Bradyrhizobium

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Bradyrhizobium
Root-nodule01.jpg
Cross section though a soybean ( Glycine max 'Essex') root nodule. Bradyrhizobium japonicum infects the roots and establishes a nitrogen fixing symbiosis. This high magnification image shows part of a cell with single bacteroids within their symbiosomes
Scientific classification Red Pencil Icon.png
Domain: Bacteria
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Hyphomicrobiales
Family: Nitrobacteraceae
Genus: Bradyrhizobium
Jordan 1982
Type species
Bradyrhizobium japonicum
Species

See text

Synonyms
  • AgromonasOhta and Hattori 1985 [1]
  • "Photorhizobium" Eaglesham et al. 1990 [2]
  • "Phytomyxa" Schroeter 1886

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.

Contents

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. [3] 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. [4] Some strains (for example, USDA 6 and CPP) are capable of oxidizing carbon monoxide aerobically. [5]

Taxonomy

Accepted Species

Bradyrhizobium comprises the following species: [6]

Provisional Species

The following species have been published, but not validated according to the Bacteriological Code. [6]

  • "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 [2]
  • "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). [6] The phylogeny is based on whole-genome analysis. [9]

Bradyrhizobium

Bradyrhizobium oligotrophicum

Bradyrhizobium manausense

Bradyrhizobium neotropicale

Bradyrhizobium yuanmingense

Bradyrhizobium ottawaense

Bradyrhizobium shewense

Bradyrhizobium stylosanthis

Bradyrhizobium arachidis

Bradyrhizobium diazoefficiens

Bradyrhizobium japonicum

Bradyrhizobium retamae

Bradyrhizobium icense

Bradyrhizobium lablabi

Bradyrhizobium jicamae

Bradyrhizobium paxllaeri

Bradyrhizobium elkanii

Bradyrhizobium pachyrhizi

Bradyrhizobium mercantei

Bradyrhizobium embrapense

Bradyrhizobium tropiciagri

Bradyrhizobium viridifuturi

outgroup

Rhodopseudomonas

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. [10] NodD is essential for the expression of the other nod genes. [11] The two different nodD genes are: nodD1 and nodD2. Only nodD1 is needed for successful nodulation. [10]

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. [12] The levels of ureide nitrogen in a plant correlate with the amount of fixed nitrogen the plant takes up. [13]

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. [14]

Diversity

This genus of bacteria can form either specific or general symbioses; [4] 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. [15]

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 . [16]

Significance

Grain legumes are cultivated on about 1.5 million km2 of land per year. [12] The amount of nitrogen fixed annually is about 44–66 million tons worldwide, providing almost half of all nitrogen used in agriculture. [17] Commercial inoculants of Bradyrhizobium are available.

Bradyrhizobium has also been identified as a contaminant of DNA extraction kit reagents and ultrapure water systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets. [18] 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. [19]

Notable species

Related Research Articles

<span class="mw-page-title-main">Leghemoglobin</span> Phytoglobin

Leghemoglobin is an oxygen-carrying phytoglobin found in the nitrogen-fixing root nodules of leguminous plants. It is produced by these plants in response to the roots being colonized by nitrogen-fixing bacteria, termed rhizobia, as part of the symbiotic interaction between plant and bacterium: roots not colonized by Rhizobium do not synthesise leghemoglobin. Leghemoglobin has close chemical and structural similarities to hemoglobin, and, like hemoglobin, is red in colour. It was originally thought that the heme prosthetic group for plant leghemoglobin was provided by the bacterial symbiont within symbiotic root nodules. However, subsequent work shows that the plant host strongly expresses heme biosynthesis genes within nodules, and that activation of those genes correlates with leghemoglobin gene expression in developing nodules.

<span class="mw-page-title-main">Rhizobia</span> Nitrogen fixing soil bacteria

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. In general, they are gram negative, motile, non-sporulating rods.

<i>Rhizobium</i> Genus of nitrogen-fixing bacteria

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.

Diazotrophs are bacteria and archaea that fix gaseous nitrogen in the atmosphere into a more usable form such as ammonia.

<i>Ensifer meliloti</i> Species of bacterium

Ensifer meliloti are an aerobic, Gram-negative, and diazotrophic species of bacteria. S. meliloti are motile and possess a cluster of peritrichous flagella. S. meliloti fix atmospheric nitrogen into ammonia for their legume symbionts, such as alfalfa. S. meliloti forms a symbiotic relationship with legumes from the genera Medicago, Melilotus and Trigonella, including the model legume Medicago truncatula. This symbiosis promotes the development of a plant organ, termed a root nodule. Because soil often contains a limited amount of nitrogen for plant use, the symbiotic relationship between S. meliloti and their legume hosts has agricultural applications. These techniques reduce the need for inorganic nitrogenous fertilizers.

<span class="mw-page-title-main">Root nodule</span> Plant part

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 as rhizobia. This process has evolved multiple times within the legumes, as well as in other species found within the Rosid clade. Legume crops include beans, peas, and soybeans.

<span class="mw-page-title-main">Nod factor</span> Signaling molecule

Nod factors, 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 relationship between legumes and rhizobia by inducing nodulation. Nod factors produce the differentiation of plant tissue in root hairs into nodules where the bacteria reside and are able to fix nitrogen from the atmosphere for the plant in exchange for photosynthates and the appropriate environment for nitrogen fixation. One of the most important features provided by the plant in this symbiosis is the production of leghemoglobin, which maintains the oxygen concentration low and prevents the inhibition of nitrogenase activity.

Actinorhizal plants are a group of angiosperms characterized by their ability to form a symbiosis with the nitrogen fixing actinomycetota Frankia. This association leads to the formation of nitrogen-fixing root nodules.

Bradyrhizobium elkanii is a species of legume-root nodulating, microsymbiotic nitrogen-fixing bacterium originally identified as DNA homology group II strains of B. japonicum . In 1988, it was discovered that only DNA homology group II strains caused a destructive bleaching of leaves, termed scientifically "microsymbiont-induced foliar chlorosis", which was widespread in soybean production fields of the southern United States . Whole cell fatty acid content together with antibiotic resistance profiles were major phenotypic differences that helped establish DNA homology group II strains as a new species, Bradyrhizobium elkanii .

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, which has three groups, taxonomy studies using DNA sequencing indicate that B. japonicum belongs within homology group II.

Bradyrhizobium arachidis is a species of legume-root nodulating, microsymbiotic nitrogen-fixing bacterium. It was first isolated from Arachis hypogaea root nodules in China. Its type strain is CCBAU 051107T.

Bradyrhizobium liaoningense is a species of legume-root nodulating, microsymbiotic nitrogen-fixing bacterium. It was first isolated from Glycine soja and Glycine max root nodules in China. Its type strain is strain 2281.

Bradyrhizobium canariense is a species of legume-root nodulating, endosymbiont nitrogen-fixing bacterium. It is acid-tolerant and nodulates endemic genistoid legumes from the Canary Islands. The type strain is BTA-1T.

Mesorhizobium plurifarium is a species of root nodule bacteria first isolated from Acacia species in Senegal. Its type strain is ORS 1032.

Bradyrhizobium yuanmingense is a species of legume-root nodulating, endosymbiont nitrogen-fixing bacterium, associated with Lespedeza and Vigna species. Its type strain is CCBAU 10071(T).

Bradyrhizobium iriomotense is a species of legume-root nodulating, endosymbiont nitrogen-fixing bacterium, first isolated from Entada koshunensis. The type strain is EK05T.

Mesorhizobium mediterraneum is a bacterium from the genus Mesorhizobium, which was isolated from root nodule of the Chickpea in Spain. The species Rhizobium mediterraneum was subsequently transferred to Mesorhizobium mediterraneum. This species, along with many other closely related taxa, have been found to promote production of chickpea and other crops worldwide by forming symbiotic relationships.

Bradyrhizobium betae is a species of legume-root nodulating, microsymbiotic nitrogen-fixing bacterium first isolated from the roots of Beta vulgaris, hence its name. It is slow-growing an endophytic. The type strain is PL7HG1T.

Ensifer medicae is a species of gram-negative, nitrogen-fixing, rod-shaped bacteria. They can be free-living or symbionts of leguminous plants in root nodules. E.medicae was first isolated from root nodules on plants in the genus Medicago. Some strains of E.medicae, like WSM419, are aerobic. They are chemoorganotrophic mesophiles that prefer temperatures around 28 °C. In addition to their primary genome, these organisms also have three known plasmids, sized 1,570,951 bp, 1,245,408 bp and 219,313 bp.

<span class="mw-page-title-main">Symbiosome</span>

A symbiosome is a specialised compartment in a host cell that houses an endosymbiont in a symbiotic relationship.

References

  1. ↑ Ramirez-Bahena, M.-H.; Chahboune, R.; Peix, A.; Velazquez, E. (2012). "Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov". International Journal of Systematic and Evolutionary Microbiology . 63 (Pt 3): 1013–6. doi:10.1099/ijs.0.041897-0. PMID   22685107.
  2. 1 2 Eaglesham AR, Ellis JM, Evans WR, Fleishman DE, Hungria M, Hardy KW (1990). "The first photosynthetic N2-fixing Rhizobium: Characteristics". In Gresshoff PM, Koth LE, Stacey G, Newton WE (eds.). Nitrogen Fixation: Achievements and Objectives. Boston, MA: Springer. pp. 805–811. doi:10.1007/978-1-4684-6432-0_69. ISBN   978-1-4684-6434-4.
  3. ↑ VanInsberghe, David; Maas, Kendra; Cardenas, Erick; Strachan, Cameron; Hallam, Steven; Mohn, William (2015). "Non-symbiotic Bradyrhizobium ecotypes dominate North American forest soils". The ISME Journal. 9 (11): 2435–2441. doi:10.1038/ismej.2015.54. PMC   4611507 . PMID   25909973.
  4. 1 2 P. Somasegaran (1994). Handbook for rhizobia: Methods in legume–rhizobium technology. New York: Springer-Verlag. pp. 1–6, 167. ISBN   978-0-387-94134-9.
  5. ↑ Gary, King (2003). "Molecular and culture-based analyses of aerobic carbon monoxide oxidizer diversity". Applied and Environmental Microbiology. 69 (12): 7257–7265. doi:10.1128/aem.69.12.7257-7265.2003. PMC   309980 . PMID   14660374.
  6. 1 2 3 "List of Prokaryotic names with Standing in Nomenclature —Bradyrhizobium" . Retrieved May 23, 2021.
  7. 1 2 3 Klepa MS, Ferraz Helene LC, O'Hara G, Hungria M (2021). "Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia". Int J Syst Evol Microbiol. 71 (3). doi: 10.1099/ijsem.0.004742 . PMC   8375429 . PMID   33709900.
  8. 1 2 Kalita, M; Małek, W (2010). "Genista tinctoria microsymbionts from Poland are new members of Bradyrhizobium japonicum bv. genistearum". Systematic and Applied Microbiology. 33 (5): 252–9. doi:10.1016/j.syapm.2010.03.005. PMID   20452160.
  9. ↑ Hördt, Anton; López, Marina García; Meier-Kolthoff, Jan P.; Schleuning, Marcel; Weinhold, Lisa-Maria; Tindall, Brian J.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Göker, Markus (7 April 2020). "Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria". Frontiers in Microbiology. 11: 468. doi: 10.3389/fmicb.2020.00468 . PMC   7179689 . PMID   32373076.
  10. 1 2 Stacey, Gary (1995). "Bradyrhizobium japonicum nodulation genetics". FEMS Microbiology Letters. 127 (1–2): 1–9. doi: 10.1111/j.1574-6968.1995.tb07441.x . PMID   7737469.
  11. ↑ Stacey, G; Sanjuan, J.; Luka, S.; Dockendorff, T.; Carlson, R.W. (1995). "Signal exchange in the Bradyrhizobium–soybean symbiosis". Soil Biology and Biochemistry. 27 (4–5): 473–483. doi:10.1016/0038-0717(95)98622-U.
  12. 1 2 Caetanoanolles, G (1997). "Molecular dissection and improvement of the nodule symbiosis in legumes". Field Crops Research. 53 (1–3): 47–68. doi:10.1016/S0378-4290(97)00022-1.
  13. ↑ van Berkum, P.; Sloger, C.; Weber, D. F.; Cregan, P. B.; Keyser, H. H. (1985). "Relationship between Ureide N and N2 Fixation, Aboveground N Accumulation, Acetylene Reduction, and Nodule Mass in Greenhouse and Field Studies with Glycine max (L.) Merr". Plant Physiol. 77 (1): 53–58. doi:10.1104/pp.77.1.53. PMC   1064455 . PMID   16664027.
  14. ↑ Hennecke, H (1990). "Nitrogen fixation genes involved in the Bradyrhizobium japonicum–soybean symbiosis". FEBS Letters. 268 (2): 422–6. doi:10.1016/0014-5793(90)81297-2. PMID   2200721. S2CID   43001831.
  15. 1 2 3 4 5 6 Rivas, Raul; Martens, Miet; De Lajudie, Philippe; Willems, Anne (2009). "Multilocus sequence analysis of the genus Bradyrhizobium". Systematic and Applied Microbiology. 32 (2): 101–10. doi:10.1016/j.syapm.2008.12.005. PMID   19201125.
  16. ↑ Chaintreuil, Clémence; Giraud, Eric; Prin, Yves; Lorquin, Jean; Bâ, Amadou; Gillis, Monique; de Lajudie, Philippe; Dreyfus, Bernard (December 2000). "Photosynthetic Bradyrhizobia Are Natural Endophytes of the African Wild Rice Oryza breviligulata". Applied and Environmental Microbiology. 66 (12): 5437–5447. Bibcode:2000ApEnM..66.5437C. doi: 10.1128/AEM.66.12.5437-5447.2000 . PMC   92479 . PMID   11097925 . Retrieved 7 May 2021.
  17. ↑ Alberton, O; Kaschuk, G; Hungria, M (2006). "Sampling effects on the assessment of genetic diversity of rhizobia associated with soybean and common bean". Soil Biology and Biochemistry. 38 (6): 1298–1307. doi:10.1016/j.soilbio.2005.08.018.
  18. ↑ Salter, S; Cox, M; Turek, E; Calus, S; Cookson, W; Moffatt, M; Turner, P; Parkhill, J; Loman, N; Walker, A (2014). "Reagent contamination can critically impact sequence-based microbiome analyses". bioRxiv   10.1101/007187 .
  19. ↑ Kulakov, L; McAlister, M; Ogden, K; Larkin, M; O'Hanlon, J (2002). "Analysis of Bacteria Contaminating Ultrapure Water in Industrial Systems". Applied and Environmental Microbiology. 68 (4): 1548–1555. Bibcode:2002ApEnM..68.1548K. doi:10.1128/AEM.68.4.1548-1555.2002. PMC   123900 . PMID   11916667.
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