Photorhizobium

''Bradyrhizobium'' is a genus of Gram-negative soil bacteria, many of which fix nitrogen. Nitrogen fixation 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. They are common soil-dwelling micro-organisms that can form symbiotic relationships with leguminous plant species where they fix nitrogen in exchange for carbohydrates 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'' 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 pentoses as carbon sources. 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.

* "''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 (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 acids and sugars into the rhizosphere. 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 factors that initiate root hair curling. 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, nitrogen fixation (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'', a free-living diazotroph. 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. 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 is highly conserved in this group of microbes, making ''Bradyrhizobium'' extremely difficult to use as an indicator of species diversity. DNA–DNA hybridizations have been used instead and show more diversity. However, few phenotypic 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'' legumes, and have also been found in the nodal roots of African wild rice ''Oryza breviligulata