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Rhizobium
Rhizobium
Rhizobium
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This article is about the bacterial genus. For the generic term that includes species in other genera, see Rhizobia.

Rhizobium
Rhizobium tropici on an agar plate (Tryptone — Yeast extract agar).
Scientific classification Edit this classification
Domain: Bacteria
Kingdom: Pseudomonadati
Phylum: Pseudomonadota
Class: Alphaproteobacteria
Order: Hyphomicrobiales
Family: Rhizobiaceae
Genus: Rhizobium
Frank 1889 (Approved Lists 1980)[1][2]
Type species
Rhizobium leguminosarum
(Frank 1879) Frank 1889 (Approved Lists 1980)
Species

See text

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 to form root nodules, where they convert atmospheric nitrogen into ammonia using the enzyme nitrogenase. The ammonia is shared with the host plant in the form of organic nitrogenous compounds such as glutamine or ureides.[3][citation needed] The plant, in turn, provides the bacteria with organic compounds made by photosynthesis. This mutually beneficial relationship is true of all of the rhizobia, of which the genus Rhizobium is a typical example.[4] Rhizobium is also capable of solubilizing phosphate.[5]

History

[edit]

Martinus Beijerinck was the first to isolate and cultivate a microorganism from the nodules of legumes in 1888.[6] He named it Bacillus radicicola, which is now placed in Bergey's Manual of Determinative Bacteriology under the genus Rhizobium.[citation needed]

Research

[edit]

Rhizobium forms a symbiotic relationship with certain plants, such as legumes, fixing nitrogen from the air into ammonia, which acts as a natural fertilizer for the plants. The Agricultural Research Service is conducting research involving the genetic mapping of various rhizobial species with their respective symbiotic plant species, like alfalfa or soybean. The goal of this research is to increase the plants' productivity without using fertilizers.[7]

In molecular biology, Rhizobium has 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.[8] The presence of nitrogen-fixing bacteria as contaminants may be due to the use of nitrogen gas in ultra-pure water production to inhibit microbial growth in storage tanks.[9]

Species

[edit]

The genus Rhizobium comprises the following species:-[10]

Species in "double quotes" have been described, but not validated according to the Bacteriological Code.[10]

Phylogeny

[edit]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN).[10] The phylogeny is based on whole-genome analysis.[16]

Notes

[edit]

References

[edit]
[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

Rhizobium

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from Grokipedia
Rhizobium is a genus of Gram-negative, rod-shaped bacteria in the family Rhizobiaceae within the phylum Proteobacteria, renowned for their ability to form symbiotic nitrogen-fixing associations with the roots of leguminous plants. These soil-dwelling microbes, typically measuring 0.5–0.9 µm in width and 1.2–3.0 µm in length, are motile via peritrichous or polar flagella and exhibit fast growth rates on yeast-mannitol agar, distinguishing them from slower-growing rhizobial genera like Bradyrhizobium. In this mutualistic relationship, Rhizobium species enter the root hairs of host plants, such as peas, beans, and alfalfa, inducing the formation of specialized root nodules where they differentiate into bacteroids. Within these nodules, Rhizobium bacteria employ the nitrogenase enzyme complex to convert atmospheric dinitrogen (N₂) into bioavailable ammonia (NH₃), a process requiring significant energy from plant-derived carbohydrates and the oxygen-binding protein leghemoglobin to maintain low oxygen levels for enzyme protection. This biological nitrogen fixation can supply 50–100 kg of nitrogen per hectare annually, enhancing plant growth while reducing the need for synthetic fertilizers. The symbiosis is mediated by specific signaling molecules, including Nod factors produced by the bacteria, which trigger plant responses for nodule development, ensuring host specificity—Rhizobium leguminosarum, for instance, primarily associates with temperate legumes like clover and vetch. Ecologically, Rhizobium plays a pivotal role in the global by linking atmospheric to organic forms, thereby improving soil fertility and supporting , particularly in -based cropping systems. Native populations in soils can reach over one million cells per gram, influenced by factors like pH (optimal 6.0–6.8), temperature (25–30°C), and prior cultivation, with commercial inoculants often used to introduce superior strains for optimized fixation. Beyond mutualism, some strains exhibit parasitic behavior, forming ineffective nodules that provide no benefit to the host.

Biology and Characteristics

Morphology and Physiology

Rhizobium species are Gram-negative, rod-shaped bacilli, typically measuring 0.5–0.9 μm in width and 1.2–3.0 μm in length, and exhibit through peritrichous or polar flagella arranged around or at the poles of the cell surface. These possess a characteristic outer membrane structure common to Gram-negative proteobacteria, including (LPS) components that contribute to cell envelope integrity and environmental interactions. Physiologically, Rhizobium bacteria are primarily aerobic respirers, though they tolerate microoxic conditions during for while maintaining aerobic respiration, with optimal growth occurring at temperatures between 25–30°C and levels of 6–7. They utilize a range of carbon sources for , such as glucose and succinate, which support heterotrophic growth in environments. Key metabolic traits include the ability to solubilize insoluble phosphates through the production of organic acids, such as gluconic and , which lower local and enhance availability. Additionally, Rhizobium produces exopolysaccharides, which are heteropolymeric structures that facilitate formation and adhesion to surfaces, aiding persistence in the . At the cellular level, precursors for nodulation factors—lipochitooligosaccharides essential for initiating symbiotic signaling—are synthesized via nod gene clusters, while symbiotic plasmids like pSym harbor nif genes encoding components of the nitrogenase complex, though these are maintained independently of active symbiosis.

Habitat and Ecology

Rhizobium species are primarily found in the rhizosphere of leguminous plants, where they colonize the root zones in soils across temperate and tropical regions worldwide. Their global distribution reflects the widespread cultivation and natural occurrence of legumes. In these environments, Rhizobium thrives in the nutrient-rich exudates from legume roots, maintaining populations that can persist even in the absence of host plants. As free-living saprophytes in , Rhizobium survive by scavenging and competing with other microbes for resources. They engage in antagonistic interactions through the production of , that inhibit competing , thereby enhancing their persistence and colonization potential. Beyond nitrogen dynamics, Rhizobium contributes to cycling by solubilizing insoluble phosphates, making more available to and supporting broader microbial community stability. Rhizobium exhibits notable adaptations to environmental stresses, including tolerance to osmotic pressures from , heavy metal contamination, and fluctuating levels, which allow survival in diverse and challenging edaphic conditions. These can persist as opportunistic colonizers in non-legume soils and even aquatic systems, where they maintain viability without forming symbioses. Such resilience is facilitated by physiological mechanisms like accumulation and efflux pumps for metal . In non-symbiotic contexts, Rhizobium associates with non-legume , promoting growth through the secretion of siderophores that chelate iron and (IAA), a phytohormone that stimulates elongation and nutrient uptake. These interactions enhance vigor in crops like and , demonstrating Rhizobium's role as a versatile growth-promoting bacterium beyond legume hosts.

Symbiosis and Nitrogen Fixation

Mechanism of Symbiosis

The establishment of symbiosis between Rhizobium and legume plants initiates with the release of flavonoids from host root exudates, which are perceived by the bacterial NodD protein, a transcriptional regulator that activates the expression of nodulation (nod) genes. This leads to the synthesis and secretion of lipochitooligosaccharide signaling molecules known as Nod factors, which are essential for host recognition and the subsequent infection process. Rhizobium cells exhibit chemotaxis toward the root surface, attaching to specific sites on elongating root hairs through pili and adhesins, facilitating close contact. Upon perception of Nod factors by lysine motif (LysM) receptors on the root hair membrane, the host responds with calcium spiking and , inducing root hair deformation into a shepherd's crook configuration, which entraps the bacteria. This deformation is followed by the localized hydrolysis of the cell wall and invagination of the plasma membrane, forming tubular threads that grow through the root hair toward the underlying cortical cells, guided by Nod factor-induced cytoskeletal rearrangements. The threads serve as conduits for bacterial invasion, preventing direct exposure to the cytoplasm and maintaining controlled entry. Nodule organogenesis commences concurrently in the root cortex, where Nod factors trigger rapid mitotic divisions in pericycle and cortical cells, establishing a meristematic nodule . As infection threads branch and penetrate deeper, bacteria are released into host cortical cells via endocytosis-like processes, where they differentiate into nitrogen-fixing bacteroids. Each bacteroid is individually enclosed by a plant-derived peribacteroid membrane, which forms the symbiosome compartment, regulating nutrient exchange and maintaining low oxygen levels to protect oxygen-sensitive processes within the nodule. This membrane, enriched with plant-specific transporters and aquaporins, ensures spatial separation and functional integration between the partners. Host specificity in the Rhizobium-legume interaction is primarily governed by the structural diversity of Nod factors, encoded by strain-specific nod gene clusters, alongside bacterial surface . The core nodABC genes, conserved across , direct the assembly of the chitooligosaccharide backbone and acylation of Nod factors, while host-specific genes (e.g., nodH, nodQ) add decorations like or groups that determine compatibility with particular receptors. For instance, Ensifer meliloti (formerly Rhizobium meliloti) nodABC mutants fail to nodulate but can be complemented by orthologs from compatible strains, underscoring their role in broad host-range determination. Exopolysaccharides (EPS) further contribute by modulating bacterial aggregation and adhesion, enhancing infection efficiency in matched host-strain pairs. The symbiotic relationship provides mutual benefits, with the plant supplying energy-rich , primarily dicarboxylic acids such as malate, transported across the peribacteroid to fuel bacterial . In exchange, Rhizobium bacteroids convert atmospheric dinitrogen into , which is exported to the plant for assimilation into , supporting host growth without external inputs. This exchange is tightly regulated, with nodule triggered if imbalances occur, ensuring the partnership's sustainability.

Nitrogen Fixation Process

The nitrogen fixation process in Rhizobium occurs within the bacteroids of legume root nodules, where the bacteria convert atmospheric dinitrogen (N₂) into (NH₃), a form assimilable by the host plant. This symbiotic biological (BNF) is catalyzed exclusively by the enzyme complex, which is highly sensitive to environmental conditions and tightly regulated to ensure efficiency. The complex consists of two main metalloproteins: the iron (Fe) protein, encoded by nifH, and the molybdenum-iron (MoFe) protein, encoded by nifD and nifK. The Fe protein acts as a reductase, transferring electrons from or flavodoxin to the MoFe protein, which serves as the site of N₂ reduction. The overall reaction catalyzed by this complex is: N2+8H++8e−+16ATP→2NH3+H2+16ADP+16Pi\text{N}_2 + 8\text{H}^+ + 8\text{e}^- + 16\text{ATP} \rightarrow 2\text{NH}_3 + \text{H}_2 + 16\text{ADP} + 16\text{P}_i This process requires 16 molecules of ATP per molecule of N₂ reduced, with the obligatory production of one molecule of H₂ representing an energy inefficiency of approximately 25%. The nifHDK genes are part of a larger nif gene cluster located on the symbiotic plasmid in Rhizobium species, which also encodes accessory proteins for nitrogenase assembly and maturation. Expression of the nif genes is activated under microaerobic conditions within the nodule, where oxygen levels are maintained at low concentrations (around 10-50 nM) to protect the oxygen-labile . This is mediated by the FixL/FixJ two-component , an oxygen-sensing kinase-response regulator pair; FixL autophosphorylates in response to decreasing O₂, phosphorylating FixJ, which then activates transcription of nifA and other fix genes, including those for respiratory protection. The plant-derived further facilitates controlled O₂ diffusion to support bacteroid respiration while preventing nitrogenase inactivation. Additionally, the transcriptional regulator NifA, downstream of FixJ, directly induces nifHDK expression in the absence of fixed . The high energy demand of nitrogenase activity is met by ATP generated from the oxidation of plant-supplied carbon sources, primarily dicarboxylates like malate, via the bacteroid tricarboxylic acid (TCA) cycle and electron transport chain. In field conditions, fixation efficiency varies by Rhizobium strain and environmental factors, typically contributing 50-200 kg of fixed N per hectare per year to legume crops. Despite these adaptations, nitrogen fixation faces several limitations. The enzyme's extreme sensitivity to oxygen leads to irreversible inactivation above threshold levels, necessitating the nodule's barrier and leghemoglobin system. Ammonia produced during fixation exerts feedback inhibition on nitrogenase activity, reducing further N₂ reduction when NH₃ accumulates. Environmental stresses, such as suboptimal pH (outside 6.5-7.5) or drought, impair nodule permeability, carbon supply, and bacteroid respiration, thereby lowering fixation rates by up to 50% in affected systems.

Taxonomy and Phylogeny

Species Diversity

The genus Rhizobium comprises over 90 validly published as of 2025, with delineation primarily based on 16S rRNA sequencing supplemented by multilocus to resolve closely related taxa. This molecular approach has facilitated the identification of adapted to diverse hosts and environmental conditions, reflecting the genus's role in and . Prominent species within the genus include R. leguminosarum, which establishes nitrogen-fixing symbioses with temperate such as peas (Pisum sativum) and faba beans (); R. etli, a specific microsymbiont of the common bean (); and R. tropici, which nodulates tropical species and exhibits notable tolerance to high temperatures, acidity, and . These representatives highlight the genus's host specificity and adaptive traits, though many species show narrower or broader symbiotic ranges. In 2024, the type strain of Rhizobium indigoferae was reclassified as Rhizobium leguminosarum. Recent taxonomic expansions have added species isolated from specific ecological niches. In 2022, R. croatiense and R. redzepovicii were described from root nodules of Phaseolus vulgaris in Croatia, distinguished by genomic and phenotypic differences from related strains. The following year, R. brockwellii, R. johnstonii, and R. beringeri were proposed as novel genospecies from Australian soils, emerging from the R. leguminosarum complex based on whole-genome comparisons. In 2025, R. kunmingense was validated as a new species isolated from rhizosphere soil. Taxonomic revisions have refined the genus boundaries, with several former Rhizobium species reclassified to adjacent genera like Ensifer and Mesorhizobium to better align with phylogenetic data. For example, the alfalfa (Medicago sativa) symbiont previously designated R. meliloti is now Ensifer meliloti. Proposed but unvalidated names, often denoted in single quotes, continue to appear in literature pending formal validation.

Phylogenetic Relationships

The genus Rhizobium is placed within the family Rhizobiaceae, which belongs to the class Alphaproteobacteria. Within this family, Rhizobium forms a core clade alongside Agrobacterium, as revealed by phylogenomic analyses that highlight their shared evolutionary history distinct from other rhizobial genera like Sinorhizobium or Mesorhizobium. Phylogenomic trees constructed from 120 core genes across hundreds of Rhizobium genomes demonstrate the monophyly of the genus, with robust support for internal branching patterns that resolve its position relative to closely related taxa. Key phylogenetic clades within Rhizobium include the R. leguminosarum supergroup, encompassing over 10 named and additional genospecies, and the tropical clade featuring such as R. tropici and R. leucaenae, which are adapted to warmer environments and show distinct symbiotic host ranges. delimitation in these clades relies on average identity (ANI) thresholds, where values exceeding 95-96% indicate conspecific strains, enabling precise genomic clustering amid the genus's high diversity. Genomic studies of reveal chromosomes typically ranging from 4 to 7 Mb, accompanied by 1 to 3 large plasmids that harbor essential symbiotic elements. Symbiotic islands, often located on these plasmids, contain clusters of nod and nif genes critical for nodulation and ; these regions exhibit signatures of (HGT), facilitating the spread of symbiotic capabilities across strains and even genera. Whole-genome sequencing has underscored how such HGT contributes to the evolutionary plasticity of the , with symbiotic loci integrating via transposon-mediated mechanisms. Recent phylogenomic reappraisals from 2022 to 2023 have refined borders using core-genome phylogenies, proposing a monophyletic framework for delimitation while addressing polyphyletic elements within traditional groupings. These analyses, incorporating metrics like identity and digital DNA-DNA hybridization, have led to the splitting of complexes such as R. leguminosarum into up to 18 distinct genospecies, enhancing taxonomic resolution and reflecting ongoing genomic divergence.

History and Classification

Discovery and Early Studies

In 1888, Dutch microbiologist Martinus Beijerinck isolated the bacterium Bacillus radicicola (now classified as a species of Rhizobium) from root nodules of Pisum sativum (pea plants), marking the first successful cultivation of these organisms in pure culture./05:_Microbial_Metabolism/5.15:_Nitrogen_Fixation/5.15B:_Early_Discoveries_in_Nitrogen_Fixation) Beijerinck demonstrated that this isolate could fix atmospheric nitrogen, providing direct evidence that symbiotic bacteria within legume nodules were responsible for enhancing plant growth in nitrogen-poor soils. This breakthrough built on concurrent work by German scientists Hermann Hellriegel and Hermann Wilfarth, who, in the same year, conducted pot experiments showing that legumes gained significant nitrogen benefits from soil microbes, unlike non-legumes, thus establishing the symbiotic nature of the process. The following year, German botanist Albert Bernhard Frank coined the term Rhizobium to describe these root-inhabiting , emphasizing their role in forming associations with . Early experiments, including controlled pot trials in the late 1880s and 1890s, confirmed that by Rhizobium far exceeded rates achieved by free-living nitrogen fixers, highlighting the efficiency of the legume- partnership. By the early 1900s, researchers recognized host specificity, observing that particular Rhizobium strains nodulated only certain legume species, limiting cross-inoculation success and underscoring the selective nature of the . Prior to the , isolating pure Rhizobium cultures remained challenging due to frequent contamination by other microbes and the bacteria's fastidious growth requirements, often leading to misidentifications and inconsistent experimental results. These issues delayed broader applications in but spurred refinements in culturing techniques, laying the groundwork for later advancements.

Taxonomic Evolution

The Rhizobium was originally proposed by Albert Bernhard Frank in 1889 to describe nitrogen-fixing associated with root nodules. Although described earlier, the received formal nomenclatural approval in 1980 through the Approved Lists of Bacterial Names, as decided by the Judicial Commission of the International Committee on Systematics of Prokaryotes, which validated the name and included initial species such as R. leguminosarum, R. meliloti, and R. loti, with R. leguminosarum designated as the . From the 1980s to the , taxonomic classification of Rhizobium shifted toward polyphasic approaches that combined phenotypic characteristics, , and genotypic analyses, particularly 16S rRNA gene sequencing and DNA-DNA hybridization, to resolve phylogenetic relationships and define species boundaries. This methodology facilitated the subdivision of species into biovars based on host specificity and symbiotic traits, exemplified by R. leguminosarum bv. viciae for strains nodulating peas and vetches. In the , advancements in phylogenomics, including multilocus of genes and whole-genome comparisons, prompted extensive reclassifications, with more than 20 species transferred to newly proposed genera such as Allorhizobium (established in 2001 for A. undicola and later A. vitis) and Neorhizobium (proposed in 2014 to accommodate R. galegae, R. vignae, R. huautlense, and R. alkalisoli). These changes addressed the polyphyletic nature of the original Rhizobium genus within the family Rhizobiaceae. A 2022 taxonomic framework for the Rhizobiaceae emphasized core-genome phylogenies and average nucleotide identity (ANI) thresholds (typically ≥95-96% for species) to delimit genera more objectively, resulting in further reassignments like the transfer of R. rhizosphaerae and R. oryzae to Xaviernesmea gen. nov. Controversies continue, particularly around species complexes like the R. leguminosarum supergroup, where genospecies boundaries remain debated due to high genomic similarity and introgression events, as well as incongruences between plasmid-based (e.g., symbiotic plasmids) and chromosomal phylogenies, which exhibit distinct topologies reflecting independent evolutionary histories.

Research and Applications

Agricultural and Environmental Uses

Rhizobium species serve as key biofertilizers in , forming symbiotic associations that enable biological and supply crops with ammonium derived from atmospheric . Inoculants applied to such as soybeans (Glycine max) and (Medicago sativa) can fix 50–465 kg of per hectare per year under favorable conditions, substantially contributing to without external inputs. This process allows for a 25–50% reduction in synthetic application while maintaining or enhancing crop yields, promoting sustainable farming practices. Commercial strains like Rhizobium tropici CIAT 899 are particularly valued for their adaptation to acidic soils ( below 5.5), where they support effective nodulation and in beans () grown in tropical regions. Beyond direct nutrient provision, Rhizobium contributes to through the production of exopolysaccharides (EPS), which bind particles into stable aggregates, improving and water retention. These EPS also mitigate in legume-based rotations by enhancing soil cohesion, particularly in vulnerable agroecosystems, and foster greater microbial by creating microhabitats that support diverse communities. Environmentally, Rhizobium inoculation reduces greenhouse gas emissions, notably (N₂O), by decreasing reliance on synthetic fertilizers that contribute up to 60% of agricultural N₂O through and processes. Additionally, certain strains exhibit capabilities, binding such as and via cell wall components, aiding in the remediation of contaminated soils when paired with metal-accumulating . Practical involves peat-based carriers to maintain bacterial viability during storage and application, often mixed with stickers for to in coating formulations that ensure even distribution. However, challenges include poor strain competitiveness against indigenous soil , which can limit nodule occupancy to below 50% in established fields, and reduced storage viability at high temperatures or low moisture, necessitating cold-chain management and strain selection for robustness.

Biotechnological and Recent Advances

Recent advances in have targeted Rhizobium species to enhance efficiency, particularly through -based tools. In 2025, researchers developed a interference (CRISPRi) system in Rhizobium etli to precisely modulate , enabling fine-tuned control over symbiotic traits without permanent genome alterations. This approach builds on broader strategies to improve legume-rhizobia symbiosis under stress, such as by optimizing clusters for higher activity in adverse conditions. efforts have further expanded Rhizobium's potential by engineering nodulation signals to extend symbiotic to non-legume crops like . For instance, a 2025 study engineered Sinorhizobium meliloti nodulation factors to initiate formation in non-legumes, mimicking natural lipo-chitooligosaccharide signals to promote biological in cereal roots. Complementary work has reprogrammed plant-microbe interactions using synthetic pathways, allowing rhizobia to respond to cereal root exudates and form functional nodules. A landmark discovery in 2024 revealed a marine between Rhizobium-like and diatoms, addressing a long-standing gap in oceanic budgets. This partnership, involving Candidatus Tectiglobus diatomicola, enables in nutrient-poor surface waters of the tropical North Atlantic, contributing fixed comparable to cyanobacterial diazotrophs and potentially accounting for up to 50% of new production in affected regions. In 2025, further insights into rhizobial emerged with the identification of type III effectors ErnA and Sup3, which hijack the SUMOylation pathway to induce nodule formation in Aeschynomene . ErnA features a SUMO-interacting motif that binds host SUMO proteins, modulating nuclear processes to bypass traditional signaling and promote nodulation even in Nod-deficient strains. Sup3 complements this by enhancing effector delivery, collectively enabling efficient in diverse . Biostimulant applications of engineered Rhizobium strains have shown promise for mitigation, particularly . The strain Rhizobium sp. PV-6, isolated from bean s, enhances drought resilience in red kidney beans () by altering root transcriptome profiles and enriching beneficial microbial communities, leading to improved water retention and yield under water-limited conditions. Beyond , Rhizobium's production of (IAA) and supports growth promotion in non-; for example, IAA aids elongation in cereals, while acts as a modulator to boost stress acclimation and uptake in crops like . These mechanisms enable rhizobial inoculants to function as versatile biostimulants, enhancing plant vigor without nodulation. The global Rhizobium biofertilizer market, driven by demand for , reached US$1.24 billion in 2022 and is projected to grow to US$1.93 billion by 2031 at a of 5.71%. However, challenges persist, including resistance in commercial strains, which can limit efficacy in contaminated soils; studies from 2024 recommend multi-strain consortia to mitigate this while maintaining symbiotic performance. adaptation remains a key hurdle, as rising temperatures and erratic reduce rhizobial survival and nodulation efficiency, necessitating engineered strains with enhanced thermal and osmotic tolerance.

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