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Rhizobacteria are root-associated
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
that can have a detrimental (parasitic varieties), neutral or beneficial effect on plant growth. The name comes from the Greek ''rhiza'', meaning root. The term usually refers to bacteria that form symbiotic relationships with many plants ( mutualism). Rhizobacteria are often referred to as plant growth-promoting rhizobacteria, or PGPRs. The term PGPRs was first used by Joseph W. Kloepper in the late 1970s and has become commonly used in scientific literature. Generally, about 2–5% of rhizosphere bacteria are PGPR. They are an important group of microorganisms used in biofertilizer. Biofertilization accounts for about 65% of the nitrogen supply to crops worldwide. PGPRs have different relationships with different species of host plants. The two major classes of relationships are rhizospheric and endophytic. Rhizospheric relationships consist of the PGPRs that colonize the surface of the root, or superficial intercellular spaces of the host plant, often forming root nodules. The dominant species found in the rhizosphere is a microbe from the genus '' Azospirillum''. Endophytic relationships involve the PGPRs residing and growing within the host plant in the apoplastic space.


Nitrogen fixation

Nitrogen fixation 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 ...
is one of the most beneficial processes performed by rhizobacteria. Nitrogen is a vital nutrient to plants and gaseous nitrogen (N2) is not available to them due to the high energy required to break the triple bonds between the two atoms. Rhizobacteria, through nitrogen fixation, are able to convert gaseous nitrogen (N2) to ammonia (NH3) making it an available nutrient to the host plant which can support and enhance plant growth. The host plant provides the bacteria with amino acids so they do not need to assimilate ammonia. The amino acids are then shuttled back to the plant with newly fixed nitrogen. Nitrogenase is an enzyme involved in nitrogen fixation and requires anaerobic conditions. Membranes within root nodules are able to provide these conditions. The rhizobacteria require oxygen to metabolize, so oxygen is provided by a hemoglobin protein called leghemoglobin which is produced within the nodules. Legumes are well-known nitrogen-fixing crops and have been used for centuries in
crop rotation Crop rotation is the practice of growing a series of different types of crops in the same area across a sequence of growing seasons. This practice reduces the reliance of crops on one set of nutrients, pest and weed pressure, along with the pro ...
to maintain the health of the soil.


Symbiotic relationships

The symbiotic relationship between rhizobacteria and their host plants is not without costs. For the plant to be able to benefit from the added available nutrients provided by the rhizobacteria, it needs to provide a place and the proper conditions for the rhizobacteria to live. Creating and maintaining root nodules for rhizobacteria can cost between 12–25% of the plant's total photosynthetic output. Legumes are often able to colonize early successional environments due to the unavailability of nutrients. Once colonized, though, the rhizobacteria make the soil surrounding the plant more nutrient rich, which in turn can lead to competition with other plants. The symbiotic relationship, in short, can lead to increased competition. PGPRs increase the availability of nutrients through the solubilization of unavailable forms of nutrients and by the production of siderophores which aids in the facilitating of nutrient transport.
Phosphorus Phosphorus is a chemical element; it has Chemical symbol, symbol P and atomic number 15. All elemental forms of phosphorus are highly Reactivity (chemistry), reactive and are therefore never found in nature. They can nevertheless be prepared ar ...
, a limiting nutrient for plant growth, can be plentiful in soil, but is most commonly found in insoluble forms. Organic acids and phosphotases released by rhizobacteria found in plant rhizospheres facilitate the conversion of insoluble forms of phosphorus to plant-available forms such as H2PO4. PGPR bacteria include '' Pseudomonas putida'', '' Azospirillum fluorescens'', and ''Azospirillum lipoferum'' and notable nitrogen-fixing bacteria associated with legumes includes ''Allorhizobium'', ''Azorhizobium'', ''Bradyrhizobium'', and ''Rhizobium''. Though microbial inoculants can be beneficial for crops, they are not widely used in
industrial agriculture Industrial agriculture is a form of modern farming that refers to the industrialized production of crops and animals and animal products like eggs or milk. The methods of industrial agriculture include innovation in agricultural machinery and ...
, as large-scale application techniques have yet to become economically viable. A notable exception is the use of rhizobial inoculants for
legumes 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 consu ...
such as peas. Inoculation with PGPRs ensures efficient nitrogen fixation, and they have been employed in North American agriculture for over 100 years.


Plant growth-promoting rhizobacteria

Plant growth-promoting rhizobacteria (PGPR) were first defined by Kloepper and Schroth to be soil
bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
that colonize the roots of plants following inoculation onto
seed In botany, a seed is a plant structure containing an embryo and stored nutrients in a protective coat called a ''testa''. More generally, the term "seed" means anything that can be Sowing, sown, which may include seed and husk or tuber. Seeds ...
and that enhance
plant growth Important structures in plant development are buds, Shoot (botany), shoots, roots, leaf, leaves, and flowers; plants produce these tissues and structures throughout their life from meristems located at the tips of organs, or between mature tissues. ...
. The following are implicit in the colonization process: ability to survive inoculation onto seed, to multiply in the spermosphere (region surrounding the seed) in response to seed exudates, to attach to the root surface, and to colonize the developing
root system In mathematics, a root system is a configuration of vector space, vectors in a Euclidean space satisfying certain geometrical properties. The concept is fundamental in the theory of Lie groups and Lie algebras, especially the classification and ...
. The ineffectiveness of PGPR in the field has often been attributed to their inability to colonize plant roots. A variety of bacterial traits and specific
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s contribute to this process, but only a few have been identified. These include
motility Motility is the ability of an organism to move independently using metabolism, metabolic energy. This biological concept encompasses movement at various levels, from whole organisms to cells and subcellular components. Motility is observed in ...
,
chemotaxis Chemotaxis (from ''chemical substance, chemo-'' + ''taxis'') is the movement of an organism or entity in response to a chemical stimulus. Somatic cells, bacteria, and other single-cell organism, single-cell or multicellular organisms direct thei ...
to seed and root exudates, production of pili or fimbriae, production of specific cell surface components, ability to use specific components of root exudates, protein secretion, and quorum sensing. The generation of
mutant In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It i ...
s altered in expression of these traits is aiding our understanding of the precise role each one plays in the colonization process. Progress in the identification of new, previously uncharacterized genes is being made using nonbiased screening strategies that rely on gene fusion technologies. These strategies employ reporter
transposon A transposable element (TE), also transposon, or jumping gene, is a type of mobile genetic element, a nucleic acid sequence in DNA that can change its position within a genome. The discovery of mobile genetic elements earned Barbara McClinto ...
s and in vitro expression technology (IVET) to detect genes expressed during colonization. Using
molecular marker In molecular biology and other fields, a molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. ...
s such as green fluorescent
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
or fluorescent
antibodies An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as bacteria and viruses, including those that caus ...
, it is possible to monitor the location of individual rhizobacteria on the root using
confocal laser scanning microscopy Confocal microscopy, most frequently confocal laser scanning microscopy (CLSM) or laser scanning confocal microscopy (LSCM), is an optical imaging technique for increasing optical resolution and contrast of a micrograph by means of using a s ...
. This approach has also been combined with an
rRNA 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 ribosomal ...
-targeting probe to monitor the metabolic activity of a rhizobacterial strain in the rhizosphere and showed that bacteria located at the root tip were most active.


Mechanisms of action

PGPRs enhance plant growth by direct and indirect means, but the specific mechanisms involved have not all been well characterized. Direct mechanisms of plant growth promotion by PGPRs can be demonstrated in the absence of plant
pathogen In biology, a pathogen (, "suffering", "passion" and , "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a Germ theory of d ...
s or other rhizosphere
microorganism A microorganism, or microbe, is an organism of microscopic scale, microscopic size, which may exist in its unicellular organism, single-celled form or as a Colony (biology)#Microbial colonies, colony of cells. The possible existence of unseen ...
s, while indirect mechanisms involve the ability of PGPRs to reduce the harmful effects of plant pathogens on crop yield. PGPRs have been reported to directly enhance plant growth by a variety of mechanisms: * fixation of atmospheric nitrogen transferred to the plant, * production of siderophores that chelate iron and make it available to the plant root * solubilization of minerals such as phosphorus, and synthesis of phytohormones. Direct enhancement of mineral uptake due to increases in specific ion fluxes at the root surface in the presence of PGPRs has also been reported. PGPR strains may use one or more of these mechanisms in the rhizosphere. Molecular approaches using microbial and plant mutants altered in their ability to synthesize or respond to specific phytohormones have increased understanding of the role of phytohormone synthesis as a direct mechanism of plant growth enhancement by PGPRs. PGPR that synthesize
auxin Auxins (plural of auxin ) are a class of plant hormones (or plant-growth regulators) with some morphogen-like characteristics. Auxins play a cardinal role in coordination of many growth and behavioral processes in plant life cycles and are essent ...
s,
gibberellin Gibberellins (GAs) are plant hormones that regulate various Biological process, developmental processes, including Plant stem, stem elongation, germination, dormancy, flowering, flower development, and leaf and fruit senescence. They are one of th ...
s and kinetins or that interfere with plant
ethylene Ethylene (IUPAC name: ethene) is a hydrocarbon which has the formula or . It is a colourless, flammable gas with a faint "sweet and musky" odour when pure. It is the simplest alkene (a hydrocarbon with carbon–carbon bond, carbon–carbon doub ...
synthesis have been identified. Development of PGPRs into biofertilisers and biopesticides could be a novel way of increasing crop yield and decreasing disease incidence, whilst decreasing dependency on chemical pesticides and fertilisers which can often have harmful effects on the local ecology and environment.


Pathogenic roles

Studies conducted on
sugar beet A sugar beet is a plant whose root contains a high concentration of sucrose and that is grown commercially for sugar production. In plant breeding, it is known as the Altissima cultivar group of the common beet (''Beta vulgaris''). Together with ...
crops found that some root-colonizing bacteria were deleterious rhizobacteria (DRB). Sugar beet seeds inoculated with DRB had reduced germination rates, root lesions, reduced root elongation, root distortions, increased fungi infection, and decreased plant growth. In one trial the sugar beet yield was reduced by 48%. Six strains of rhizobacteria have been identified as being DRB. The strains are in the genera ''
Enterobacter ''Enterobacter'' is a genus of common Gram-negative, Facultative anaerobic organism, facultatively anaerobic, bacillus (shape), rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Cultures are found in soil, water, sewage, ...
'', '' Klebsiella'', '' Citrobacter'', ''
Flavobacterium ''Flavobacterium'' is a genus of Gram-negative, nonmotile and motile, rod-shaped bacteria that consists of 130 recognized species. Flavobacteria are found in soil and fresh water in a variety of environments. Several species are known to cause ...
'', '' Achromobacter'', and ''
Arthrobacter ''Arthrobacter'' (from the Greek, "jointed small stick”) is a genus of bacterium, bacteria that is commonly found in soil. All species in this genus are Gram-positive obligate aerobes that are bacterial shape, rods during exponential growth and ...
''. Due to a large number of taxonomic species yet to be described, complete characterization has not been possible as DRB are highly variable. The presence of PGPRs has proven to reduce and inhibit the colonization of DRB on sugar beet roots. Plots inoculated with PGPRs and DRBs had an increase in production of 39% while plots only treated with DRBs had a reduction in production of 30%.


Biocontrol

Rhizobacteria are also able to control plant diseases that are caused by other bacteria and fungi. Disease is suppressed through induced systemic resistance and through the production of antifungal metabolites. ''Pseudomonas''
biocontrol Biological control or biocontrol is a method of pest control, controlling pests, whether pest animals such as insects and mites, weeds, or pathogens affecting animals or phytopathology, plants by bioeffector, using other organisms. It relies o ...
strains have been genetically modified to improve plant growth and improve the disease resistance of agricultural crops. In agriculture, inoculant bacteria are often applied to the seed coat of seeds prior to being sown. Inoculated seeds are more likely to establish large enough rhizobacterial populations within the rhizosphere to produce notable beneficial effects on the crop. They can also combat pathogenic microbes in
cattle Cattle (''Bos taurus'') are large, domesticated, bovid ungulates widely kept as livestock. They are prominent modern members of the subfamily Bovinae and the most widespread species of the genus '' Bos''. Mature female cattle are calle ...
. Different forage species regulate their own rhizosphere to varying degrees and favouring various microbes. Kyselková et al 2015 find planting forage species known to encourage native rhizobacteria retards the spread within the soil of antibiotic resistance genes of cow faeces bacteria.


References

{{Reflist Bacteria Soil biology Botany