' genes.

Diversity

This genus of bacteria can form either specific or general symbioses; one species of ''Bradyrhizobium'' may only be able to nodulate one legume species, whereas other ''Bradyrhizobium'' species may be able to nodulate several legume species.

Ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosom ...

is highly conserved in this group of microbes, making ''Bradyrhizobium'' extremely difficult to use as an indicator of species diversity.

DNA–DNA hybridization In genomics, DNA–DNA hybridization is a molecular biology technique that measures the degree of genetic similarity between pools of DNA sequences. It is usually used to determine the genetic distance between two organisms and has been used ex ...

s have been used instead and show more diversity. However, few

phenotypic In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological proper ...

differences are seen, so not many species have been named. Some strains are photosynthetic, these ''Bradyrhizobium'' often form nodules in the stems of semi-aquatic ''

Aeschynomene ''Aeschynomene'' is a genus of flowering plants in the family Fabaceae, and was recently assigned to the informal monophyletic ''Dalbergia'' clade of the Dalbergieae. They are known commonly as jointvetches. These legumes are most common in wa ...

'' legumes, and have also been found in the nodal roots of African wild rice '' Oryza breviligulata''.

Significance

Grain legumes are cultivated on about 1.5 million km² of land per year. The amount of nitrogen fixed annually is about 44–66 million tons worldwide, providing almost half of all nitrogen used in agriculture. Commercial inoculants of ''Bradyrhizobium'' are available. ''Bradyrhizobium'' has also been identified as a contaminant of DNA extraction kit reagents and

ultrapure water Ultrapure water (UPW), high-purity water or highly purified water (HPW) is water that has been purified to uncommonly stringent specifications. Ultrapure water is a term commonly used in manufacturing to emphasize the fact that the water is treated ...

systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets. The presence of nitrogen-fixing bacteria as contaminants may be due to the use of nitrogen gas in ultrapure water production to inhibit microbial growth in storage tanks.

Notable species

* '' Bradyrhizobium betae'' was isolated from tumor-like root deformations on sugar beets; they have an unknown symbiotic status. * '' Bradyrhizobium elkanii'', ''

Bradyrhizobium diazoefficiens ''Bradyrhizobium diazoefficiens'' is a species of bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), d ...

'', and '' Bradyrhizobium liaoningense'' establish symbiosis with soybeans. * ''

Bradyrhizobium japonicum ''Bradyrhizobium japonicum'' is a species of legume- root nodulating, microsymbiotic nitrogen-fixing bacteria. The species is one of many Gram-negative, rod-shaped bacteria commonly referred to as rhizobia. Within that broad classification, w ...

'' nodulates

soybean The soybean, soy bean, or soya bean (''Glycine max'') is a species of legume native to East Asia, widely grown for its edible bean, which has numerous uses. Traditional unfermented food uses of soybeans include soy milk, from which tofu a ...

cowpea The cowpea (''Vigna unguiculata'') is an annual herbaceous legume from the genus ''Vigna''. Its tolerance for sandy soil and low rainfall have made it an important crop in the semiarid regions across Africa and Asia. It requires very few inputs, ...

s, mung beans, and siratro. * '' Bradyrhizobium yuanmingense'' nodulates ''

Lespedeza ''Lespedeza'' is a genus of some 40 species (including nothospecies) of flowering plants in the pea family (Fabaceae), commonly known as bush clovers or (particularly East Asian species) Japanese clovers (''hagi''). The genus is native to warm t ...

''. * ''

Bradyrhizobium canariense ''Bradyrhizobium canariense'' is a species of legume- root nodulating, endosymbiont nitrogen-fixing bacterium. It is acid-tolerant and nodulates endemic Endemism is the state of a species being found in a single defined geographic location ...

'' nodulates genistoid legumes endemic to the Canary Islands. It has also been found in lupin and serradella nodules in western Australia and southern Africa.

References

{{Taxonbar, from=Q4955276 Bacteria genera Nitrobacteraceae