''Bradyrhizobium japonicum'' is a species of

legume Legumes are plants in the pea family Fabaceae (or Leguminosae), or the fruit or seeds of such plants. When used as a dry grain for human consumption, the seeds are also called pulses. Legumes are grown agriculturally, primarily for human consum ...

nitrogen-fixing Nitrogen fixation is a chemical process by which molecular dinitrogen () is converted into ammonia (). It occurs both biologically and abiological nitrogen fixation, abiologically in chemical industry, chemical industries. Biological nitrogen ...

bacteria. The species is one of many

Gram-negative Gram-negative bacteria are bacteria that, unlike gram-positive bacteria, do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. Their defining characteristic is that their cell envelope consists ...

rod-shaped Bacterial cellular morphologies are the shapes that are characteristic of various types of bacteria and often key to their identification. Their direct examination under a light microscope enables the classification of these bacteria (and archae ...

bacteria commonly referred to as

rhizobia Rhizobia are diazotrophic bacteria that fix nitrogen after becoming established inside the root nodules of legumes (Fabaceae). To express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen. I ...

. Within that broad classification, which has three groups,

taxonomy image:Hierarchical clustering diagram.png, 280px, Generalized scheme of taxonomy Taxonomy is a practice and science concerned with classification or categorization. Typically, there are two parts to it: the development of an underlying scheme o ...

studies using

DNA sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, thymine, cytosine, and guanine. The ...

indicate that ''B. japonicum'' belongs within homology group II.

Uses

Agriculture

''B. japonicum'' is added to legume seed to improve

crop yield In agriculture, the yield is a measurement of the amount of a crop grown, or product such as wool, meat or milk produced, per unit area of land. The seed ratio is another way of calculating yields. Innovations, such as the use of fertilizer, the ...

s, particularly in areas where the bacterium is not native (e.g.

Arkansas Arkansas ( ) is a landlocked state in the West South Central region of the Southern United States. It borders Missouri to the north, Tennessee and Mississippi to the east, Louisiana to the south, Texas to the southwest, and Oklahoma ...

soils). Often the inoculate is adhered to the seeds prior to planting using a sugar solution.

Research

A strain of ''B. japonicum'', USDA110, has been in use as a

model organism A model organism is a non-human species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. Mo ...

since 1957. It is widely used to study

molecular genetics Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the st ...

plant physiology Plant physiology is a subdiscipline of botany concerned with the functioning, or physiology, of plants. Plant physiologists study fundamental processes of plants, such as photosynthesis, respiration, plant nutrition, plant hormone functions, tr ...

, and

plant ecology Plant ecology is a subdiscipline of ecology that studies the distribution and abundance (ecology), abundance of plants, the effects of environmental factors upon the abundance of plants, and the interactions among plants and between plants and ...

due to its relatively superior symbiotic nitrogen-fixation activity with

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. Soy is a staple crop, the world's most grown legume, and an important animal feed. Soy is a key source o ...

(i.e. compared to other rhizobia species). Its entire

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

was sequenced in 2002, revealing that the species has a single

circular chromosome A circular chromosome is a chromosome in bacteria, archaea, mitochondria, and chloroplasts, in the form of a molecule of circular DNA, unlike the linear chromosome of most eukaryotes. Most prokaryote chromosomes contain a circular DNA molecule. ...

with 9,105,828

base pairs A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

Metabolism

''B. japonicum'' is able to degrade

catechin Catechin is a flavan-3-ol, a type of secondary metabolite providing antioxidant roles in plants. It belongs to the subgroup of polyphenols called flavonoids. The name of the catechin chemical family derives from ''catechu'', which is the tannic ...

with formation of

phloroglucinol carboxylic acid Phloroglucinol carboxylic acid, also called ‘Phloroglucinic acid’ or simply ‘PGCA’, is a trihydroxybenzoic acid, a type of phenolic acid. It can be encountered in nature were it is produced by plants or microorganisms. Structurally, the m ...

, further decarboxylated to

phloroglucinol Phloroglucinol is an organic compound with the formula C6H3(OH)3. It is a colorless solid. It is used in the organic synthesis, synthesis of pharmaceuticals and explosives. Phloroglucinol is one of three isomeric benzenetriols. The other two isom ...

, which is dehydroxylated to

resorcinol Resorcinol (or resorcin) is a phenolic compound. It is an organic compound with the formula C6H4(OH)2. It is one of three isomeric benzenediols, the 1,3-isomer (or ''meta- (chemistry), meta''-isomer). Resorcinol crystallizes from benzene as co ...

and

hydroxyquinol Hydroxyquinol is an organic compound with the formula C6H3(OH)3. It is one of three isomeric benzenetriols. The compound is a colorless solid that is soluble in water. It reacts with air to give a black insoluble solid. Production It is prepare ...

. ''B. japonicum'' possess the ''nosRZDFYLX'' gene, which aides in denitrification and has two catalytic subunits - Cu-a and Cu-z (with several histidine residues). It manages an expression cascade that can sense oxygen gradients, termed 'FixJ-FixK2-FixK1.' FixJ positively regulates FixK2, which activates nitrogen respiration genes, as well as FixK1. FixK1 mutants are unable to respire from nitrogen due to a defective catatylic copper subunit (Cu-z) in ''nosRZDFYLX''.

Genetic transformation

Natural genetic transformation in bacteria is a sexual process involving transfer of DNA from one cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by

homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in Cell (biology), cellular organi ...

. ''B. japonicum'' cells are able to undergo transformation. They become competent for DNA uptake during late log phase.

References

External links

Bradyrhizobium on www.bacterio.cict.frType strain of ''Bradyrhizobium japonicum'' at Bac''Dive'' - the Bacterial Diversity Metadatabase
{{DEFAULTSORT:Bradyrhizobium japonicum Nitrobacteraceae Gram-negative bacteria Model organisms Bacteria described in 1896