An Overview of Plant Growth Promoting Rhizobacteria (PGPR) for Sustainable Agriculture

  • Rifat Hayat
  • Iftikhar Ahmed
  • Rizwan Ali Sheirdil


Soil bacteria beneficial to plant growth usually referred to as plant growth promoting rhizobacteria (PGPR), are capable of promoting plant growth by colonizing the plant root. The mechanisms of PGPR-mediated enhancement of crop growth includes (i) a symbiotic and associative nitrogen fixation; (ii) solubilization and mineralization of other nutrients; (iii) production of hormones e.g. auxin i.e. indole acetic acid (IAA), abscisic acid (ABA), gibberellic acid and cytokinins; (iv) production of ACC-deaminase to reduce the level of ethylene in crop roots thus enhancing root length and density; (v) ability to produce antagonistic siderophores, ß-1-3-glucanase, chitinases, antibiotics, fluorescent pigment and cyanide against pathogens and (vi) enhanced resistance to drought and oxidative stresses by producing water soluble vitamins niacin, thiamine, riboflavin, biotin and pantothenic acid. Increased crop production through biocontrol is an indirect mechanism of PGPR that results in suppression of soil born deleterious microorganisms. Biocontrol mechanisms involved in pathogen suppression by PGPR include substrate competition, antibiotic production, and induced systemic resistance in the host. PGPR can play an essential role in helping plants to establish and grow in nutrient deficient conditions. Their use in agriculture can favour a reduction in agro-chemical use and support ecofriendly crop production. Trials with rhizosphere-associated plant growth-promoting P-solubilizing and N2-fixing microorganisms indicated yield increase in rice, wheat, sugar cane, maize, sugar beet, legumes, canola, vegetables and conifer species. A range of beneficial bacteria including strains of Herbaspirillum, Azospirillum and Burkholderia are closely associated with rhizosphere of rice crops. Common bacteria found in the maize rhizosphere are Azospirillum sp., Klebsiella sp., Enterobacter sp., Rahnella aquatilis, Herbaspirillum seropedicae, Paenibacillus azotofixans, and Bacillus circulans. Similarly, strains of Azotobacter, Azorhizobium, Azospirillum, Herbaspirillum, Bacillus and Klebsiella can supplement the use of urea-N in wheat production either by BNF or growth promotion. The commonly present PGPR in sugarcane plants are Azospirillum brasilense, Azospirillum lipoferum, Azospirillum amazonense, Acetobacter diazotrophicus, Bacillus tropicalis, Bacillus borstelensis, Herbaspirillum rubrisubalbicans and Herbaspirillum seropedicae. Symbiotic N2-fixing bacteria collectively known as Rhizobia are currently classified into six genera; Rhizobium, Allorhizobium, Azorhizobium, Bradyrhizobium, Mesorhizobium and Sinorhizobium and 91 species. Their inoculation may increase nodulation and N2-fixation in legumes. All these Rhizobiumn spp. can minimize chemical N fertilizers by BNF, but only if conditions for expression of N2-fixing activity and subsequent transfer of N to plants are favourable. In this Chapter, PGPR role has been discussed in the process of crop growth promotion, their mechanisms of action and their importance in crop production on sustainable basis.


PGPR BNF P-solubilization Phytohormones Biocontrol Cereals Sugarcane and legumes crops 

1 Introduction

Plant growth promoting rhizobacteria (PGPR) are capable of promoting plant growth by colonizing their roots and can play an essential role in helping plants to establish and grow in nutrient deficient conditions. Their use in crop production can reduce the agro-chemical use and support ecofriendly sustainable food production. Plant growth promotion by PGPR is due to root hair proliferation, root hair deformation and branching, increase in seedling emergence, early nodulation, nodule functioning, enhanced leaf surface area, vigor, biomass, increasing indigenous plant hormones levels, mineral and water uptake, promoted accumulation of carbohydrates and yield in various plant species (Podile and Kishore 2006). The demand of PGPR biofertilizers has been increasing day by day with increase in the importance of organic agriculture with minimum inputs of chemicals. The population of PGPR in rhizospheric soil varies and depends largely on crop species and soil health (Tilak et al. 2005). Numerous studies clearly indicated the positive effect of PGPR on growth of different crops at different agroecological boundaries. Trials with soil rhizospheric N2-fixing and P-solubilizing Bacillus species showed yield increase in wheat (de Freitas 2000), rice (Sudha et al. 1999), maize (Pal 1998), sugar beet (Çakmakçi et al. 2006), canola (de Freitas et al. 1997), and conifer species (Bent et al. 2002). One of the most important and oftenly reported PGPR is Bacillus polymyxa, also known as Paenibacillus polymyxa (Timmusk et al. 1999) with a range of properties, including P-solubilization (de Freitas et al. 1997), nitrogen fixation (Coelho et al. 2003); production of cytokinin (Timmusk et al. 1999), antibiotic (Rosado and Seldin 1993), hydrolytic enzymes (Nielson and Sorenson 1997), colonization hair and cortical cells (Shishido et al. 1999), and increased root and shoot growth of crops (Sudha et al. 1999). Some strains of Rhodobacter are known to fix N2 (Drepper et al. 2002), but extensive studies are needed to validate its ability to fix N2. Pseudomonas sp. effectively adapt to new environments and colonize winter wheat roots (Misko and Germida 2002) thus significantly increasing root dry weight in spring wheat (Walley and Germida 1997), yield in sugar beet (Çakmakçi et al. 2001), and promote the growth of spinach (Urashima and Hori 2003).

Sustainable agriculture production can be achieved by emphasizing the use of PGPR as biofertilizer inoculants (Schippers et al. 1995). Generally, bacteria promote plant growth in three different ways (Glick 1995, 2001): synthesizing growth promoting harmones for the plants (Dobbelaere et al. 2003), facilitating the uptake of nutrients from the soil (Çakmakçi et al. 2006), and lessening or preventing the plants from diseases (Saravanakumar et al. 2008). The indepth mechanisms involved in plant growth by PGPR are yet to be investigated (Dey et al. 2004). However, the possible explanations include (i) solubilization of mineral phosphates and mineralization of other nutrients (Richardson 2001; Banerjee and Yasmin 2002); (ii) a biological nitrogen fixation (Kennedy et al. 2004a, b); (iii) ability to produce hormones like auxin i.e. indole acetic acid (IAA) (Patten and Glick 2002), abscisic acid (ABA) (Dobbelaere et al. 2003), gibberellic acid and cytokinins (Dey et al. 2004); (iv) ability to produce ACC-deaminase to reduce the level of ethylene in root of developing plants thereby increasing the root length and growth (Li et al. 2000; Penrose and Glick 2001); (v) antagonism against phytopathogenic bacteria by producing siderophores, ß-1,3-glucanase, antibiotics, chitinases, fluorescent pigment and cyanide (Glick and Pasternak 2003); and (vi) mediated resistance to drought (Alvarez et al. 1996) and oxidative stresses (Stajner et al. 1995, 1997) and production of water soluble vitamins thiamine, niacin, pantothenic acid, biotin and riboflavin (Revillas et al. 2000).

2 Biological Nitrogen Fixation (BNF)

Nitrogen is the most important nutrient and its deficiency severely affects crop yields. Most of the soils around globe are deficient in nitrogen and applications of nitrogenous fertilizer are essential for achieving maximum crop yield. Nitrogen is required for all living organisms. Although 78% of the atmosphere consists of dinitrogen, but it cannot be used by most organisms and consequently the availability of nitrogen in a form suitable for assimilation is often a major limiting factor for crop growth. The production of chemical nitrogen fertilizers not only depletes non-renewable energy resources but also poses human and environmental hazards, besides being very expensive. Urea is the cheapest and readily available N source, but unfortunately less than 50% of the applied urea is used by plants. This low efficiency of use is mainly caused by NH3 volatilisation and denitrification, and losses from leaching. Leaching of NO3-N causes ground water toxicity. Volatilisation and denitrification pollute the atmosphere through the evolution of greenhouse gases like N2O, NO and NH3. BNF not only complements and substitutes the mineral fertilizers but can be an economically beneficial and ecologically sound alternative (Glick et al. 1999).

BNF is a major source of nitrogen for plants as a part of environment friendly agricultural practices. It contributes for 65% of the total nitrogen currently utilized in crop production and will be important contributor for future agriculture (Matiru and Dakora 2004). This fixation is an important biochemical reaction next to plant photosynthesis for life on earth and occurs through symbiotic N2-fixing bacteria possessing the nitrogenase enzyme and in association with legumes (and some woody species) that converts atmospheric elemental dinitrogen (N2) into ammonia (Shiferaw et al. 2004). The potential of nitrogen fixation for most legumes species is in the range of 200–300 kg N ha−1 crop−1 (Peoples et al. 1995).

In the recent years, use of biological inoculants for sustainable crop production is attaining popularity in various parts of the world and biological nitrogen fixation represents the major source of N input in agricultural soils including those in arid regions. Symbiotic nitrogen-fixing bacteria include the cyanobacteria, the genera Rhizobium, Azorhizobium, Bradyrhizobium, Sinorhizobium, Allorhizobium, Mesorhizobium and Frankia (Paul and Clark 1996; Brock et al. 2000). The mechanisms of symbiotic N2-fixation between Rhizobium and legumes has been studied intensively. The symbiosis between Frankia and non-leguminous actinorhizal plants, is also been investigated now a days. Symbiotic system is the major N2-fixation system, playing a significant role in improving the fertility and maximizing productivity of low-N soils. Biological N2-fixed through rhizobium-legume symbiosis can also be beneficial to cereals growing in intercrops or to subsequent crops rotated with legumes. In many natural grassland systems, the grasses use N2 fixed by their legume counterparts for their nitrogen requirement and the protein available through this association enhances the forage quality for livestock production (Paynel et al. 2001). In addition to symbiotic N2-fixation in legumes, rhizobia as PGPR are also capable of contributing to growth promotion in non-legume species (Hoflich 2000). To act as PGPR, rhizobia naturally produce molecules (auxins, abscisic acids, cytokinins, riboflavin, lumichrome, lipo-chitooligosaccharides and vitamins) that promote crop growth, and their colonization and infection of cereal root would be expected to increase vigor and grain yield (Matiru and Dakora 2004). Other PGPR role of Rhizobium includes their ability to produce phytohormones (Arshad and Frankenberger 1998), solubilization of inorganic phosphorus (Chabot et al. 1996), siderophore release (Plessner et al. 1993; Jadhav et al. 1994) and antagonism against plant pathogenic microorganisms (Ehteshamul-Haque and Ghaffar 1993). Application of rhizobium inoculants under rainfed conditions on legumes like guar (Cyamopsis tetragonoloba L. Taub), moth (vigna acontifolia), mung (vigna ­radiate), and mash (vigna mungo) give up to 10–25% yield benefits (Rao 2004; Hayat et al. 2008a, b).

Free living bacteria as well as rhizobial strains can promote the growth of cereals by contributing to N-economy through their ability to fix N2 (Zahir et al. 2004). It is reported that biological N2-fixed by the diazotrophic PGPR may be a contributing factor of rice growth promotion in addition to other mechanisms (Biswas et al. 2000). Kennedy and Islam (2001) also explained the possible role and mechanisms of non-symbiotic bacteria to crop growth from BNF view point. Providing the plant with essential nutrients, e.g. NH4-N through atmospheric nitrogen fixation or aiding the plant in nutrient uptake is also considered as direct plant growth promotion. The important free living and associative nitrogen fixing genera are; Azospirillum, Azotobacter, Acetobacter (also known as Gluconacetobacter) Azoarcus, Achromobacter, Bacillus, Burkholderia, Clostridia, Citrobacter, Enterobacter, Herbaspirillum, Kelbsiella, Mycobacterium, Pseudomonas, Rhodobacter and Serratia. This list is increasing day by day.

3 Mineral-Solubilization and Uptake

PGPR directly contribute to the plant growth by facilitating plant nutritions through solubilization of inorganic phosphates and production of iron chelating siderophores thus increasing phosphorous and iron uptake.

3.1 Phosphorus Solubilization

Phosphate-solubilizing bacteria (PSB) could play an important role in supplying phosphate to plants in a more environment friendly and sustainable manner. The naturally abundant PSB solubilize Calcium-bound phosphatic compounds in an alkaline soil environment and convert the insoluble phosphatic compounds into soluble forms and make them available to crop plants. PSB are widely applied in agronomic practices in order to increase the productivity of crops while maintaining the health of soils. The beneficial effects of PSB on plant growth vary significantly depending on environmental conditions, bacterial strains, plant and soil conditions (Şahin et al. 2004; Çakmakçi et al. 2006). Various bacterial species in the genera Bacillus, Rhizobium and Pseudomonas, have proven to be the most powerful phosphate-solubilizing bacteria (Banerjee et al. 2006). There are also reports of phosphate solubilization by non-symbiotic nitrogen fixer, Azotobacter (Kumar et al. 2001). The phosphate-solubilizing activity of Rhizobium (e.g., Rhizobium/Bradyrhizobium) is associated with the production of 2-ketogluconic acid, indicating that phosphate-solubilizing activity of the organism is entirely due to its ability to reduce pH of the medium (Halder and Chakrabarty 1993). The phosphate-solubilizing ability also depends on nature of nitrogen source used in the media, with greater solubilization in presence of ammonium salts than when nitrate is used as nitrogen source. This has been attributed to extrusion of protons to compensate for ammonium uptake, leading to a decreased extra-cellular pH (Roos 1984). In some cases, however, ammonium can lead to decrease in phosphorus solubilization (Reyes et al. 1999). Several strains of P-solubilizers have been identified in vitro as Bacillus brevis, B. megaterium, B. polymyxa, B. sphaericus, B. thuringiensis and Xanthomonas maltophilia (de Freitas et al. 1997). P-solubilizing bacteria of Bacillus and Paenibacillus (formerly Bacillus) sp. have been applied to soils to successfully enhance the phosphorus status of plants (van Veen et al. 1997).

Since 1950s it is reported that P-solubilizing bacteria release phosphorus from organic and inorganic soil phosphorus pools through mineralization and solubilization (Fig. 22.1; Khan et al. 2009). Lowering of soil pH by microbial production of organic acids such as acid phosphatases, lactate, citrate, and succinate gluconic and keto gluconic acids etc. (Goldstein 1995; Deubel et al. 2000) and proton extrusion is the main principal mechanism of mineralization of organic form of phosphorus. Release of phosphorus from insoluble and adsorbed forms is also an important aspect of phosphorus solubilizing bacteria regarding phosphorus availability in soils. Phosphorus solubilizing bacteria transform soil phosphorus to forms that can easily be taken up by crops. Bacteria assimilate soluble phosphorus, and make it available by preventing it from adsorption (Khan and Joergensen 2009). Bacteria also enhance phosphorus availability to crops by solubilizing precipitated forms of phosphorus (Chen et al. 2006).
Fig. 22.1

Schematic diagram of soil phosphorus mobilization and immobilization by bacteria (Khan et al. 2009)

Fe - and Al - P and Ca - P are the main precipitated forms in acidic and alkaline soils respectively and can be solubilized involving organic anions and associated protons. Complex form of adsorbed phosphorus my be released by chelating metal ions through ligand exchange reactions. Soil bacteria use carbon and serve as a sink for phosphorus by immobilizing it from soil (Bünemann et al. 2004). Phosphorus solubilizing bacteria mainly depend on soil phosphorus and organic matter contents and release phosphorus from their cells for crops (Kim et al. 1998a). Agricultural and range land soils are main habitat of phosphorus solubilizing bacteria (Yahya and Azawi 1998) and their use in crop production can reduce chemical P by 50% without any significant reduction of crop yield (Yazdani et al. 2009). PSB biofertilizers have great potential for sustaining crop yield along with optimized phosphorus fertilization. Examples of P-solubilizing PGPR include Azotobacter chroococcum (Kumar and Narula 1999) and Bacillus circulans in wheat (Singh and Kapoor 1998), Enterobacter agglomerans in tomato (Kim et al. 1998b), Pseudomonas chlororaphis or Pseudomonas putida in soybean (Catellan et al. 1999) and other prominent P-solubilizing genera are Klebsiella, Balkhurdaria and Azospirillum etc. The availability of nutrients i.e. C, N and metals ions are the determining factors of P-solubilizing ability of PGPR. The activity of P-solubilizing rhizobacteria varies with nitrogen source and increases in the presence of low levels of Ca2+ and EDTA (Nautiyal et al. 2000). Soil bacteria could increase the P nutrition of plants through increased solubility of Ca-phosphates. Phosphate solubilization is the result of combined effect of pH decrease and production of organic acids (Fankem et al. 2006). Bacteria through secretion of different types of organic acids e.g. carboxylic acid and rhizospheric pH lowering mechanisms (He and Zhu 1988) dissociate the bound forms of phosphate like Ca3(PO4)2. Nevertheless, buffering capacity of the medium reduce the effectiveness of PSB in releasing P from tricalcium phosphates (Stephen and Jisha 2009). Acidification due to proton substitution/excretion of H+ (accompanying greater absorption of cations than anions) or release of Ca2+ by microbial population releases P from apatite (Goldstein 1994; Villegas and Fortin 2002). The reverse phenomenon become operative when uptake of anions increases than that of cations, with excretion of OH/HCO3 (Tang and Rengel 2003). PSB produce carboxylic anions, which have high affinity to calcium. This phenomenon results in more solubilization of phosphorus than acidification alone (Staunton and Leprince 1996). Complexation favoured by organic acids results in cations complexing structures in P solubilization, which is an important mechanism. Decrease in pH as well as synthesis of carboxylic acids results in the release of calcium phosphate (Ca-P); however, release of protons cannot be the single mechanism (Deubel et al. 2000). Crop yields improve with increased solubilization of the fixed soil P as well as the applied phosphates by PSB (Gull et al. 2004).

Most annual crops often do not get benefitted by direct application of phosphate rock in a short time. Phosphatic rocks can be solubilized by acid producing microorganisms (Gyaneshwar et al. 2002) to release more P for plant uptake. The inorganic P-solubilizing activities by PSB ranges between 25 and 42 μg P mL−1, whereas the organic P mineralization may occur between 8 and 18 μg P mL1 (Tao et al. 2008). The application of P fertilizers can be reduced by 25% and 50%, by using PSB inocula along with single super phosphate and rock phosphate, respectively (Sundara et al. 2002). It is reported that 29–62% P can be released by Pseudomonas putida, P. fluorescens Chao and P. fluorescens Tabriz; along with highest value of 0.74 mg P/50 mL from Fe2O3 (Ghaderi et al. 2008). Pseudomonas fluorescens is very effective and can solubilize 100 mg P L−1 containing Ca3(PO4)2 or 92 and 51 mg P L−1 containing AlPO4 and FePO4, respectively (Henri et al. 2008). Rock phosphatic minerals are often insoluble to provide sufficient P for plant uptake; however, using PSBs can release P from the fixed insoluble minerals and thus help to increase crop yields (Zaidi 1999). PGPR not only improves BNF but also contribute in increasing the availability of soluble P and thus, enhance plant growth (Ponmurugan and Gopi 2006). It is reported that PSB enhanced seedling length of Cicer arietinum (Sharma et al. 2007) and increase sugarcane yield (Sundara et al. 2002). Co-inoculation of PSB and PGPR can reduce application of P fertilizers by 50% without affecting corn yield (Yazdani et al. 2009). Grain yield of wheat increased 20–40% by the application of inoculation along with P fertilizers against sole P fertilization (Afzal and Bano 2008). The indigenous PSB populations often are not effective in releasing P from bound phosphates mainly due to high buffering capacity of soil; however, inoculants of PSB biofertilizers may contribute considerably in more plant P uptake. Plant available P increased by the activity of PSB especially belonging to the genera: Bacillus, Pseudomonas and Enterobacter. So, PSB has enormous potential in biofertilizer formulations to be exploited in increasing crop yields by increasing fixed P in the soil, as well as by making good use of natural reserves of phosphate rocks.

3.2 Iron Uptake

Iron being essential micronutrient of plants plays a key role in several enzymes with redox activity. Its role is important in photosynthesis, NO2 and SO4 reduction and N2 assimilation, and is therefore indispensable for chlorophyll biosynthesis (Rashid 1996). Iron is essential component of different steps involved in biosynthetic pathways and formation of chlorophyll required physiologically available iron to the plant (Lopez-Millan et al. 2001). Catalase and peroxidase are considered as important protoheme enzymes which can be used as biological markers in iron acquisition studies. Around 30% of the agronomic crops growing around the globe are facing the problem of chlorosis due to iron deficiency (Imsande 1998). Total soil Fe is always in excess of crop requirements, which is present in highly insoluble form of ferric hydroxide. In nature, various forms of iron are present in abundance but remain unavailable to plants due to their different solubility and bioavailability behaviour. The amount of soluble Fe in soil is much less than the total Fe contents thus iron remains unavailable for crops even in iron rich soils and contributes little in crop production (Podile and Kishore 2006). When iron availability to crops is inadequate for growth, leaves become pale green, yellow or white and eventually brown (Brittenham 1994). The availability of iron in soil solution is 10–18 M, a concentration even not sufficient for sustaining microbial growth. A large number of soil bacteria produce siderophores that bind Fe3+ and help in iron uptake (Podile and Kishore 2006). These siderophores can be used by rhizosphere bacteria and crops can absorb bacterial Fe3+ siderophore complexes. This mechanism is involved in iron absorption by crops especially in calcareous soils. Different kind of PGPR produce different kinds of siderophores. Pseudomonads are leading siderophore producers among PGPR and siderophore producing strains of fluorescent psuedomonas may be inoculated in calcareous soils for solubilization of non-available forms of iron (Sharma and Johri 2003).

Siderophores are iron chelating compounds having low molecular weight which are released under iron limited rhizospheric soils. These siderophores possess high binding affinity and specificity for iron (III) and help to facilitate its bioavailability into the biological cell (Schalk et al. 2001). The transportation of ferric siderophore complexes is a heterologous uptake and mediated by specific receptor proteins (Meyer et al. 2000). PGPR with the ability to produce siderophore play a vital role for iron acquisition in rhizo spheric soil. It is reported that under non-sterile soil system, crops show no iron-deficiency symptoms and have more iron uptake in roots as compared to crops grown in sterile soil (Masalha et al. 2000). This supports the possible role of PGPR in iron acquisition. Iron is present in different complexes each having different solubilities in natural system; therefore, the bioavailability of iron depends upon the potential of siderophores to chelate the iron from its complexes (Hersman et al. 2001). A cold-tolerant mutant of Pseudomonas fluorescens with 17-fold increase in siderophore production enhances colonization and PGP effect on mungbean (Katiyar and Goel 2004). Similarly, seed inoculation of maize with siderophore-producing Pseudomonas Pseudomonas chlororaphis enhances seed germination and root shoot biomass (Sharma and Johri 2003). Siderophores producing PGPR suppressed root pathogens by consuming available soil iron (Kloepper et al. 1980) and with the addition/availability of iron even in acidic soils (pH  <  6.0), these siderophores becomes less effective (Neilands and Nakamura 1991). Different bacterial proteins are involved in iron uptake and transport. This uptake by different bacterial species depends on the available concentration of soil iron.

4 Plant Growth Regulators

PGPR synthesize and export phytohormones also called as plant growth regulators (PGRs), that may be synthesized in defined organs of plant and can be translocated to other sites, where these trigger specific biochemical, physiological, and morphological role in plant growth and development (Hayat et al. 2011). PGRs are organic in nature that promote physiological processes of plants even at low concentrations and also take part in the development of tissues where they are produced. Among PGRs, gibberellins, cytokinins, auxins, abscisic acid and ethylene are well documented. The most common and active auxin in plants is indole-3-acetic acid (IAA), that regulates many aspects of plant growth and development throughout the plant cell cycle, from cell division, cell elongation and differentiation to root initiation, apical dominance, tropistic responses, flowering, fruit ripening, senescence and stimulation of plant growth. Regulation of these processes by auxin is believed to involve auxin-induced changes in gene expression (Guilfoyle et al. 1998). In addition to IAA, bacteria such as Paenibacillus polymyxa and Azospirillum also release other compounds in rhizosphere that could indirectly contribute to plant growth promotion like indole-3-butyric acid (IBA), Trp and tryptophol or indole-3-ethanol (TOL).

Cytokinins too are important phytohormones usually present in small amounts in biological samples (Vessey 2003). These enhance cell division, root development and root hair formation (Frankenberger and Arshad 1995), and are also involved in the processes such as photosynthesis or chloroplast differentiation. They are also known to induce opening of stomata, suppress auxin-induced apical dominance, and inhibit senescence of plant organs, especially in leaves (Crozier et al. 2001). More than 30 growth promoting compounds of cytokinin group are reported that are produced by plant associated PGPR. Cytokinin producing bacteria Azotobacter chroococcum and cytokinin precursor’s isopentyl alcohol (IA) and adenine (ADE) have been tested on maize crop under controlled and field conditions by Nieto and Frankenberger (1991). They observed improvement in crop growth. PGPR also produce widely recognized gibberellic acid (GA) and gibberellins (GAs).Over 89 GAs are known to date, most of which are primarily responsible for stem elongation (Dobbelaere et al. 2003). GAs also affect reproductive processes in a wide range of plants (Crozier et al. 2001). PGPR like Azospirillum and Pseudomonas sp. produce cytokinins and gibberellins (gibberellic acid). In addition to IAA, abscisic acid (ABA) has also been detected by radio-immunoassay or TLC in supernatants of Azospirillium sp. and Rhizobium sp. cultures (Dobbelaere et al. 2003).

Ethylene is a plant growth regulator synthesized by almost all species of bacteria (Primrose 1979). It acts as a ripening hormone, promotes adventitious root and root hair formation, stimulates germination, breaks dormancy of seeds; promote plant growth, development, and senescence. However, if ethylene concentration remains high after germination, root elongation, as well as symbiotic N2 fixation in leguminous plants is inhibited. PGPR produces enzyme like 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which hydrolyzes ACC and lowers the level of ethylene in crop rhizosphere. The product of this hydrolysis, ammonia and α-ketobutyrate, can be used by the bacterium as a source of nitrogen and carbon for growth. In this way the bacterium acts as a sink for ACC and thus lowers the ethylene level in plants, preventing some of the potentially deleterious consequences of high ethylene concentrations (Glick et al. 1998). PGPR with ACC-deaminase characteristics improve crop growth and yield and may be included bio-fertilizer biotechnology (Shaharoona et al. 2006). Role of PGPR in the production of phosphatase, β-glucanase, dehydrogenase and antibiotics has also been recognized. Another recently identified mechanism for plant growth promotion is due to production of volatiles by PGPR. Ryu et al. (2004) discussed in detail the role of bacterial volatiles in plant growth promotion in vitro. PGPR release different volatile blends and the differences in these volatile blends stimulate the plant growth. Volatile compounds like 3-hydroxy-2-butanone (acetoin) and 2,3-butanediol, produced by Bacillus subtilis and B. amyloliquefaciens stimulated the growth of Arabidopsis thaliana in in-vitro experiments. The volatile-mediated growth promotion by PGPR is by activation of cytokinin-signaling pathways.

5 Role of PGPR in Biocontrol Aspects

PGPR indirectly help in plant growth by suppression of deleterious microorganisms that inhibit plant growth or root pathogens through antibiosis, parasitism, competition for nutrients and space within the vicinity of plant roots, and/or activation of host defense responses (Podile and Kishore 2006). The strains of Bacillus subtilis are the most widely used PGPR due to their disease reducing and antibiotic producing capabilities (Kokalis-Burelle et al. 2006). Fluorescent pseudomonads are also known to suppress soil born fungal pathogens by producing antifungal metabolites and by sequestering iron in rhizosphere through the release of iron-chelating siderophores, rendering it unavailable to other organisms (Dwivedi and Johri 2003).

Suppression of deleterious microorganisms by PGPR is mainly by parasitism, by competing for available nutrients, production of enzymes or toxins and inducing resistance by activating plant defense response against pathogens (Podile and Kishore 2006). Fluorescent pseudomonads establish themselves on plant roots and sink the available nutrients, thus limiting the available nutrients required for the growth of pathogen (Walsh et al. 2001). PGPR also compete for nutrients with native rhizosphere microbes for elimination of pathogens. Siderophore production by PGPR, sequester most of available Fe3+ in the rhizosphere and force the pathogens for iron starvation, thus is a major contributor for pathogen suppression (O’Sullivan and O’Gara 1992). Suppression of Fusarium wilt of radish by Pseudomonas strain WCS358 through siderophore-mediated competition for iron (Costa and Loper 1994) is another example. Some PGPR’s degrade the cell wall of pathogenic fungi through production of hydrolytic enzymes (chitinase, β-1,3-glucanase). Purified chitinases of Bacillus subtilis AF 1 (Manjula et al. 2004), Serratia marcescens (Kishore et al. 2005b; Ordentlich et al. 1988) and S. plymuthica (Frankowski et al. 2001) are highly antifungal. β-1,3-glucanase producing strain of Pseudomonas cepacia inhibits the rhizosphere proliferation of various phytopathogenic fungi including Rhizoctonia solani, Sclerotium rolfsii and Pythium ultimum (Fridlender et al. 1993) and synergistic action of the two hydrolytic enzymes chitinases and β-1,3-glucanases was more effective in the inhibition of fungal pathogens than either enzyme alone (Tanaka and Watanabe 1995). Hydrolytic enzyme produced by pathogenic fungi includes pectolytic enzymes (polygalacturonases, pectin, lysis), cellulases and cutinase. PGPR’s inhibit (Podile and Kishore 2006) these pathogenic fungi and thus activity of these enzymes can be reduced with the reduction in virulence (Beraha et al. 1983). Bacillus megaterium B 153-2-2 inhibits the activities of extracellular enzymes, like cellulase, pectin lyase and pectinase produced by Rhizoctonia solani, by producing an extracellular endoproteinase (Bertagnolli et al. 1996). A groundnut seed endophytic bacterium Pseudomonas aeruginosa GSE 18, effective in control of groundnut stem rot disease, when applied as seed treatment or soil amendment, inhibits the production of cell wall-degrading enzymes (CWDE) polygalacturonase and cellulase by the pathogen Sclerotium rolfsii tested in vitro (Kishore et al. 2005c).A few strains of rhizobacteria activate plant defense responses against a broad spectrum of plant pathogens, termed as induced systemic resistance (ISR). Rhizobacteria-mediated ISR has been demonstrated in many plant-pathogen systems wherein the bacterium and the challenging pathogen remained spatially separated, and these observations indicate that ISR is genetically determined (Pieterse et al. 2001).

Inoculation of different strains of Pseudomonas fluorescens strains reduce the seedling mortality caused by Aspergillus niger (Dey et al. 2004) and show strong inhibition to Sclerotium rolfsii by reducing the incidence of stem rot severity. They also produce siderophores and antifungal metabolites. Production of antifungal metabolites by fluorescent Pseudomonads has been found to suppress soil-borne fungal pathogens on many occasions (Dey et al. 2004; Catellan et al. 1999). Similarly, Pseudomonas putida produces siderophores which convert a fusarium-conducive soil into a fusarium-suppressive soil for growth of different crops. Improvement in plant growth and disease resistance to a broad array of plant pests can be accomplished using PGPR (Kloepper et al. 2004). It is well recognized that PGPR can influence plant growth through creating resistance against pathogens. Bacillus subtilis is one such commercialized PGPR and it acts against a wide variety of pathogenic fungi (Banerjee et al. 2006).

6 Role of PGPR in Crop Production

Rice, wheat and maize are the three major staple food crops for world’s population. A variety of PGPR’s participate in interaction with C3 and C4 plants and can significantly increase their yield (Kennedy et al. 2004a, b). Rice crop removes around 16–17 kg N to produce 1 t dry weight of rice including straw. Wheat crop requires about 26–28 kg N to produce 1 t of grain including straw (Angus 2001). Maize plants require 9–11 kg N to produce 1 t biomass (Kennedy et al. 2004a, b). The N requirement of cereals is normally met by fertilization at a rate depending on soil fertility with chemical urea (Scharf 2001). PGPR inoculant biofertilizers can, in principle, be used to supplement or reduce the use of urea-N (Kennedy et al. 2004a, b). Those closely associated with rice rhizosphere are Azospirillum, Burkholderia and Herbaspirillum. A free living heterotrophic diazotroph like Azotobacter (A. vinelandii and A. chroococcum) uses C from sugar as energy source (Kennedy and Tchan 1992). There are obligatory anaerobic heterotrophs like Clostridia which are only capable of fixing N2 in the complete absence of oxygen (Kennedy and Tchan 1992; Kennedy et al. 2004a, b) and are usually isolated from rice fields (Elbadry et al. 1999). Their activity in rice may be enhanced with the addition of organic source like straw (Kanungo et al. 1997), presumably as a result of microbial breakdown of cellulose into cellobiose and glucose. Yield of rice can be increased with the application of Azotobacter, Azospirillum lipoferum and Azospirillum brasilense, Azospirillum (Reis et al. 2000). Similarly, Burkholderia vietnamiensis increases rice grain yields significantly up to 8 t ha−1 (Tran Vân et al. 2000) by supplementing 25–30 kg N ha−1 as synthetic fertilizer. Family Enterobacteriaceae has several diazotrophs like Klebsiella (K. pneumonia), Enterobacter (E. cloacae), Citrobacter (C. freundii), and Pseudomonas (Ps. putida or Ps. fluorescens) isolated from rice rhizosphere with plant growth promoting traits (Kennedy et al. 2004a, b). Another rice endophyte Herbaspirillum seropedicae (James et al. 2000) can fix upto 45% of total plant N in rice from the atmosphere (Baldani et al. 2000). The N2- fixation range by Herbaspirillum was assessed upto 58 mg tube−1 under aseptic conditions (Reis et al. 2000). Azoarcus sp. is also endophytic Gram-negative N2-fixing bacterium firstly isolated from Kallar grass (Leptochloa fusa Kunth) growing in saline-sodic soils of Pakistan (Reinhold-Hurek et al. 1993). Azoarcus colonise rice under both laboratory and field condition (Hurek et al. 1994; Reinhold-Hurek et al. 2002). Multi-strain biofertilizer (BioGro) containing three different PGPR like Pseudomonas (Ps. fluorescens, Ps. putida), Klebsiella (K. pneumonia) and Citrobacter (C. freundii) isolated from rice rhizospheric soil of Hanoi, Vietnam (Nguyen et al. 2003) significantly increased rice grain yield in Vietnam and Australia (Williams and Kennedy 2002). National Institute for Biotechnology and Genetic Engineering (NIBGE) of Pakistan also prepared a multi-strain rice biofertilizer rice with the commercial name “BioPower” (Malik et al. 2002) and similar product is also available in Egypt (Hegazi et al. 1998). These inoculants are claimed to give similar yield increases on rice farms upto 20% (Kennedy et al. 2004a, b).

Similarly, strains of Azospirillum, Azotobacter, Azorhizobium, Bacillus, Herbaspirillum and Klebsiella can supplement the use of urea-N in wheat production either by BNF or growth promotion (Kennedy and Islam 2001). The N requirement of wheat is higher than that for rice, because of its higher grain protein content. Wheat yields vary widely from 1 to 7 t ha−1 dependent on inherent soil fertility, amount of applied fertilizer, wheat variety, diseases, other management practices and environmental conditions (Angus 2001).Thus, estimated amount of N removed by wheat crop varies between 26 and 200 kg N ha−1, depending on the yield (Reeves et al. 2002). To maximize wheat yields in soils that are not capable of supplying enough N, chemical fertilizers such as urea are used to enhance N supply. Biofertilizers are also being used to supplement the use of urea worldwide. The estimated amount of BNF by such wheat-bacterial associations was between 10 and 30 kg N ha−1 (Kennedy and Islam 2001) or about 10% of their total-N requirement. Wheat transformed about 30% of carbon assimilates into the process of rhizodeposition and part of this below ground translocated C is incorporated by rhizosphere micro-organisms (Kuzyakov and Domanski 2000). Studies indicate that PGPR may act as natural elicitor for improving the growth and yield of wheat. Important PGPR responsible for increased wheat yield in different parts of world are Pseudomonas (ps. cepacia, ps. aeruginosa, ps. fluorescens and ps. putida, ps. chlororaphis), Bacillus (B. cereus), Azospirillum (A. brasilense, A. lipoferum) and Herbaspirillum (H. seropedicae). Common PGPR species found in rhizosphere of maize are Enterobacter sp., Rahnella aquatilis, Paenibacillus azotofixans, Herbaspirillum seropedicae, Bacillus circulans, Klebsiella sp. and Azospirillum sp. (Chelius and Triplett 2000). The positive effects of Azospirillum on maize growth are mainly derived from physiological changes of the inoculated plant roots, which enhance water and mineral nutrient uptake (Okan and Kapulnik 1986). Both Azospirillum brasilense and Azospirillum irakense are used as inoculant biofertilizer for maize. Other species of Azospirillum capable of increasing the yield of maize are A. lipoferum, and A. indigens. Azorhizobium caulinodans is also capable of giving such beneficial effects (Riggs et al. 2001). Herbaspirillium seropedicae can improve the ability of maize plant to use fertilizer N more efficiently and the yield increase due to H. seropedicae was up to 19.5% (Riggs et al. 2001). PGPR strains Burkholderia (B. cepacia), Pseudomonas (P. fluorescens), Serratia (S. proteamaculans, and S. liquefaciens), Rhizobium (R. etli bv. Phaseoli, R. leguminosarum bv. Trifolii) and Sinorhizobium sp. increase corn growth, plant height and grain yield of maize in different agro-ecological zones. The diazotrophs commonly present in sugarcane plants are Acetobactor also known as Gluconacetobacter (A. diazotrophicus), Azospirillum (A. brasilense, A. lipoferum, A. amazonense), Burkholderia (B. brasilensis, B. tropicalis), and Herbaspirillum (H. seropedicae, H. rubrisubalbicans) (Kennedy and Islam 2001). Sugarcane requires approximately 1.45 kg N ha−1 to produce 1 t moist biomass (Bhuiyan 1995) or about 7 kg N ha−1 for 1 t of dry cane. Generally 150–250 kg urea-N ha−1 is applied for sugarcane cultivation depending on soil fertility, genotype and the targeted yield. Evidence from Brazil indicates fertilizer-N of sugarcane can be reduced to half by exploiting BNF systems, claimed to be based on diazotrophic PGPR such as Acetobacter (Gluconacetobacter) and Herbaspirillum (Döbereiner 1997; Döbereiner and Baldani 1998). More than 70% of sugarcane N (200 kg N ha−1 y−1) was derived from biological fixed N2 by Azospirillum (A. diazotrophicus) (Boddey et al. 1991). Similarly, Acetobacter (with nifH+) -sugarcane system has also been well established (Lee et al. 2002). Azotobacter sp. and Klebsiella mobilis are reported for improving potato yield. Similarly Pseudomonas fluorescent and Achromobacter piechaudii increase tomato yield. Positive effect of PGPR (Bacillus cereus; Pseudomonas putida; Pseudomonas fluorescens; Serratia liquefaciens; Arthrobacteer cetreus; Escherichia coli, Mesorhizobium loti and Delftia acidovorans) inoculation on the growth and yield of rapeseed have been reported by many researchers. Burkholderia cepacia alone or in combination with Enterobacter spp. and Pseudomonas fluoroscens have also been tested for its ability to promote growth of sorghum (Sorghum bicolar) (Chiarini et al. 1998). Inoculation with effective bacterial strains (Pseudomonas alcaligenes, Pseudomonas denitrificans, Bacillus polymyxa, Azospirillum brasilense and Mycobacterium phlei) increases the root and shoot growth of cotton (Anjum et al. 2007). Çakmakçi et al. (2007) also conducted a study on barley under greenhouse conditions in order to investigate seed inoculation with five different N2-fixing (Bacillus licheniformis, Rhodobacter capsulatus, Paenibacillus polymyxa, Pseudomonas putida, and Bacillus spp. OSU-142) and two different phosphate-solubilising (Bacillus megaterium and Bacillus spp. M-13) bacteria in comparison to control and mineral fertiliser (N and P) application. Co-inoculation of legumes with PGPR and Rhizobium has received increasing attention in recent years. Co-inoculation with symbiotic bacteria and rhizosphere bacteria may increase nodulation through a variety of mechanisms. PGPR strains, from a range of genera, enhance legume growth, nodulation and nitrogen fixation when co-inoculated with their effective rhizobia. Examples of these are Azospirillum (A. lipoferum, A. brasilense), Azotobacter (A. chroococcum), Bacillus (B. cereus, B. endophyticus, B. pumilus, B. subtilis, B. firmis, B. megaterium), Paenibacillus (P. lautus, P. macerans, P. polymyxa,), Pseudomonos (Ps. fluorescens, Ps. putida, Ps. aeruginosa) Serratia (S. lequefacians, S. proteamaculans), Aeromonas hydrophia and, Streptomyces (Pal et al. 2004; Kishore et al. 2005a; Figueiredo et al. 2007) . All these bacteria including cyanobacteria can supplement urea-N by BNF, but only if conditions for expression of N2-fixing activity and subsequent transfer of N to plants are favourable. In general, it is believed that PGPR are more effective in promoting plant growth under limited supply of nutrients; however, present scenario does not allow to compromise on actual potential of crop productivity by reducing use of chemical fertilizers. Hence, it is of prime importance to isolate such PGPR strains that could be effective even under optimum nutrition. The biosynthesis of ethylene in plant roots is significantly affected by concentration of NO3-N present around the roots (Ligero et al. 1999). Higher levels of NO3 in rooting medium stimulate ACC-oxidase activity leading to increased ethylene production, which is generally believed to be inhibitory to root growth (Glick et al. 1998). The nitrogenous fertilizer applied in ammonical form is readily oxidized to NO3-N under aerobic conditions. It is very likely that NO3-N present in the vicinity of roots reduces the efficiency of PGPR by inducing ethylene synthesis. However, PGPR containing ACC-deaminase minimizes the NO3 induced ethylene synthesis.

7 Conclusion

PGPR are able to enhance significantly the yield of cereals, legumes and sugarcane crops etc. Soil and plant health can be enhanced through PGPR-crops rhizospheric interactions. From the agricultural viewpoint, the aim will be to increase the yield on sustainable basis, while maintaining soil health. To achieve this, knowledge about indigenous PGPR for different crop rhizospheric environment must be improved. It is also necessary to adopt and maintain minimal standards for production of PGPR inoculants/biofertilizers. PGPR biofertilizers not only promote crop growth but also enhance the resistance against pathogens. Integrated use of PGPR along with inorganic and organic nutrient sources provides a sustainable agricultural ecosystem.


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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Rifat Hayat
    • 1
  • Iftikhar Ahmed
    • 2
  • Rizwan Ali Sheirdil
    • 1
  1. 1.Department of Soil Science and SWCPMAS Arid Agriculture UniversityRawalpindiPakistan
  2. 2.Plant Biotechnology ProgramNational Agricultural Research CentreIslamabadPakistan

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