PLANT GROWTH PROMOTING RHIZOBACTERIA (PGPR)

PLANT GROWTH PROMOTING RHIZOBACTERIA (PGPR)

• The group of bacteria that colonize roots or rhizosphere soil and beneficial to crops are referred to as Plant Growth Promoting Rhizobacteria (PGPR).
• Rhizosphere consists of bacteria named rhizobacteria which either directly or indirectly exert positive effects on plants. These soil bacteria colonize plant root and benefit the plants by stimulating its growth and are therefore called plant growth promoting rhizobacteria (PGPR).
• PGPR can also be referred to as Plant Health Promoting Rhizobacteria (PHPR)
• The concept of Rhizosphere was first given by Hiltner in 1904.
• The term PGPR was first coined by Joseph W. Kloepper and Schroth in the late 1970s.
• Bacteria belonging to the genera Azospirillum sp., Azotobacter sp., Azoarcus sp., Arthrobacter sp., Klebsiella sp., Burkholderia sp., Citrobacter sp., Pseudomonas sp., Bacillus sp., Paenibacillus sp., Herbaspirillum sp., Erwinia sp., Flavobacterium sp., Serratia sp., Xanthomonas sp., Rhizobium sp., Alcaligenes faecalis, Enterobacter cloacae, Gluconacetobacter diazotrophicus and Bradyrhizobium japonicum have been shown to produce plant growth promoting substances.
• PGPRs have different relationships with different species of host plants. The two major classes of relationships are (a) Rhizospheric and (b) Endophytic.

a)    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 Azospirillum sp. 

b)    Endophytic relationships involve the PGPRs residing and growing within the host plant in the Apoplastic space (the space outside the plasma membrane).

•          PGPR are potential biofertilizers. It stimulates plant growth and increase crop yields.
•      PGPR are less harmful to the environment and they also reduce the cost of Chemical fertilizers.

MECHANISMS OF PGPR

• Plant growth promoting rhizobacteria are free - living, soil - borne bacteria, which enhance the growth of the plant either directly or indirectly.

a)     The direct mechanisms involve

ü  Nitrogen fixation

ü  Phytohormones production (Auxin and Gibberellins)

ü  Lowering of Ethylene concentration (ACC deaminase activity)

ü  Siderophores production

ü  Solubilization of Phosphorous

ü  Solubilization of Potassium

ü  Ammonia production

b)     Some bacteria support plant growth indirectly by

ü  Production of Antagonistic substances (Antibiotics and Lytic enzymes)

ü  Induced Systemic Resistance (ISR) towards plant pathogens.

ü  Hydrogen cyanide (HCN) production

ü  Competition

ü  Exopolysaccharide (EPS) production

 

DIRECT MECHANISMS OF PGPR

a) Nitrogen Fixation

• Nitrogen is the most important plant nutrient required for growth and productivity. This is because nitrogen is the basic building block of plant, animal and microorganisms.
• Nitrogen fixation is the conversion of molecular or atmospheric nitrogen into form utilizable to plant by nitrogen fixing microorganisms using an enzyme system called Nitrogenase. This is also known as Biological Nitrogen Fixation.
• Biological Nitrogen Fixation mostly occurs at mild temperatures. This process consumes significant amount of energy in the form of ATP. The nitrogenase gene (nif) required for Biological Nitrogen Fixation is sensitive to oxygen. Therefore, to prevent oxygen from inhibiting nitrogen fixation while at the same time providing sufficient oxygen for the bacteroides within the nodule to respire, it is essential that bacterial hemoglobin which can bind free oxygen is introduced.
• Biological nitrogen fixation includes both symbiotic nitrogen fixation and the free living nitrogen fixing system.
• Symbiotic nitrogen fixers include the following genera, Rhizobium, Achromobacter, Sinorhizobium, Azoarcus, Mesorhizobium, Frankia, Allorhizobium, Bradyrhizobium, Burkholderia, Azorhizobium and Herbaspirillum.
• Some of the important non-symbiotic nitrogen-fixing bacteria include: Azoarcus sp., Herbaspirillum sp., Gluconacetobacter diazotrophicus and Azotobacter sp.

b) Phytohormones production

• Phytohormones are the chemical messengers that induces gene expression and transcription levels, cellular division and hence improves plant growth.
• Phytohormones also influences the seed germination, emergence of flowering, sex of flowers, senescence of leaves, and fruits.
• Examples of phytohormones produced by PGPR include Auxin and Gibberellins.

Auxin

• Indole-3-acetic acid (Indole acetic acid, IAA) is one of the commonly studied auxins.
• IAA is synthesized by at least three biosynthetic pathways. These pathways include: Indole acetamide (IAM) pathway, Indole pyruvic acid (IPyA) pathway and Indole acetaldoxime (IAOx)/Indoleacetonitrile (IAN) pathway. Many PGPR can have one, two, or even three functional IAA biosynthesis pathway.
• IAA also plays an ultimate role in growth stimulation by being involved in DNA synthesis.
• The main function of IAA is cell division, differentiation, cell elongation, and extension.
• IAA causes a rapid increase in cell wall extensibility in young stems.
• IAA promotes growth of auxiliary bud and bud formation. It also plays important role in leaf and flower abscission.
• Some other compounds like Indole-3-acetamide, Indole-3-pyruvate, Indole-3-acetaldehyde and 4-chloroindole-3-acetic acid have been reported to have Auxin activity.

Gibberellins

• Gibberellins (GAs) are tetracyclic diterpenoid carboxylic acids with either C20 or C19 carbon skeletons.
• Even though, 136 Gibberellins structures have been identified, only four have been identified in bacteria.
• GAs activates important growth processes such Seed germination, Stem elongation, Flowering and Fruit setting.
• GAs improves photosynthesis rate, and chlorophyll content.
• GAs stimulates shoot growth and inhibit root growth via the actions of the GA signaling system, and the DELLA repressor which trigger GA-inducing genes

c) Lowering of Ethylene concentration by ACC Deaminase Activity

• 1-Aminocyclopropane-1-carboxylate (ACC) deaminase is another enzyme produced by some PGPR which facilitate plant growth and development by decreasing Ethylene levels.
• Ethylene is a plant growth hormone produced by approximately all plants and also by different Biotic and Abiotic processes in soils.
• Ethylene induces multifarious physiological changes in plants. Ethylene has also been established as a stress hormone.
• Biotic and abiotic stress such as insect and nematode damage, drought or flood, presence of metals, chemicals (both organic and inorganic), ultraviolet light, extreme temperatures, mechanical wounding as well as fungal and bacterial pathogens triggers increased production of ethylene in plants. However, its production beyond the threshold levels in plant tissue affects the shoot and root development in plant negatively, but ACC deaminase produced by PGPR will reduce ethylene levels by converting ACC (ethylene precursor) to α-Ketobutyrate and ammonia and thereby restoring normal plant development.
• Prior application of ACC deaminase-containing PGPR to plants typically reduce the concentration of ethylene produced by the plants as a result of stress and thereby decreases the damage that the plant incurs from the stress.

d) Siderophores production

• Siderophores are small peptidic molecules which contain side chains and functional groups that provide a high-affinity set of ligands to which ferric ions can bind.
• Microorganisms evolved these highly specific pathways to satisfy nutritional requirements of iron.
• Siderophores producing microbes can therefore be classified into four main classes (based on their iron-coordinating functional groups, structural features and type of ligands) namely; a) Carboxylate, b) Hydroxamates, c) Phenol catecholates and d) Pyoverdines.
• Bacteria siderophore can prevent or lessen proliferation of pathogen by reducing the amount of iron that is available to a pathogen.
• Siderophore producing PGPR therefore has competitive advantages over other microorganisms in the rhizosphere. Siderophores produced by Chryseobacterium spp. when delivered to the root were effective in the supply of iron in tomato plant. Likewise, Siderophore producing Pseudomonas strain showed significant increase in germination and plant growth

e) Phosphorous solubilization

• Phosphorus is an essential element that is necessary for plant growth and development and it is second only to Nitrogen.
• Phosphorus occurs in soil in both organic and inorganic forms which are not available to plant. However, a number of PGPR have been reported to mobilize poorly available phosphorus via Solubilization and Mineralization.
• Examples of Phosphorus solubilizers include Pseudomonas sp., Agrobacterium sp., Bacillus circulans, Azotobacter sp., Bacillus sp., Burkholderia sp., Enterobacter sp., Erwinia sp., Kushneria sp., Paenibacillus sp., Ralstonia sp., Rhizobium sp., Rhodococcus sp., Serratia sp., Bradyrhizobium sp., Salmonella sp., Sinomonas sp. and Thiobacillus sp.
• The mechanism employed by Phosphorus solubilizing bacteria in promoting plant growth include (i) Production of plant growth hormones; (ii) Promoting the efficiency of Biological nitrogen fixation and (iii) Enhancing the availability of some nutrient elements such as iron, zinc, etc.
• The most important mechanism of inorganic phosphorus solubilization by PGPR is the production of mineral dissolving compounds such as organic acids, hydroxyl ions, protons, and CO₂.
• Some other mechanisms of mineral phosphate solubilization by PGPR includes (i) Production of inorganic acids (such as sulphuric, nitric, and carbonic acids); (ii) Production of chelating substances and (iii) Enzymolysis or liberation of enzymes. 

f) Potassium solubilization

• Potassium in the soil occurs mostly as silicate minerals which are inaccessible to plants.
• Potassium minerals are made available only when they are slowly weathered or solubilized.
• Potassium solubilizing microorganisms (Bacillus sp.) solubilize silicates by producing organic acids which cause the decomposition of silicates and helps in the removal of metal ions thereby making them available to plants.
• Potassium solubilizing biofertilizers are broad spectrum biofertilizers.

g) Ammonia production

• The soil consists of plant, microbial, and animal residues. The quantitatively most important Nitrogen containing molecules in the residue are proteins; chitin and peptidoglycan with the proteins alone comprise 60 % or more of the Nitrogen in plant and microbial cells.
• Organic nitrogen residues in soil organic matter is converted by some PGPR such as the Ammonia nitrifyers like Pseudomonas sp. and Bacillus sp. to Amino acid and, the amino acid is then digested to produce ammonia through the process called Ammonification (an important step in Nitrogen cycle).
• Ammonification is a very important biochemical process in soil because some soil bacteria use the Ammonia produced to build their own body protein while some other soil bacteria convert the Ammonia to Nitrite, e.g., Nitrobacter sp. and then to Nitrate, e.g., Nitrosomonas sp.
• Still other bacteria can reduce Ammonia to Nitrogen gas.

INDIRECT MECHANISMS OF PGPR

a) Production of Antagonistic substances

Antibiotics

• The major mechanism employed by PGPR to combat deleterious effects of plant pathogens is the production of one or more Antibiotics.
• Antibiotics are low molecular weight compounds that are produced by PGPR which are deleterious and critical to important enzymes and metabolism of other microorganisms and thus retard the growth.
• Some plant pathogens can develop resistance against specific antibiotics hence the ability of PGPR to produce one or more antibiotics, enhance their ability to act as effective antagonistic agents against plant pathogens.
• Antibiotics produced by antagonistic microbes have biostatic and biocidal effects on soil-borne plant pathogens.
• Bacillus and Pseudomonas spp. have been recognized to produce a variety of antibiotics.
• From Bacillus sp., Tas A, Subtilin, Bacilysin, Sublancin, Iturin, Chlorotetain, Fengycin, Subtilosin and Bacillaene.
• From Pseudomonas sp., Phenazine-1-carboxylic acid (PCA), Zwittermycin A, Cepaciamide A, Karalicin, Pseudomonic acid, Kanosamine, Rhamnolipids, Cepafungins, Azomycin, Butyrolactones, 2,4-Diacetyl Phloroglucinol (DAPG), Aerugine, Pyrrolnitrin and Oomycin A.

Lytic Enzymes

• Some PGPR isolates produce lytic enzymes including Chitinases, Proteases, Cellulases, Lipases and 1,3-glucanases.
• The Lytic enzymes can lyse a portion of the cell walls of many pathogenic fungi.

b) Induced Systemic Resistance (ISR)

• Induced Systemic Resistance (ISR) is a mechanism in which non-pathogenic microbes, such as PGPR, reduce the deleterious effects of plant pathogens by stimulating a resistance mechanism in the plants.
• ISR mechanism increases resistance at the particular sites of plants at which induction had occurred, i.e., the defense mechanism of ISR is activated only when there is an attack of pathogenic agent.
• ISR is not pathogen specific but rather top the plant against a range of different pathogens.
• Jasmonate and Ethylene are plant hormones that stimulate plants defense response to pathogens, hence ISR employ these hormones to stimulate resistance mechanism in the plants.
• ISR activates the “dormant” defense mechanisms which become expressed in response to external contacts from pathogens or insect.
• PGPR contribute to sustaining the intrinsic resistance of plant to pathogenic organisms.
• Plant protection by ISR is controlled by a network of coordinated signaling pathways and these are dominated and regulated by plant hormones sharing signaling components.
• ISR is regulated by the redox-regulated protein Non-expressor of PR genes1 (NPR1) which is produced in the cytoplasm as an oligomer via intermolecular disulfide bonds.
• Many PGPR has been documented to activate ethylene dependent ISR.
• Volatile organic compounds (Hydrogen cyanide synthesized by Pseudomonas sp.; Acetoin and 2,3 – butanediol synthesized by Bacillus sp.) produced by PGPR are heavily involved in improving plant growth and ISR towards pathogens.

c) Hydrogen cyanide (HCN) production

• Hydrogen cyanide (HCN) are secondary metabolite that acts as an effective agent for the biocontrol of weeds.
• HCN produced by PGPR has the ability to inhibit Electron Transport Chain and energy supply to cell, resulting to death of Weed cells. Therefore, HCN producing rhizobacteria are an effective agent of biological weed control.
• Biocontrol PGPR that produces HCN can also synthesize some cell wall degrading enzymes or antibiotics.
•  HCN can also act as an anti-fungi agent.
• HCN synthesized by PGPR is usually in small quantity, this ensures that the fungi do not develop resistance to the synthesized antifungal thereby enhancing the effectiveness of antifungal.
• HCN ability to inhibit important metalloenzymes including Cytochrome - c oxidase affects its toxicity effectiveness.

d) Competition

• PGPR can limit the proliferation of pathogenic organisms by competing with them for the sparsely available nutrients.
• Some biocontrol PGPR outcompete plant pathogens, either for binding sites on the plant root or for nutrient. As a result, limit the binding of the pathogen to the plant and thereby making it difficult for it to proliferate.
• PGPR competitiveness works in synergy with other biocontrol mechanisms to inhibit the functioning of phytopathogens.

e) Exopolysaccharides (EPS) production

• Exopolysaccharides (EPS) are the active constituents of soil organic matter.
• EPS are most important part of extracellular matrix that often represent 40 –95 % of bacterial weight.
• Bacteria produce EPS in two forms: (a) Slime EPS and (b) Capsular EPS.
• The important roles exhibited by EPS are a) Protective; b) Surface attachment; c) Biofilm formation; d) Microbial aggregation; e) Plant - microbe interaction and f) Bioremediation.
• Some EPS-producing bacteria like Pseudomonas have the ability to survive even under drought stress due to the production of their EPS.
• EPS of bacteria are hydrated compounds with 97% of water in polymer matrix which impart protection against Desiccation.
• The EPS protect these bacteria from Desiccation under Drought stress by enhancing the water retention and by regulation of organic carbon source's diffusion.
• Water availability in the soil also affects the soil structure. Plants treated with EPS-producing bacteria Azospirillum showed resistance to water stress through improvement in the soil structure and soil aggregation.