Piriformospora indica: Potential and Significance in Plant Stress Tolerance

1In natural ecosystems, a variety of microorganisms seek to obtain nutrients for their survival by interacting with plants, where the interaction can be neutral, harmful (parasitism), or beneficial (mutualism or symbiosis) to the host. However, most plants in natural ecosystems have been reported to display their high degree of colonization/symbiosis with mycorrhizal fungi and/or fungal endophytes. Biotrophy, necrotrophy and hemibiotrophy are among the major lifestyles that plant-associated fungi can exhibit. The actively metabolizing plant tissues are required by biotrophic fungi where host is kept alive; whereas, the host is killed by necrotrophic fungi to obtain nutrients from the dead cells for their own growth and survival. The hemibiotrophic fungi belongs to an intermediate category, which requires living host cells during the initial part of their life cycles, and later acts as a necrotrophic fungi.

2Piriformospora indica, an axenically cultivable phytopromotional, biotrophic mutualistic root endosymbiont belongs to order Sebacinales (Basidiomycota) and has been reported to mimic capabilities of typical arbuscular mycorrhizal (AM) fungi. This fungus can colonize roots of a wide range of higher plants and provide plants multifaceted amenities (such as nutrient uptake, disease resistance, stress tolerance and growth-promotion involving value addition). In plant groups other than crops, for example orchids, P. indica has been reported to be primarily existed as a partner of mycorrhiza. This fungus has been reported to perform multifarious functions, including its role in biological hardening during transplantation of micro-propagated plantlets, increased endogenous content of spilanthol after realization of its mutual interaction with medicinal plants such as Spilanthes calva. P. indica infestation in Helianthus annus and Aristolochia elegans has resulted into the stimulated synthesis of valuable compounds. Additionally, Bacopa monnieri co-cultivated with P. indica exhibited an enhanced growth, elevated bacoside endogenous level, antioxidant activity and nuclear hypertrophy. Notably, compared to many other endophytes, P. indica can be cultured very easily in a bioreactor in order to prepare effective biofertilizer formulations. P. indica inocula are very effective for their commercial applications to various crops within the defined parameters viz., inocula quantity, inoculation time point, as well as soil selection for plant cultivation. Moreover, P. indica root endophyte has been credibly evidenced to minimize the use of chemical fertilizers, control crop yield, and also to provide increased resistance and tolerance in plants against biotic and abiotic stresses. In our recent effort, P. indica-mediated improvements in the biomass, seed germination, plant growth and development and crop productivity under favorable environmental conditions were highlighted, and P. indica was argued as a powerful tool for crop improvement.

3Taking into account of recent literature, this paper: (a) overviews P. indica-strategies for root colonization; (b) gives insights into P. indica–plant mutualistic interaction and the role of calcium; (c) enlightens the association of P. indica with programmed cell death (PCD); (d) dissects information related with P. indica genome; (e) appraises literature available on P. indica-services to plants; (f) evaluates interaction of P. indica with other microorganisms, and appraises biotechnological significance of P. indica; (g) cross-talks information related with regulatory role of P. indica for the genes involved in plant metabolism, mineral uptake, in plant stress resistance and defense; and finally, (h) highlights the least explored aspects in the present context so far.

4The fact that P. indica has a broad host range, which is not only confined to vascular plants but also to colonized mosses, implies that this fungus has evolved highly effective colonization strategies. Some facts related with the lifestyle and the mechanisms underlying root colonization of P. indica from its interaction with many plants (such as Hordeum vulgare and Arabidopsis thaliana) have been unraveled. Generally, symbionts colonize rhizodermal and cortical cell layers of roots. Root colonization by P. indica is also known to start with interacellular chlamydospore germination and forming extracellular hyphal mats, and simultaneously penetrating rhizodermal and cortical cells. As colonization proceeds, roots are densely covered with extracellular hyphae and harbor through inter- and intracellular networks; however, the fungus never enters into the vascular tissues. At cellular level, this fungus colonizes living root cells by its direct penetration. No microscopic evidence for impairment or even necrotization was found in H. vulgare and P. indica-colonized A. thaliana roots. The colonization patterns of the various root regions harbor some quantitative as well as qualitative differences, which distinguish P. indica on H. vulgare (and A. thaliana) from endomycorrhizal fungi. The fungal root colonization increases with root maturation and the highest fungal biomass has been found in the differentiation, particularly in the root hair zones. Cytological studies have revealed the diverse types of P. indica-interaction with different root regions of H. vulgare, where the root hair zone (as the oldest root zone) was observed to be highly colonized by intracellular hyphae. Cells in the differentiation zone can be filled with fungal hyphae reminiscent of hyphal coils; whereas, scarcely and solely extracellularly colonization can be evidenced in the cells of meristematic zone. Importantly, the physiological activity of host cells has been considered as a prerequisite for efficient nutrient exchange between the symbiotic partners. Thus, root colonization pattern of P. indica differs from that of AM fungi, which are known to preferentially colonize younger root parts (Figure 1).

5presented the first in-depth genomic study and unveiled a mutualistic symbiont with a biphasic lifestyle. On the 25 Mb genome of the mutualistic root symbiont P. indica, the authors characterized fungal transcriptional responses associated with the colonization of living and dead H. vulgare roots. A biphasic root colonization strategy of P. indica was revealed by microarray analysis, where a tightly controlled expression of the lifestyle-associated gene-sets was reported during the onset of the symbiosis. It has been observed that about 10% of the fungal genes induced during the biotrophic colonization encoded putative small secreted proteins (SSP). SSP included several lectin-like proteins and members of a P. indica-specific gene family (DELD) with a conserved novel seven-amino acids motif at the C-terminus. The occurrence of the DELDs was further correlated with the presence of transposable elements in gene-poor repeat-rich regions of the genome similar to the effectors found in other filamentous organisms. These findings together, helped to understand the development of biotrophic plant symbionts and also suggested a series of incremental shifts along the continuum from saprotrophy toward biotrophy in the evolution of mycorrhizal association from decomposer fungi.

6On the perspective of the biotrophic colonization pattern of P. indica, it has been reported that the P. indica biotrophic colonization pattern can be accompanied by a broad-spectrum suppression of root innate immunity. In the support of the large host range of P. indica, molecular and genetic analyses revealed that plant roots, similar to leaves, are equipped with an effective innate immune system where immune suppression by P. indica was considered as a prerequisite for successful root colonization. A little work has been performed in order to decipher the underlying mechanisms of suppression of root innate immunity by P. indica for a successful colonization. However, there are evidences that signify the involvement of several phytohormones in this context. H. vulgare and Arabidopsis mutants impaired in gibberelic acid (GA) and jasmonic acid (JA) metabolism, respectively exhibited elevated root immune responses together with reduced root colonization. Studies have also revealed the dependency of P. indica on JA-mediated suppression of early immune responses (e.g., root oxidative burst) as well as salicylic acid (SA)- and glucosinolate-related defense pathways. For example, Arabidopsis mutants impaired in SA- and glucosinolate-associated defense were reported to be more susceptible to P. indica. The disturbance of endoplasmic reticulum (ER) integrity by P. indica has been advocated to have potential for impairing the secretion of immunity-associated proteins (e.g., PR1 and PRRs). This suppression of early immune signaling (which disturbs immune execution) may potentially disarm the root, and thereby may facilitate root colonization. Since the genome of P. indica is available, it is possible to identify effector molecules targetting immune signaling components.

7Both mutualists and commensals are identical for many fungi during the initial phases of infection and colonization by pathogens. Thus, the mode of recognition and early signaling processes are crucial in understanding how plants can differentiate between a beneficial and a detrimental microbe which in turn can modulate the expression of lifestyle in plants. Notably, within seconds or minutes after the recognition of the two partners, an increase in the level of intracellular calcium (Ca2+) in a plant cell has been considered as an early signaling event in the interaction of pathogenic, mycorrhizal or endophytic microbes with plants. Nevertheless, in various plant-signaling pathways, Ca2+ ions act as a second messenger in order to couple extracellular stimuli with intracellular and whole plant responses. Endophytic and mycorrhizal fungus interactions result in a better plant performance through sequential cytoplasmic and nuclear Ca2+elevations.

8Ca2+ ions have been evidenced as a key participant in the mutualistic interaction of both P. indica and Arabidopsis. It is also one of the earliest signaling events during the recognition of these two symbionts, where a rapid induction of [Ca2+]cyt elevation follows a nuclear Ca2+ response. Quite a few mutants which do not respond to P. indica concerning growth promotion and higher biomass production are also impaired in [Ca2+]cyt elevation. Additionally, elevations in the [Ca2+]cyt can also be induced by an autoclaved cell wall extract (CWE) from P. indica, which also can promote growth of Arabidopsis and other plant species. Previous facts together suggest insignificance of root colonization by the living fungus in the highlighted above response. Inductions in the elevation of [Ca2+]cyt by autoclaved CWE, preferentially in the roots confirm that the endophyte is a root-colonizing fungus. The very same CWE can induce a slightly different Ca2+ signature in tobacco roots hinting at the possibility of species-specific plant responses. CWE from P. indica also induces tuberization in vitro and promotes tuber growth and yield in potato due to increased transcript expression of the two Ca2+ dependant proteins (such as CaM1 and St-CDPK1) and the lipoxygenase (LOX) mRNA, which are known to play distinct roles in potato tuberization.

9At the contact surface of plants, P. indica exchanges various signals which can result into influx of phosphorus and efflux of Ca2+ within plant cell. The external stimuli from endophyte signaling cascade of cellular network either signifies phytohormones to mainly be involved in PCD via endoplasmic reticulum stress or directly be involved in growth and development. Exhibition of the reduced colonization, plant growth and development were reported by the plant mutants impaired in GA and JA metabolism. Generally, in PCD, Ca2+ and phytohormone signal as internal or external stimuli that down-regulates (PR1b, PR5, β-gulcanase etc.) and up-regulates (auxin) (BI-1 gene). PCD as DNA fragmentation and cell shrinkage were common during P. indica colonization. The host cell death in H. vulgare plants via constitutively overexpressing the negative cell death regulator Bax Inhibitor-1 (BI-1) was reported to reduce colonization of roots. Arabidopsis roots displayed ultrastructural alterations at the time of cell death that was linked with the colonization by P. indica. This can be explained by the fact that P. indica induces ER stress in colonized roots and also suppresses the adaptive ER stress response pathway (unfolded protein response, UPR). The inability of colonized cells to relieve ER stress via the UPR leads to activation of a pro-apoptotic signaling cascade. Phytohormones and Ca2+ (which might occur at the plant-fungus interface) can direct the molecular and physiological processes responsible for the actual mechanism of P. indica colonization with plants providing various benefits to plants (Figure 2).

10Generally, PCD is a natural response of plants to face physiological constraints provoked by varied internal or external stimuli. PCD is a metabolically regulated mechanism (e.g., nutrient recycling) vital for plant development. However, in the case of hypersensitive response (HR), PCD has a protective function in local and systemic tissue, characterized by defense gene expression to check the growth and propagation of pathogens. Plant-PCD shares some common characteristics to apoptosis in animals such as chromatin condensation, cell shrinkage and DNA fragmentation followed by the nucleus breakdown. The fungal colonization of roots begins with a biotrophic growth phase, in which living cells are colonized, and followed by a cell death-dependent phase, in which root cells are actively killed by the fungus. Earlier, P. indica was reported to colonize roots (such as that of Arabidopsis) by an initial biotrophic phase, which was evidenced to follow a cell death-dependent phase that may not show any disease symptoms on plant roots. DNA fragmentation and cell shrinkage, common features of PCD can also be observed in P. indica-colonized roots. It is assumed that P. indica uses these dead cells for intracellular sporulation. In contrary to their pronounced induction during pathogen-induced HR, argued that the kind of cell death occurred during P. indica colonization in H. vulgare may not be regarded as a microorganism-antagonizing plant response, since the defense marker genes (e.g., PR1b, PR5 and 1,3-β-glucanase) are weakly and transiently up-regulated solely at early interaction stages. Besides, accumulation of ROS (e.g., hydrogen peroxide, H2O2), as well as whole-cell auto-fluorescence mediated by phenolic compounds as characteristics of HR have never been detected in the P. indica colonized roots.

11Transmission electron microscopic studies have revealed that cells are not dead at the penetration stages but show ultrastructural changes as cell-colonization is ascertained. It implies that the fungal-colonization strategy is not merely focused on the perception and subsequent colonization of dead cells though the penetrated host cells certainly die at one defined point of cell-colonization. Evidences also confirm the dependency of this colonization strategy merely on the host cell death. Reduced colonization of roots was observed in H. vulgare plants constitutively overexpressing the negative cell death regulator Bax Inhibitor-1 (BI-1). The expression of BI-1 in P. indica-infested H. vulgare was suppressed from 5 days after inoculation onward, which corresponded with cellular mycelial proliferation, and did not match with earlier root penetration events. Additionally, in comparison to the wild-type plants, the constitutive overexpression of HvBI-1 in H. vulgare led to a significant reduction in fungal biomass at 20 days after inoculation. These findings also agreed with the significant role of BI-1 in plant defense and cell survival. BI-1, known to be an integrator of ER stress, supports cell integrity and viability under unfavorable conditions. Besides its involvement in cell death, the ER is also significant for correct processing of immunity-related proteins with an extracellular or plasma membrane-associated destination, including the pattern recognition receptor EFR. After recognition of the bacterial elongation factor TU, EFR activates basal immunity and effectively halts bacterial invasion of plants. Recent cellular analyses of Arabidopsis roots revealed ultrastructural alterations during cell death-associated colonization by P. indica. According to these studies, P. indica induces ER stress in colonized roots, nevertheless, at the same time suppresses the adaptive ER stress i.e., unfolded protein response pathway (UPR). The inability of colonized cells to relieve ER stress via the UPR leads to activation of a pro-apoptotic signaling cascade. Thus, vacuolar collapse was identified to be downstream of ER stress and to represent a key element of the P. indica-induced cell death pathway. This vacuolar collapse has been considered essential for both cell death execution and root colonization, which is mediated by vacuolar processing enzymes (VPEs). For example, Arabidopsis mutants lacking VPEs were found incapable of undergoing cell death-associated vacuolar collapse and exhibited reduced fungal colonization. It has been suggested that P. indica achieved its large host range through a biphasic colonization strategy, which consists of biotrophic accommodation by effective host immune suppression, followed by an ER stress-induced caspase-dependent vacuolar cell death. The exact execution of both colonization phases is a prerequisite for a successful symbiosis with Arabidopsis. PYK10, a gene for an abundant β-glucosidease/myrosinase of 65 kDa is located in the ER and has been identified as a target of P. indica in Arabidopsis roots. PYK10 was argued as a requirement for the beneficial interaction between Arabidopsis and P. indica. In fact, non-toxic glucosinolates can be hydrolyzed by myrosinases to biologically active isothiocyanates, thiocyanates, nitriles or epithio nitriles. However, the nature of the aglycon moieties released from the substrates basically controls the biological function of a myrosinase. The involvement of these aglycons in the plant defense against herbivores and microbes has been reported. Thus, myrosinases can be exploited for their applications in plant biotic/abiotic stress defense.

12hypothesized that the broad host range of P. indica is possibly due to its interaction(s) based on general recognition and signaling processes. In order to identify plant genes, which are targeted by the fungus, Arabidopsis mutants were screened that do not respond to the fungus with regard to growth promotion and enhanced seed production. The authors reported that the growth of a T-DNA insertion line in PYK10 is not promoted and the plants do not produce more seeds in the presence of P. indica, although their roots are more colonized by the fungus in comparison with the wild-type roots. Overexpression of PYK10 mRNA did not affect either root colonization or the response to the fungus. The basic helix-loop-helix domain containing transcription factor NAI1 activates expression of PYK10, and two Arabidopsis lines with mutations in the NAI1 gene show similar response to P. indica as that of PYK10 insertion line. PYK10 transcript and PYK10 protein levels are severely reduced in a NAI1 mutant, signifying that PYK10 is responsible for the response to the fungus not the transcription factor NAI1. The message level for a leucine-rich repeat protein LRR1 is upregulated in wild-type roots in the presence of P. indica but not for plant defensin 1.2 (PDF1.2). Contrary to that, the message level for PDF1.2 is upregulated in the presence of the fungus in lines with reduced PYK10, not for LRR1. concluded that PYK10 restricts root colonization by P. indica, which leads into repression of defense responses and the upregulation of responses directing to a mutualistic interaction between the two symbiotic partners.

13A comparison of the P. indica genome with other fungi has revealed its classical features related with biotrophism as well as saprotrophism. The colonization of P. indica with Arabidopsis roots has been report to involve an initial biotrophic phase followed by cell death dependent phase, leading ultimately to no disease symptoms on roots. However, P. indica was reported to use the dead cells formed therein during the course of infection for intracellular sporulation. The endophyte infection was earlier considered entirely symptomless, involving certain genes to indicate systemic root colonization by different fungal groups. Exhibition of biotroph-associated genomic adaptations has been evidenced in P. indica, where genes involved in N metabolism are lacking and also a limited potential is displayed by this mutualistic symbiont for host-damage and destruction. In fact, P. indica lacks genes potentially involved in biosynthesis of toxic secondary metabolites and cyclic peptides. Nevertheless, genomic traits with saprotrophic and hemibiotrophic phytopathogenic fungi (such as the presence of an expanded enzyme arsenal which is weakly expressed during the initial biotrophic phase) are also shared by P. indica. The analyses of the colonized young H. vulgare roots has revealed 579 genes in the phase of pre-penetration (36–48 hpi), 397 genes at early colonization (3 dpi) and 641 genes (5 dpi) as distinctively regulated when compared to fungal free roots. In addition, the majority of genes (≈40%) induced via symbiosis were found to be non-orthologous to either species; rather, these were reported specific to P. indica. Plant hormones such as JA, methyl-jasmonate and ethylene signals from the roots were reported to decide the shoots to become preconditioned prior to foliar pathogens infection in P. indica-colonized roots via activating defense responses which in turn were evidenced to lead to enhanced disease resistance. In a signaling cascade, the JA (VSP, PDF1.2, LOX2) plus ET (ERF1) signaling and not the SA signaling (PR1, PR5) genes were up-regulated in the P. indica plants in order to cope the powdery mildew fungus. The indole-3-acetic acid (IAA) and ethylene role has been implicated in establishing a biotrophic symbiosis representing a compatibility factor at contact surface between endophyte and plants. The augmented intracellular Ca2+ pool after attaining the basic compatibility between the two partners in an early signaling event in the interaction of endophyte with plants, acts as a second messenger in various plant signaling pathways.

14Soil signifies a positive environment for a wide range of microorganisms including algae, bacteria, and fungi and the chemical changes that happen within the soil environment involve the active contribution of soil microflora. They chiefly participate in the processes which are necessary for plant growth and survival such as C and N cycle, nutrient acquisition and soil formation. On the other hand, owing to their role in C-input in soils through root exudates, plants can also have profound effects on soil microbial communities especially those colonizing the rhizosphere.

15Being immobile organisms, plants have to cope with unfavorable conditions such as nutrient deficiency, salinity, drought, and pathogen attacks etc. Thus, to avoid such adverse situations, plants tend to establish their associations with beneficial microorganisms. In particular, symbiosis with beneficial fungi are known to be vital for nutrient acquisition by the root systems of most plants. Thus, application of beneficial microorganisms as biofertilizer plays a key role in today’s agricultural scenario through enhancement of soil fertility and crop production. For example, mycorrhizal fungi and AM fungi under the order Glomales, are known to have symbiotic relationship with the majority of terrestrial plant species, where the fungi facilitate plants in their accession to soil nutrients, mainly phosphate. Interestingly, AM symbiosis is described relatively primordial with that of rhizobium-legume association where ‘Myc factor,’ a AM fungal signal, is a mixture of sulphated and non-sulphated simple lipochitooligosaccharides, might turn on signaling pathways having similar components of doesn’t make infections (DMI)-signal transduction pathway to establish the mycorrhiza formation to promote plant growth. Endophytic fungi P. indica which is phylogenetically close to mycorrhizal endosymbionts of orchid and ericoid roots has also been recognized as a growth promoter of numerous plant species. Although mutual nutrient exchange through specialized structures is generally accepted as the main beneficial factor in mycorrhiza, however, major mechanisms of interaction in other endophytic systems are still not clear.

16Phosphorous (P), one of the most essential mineral nutrients constitutes up to 0.5% of the dry weight of plant cell, and plays diverse regulatory, structural, and energy transfer roles. Plants cannot directly access P present in the soil as it is mostly in the form of scarcely soluble complexes; hence, its deficiency impedes crop production throughout the world. Plants acquire P from the soil through direct uptake by its own transporters and indirect uptake through mycorrhizal associations. P. indica was reported to mediate the uptake of radiolabelled P from the culture medium and its translocation to the host in an energy-dependent process. P. indica also produce significant amounts of acid phosphatases which can enable the host plant to access adequate amount of insoluble, condensed or complex forms of phosphate reserve in the soil. The association of P ectomycorrhiza and its role in plant P-aacquisition has been the focuss of recent studies. Identification and characterization of high affinity phosphate transporters were also done in several plant and fungal species including A. thaliana, Medicago truncatula, Lycopersicon esculentum, Solanum tuberosum, Saccharomyces cerevisiae, and Neurospora crassa (reviewed by ). Notably, due to the lack of a stable transformation system in AM fungal species the role of phosphate transporters could not be established. Isolation, identification, and functional characterization of a high affinity phosphate transporter from root endophyte fungus P. indica revealed the essentiality of phosphate transporter (PiPT) for phosphate transport to the host plant. Nevertheless, the mechanism of this phosphate transfer from the fungus to the plant is not yet clear, though it has been hypothesized that the process might occur at the plant-fungus interface. This process essentially requires two transporters: the first to enable efflux of phosphate from the fungus and the second to mediate uptake of phosphate by the plant.

17The reports concerning the involvement of P. indica in phosphate transfer and improvement in host plant are contradictory. reported that P. indica enhances the phosphate uptake 2–3 times higher in Arabidopsis seedlings and suggested that P. indica stimulates Arabidopsis growth in a manner parallel of mycorrhizal fungi. On the contrary, it has also been reported that P. indica does not induce significant increase of leaf P and N and phosphate has no role in the improved biomass of Nicotiana attenuata. reported that P. indica is involved in the phosphate transfer to the host Zea mays plant and proposed that involvement of PiPT in indirect phosphate transport to host plants presents the information regarding the molecular mechanism underlying P. indica-mediated phosphate transport to the host plant. However, it was resported earlier that P. indica does not induce potato phosphate transporter gene (StPT3) and that P. indica is not involved in the phosphate transfer to host plant. Correspondingly, no improved phosphate supply (a central mechanism of host plant fortification by AM fungi) was evidenced in P. indica–H. vulgare symbiosis. However, the improved grain yield induced by the fungus was found to be independent of different P and N fertilization levels. Also, the total phosphate contents of host plant roots and shoots were not significantly affected by P. indica. The authors concluded that positive influence of P. indica on H. vulgare grain yield was independent of P and N supply and rather due to accelerated growth that leads to early development.

18Contrary to the reports discussed above, found the impact of phosphate on the biomass of the Z. mays plant colonized with P. indica. Increased total phosphate content as well as biomass in the plants colonized with wild-type P. indica as compared with non-colonized and KD-PiPT P. indica-colonized plants were observed. These findings imply that phosphate play a significant role in the improvement of yield or biomass of Zea mays, and that enhanced biomass is in fact due to the PiPT. Furthermore, the growth-promoting activity (in terms of biomass) of P. indica was two-fold higher at low phosphate condition as compared with high phosphate condition (1.2-fold). further investigated to ascertain whether growth-promoting activity of P. indica is an inherent trait of the fungus or it is dependent on the availability of P, under P-rich and -deprived conditions. No significant change in the biomass was found at seedling stage; however, the difference in biomass was significant between colonized plants grown in P deprived conditions and non-colonized plants in rich P conditions at later stage. P. indica enhances biomass more efficiently in P-deprived condition than P-rich condition. The growth of colonized plant at 40 μM phosphate was equal to non-colonized plants grown at 400 μM indicating that P. indica can mimic the growth even at 10-fold lower P supplement. Bicompartment assay for 32P transportation revealed that the fungal hyphae transport P to host plant in P-deprived condition but unable to transfer more P in P-rich condition though, there was no difference in the colonization at both the conditions. Hence, it has been concluded that P. indica has an ability to increase the biomass of the maize plant specifically under low phosphate condition thus; P. indica could be a good candidate for utilization in sustainable agriculture for the improvement of crop production in land deficient in P. Furthermore, RT-PCR analysis showed the expression of PiPT gene in P-deprived condition but not in P-rich condition. Therefore it was concluded that PiPT is actively involved in transporting P to the seedlings and that PiPT expression is dependent on the P availability. Though the mechanism for the transfer of P from P. indica to plant is not fully understood; however, it was hypothesized that Pi and organic P (such as polyphosphate) can be carried within the fungus by cytoplasmic streaming or by bulk flow to the plant root from external hyphae located in the soil.

19Conflicting results discussed above may be due to the host-specific nature of P. indica since all the studies were conducted on different crop plants. Therefore, a complete range of different host plants would only provide a clear picture of whether P. indica and PiPT are host-specific or not. Exploitation of P. indica and its PiPT not only can complement crop improvement strategies but may also serve as a model system to study molecular mechanism and indirect uptake of phosphate by plants. Recently, the crystal structure of PiPT has been elucidated. With reference to the root colonization strategy of P. indica, i.e., the program cell death, the authors emphasized that the main part of the root further develops and is not necrotized when colonized by the fungus. Hence, it was hypothesized that once the fungus releases phosphate into dead cells, it might be taken up by the non-affected living adjacent cells and further distribute into different parts of the plant. Future research should be designed to perform gene function analysis studies in P. indica which has been a major constraint in genetic manipulation this fungus until now. In this context, the recently established electroporation-mediated transformation system based on the polyethylene glycol method for P. indica in combination with RNAi-mediated gene silencing have been suggested as major genetic engineering tools.

20Deficiency of other important nutrients such as nitrogen (N) and zinc (Zn) in soil has been reported to restrict plant growth and development. Plants recruit N either as nitrate or ammonium but in some species by N fixation with the help of rhizobia. Mycorrhizal fungi also play an important role in delivering either nitrate or ammonium to the root cells. It is believed that mycorrhizal fungi preferentially recruit ammonium rather than nitrate from the soil and that amino acids represent the major compounds that serve to transfer nitrogen to the host plant. reported that the co-cultivation of Nicotiana tabaccum and Arabidopsis seedlings with P. indica is accompanied by a huge transfer of N from the agar plates into the aerial part of the seedlings. This effect is associated with activation of the NADH-dependent nitrate reductase (NR), the enzyme which plays a key role in nitrate acquisition in plants. However, the stimulation of nitrate assimilation by P. indica is the reason for the growth promotion is not known. P. indica activates NR which in turn plays a key role in nitrate acquisition and also a starch-degrading enzyme, glucan-water dikinase is involved in the early events of starch degradation in N. tabaccum and Arabidopsis. P. indica also activates the expression of the genes for the starch-degrading enzyme, glucan-water dikinase (SEX1) in roots which is involved in early events of starch degradation in N. tabaccum and Arabidopsis. Both the growth promotion and stimulation of the two enzymes do not require heterotrimeric G-proteins. P. indica also stimulates the expression of the uidA gene under the control of the Arabidopsis NR (Nia2) promoter in transgenic tobacco seedlings. A homeodomain transcription factor responds to the fungus and binds to promoter regions of the P. indica-responsive Nia2, SEX1, and 2-nitropropane dioxygenase genes, indicating that the expression of P. indica-responsive target genes may be controlled by common regulatory elements and trans-factors. It is proposed that the growth promoting effect initiated by P. indica is accompanied by a co-regulated stimulation of enzymes involved in nitrate and starch metabolisms. Application of bioinoculants prepared with the of fluorescent pseudomonas strains R81, and P. indica can efficiently promote growth in tomato plants probably due to the colonization strategies of plant growth promoting rhizobacteria (PGPR) and P. indica. It has also been suggested that the better root density of the inoculated plants facilitate and improve uptake of the nutrients from the rhizosphere. Fluorescent pseudomonad strain (R81) being a phosphate solubilizing strain and acid phosphatases produced by P. indica were reported to mobilize and assist L. esculentum plant in phosphate-acquisition, and growth promotion. Recently, a model has been proposed to study an interaction between different strains of Azotobacter and P. indica. The interaction with P. indica is proposed as a useful tool for mitigating zinc (Zn)-deficiency stress in Triticum aestivum. Improved uptake of mineral nutrients, antioxidant enzyme activities, photosynthetic pigments, and low lipid peroxidation have been observed in T. aestivum plants under Zn-deficiency conditions with co-inoculation of two plant-growth-promoting microorganisms; Azotobacter chroococcum and P. indica.

21Piriformospora indica can also significantly mediate improvements in the growth and yield of various crop plants, horticultural and medicinal plants. P. indica-induced seed germination and development have been reported in several crop plants. P. indica-mediated seed development and enhanced seed production in A. thaliana were reported as a result of the pii-2 and At5g16590 located in the micro-domains of plasma membrane. P. indica-inoculated H. vulgare seeds exhibited higher viability. Moreover, germinated seedlings immersed in P. indica-homogenate exhibited a good survival rate under adverse conditions. P. indica filtrate can facilitate early seed germination in vascular plants. In Helianthus annus, P. indica culture filtrate was evidenced to influence the seed-oil yield. A higher seed yield was also reported in the members of bryophytes, pteridophytes, gymnosperms and angiosperms as a result of the colonization of P. indica in their roots (Table 1).

22The role of P. indica inoculation/colonization in medicinal plants has been considered of utmost significance. The colonization of P. indica has been reported in a number of medicinal plants including Coleus forskohlii, Bacopa monnieri, Stevia rebaudiana, Artemisia annua, Linum album, Trigonella foenumgraecum, Spilanthes calva, Withania somniferra, Chlorophytum borivilianum, Curcuma longa, Podophyllum peltatum, Azadirachta indica, Oscimum sanctum, Linum album and Lantana camara (Table 2). Increased contents of chemical compounds and secondary metabolites were reported in P. indica-colonized C. forskohlii. P. indica has also been reported to enhance the growth, bacoside endogenous level, antioxidant activity as well as hypertrophy of nuclei in B. monnieri. Medicinal properties of A. indica, A. elegans, and H. annuus were increased with their colonization with P. indica. P. indica-inoculation in L. album cell culture improved the production of anticancer drug podophyllotoxin. Leaf area and fresh biomass were improved in herbaceous plants namely S. rebaudiana and A. annua with their cultivation with P. indica. Earlier, reported a positive response of the growth of medicinal plants such as S. calva and W. somnifera in a field trial with P. indica inoculum (Table 2). Recently, in vitro co-cultivation of P. indica filtrate was reported to improve biomass productivity in A. annua and W. somniferra. Cell suspension cultures of W. somnifera offers the potential for continuous production of withaferin A. Further, it can be concluded that the symbiotic effect of P. indica can be used as a biopriming agent for the overall growth of plant biomass.

23On the perspective of P. indica colonization role in crop plants, P. indica-mediated improvements in the growth and biomass have been reported in a number of crop plants including Oryza sativa, Saccharum officinarum, Abrus precatorius, Zea mays, Phaseolus vulgaris, and Tridax procumbans. P. indica can produce auxin (IAA) which in turn can promote plant root growth. In contrast to the auxin mediated least impact on the regulation of the gene expression in Arabidopsis, auxin regulated gene expression was found upregulated in H. vulgare and Chinese cabbage. Interestingly, P. indica has been reported to interfere with ethylene signaling in plants where, it promotes the plant growth. However, the exact mechanism underlying P. indica-mediated ethylene signaling inhibition is still unclear in plants. The stimulation of secondary metabolite synthesis by the endophytic fungus, P. indica has also been reported for the production of pentacyclic triterpenoids (e.g., ursolic acid, oleanolic acid and betulinic acid) in the suspension cultures of L. camara.

24Piriformospora indica has been extensively reported to improve crop tolerance to a number of abiotic stresses including salinity, low temperature and heavy metal toxicity. P. indica colonization-mediated high salinity tolerance was reported in Triticum aestivum, that of drought stress tolerance in Arabidopsis seedlings, Chinese cabbage and strawberry. P. indica colonization has extensively been reported to mediate the activation of defense related genes (such as PR, LOX2, and ERF1 genes), abiotic stress responsive genes (DREB2A, CBL1, RD29A) and osmoprotectants (proline, glycine betaine) (Figure 3). The interaction of P. indica with A. thaliana roots is a unique model system to study symbiotic relationships. Recently, has reported a co-cultivation system which allowed them to investigate the effects of fungal exudates on the root transcriptome before and after the establishment of a physical contact, and during early phases of root colonization.

25Mutualistic fungi P. indica has also evolved the ability to deliver molecules, called effectors, inside the cells to enhance microbial infection, and manipulate the host metabolism. The effector protein is involved in the establishment and maintenance of symbiosis in endo- and ectomycorrhiza, allowing the fungus to manipulate the plant defense response. Recently, reported the function of P. indica effector candidate PIIN_08944, a non-DELD effector, during the interaction of plants with P. indica. The authors noted the contribution of the candidate effector to plant colonization where the mutualistic fungus suppressed the salicylate -mediated basal resistance response. Effector protein, PIIN_08944 expression was detected during chlamydospore germination, and fungal deletion mutants (PiΔ08944) showed delayed root colonization. PIIN_08944-expressing A. thaliana showed a reduced expression of flg22-induced marker genes of pattern-triggered immunity (PTI) and the SA-defense pathway. In H. vulgare, the expression of PIIN_08944 reduced the burst of reactive oxygen species (ROS) triggered by flg22. Therefore, PIIN_08944 was advocated to contribute to the root colonization by P. indica by interfering with SA-mediated basal immune responses of the host plant.

26Piriformospora indica has also been reported to modulate major antioxidant defense enzymes monodehydroascorbate reductase and dehydroascorbate reductase and the other components of ROS-scavenging system. P. indica-colonization was reported to mediate the up-regulation in a number of enzymes involved in ROS-metabolism in salinity exposed plants. In addition, the establishment of ROS-scavenging system as a result of P. indica inoculation has been reported to confer plant tolerance to major abiotic stresses including salinity, drought, heat and heavy metal, and protection against fungal and viral pathogens. Interestingly, down-regulation of genes encoding enzymes for ascorbate synthesis in Arabidopsis exhibited a greater colonization by this endophyte. However, a greenhouse study of ‘Hildares’ tomato (Solanum lycopersicum Mill.) inoculation with P. indica under osmotic stress and specific chloride toxicity conditions showed insignificant increases in the growth of P. indica-inoculated plants grown under severe salinity stress, and the responses corresponded a significant increase in CO2 assimilation rate in the final harvest and leaf water potential and transpiration rate in the first harvest. Though the mechanisms underlying P. indica-induced resistance has already been much explained for abiotic and biotic stress response in rhizobacteria-colonized plants little is known for mechanisms underpinning P. indica-induced resistance in abiotic and biotic stressed-plants.

27Piriformospora indica has its well defined roles in the protection of plants against a range of biotic stress factors such as pathogenic fungi, bacteria and virus. The analyses of the beneficial interaction between P. indica and host plants has revealed the upregulation of various defense related genes including pathogenesis related PR genes, jasmonate JA (VSP, PDF1.2, LOX2) and ethylene ET (ERF1) signaling genes in response to pathogen attack (Figure 3). P. indica has found to confer protection to H. vulgare plant against root damage caused by Fusarium culmorum and against shoot infection with Blumeria graminis. Many root pathogens have been found to be directly inhibited by antagonistic activities of the endophytic fungus except F. culmorum, P. herpotrichoides, F. oxysporum. To the other, systemically induced resistance by P. indica root-colonization has also been reported for many leaf pathogens. Recently, in root endophyte-colonized H. vulgare plants, a sub-set of defense-related genes was observed highly induced by leaf pathogens. The role of P. indica in the protection of a number of plants against losses due to fungal pathogens infection has been summarized in Table 1.

28Piriformospora indica has been credibly reported to defend crop plants against attack of viral as well as fungal pathogens and thereby providing them a better vegetative or generative development. Recently, P. indica has been found to provide massive bioprotective potential to economically important different agricultural and horticultural crops against various plant pathogens and insect pests attack. P. indica fungus could be utilized to increase fungal disease resistance in plants where, P. indica-infested crop plants were reported to exhibit their additional resistant against pathogenic fungi. H. vulgare plants subjected to the fungal pathogen such as F. culmorum, become free from root diseases when colonized with P. indica. Similarly, P. indica treated plants were also protected against root-pathogenic Cochliobolus sativus fungus. P. indica fungus-mediated improved resistance of H. vulgare has been noted against the attack of root- and leaf-pathogens such as Fusarium culmorum and Blumeria graminis. Recently, P. indica colonized H. vulgare roots incited systemic resistance against the biotrophic leaf pathogen B. graminis f. sp. hordei. P. indica was reported to be an effective candidate in biocontrol of take-all diseases of T. aestivum (such as Gaeumannomyces graminis var. tritici) and Fusarium wilt disease of lentil. Greenhouse experiments on P. indica-colonization with winter T. aestivum’s roots were resulted into significant reduced of incidence of leaf, stem, and root diseass caused by B. graminis f. sp. tritici, Pseudocercosporella herpotrichoides and F. culmorum. In a field trial, P. herpotrichoides infection was considerably decreased in endophyte-colonized plants. Systemic resistance against B. graminis attack was induced in P. indica-colonized plants. P. indica-induced powdery mildew (Golovinomyces orontii) resistance in Arabidopsis necessitated JA-signaling involving JA-regulated genes to confer G. orontii tolerance. Furthermore, fungus has been evidenced to require merely cytosolic and not nuclear localized NPR1 to provoke systemic induced resistance in Arabidopsis. Recent reports have evidenced that P. indica-induced GA can positively modulate plant defense response in roots. It has similar potential to induce systemic resistance (ISR) like Trichoderma spp. Pathogens attack requires basic compatibility to attain with their host plants involving definite upstream regulatory genes. The key mechanism has been defined either in rhizobacteria-mediated ISR or by plant inoculation with P. indica. Nevertheless, the majority of expression studies regarding P. indica-host communication center on root physiology. Further, systemic stimulation of a small number of defense-related genes or proteins have been depicted based on more or less a similar mechanism.

29Piriformospora indica interaction (antagonism and cooperation) with other microorganisms has been reported to improve plant protection against environmental stresses. P. indica interacts with a diverse group of microorganisms such as Sebacina vermifera, Pseudomonas fluorescens (rhizobacteria), Chlamydomonas reinhardtii, G. graminis, and other soil fungi (i.e., Aspergillus niger, A. sydowii and Rhizopus stolonifer). P. indica invaded H. vulgare roots were reported resistant against Fusarium infections. These authors provided evidences that pathogenesis-related (PR) proteins do not affect P. indica-mediated response to confer resistance against Fusarium infections. P. indica was found to diminish the severity of disease caused by V. dahliae. The interaction of P. indica with the Pepino mosaic virus (PepMV) was evaluated in hydroponically grown L. esculentum where, the authors observed 30% reduction on the disease severity by V. dahliae. The growth of pathogenic fungi such as A. sydowii, R. stolonifer and A. niger has been reported to be entirely obstructed by P. indica. However, stimulation was noticed in the growth of the alga such as C. reinhardtii when cultured with P. indica. Though P. indica interacts with diverse class of bryophyte including mosses and liverworts but no growth promotion has been reported as a result of the interaction.

30Among the Sebacinales, P. indica shows its interaction with S. vermifera in addition to multinucleate Rhizoctonia. The pure cultures of closely related species such as P. indica and S. vermifera were reported essential for the germination, growth, development and yield and herbivore resistance of Nicotiana attenuate. It has been reported that P. indica, S. vermifera and Trichoderma species act as effective biocontrol agent for take-all diseases in T. aestivum. P. indica has been reported to support the growth and development of Azotobacter chroococcum, Azospirillum brasilensis, and Bradyrhizobium sp.; however, P. indica-mediated inhibition was noted in Pseudomonas fluorescens. Interestingly, there is an evidence that P. indica subsist rod-shaped 1–1.5 μm long bacteria in its cytoplasm and is characterized as Rhizobium radiobacter. In a field experiment, P. indica-colonized plants exhibited significantly reduced disease severity caused by P. herpotrichoides. P. indica and R. leguminosarum inoculated Phaseolus bean along with vermicompost revealed enhanced length and dry weight of both root as well as shoot with respect to treatment either deficient in vermicompost or with single inoculation. P. indica either alone or in an interaction with S. vermifera, Trichoderma viride and T. harzianum was found to be more effective in reducing the severity of Fusarium wilt disease of lenti.

31The studies on 18S rRNA and 20S rRNA sequence identity have revealed the fact that P. indica is closed relatives to the Rhizoctonia group and Sebacinaceae (Basidiomycetes). In adition, P. indica affinity with Glomeromycota members such as Glomerales, Diversisporales as well as Archeosporales has been deciphered through P. indica characterization via immunofluorescence, Western blot, enzyme-linked immunosorbent assay along with immuno-gold. In response to signals from P. indica, MATH protein, LRR1, LRR2, PDK, OXII, MAPK genes were upregulated in the roots of A. thalina prior to colonization. On the other hand, [Ca2+]cyt either induced various signaling course of actions, or defense interrelated responses were suppressed by supplementary factors (e.g., effectors) liberated by the fungus. These signaling events may be useful to understand the interactions of other beneficial fungi associated with economically important diverse crops for possible biotechnological applications.

32It is believed that P. indica-colonization results into the activation of antioxidant system, which in turn improves crop plant tolerance against abiotic as well as biotic stresses. The bio-protection performance of P. indica in T. aestivum has been evidenced against B. graminis f. sp. tritici, P. herpotrichoides and Fusarium culmorum, and in Z. mays against the root parasite Fusarium verticillioides. The fungus colonized plants were less susceptible to Alternaria alternate and Colletotrichum falcatu compared to non-colonized plants. The ability of P. indica to synthesize hydroxamic acids – a secondary metabolite has been reported, which functions like a natural pesticide. The significance of P. indica as a bio-fertilizer as well as a bio-control agent has been strongly advocated. Now, P. indica has become a paramount important candidate in microbiological and biotechnological research revealing several positive consequences on diverse crop plants.

33Ethylene, a gaseous plant hormone is produced in the majority of plant cells and controls various aspects of plant growth and development. Its positive and/or negative consequences has already been realized on flower, fruit ripening and leaf epinasty and abscission, suppression of apical dominance, leaf senescence, PCD, root nodulation, seed dormancy, seed germination and responsiveness to environmental stress including pathogen attack. The beneficial interaction of A. thaliana roots with mutualistic root endophytic fungus P. indica has been reported to induce ethylene, a gaseous plant hormone. Ethylene contributed a significant role in retaining the stability between beneficial as well as non-beneficial traits via signaling components ETR1, EIN2 and EIN2/EIL1 in a P. indica mutualism with plant’s roots. In another study, the P. indica induced methionine synthase activity was reported to facilitate methionine cycle of ethylene biosynthetic pathway during its colonization with plant roots via immuno suppression explaining surprisingly broad host range of the fungus. In a DNA microarray study, expression analysis of gene of P. indica colonized H. vulgare roots depicted differentially expressed ethylene related genes. Ethylene was reported to positively modulate the P. indica-plant interaction via signal molecules of fungi as well as plant receptors at the root cells surface after landing the fungal spores to attain the desired compatibility. Interestingly, ethylene signal magnitude also plays an important part in the colonization of plant roots by P. indica; where, ethylene signaling either inhibits or promotes the growth of hyphae depending upon magnitude of signaling. It is now clear that to establish the symbiosis, ethylene signaling network requires definite biochemical or genetic actions to sustain a communication across the symbionts as well as host plants to provide physiological benefits to each partner.

34Piriformospora indica interaction studies in Arabidopsis and H. vulgare have provided molecular basis of the beneficial plant–microbe interaction. The fungus in a mutual interaction with plants has already been known to provide enhanced nitrate/nitrogen uptake. The up-regulation of Nia2 gene of NR and SEX1 gene of starch degrading enzymes was reported to influence a substantial source and sink relation. The additional sinks were remained balanced via higher rates of CO2 assimilation in H. vulgare plants colonized by P. indica with respect to the subsequent controls. The elevated N, P and K endogenous content were reported in chickpea as well as black lentil plants colonized with P. indica. In contrast, Fe and Cu deficiencies in sugar cane plants were surpassed if inoculated with P. indica. The expression profile of receptor kinase in roots of Arabidopsis and enhanced uptake of radio-labeled P was observed after colonization of the endophytic fungus. P. indica-mediated P-uptake and transport were evidenced to improve plant growth and development via their impact on various regulatory, structural and addition to energy transfer processes. Further, reduced endogenous content of phosphate in Z. mays plants were detected upon its colonization by P. indica mutant where, a phosphate transporter was knocked out.

35Piriformospora indica colonization provides certain benefits to the host plant such as tolerance to high salt and drought, resistance against heavy metal toxicity and protection from pathogen attack. P. indica colonized T. aestivum showed an optimum growth under rising concentrations of salt. Plants such as Arabidopsis, Chinese cabbage and strawberry were recovered from drought stress when pre-inoculated with endophyte P. indica. The expression profile of the drought responsive genes such as DREB2A, ANAC072, CBL1 in addition to RD29A were positively modulated in the leaves of P. indica-colonized plants under drought stress exposure. The drought tolerance was exhibited as higher endogenous proline level which in turn led to increased tolerance to osmotic stress in endophyte colonized plants when compared to non-colonized one. H. vulgare plants pre-inoculated with P. indica displayed augmented profile of enzymatic and non-enzymatic antioxidants levels resulting increased tolerant to drought and high salt. The increased antioxidants level was evident by reduced dehydroascorbate level via dehydroascorbate conversion to ascorbate and elevated glutathione level. The stress tolerance response of P. indica-colonized plants was found to be associated with burst accumulation of plastid-localized proteins such as Ca2+-sensing regulator (CAS) in the leaves of colonized plants. The use of P. indica was found to be more effective in improving salt stress tolerance in crop plants that consequently has opened an innovative and promising application of this fungus in sustainable agriculture, especially in the areas affected by salinity. The differential expression profile of abiotic stress responsive genes putatively engaged in various stress response in P. indica-colonized plants is required for in-depth interpretation of the mechanism functions via induction of osmoprotectants and heat shock proteins in plant cell.

36In P. indica-inoculated host plants, pathogenesis related PR genes, JA (VSP, PDF1.2, LOX2) and ethylene ET (ERF1) signaling genes were reported up-regulated in response to pathogen attack. P. indica mediated H. vulgare plant protection was first observed against F. culmorum and B. graminis in root and shoot part, respectively. Enhanced antioxidant defense system has been evidenced as a major factor involved in P. indica colonization mediated beneficial effects in H. vulgare, T. aestivum and Z. mays roots. It is also evident from mutant study that not nuclear but the cytosolic non-expressor of PR-genes 1 (NPR1) form is required by the fungus in order to induce systemic resistance. For this reason, the mechanisms involved in P. indica-induced resistance in plants is more or less similar to systemic resistance induced by plant growth-promoting rhizobacteria-colonized plants. The endophyte provides inducing systemic resistance against pathogenic fungi and also protects the plant against damages caused by the invading pathogens via direct antagonism.

37Piriformospora indica is a mycorrhiza like endophytic fungus which exhibits its versatility for colonizing the plant species with direct manipulation of plant hormone signaling and induces both local and systemic resistance to several fungal and viral plant diseases through signal transduction. P. indica is multifunctional in providing its services such as nutrient uptake, disease resistance, stress tolerance and growth-promotion. This fungus has become an outstanding tool for biological hardening during transplantation of micro-propagated plantlets. P. indica-infestation in a number of medicinal plants has been reported to stimulate the synthesis of valuable secondary metabolites, therefore possess commercial and biotechnological importance. The comparison of the P. indica genome with other fungi has revealed its classical features related with biotrophism as well as saprotrophism. P. indica has also evolved highly effective colonization strategies in diverse plant species. The significant number of reports accumulated during last one decade has confirmed the P. indica-mediated improvements in the growth and yield of various plants, which includes crop plants, horticultural and medicinal plants. These reports also support the role of P. indica in crop tolerance to a number of abiotic as well as biotic stresses. Therefore, P. indica can be used as: (i) bio-control agent and plant stress response mediator, (ii) regulator of genes involved in metabolism and mineral uptake, and (iii) regulator of genes involved in resistance and defense of plants. It needs elaboration of a few studies done on the role of nano(bio)technology in acheiving major insights into and benefits of plant-interaction with fungi/P. indica. Furthermore, in order to commercially exploit the potentialities of P. indica in improving biotic and abiotic stress tolerance in crop plants, in addition to establishing P. indica inoculum production conditions and its formulation and stability; and exploring the persistence of the fungus in the environment, the future research should focus on revealing: (i) the mechanisms underpinning broad compatibility in root symbiosis, (ii) functional analyses of the effector-like proteins, (iii) symbiosis determinants, and (iv) identification of novel symbiosis/pathogenicity genes.

38SSG, RG, AJ, AV, NAA, NT, and EP developed the idea and wrote/finalized the MS. SSG, DT, MA, NAA, EP, RP, KKS, MWA, AAA made the figures and developed table and helped in writing. All authors read and approved the approved the final manuscript.

39The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.