Fungal Endophytes as Mitigators against Biotic and Abiotic Stresses in Crop Plants

The escalating global food demand driven by a gradually expanding human population necessitates strategies to improve agricultural productivity favorably and mitigate crop yield loss caused by various stressors (biotic and abiotic). Biotic stresses are caused by phytopathogens, pests, and nematodes, along with abiotic stresses like salt, heat, drought, and heavy metals, which pose serious risks to food security and agricultural productivity. Presently, the traditional methods relying on synthetic chemicals have led to ecological damage through unintended impacts on non-target organisms and the emergence of microbes that are resistant to them. Therefore, addressing these challenges is essential for economic, environmental, and public health concerns. The present review supports sustainable alternatives, emphasizing the possible application of fungal endophytes as innovative and eco-friendly tools in plant stress management. Fungal endophytes demonstrate capabilities for managing plants against biotic and abiotic stresses via the direct or indirect enhancement of plants' innate immunity. Moreover, they contribute to elevated photosynthesis rates, stimulate plant growth, facilitate nutrient mineralization, and produce bioactive compounds, hormones, and enzymes, ultimately improving overall productivity and plant stress resistance. In conclusion, harnessing the potentiality of fungal endophytes represents a promising approach toward the sustainability of agricultural practices, offering effective alternative solutions to reduce reliance on chemical treatments and address the challenges posed by biotic and abiotic stresses. This approach ensures long-term food security and promotes environmental health and economic viability in agriculture.

Analysis of growth dynamics in five different media and metabolic phenotypic characteristics of Piriformospora indica

Piriformospora indica is an important endophytic fungus with broad potential for alleviating biotic and abiotic stress on host plants. This study monitored the growth dynamics of P. indica on five commonly used artificial media for microorganisms and analyzed its metabolic characteristics using Biolog Phenotype Microarray (PM) technology. The results showed that P. indica grew fastest on Potato Dextrose Agar (PDA), followed by Kidney Bean Agar (KBA), Alkyl Ester Agar (AEA), Oatmeal Agar (OA), and Luria-Bertani Agar (LB), and the most suitable medium for spore production was OA. Using Biolog PM1-10, 950 metabolic phenotypes of P. indica were obtained. P. indica could metabolize 87.89% of the tested carbon sources, 87.63% of the tested nitrogen sources, 96.61% of the tested phosphorus sources, and 100% of the tested sulfur sources. P. indica displayed 92 kinds of tested biosynthetic pathways, and it could grow under 92 kinds of tested osmotic pressures and 88 kinds of tested pH conditions. PM plates 1-2 revealed 43 efficient carbon sources, including M-Hydroxyphenyl acid, N-Acetyl-D-Glucosamine, Tyramine, Maltotrios, α-D-Glucosine, I-Erythritol, L-Valine, D-Melezitose, D-Tagatose, and Turanose. PM plates 3,6-8 indicated 170 efficient nitrogen sources, including Adenosine, Inosine Allantoin, D, L-Lactamide, Arg-Met, lle-Trp, Ala-Arg, Thr-Arg, Trp-Tyr, Val-Asn, Gly-Gly-D-Leu, Gly-Gly-Phe, and Leu-Leu-Leu. This study demonstrates that P. indica can metabolize a variety of substrates, such as carbon and nitrogen sources, and has a wide range of environmental adaptability. The growth dynamics on artificial culture media and metabolic phenotypes of P. indica can be used to investigate its biological characteristics, screen for more suitable growth and sporulation conditions, and elucidate the physiological mechanisms that enhance the stress resistance of host plants. This study provides a theoretical basis for its better application in agriculture.

Endophytic fungi: an overview on biotechnological and agronomic potential

Abstract Endophytic fungi colonize the inter- and/or intracellular regions of healthy plant tissues and have a close symbiotic relationship with their hosts. These microorganisms produce antibiotics, enzymes, and other bioactive compounds that enable them to survive in competitive habitats with other microorganisms. In addition, secondary metabolites confer protection to their host plant against other bacterial and fungal pathogens and/or can promote plant growth. Endophytic fungi are viewed as a promising source of bioactive natural products, which can be optimized through changes in growing conditions. The exploration of novel bioactive molecules produced by these microorganisms has been attracting attention from researchers. The chemical and functional diversity of natural products from endophytic fungi exhibits a broad spectrum of applications in medicine, agriculture, industry and the environment. Fungal endophytes can also enhance the photoprotective effects and photochemical efficiency in the host plants. Modern omic approaches have facilitated research investigating symbiotic plant-endophytic fungi interactions. Therefore, research on endophytic fungi can help discovery novel biomolecules for various biotechnological applications and develop a sustainable agriculture.

Advances in Identifying the Mechanisms by Which Microorganisms Improve Barley Salt Tolerance

As the global human population continues to increase, the use of saline-alkali land for food production is an important consideration for food security. In addition to breeding or cultivating salt-tolerant crop varieties, microorganisms are increasingly being evaluated for their ability to improve plant salt tolerance. Barley is one of the most important and salt-tolerant cereal crops and is a model system for investigating the roles of microorganisms in improving plant salt tolerance. However, a comprehensive review of the mechanisms by which microorganisms improve barley salt tolerance remains lacking. In this review, the mechanisms of barley salt tolerance improvement by microorganisms are summarized, along with a discussion of existing problems in current research and areas of future research directions. In particular, with the development of sequencing technology and the great reduction of prices, the use of omics can not only comprehensively evaluate the role of microorganisms but also evaluate the impact of the microbiome on plants, which will provide us with many opportunities and challenges in this research area.

Physiological and TMT-based quantitative proteomic responses of barley to aluminium stress under phosphorus-Piriformospora indica interaction

Barley (Hordeum vulgare L.) is one of the most important cereal crop in the world, and is also the one being seriously affected by heavy metals, particularly aluminium (Al). Keeping in view the utility of barley as food, fodder and raw material for traditional beer brewing, the top-notch quality and higher production of this crop must be sustained. Phosphorus (P) has a quintessential role in plant growth with a potential to relieve symptoms caused by Al poisoning. Displaying a phytopromotive and stress alleviatory potential, Piriformospora indica (P. indica) can improve the stress tolerance in crops. Several studies have been conducted to evaluate the mechanism of Al translocation in a variety of crops including barley, however, the bio-remediative studies related to detoxification and/or sequestration of metals are scarce. Therefore, the current study was carried out to elucidate the tolerance mechanism of an Al-sensitive barley cultivar ZU9 following the colonization with P. indica and exogenous P supply by physio-biochemical, elemental, leaf ultrastructural and root proteome analyses. When compared to the Al alone treated counterparts, the Al + P + P.i treated plants exhibited 4.1-, 1.38-, 2.7 and 1.35-fold improved root and shoot fresh and dry weights, respectively. With the provision of additional phosphorus, the content of P in the root and shoot for Al + P + P.i group was reportedly higher (71.6% and 49.5%, respectively) as compared to the control group. Moreover, inoculation of P. indica combined with P improved barley leaves' cell arrangement and also maintained normal cell wall shape. The root protemics experiment was divided into three groups: Al, Al + P.i and Al + P + P.i. In total, 28, 598, and 823 differentially expressed proteins were found in Al + P.i vs. Al and Al + P + P.i vs. Al, and phenylpropanoid biosynthesis was the most prominently enriched pathway, which contributed significantly to the recuperating effects of P-P. indica interaction. Conslusively, it was found that the percentage of protein related to peroxidase was 70/359 (Al + P + P.i vs. Al) and 92/447 (Al + P + P.i vs. Al + P.i), respectively, which indicated that P. indica in combination with P might be involved in the regulation of peroxidases, increasing the adaptability of barley plants by enhanced reactive oxygen species (ROS) scavenging mechansism.

Enhancing growth and salinity stress tolerance of date palm using Piriformospora indica

Endophytic fungi are known to enhance plant growth and performance under salt stress. The current study investigated the growth, as well as biochemical and molecular properties of Phoenix dactylifera colonized with the mutualistic fungus Piriformospora indica, under control and salinity stress. Our findings indicated an increase in the plant biomass, lateral root density, and chlorophyll content of P. indica-colonized plants under both normal and salt stress conditions. Furthermore, there was a decline in the inoculated plants leaf and root Na⁺/K⁺ ratio. The colonization enhanced the levels of antioxidant enzymes such as catalase, superoxide dismutase, and peroxidase in plants. Increased ionic content of Zn and P were also found in salt-stressed date palm. The fungus colonization was also associated with altered expression levels of essential Na⁺ and K⁺ ion channels in roots like HKT1;5 and SOS1 genes. This alteration improved plant growth due to their preservation of Na⁺ and K⁺ ions balanced homeostasis under salinity stress. Moreover, it was confirmed that RSA1 and LEA2 genes were highly expressed in salt-stressed and colonized plant roots and leaves, respectively. The current study exploited P. indica as an effective natural salt stress modulator to ameliorate salinity tolerance in plants.

Transcriptome analysis of perennial ryegrass reveals the regulatory role of Aspergillus aculeatus under salt stress

Perennial ryegrass (Lolium perenne) is an important turf grass and forage grass with moderately tolerant to salinity stress. Aspergillus aculeatus has been documented to involved in salt stress response of perennial ryegrass, while the A. aculeatus-mediated molecular mechanisms are unclear. Therefore, to investigate the molecular mechanisms underlying A. aculeatus-mediated salt tolerance, the comprehensive transcriptome analysis of the perennial ryegrass roots was performed. Twelve cDNA libraries from roots were constructed after 12 h of plant-fungus cocultivation under 300 mM salt stress concentrations. A total of 21,915 differentially expressed genes (DEGs) were identified through pairwise comparisons. Enrichment analysis revealed that potentially important A. aculeatus-induced salt responsive genes belonging to specific categories, such as hormonal metabolism (auxin and salicylic acid metabolism related genes), secondary metabolism (flavonoid's metabolism related genes) and transcription factors (MYB, HSF and AP2/EREBP family). In addition, weighted gene co-expression network analysis (WGCNA) showed that blue and black modules were significantly positively correlated with the peroxidase activity and proline content, then the hub genes within these two modules were further identified. Taken together, we found the categories of A. aculeatus-induced salt responsive genes, revealing underlying fungus-induced molecular mechanisms of salt stress response in perennial ryegrass roots. Besides, fungus-induced salt-tolerant hub genes represent a foundation for further exploring the molecular mechanisms.

Growth-Promoting Endophytic Fungus (Stemphylium lycopersici) Ameliorates Salt Stress Tolerance in Maize by Balancing Ionic and Metabolic Status

Climate change is a major cause of the world's food security problems, and soil salinity is a severe hazard for a variety of crops. The exploitation of endophytic fungi that are known to have a positive association with plant roots is preferred for improving plant growth, yield, and overall performance under salt stress. The current study thus rationalized to address how salt stress affected the growth, biochemical properties, antioxidant capacity, endogenous indole-3-acetic acid (IAA), and the ionic status of maize associated with endophytic fungus (Stemphylium lycopersici). According to the findings, salt stress reduced chlorophyll a and b, total chlorophyll, total protein, sugars, lipids, and endogenous IAA levels. Enhanced values of chlorophyll a/b ratio, carotenoids, secondary metabolites (phenol, flavonoids, and tannins), antioxidant enzyme activity (catalase, ascorbate peroxidase), proline, and lipid peroxidation were noticed in maize plants under salt stress. Increased ionic content of Na+, Cl-, Na+/K+, and Na+/Ca2+ ratio, as well as decreased Ca2+, K+, Mg2+, N, and P contents, were also found in salt-stressed maize plants. In comparison to the non-saline medium, endophytic association promoted the antioxidant enzyme activities (798.7 U/g protein; catalase activity, 106 U/g protein; ascorbate peroxidase activity), IAA content (3.47 mg/g FW), and phenolics and flavonoids (88 and 1.68 μg/g FW, respectively), and decreased MDA content (0.016 nmol/g FW), Na+ ion content (18 mg/g dry weight), Cl- ion (16.6 mg/g dry weight), and Na+/K+ (0.78) and Na+/Ca2+ (1.79) ratios, in maize plants under salt stress, whereas Ca2+, K+, Mg2+, N, and P contents were increased in maize plants associated with S. lycopersici under salt stress. Current research exposed the role of S. lycopersici as an effective natural salt stress reducer and maize growth promoter; hence, it can be used as a biofertilizer to ameliorate salt stress tolerance in crops along with better growth performance in saline regions.

Inducing Tolerance to Abiotic Stress in Hordeum vulgare L. by Halotolerant Endophytic Fungi Associated With Salt Lake Plants

A characteristic trait of plants living in harsh environments is their association with fungal endophytes, which enable them to survive under extreme stress. Abiotic stress resistance in agro-ecosystems, particularly in arid and semi-arid regions, can be increased by inoculating these fungal endophytes on plants other than their original hosts. The present study is therefore focused on the possible role of three halotolerant endophytic fungi, i.e., Periconia macrospinosa, Neocamarosporium goegapense, and N. chichastianum, isolated from roots of salt lake plants growing in the central desert of Iran, in alleviating the adverse effects of salinity and drought stresses on barley under greenhouse conditions. To perform this experiment, a randomized block design was applied with three factors: fungi (four levels including three halotolerant endophytic species and control), salinity (three levels including 8, 12, and 16 dS/m), and drought (four levels including 100, 80, 60, 40 percent field capacity). All plants were measured for growth characteristics, chlorophyll concentration, proline content, and antioxidant enzyme activities. A three-way analysis of variance indicated that all three fungal endophytes, to varying extents, induced the barley plants’ resistance to salinity and drought, and their combined effects. Additionally, we found that fungal endophytes were more effective when the barley plants were subjected to higher levels of salinity and drought. Under the stress of salinity and drought, a strong relationship between inoculation of fungal endophytes and enhancement of biomass, shoot length, chlorophyll concentration, proline content, and activity of catalase, peroxidase, and superoxide dismutase was indicated. We discussed that increased root growth, proline content, and antioxidant enzyme activity are the main physiological and biochemical mechanisms causing stress resistance in barley plants inoculated with endophytes. Our research findings illustrate that fungal endophytes have a substantial potential for increasing abiotic stress tolerance in barley plants, which can be applied in agricultural ecosystems.

Piriformospora indica recruits host-derived putrescine for growth promotion in plants

Growth promotion induced by the endosymbiont Piriformospora indica has been observed in various plants; however, except growth phytohormones, specific functional metabolites involved in P. indica-mediated growth promotion are unknown. Here, we used a gas chromatography-mass spectrometry-based untargeted metabolite analysis to identify tomato (Solanum lycopersicum) metabolites whose levels were altered during P. indica-mediated growth promotion. Metabolomic multivariate analysis revealed several primary metabolites with altered levels, with putrescine (Put) induced most significantly in roots during the interaction. Further, our results indicated that P. indica modulates the arginine decarboxylase (ADC)-mediated Put biosynthesis pathway via induction of SlADC1 in tomato. Piriformospora indica did not promote growth in Sladc1-(virus-induced gene silencing of SlADC1) lines of tomato and showed less colonization. Furthermore, using LC-MS/MS we showed that Put promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4 and GA7) levels in tomato. In Arabidopsis (Arabidopsis thaliana) adc knockout mutants, P. indica colonization also decreased and showed no plant growth promotion, and this response was rescued upon exogenous application of Put. Put is also important for hyphal growth of P. indica, indicating that it is co-adapted by both host and microbe. Taken together, we conclude that Put is an essential metabolite and its biosynthesis in plants is crucial for P. indica-mediated plant growth promotion and fungal growth.

A comparison between the function of Serendipita indica and Sinorhizobium meliloti in modulating the toxicity of zinc oxide nanoparticles in alfalfa (Medicago sativa L.)

Zinc oxide nanoparticles (ZnO-NPs) are among the most commonly used nano-fertilizers (NF). However, elevated levels of ZnO-NPs in soil may affect plant growth and development due to its potential toxicity when accumulated in large amounts in plant tissues. This research was conducted using an in situ rhizobox system with the aims of evaluating zinc uptake from nano-zinc oxide amended rhizosphere soil by alfalfa plant and the effect of plant growth-promoting microorganisms on alleviating the phytotoxicity of ZnO-NPs. Treatments included microbial inoculations (Sinorhizobium meliloti, Serendipita indica) and different ZnO-NP concentrations (0, 400, and 800 mg kg^-1) with three replications. The results indicated that S. indica minimized the phytotoxicity of ZnO-NPs to alfalfa by enhancing growth rate and decreasing zinc (Zn) translocation from root to shoot. Compared with plants inoculated with S. meliloti, co-inoculation with S. indica increased the shoot dry weight by 18.33% and 8.05% at 400 and 800 mg kg^-1 ZnO-NPs, respectively. However, at the highest level of ZnO-NPs (800 mg kg^-1), root inoculation of S. indica and S. indica + S. meliloti decreased Zn translocation factor by 60.2% and 44.3% compared to S. meliloti, respectively. Furthermore, a distinct relation between tolerance of S. indica-colonized plant to ZnO-NPs and the ability of S. indica in inhibiting or retarding degradation of polyunsaturated lipids through prevention of excess reactive oxygen species formation was observed. Malondialdehyde content of inoculated plants with S. indica either alone or in combination with S. meliloti was significantly lower than non-inoculated plants (p< 0.01). Zn-induced oxidative stress was mitigated by S. indica through enhanced activities of catalase and peroxidase enzymes. The findings of the present study indicate the potential use of endophytes fungus S. indica for ensuring food safety and security, and human health in heavy metal-polluted soil by reducing the phytoavailability of heavy metals in the aerial parts of the host plants.

Elucidating the Molecular Mechanisms by which Seed-Borne Endophytic Fungi, Epichloë gansuensis, Increases the Tolerance of Achnatherum inebrians to NaCl Stress

Seed-borne endophyte Epichloë gansuensis enhance NaCl tolerance in Achnatherum inebrians and increase its biomass. However, the molecular mechanism by which E. gansuensis increases the tolerance of host grasses to NaCl stress is unclear. Hence, we firstly explored the full-length transcriptome information of A. inebrians by PacBio RS II. In this work, we obtained 738,588 full-length non-chimeric reads, 36,105 transcript sequences and 27,202 complete CDSs from A. inebrians. We identified 3558 transcription factors (TFs), 15,945 simple sequence repeats and 963 long non-coding RNAs of A. inebrians. The present results show that 2464 and 1817 genes were differentially expressed by E. gansuensis in the leaves of E+ and E− plants at 0 mM and 200 mM NaCl concentrations, respectively. In addition, NaCl stress significantly regulated 4919 DEGs and 502 DEGs in the leaves of E+ and E− plants, respectively. Transcripts associated with photosynthesis, plant hormone signal transduction, amino acids metabolism, flavonoid biosynthetic process and WRKY TFs were differentially expressed by E. gansuensis; importantly, E. gansuensis up-regulated biology processes (brassinosteroid biosynthesis, oxidation–reduction, cellular calcium ion homeostasis, carotene biosynthesis, positive regulation of proteasomal ubiquitin-dependent protein catabolism and proanthocyanidin biosynthesis) of host grass under NaCl stress, which indicated an increase in the ability of host grasses’ adaptation to NaCl stress. In conclusion, our study demonstrates the molecular mechanism for E. gansuensis to increase the tolerance to salt stress in the host, which provides a theoretical basis for the molecular breed to create salt-tolerant forage with endophytes.

Understanding the potential of root microbiome influencing salt-tolerance in plants and mechanisms involved at the transcriptional and translational level

Soil salinity severely affects plant growth and development and imparts inevitable losses to crop productivity. Increasing the concentration of salts in the vicinity of plant roots has severe consequences at the morphological, biochemical, and molecular levels. These include loss of chlorophyll, decrease in photosynthetic rate, reduction in cell division, ROS generation, inactivation of antioxidative enzymes, alterations in phytohormone biosynthesis and signaling, and so forth. The association of microorganisms, viz. plant growth-promoting rhizobacteria, endophytes, and mycorrhiza, with plant roots constituting the root microbiome can confer a greater degree of salinity tolerance in addition to their inherent ability to promote growth and induce defense mechanisms. The mechanisms involved in induced stress tolerance bestowed by these microorganisms involve the modulation of phytohormone biosynthesis and signaling pathways (including indole acetic acid, gibberellic acid, brassinosteroids, abscisic acid, and jasmonic acid), accumulation of osmoprotectants (proline, glycine betaine, and sugar alcohols), and regulation of ion transporters (SOS1, NHX, HKT1). Apart from this, salt-tolerant microorganisms are known to induce the expression of salt-responsive genes via the action of several transcription factors, as well as by posttranscriptional and posttranslational modifications. Moreover, the potential of these salt-tolerant microflora can be employed for sustainably improving crop performance in saline environments. Therefore, this review will briefly focus on the key responses of plants under salinity stress and elucidate the mechanisms employed by the salt-tolerant microorganisms in improving plant tolerance under saline environments.

Physio-ultrastructural footprints and iTRAQ-based proteomic approach unravel the role of Piriformospora indica-colonization in counteracting cadmium toxicity in rice

Due to its immense capability to concentrate in rice grain and ultimately in food chain, cadmium (Cd) has become the cause of an elevated concern among agriculturists, scientists and the environmental activists. Symbiotic association of Piriformospora indica (P. indica) has been characterized as a potential aid in combating heavy metal stress in plants for sustainable crop production but our scant knowledge regarding ameliorative tendency of P. indica against Cd, specifically in rice, necessitates an in-depth investigation. This study aimed at elaborating the underlying mechanisms involved in P. indica-mediated tolerance against Cd stress in two rice genotypes, IR8 and ZX1H, varying in Cd accumulation pattern. Either colonized or un-inoculated with P. indica, seedlings of both genotypes were subjected to Cd stress. The results showed that P. indica colonization significantly supported plant biomass, photosynthetic attributes and chlorophyll contents in Cd stressed plants. P. indica colonization sustained chloroplast integrity and reduced Cd translocation (46% and 64%), significantly lowering malondialdehyde (MDA) content (11.3% and 50.4%) compared to uninoculated roots under Cd stress in IR8 and ZX1H, respectively. A genotypic difference was evident when a 2-fold enhancement in root peroxidase (POD) activity was recorded in P. indica colonized IR8 plants as compared to ZX1H. The root proteomic analysis was performed using isobaric tags for relative and absolute quantification (iTRAQ) and the results showed that P. indica alleviates Cd stress in rice via down-regulation of key glycolysis cycle enzymes in a bid to reduce energy consumption by the plants and possibly re-directing it to Cd defense response pathways; and up-regulation of glutamine synthetase, a key enzyme in the L-Arg-dependent pathway for nitric oxide (NO) production, which acts as a stress signaling molecule, thus conferring tolerance by reduction of NO-mediated modification of essential proteins in response to Cd stress. Conclusively, both the tested genotypes benefited from P. indica symbiosis at varying levels by an enhanced detoxification capacity and signaling efficiency in response to stress. Hence, a step forward towards the employment of an environmentally sound and self-renewing approach holding the hope for a healthy future.

Proteomic analysis of young sugarcane plants with contrasting salt tolerance

Soil salinity affects sugarcane (Saccharum officinale L.) production in arid and semiarid climates, severely reducing productivity. This study aimed to identify differentially regulated proteins in two cultivars that differ markedly in tolerance of saline soil. Plants were grown for 30 days and then subjected to treatments of 0 and 160 mM NaCl for 15 days. The tolerant cultivar showed a 3-fold upregulation of lipid metabolising enzymes, GDSL-motif lipases, which are associated with defence to abiotic stress, and which were not upregulated in the sensitive cultivar. Lipoxygenase was 2-fold upregulated in the tolerant cultivar but not in the sensitive cultivar, as were Type III chlorophyll a/b binding proteins. Other differences were that in the sensitive cultivar, the key enzyme of C4 photosynthesis, phosphoenolpyruvate carboxylase was downregulated, along with other chloroplast enzymes. Na+ concentrations had not reached toxic concentrations in either cultivar by this time of exposure to salt, so these changes would be in response to the osmotic effect of the soil salinity, and likely be in common with plants undergoing drought stress.

Root endophytic fungus Serendipita indica modulates barley leaf blade proteome by increasing the abundance of photosynthetic proteins in response to salinity

AIMS

The present study aimed at analysing the proteome pattern of the leaf blade of barley (Hordeum vulgare L.) in Serendipita indica-colonised plants to decipher the molecular mechanism of S. indica-mediated salt stress. This work is aligned with our previous research on barley leaf sheath to study proteomic pattern variability in leaf blade and sheath of barley plant in response to salinity and S. indica inoculation.

METHODS AND RESULTS

The experiment was conducted using a completely randomised factorial design with four replications and two treatments: salinity (0 and 300 mmol l^-1 NaCl) and fungus (noninoculated and S. indica-inoculated). The leaf blades of the salt-treated S. indica-colonised and noninoculated plants were harvested after 2 weeks of salt treatment for the physiological and proteomic analyses. After exposure to 300 mmol l^-1 NaCl, shoot dry matter production in noninoculated control plants decreased 84% which was about twofold higher than inoculated plants with S. indica. However, the accumulation of sodium in the shoot of S. indica-inoculated plants was significantly lower than the control plants. Analysis of the proteome profile revealed a high number of significantly up-regulated proteins involved in photosynthesis (26 out of 42 identified proteins).

CONCLUSIONS

The results demonstrated how the enhanced plant growth and salt stress resistance induced by S. indica was positively associated with the up-regulation of several proteins involved in photosynthesis and carbohydrate metabolism. In fact, S. indica improved photosynthesis in order to reach the best possible performance of the host plant under salt stress.

SIGNIFICANCE AND IMPACT OF THE STUDY

Current research provides new insight into the mechanism applied by S. indica in reducing the negative impacts of salt stress in barley at physiological and molecular levels.

Insights Into Microbially Induced Salt Tolerance and Endurance Mechanisms (STEM) in Plants

Salt stress threatens the achievement of sustainable global food security goals by inducing secondary stresses, such as osmotic, ionic, and oxidative stress, that are detrimental to plant growth and productivity. Various studies have reported the beneficial roles of microbes in ameliorating salt stress in plants. This review emphasizes salt tolerance and endurance mechanisms (STEM) in microbially inoculated (MI) plants that ensure plant growth and survival. Well-established STEM have been documented in MI plants and include conglomeration of osmolytes, antioxidant barricading, recuperating nutritional status, and ionic homeostasis. This is achieved via involvement of P solubilization, siderophore production, nitrogen fixation, selective ion absorption, volatile organic compound production, exopolysaccharide production, modifications to plant physiological processes (photosynthesis, transpiration, and stomatal conductance), and molecular alterations to alter various biochemical and physiological processes. Salt tolerance and endurance mechanism in MI plants ensures plant growth by improving nutrient uptake and maintaining ionic homeostasis, promoting superior water use efficiency and osmoprotection, enhancing photosynthetic efficiency, preserving cell ultrastructure, and reinforcing antioxidant metabolism. Molecular research in MI plants under salt stress conditions has found variations in the expression profiles of genes such as HKT1, NHX, and SOS1 (ion transporters), PIPs and TIPs (aquaporins), RBCS, RBCL (RuBisCo subunits), Lipoxygenase2 [jasmonic acid (JA) signaling], ABA (abscisic acid)-responsive gene, and APX, CAT, and POD (involved in antioxidant defense). Proteomic analysis in arbuscular mycorrhizal fungi-inoculated plants revealed upregulated expression of signal transduction proteins, including Ca²⁺ transporter ATPase, calcium-dependent protein kinase, calmodulin, and energy-related proteins (NADH dehydrogenase, iron-sulfur protein NADH dehydrogenase, cytochrome C oxidase, and ATP synthase). Future research should focus on the role of stress hormones, such as JA, salicylic acid, and brassinosteroids, in salt-stressed MI plants and how MI affects the cell wall, secondary metabolism, and signal transduction in host plants.

Plant-Microbe Symbiosis: What Has Proteomics Taught Us?

Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.

Proteomic and metabolomic analysis of desiccation tolerance in wheat young seedlings

Young wheat seedlings are desiccation tolerant and have the capacity to withstand long dehydration period. In this study, we characterized the proteome and metabolome of wheat seedlings during desiccation and after recovery. Functional classification of differentially identified proteins revealed dynamic changes in the number and abundance of proteins observed during stress and recovery. Desiccation resulted in a decline in the abundance of proteins associated with photosynthesis and carbohydrate reserves, along with an increase in the presence of proteins associated with stress and defense response, such as peroxiredoxins and antioxidant enzymes. Following recovery, the abundance of stress-responsive proteins returned either partially or completely to their baseline level, confirming their importance to the seedling's desiccation response. Furthermore, proteins involved in carbohydrate metabolism, as well as fructose-bisphosphate aldolase and fructokinase-2 and phosphorylated metabolites as the substrate or the end-product, showed the inverse pattern during desiccation and after re-watering. This may reflect the fact that plants maintained energy supply during stress to protect seedlings from further damage, and for use in subsequent recovery after rewatering period. This study provides novel insights into the molecular mechanisms underlying the desiccation tolerance of wheat seedlings, and paves the way for more detailed molecular analysis of this remarkable phenomenon.

Tackling Salinity in Sustainable Agriculture—What Developing Countries May Learn from Approaches of the Developed World

Soil salinity is a common problem of the developing world as well as the developed world. However, the pace to reduce salinity is much slower in the developing world. The application of short-term approaches with an unsustainable supply of funds are the major reasons of low success. In contrast, the developed world has focused on long-term and sustainable techniques, and considerable funds per unit area have been allocated to reduce soil salinity. Here, we review the existing approaches in both worlds. Approaches like engineering and nutrient use were proven to be unsustainable, while limited breeding and biosaline approaches had little success in the developing countries. In contrast, advanced breeding and genetics tools were implemented in the developed countries to improve the salinity tolerance of different crops with more success. Resultantly, developed countries not only reduced the area for soil salinity at a higher rate, but more sustainable and cheaper ways to resolve the issue were implemented at the farmers’ field. Similarly, plant microbial approaches and the application of fertigation through drip irrigation have great potential for both worlds, and farmer participatory approaches are required to obtain fruitful outcomes. In this regard, a challenging issue is the transition of sustainable approaches from developed countries to developing ones, and possible methods for this are discussed.

Comparative analyses of albumin/globulin grain proteome fraction in differentially salt-tolerant Tunisian barley landraces reveals genotype-specific and defined abundant proteins

Salinity is one of the major abiotic stresses threatening crop production and yield worldwide. Breeding programmes are therefore needed to improve yield under cultivation in soil. Traits from locally adopted landraces provide a resource to assist breeding of novel elite genotypes. Here, we examine differentially expressed proteins by performing comparative proteomic profiling of the albumin/globulin grain fraction of Tunisian barley genotype landraces with contrasting salinity tolerance. Tunisian barley Boulifa (B, tolerant) and Testour (T, sensitive) mature grains were assessed in 2-DE profiles. Differentially expressed spots, with an abundance enhanced 1.5-fold in the grain, were subjected to MALDI TOF/TOF MS for identification. Distinctiveness between tolerant and sensitive genotypes was proved in the albumin/globulin fraction using PCA; 64 spots showed significant differential abundance. Increased accumulation of 40 spots was confirmed in Boulifa with, interestingly, four genotype-specific spots. Two of these four spots were sHSP. Proteins with highest abundance were serpin Z7, 16.9 KDa Class I HSP and phosphogluconolactonase 2. Proteins such as expansin, kiwellin, kinesin and succinyl-CoA ligase were identified for the first time in barley grain. Moreover, ß-amylase, LEA family and others were identified as abundant in Boulifa. On the other hand, proteins more accumulated in Testour are implicated mainly in ROS scavenging and protease inhibition. Our results clearly indicate proteomic contrast between the two selected genotypes. With identification of specific HSP, high abundant stress-protective and other defined proteins, we provide biochemical traits that will support breeding programmes to address the threat of salinity in agricultural production.

Symbiotic Root-Endophytic Soil Microbes Improve Crop Productivity and Provide Environmental Benefits

Plants should not be regarded as entities unto themselves, but as the visible part of plant-microbe complexes which are best understood as "holobiomes." Some microorganisms when given the opportunity to inhabit plant roots become root symbionts. Such root colonization by symbiotic microbes can raise crop yields by promoting the growth of both shoots and roots, by enhancing uptake, fixation, and/or more efficient use of nutrients, by improving plants' resistance to pests, diseases, and abiotic stresses that include drought, salt, and other environmental conditions, and by enhancing plants' capacity for photosynthesis. We refer plant-microbe associations with these capabilities that have been purposefully established as enhanced plant holobiomes (EPHs). Here, we consider four groups of phylogenetically distinct and distant symbiotic endophytes: (1) Rhizobiaceae bacteria; (2) plant-obligate arbuscular mycorrhizal fungi (AMF); (3) selected endophytic strains of fungi in the genus Trichoderma; and (4) fungi in the Sebicales order, specifically Piriformospora indica. Although these exhibit quite different "lifestyles" when inhabiting plants, all induce beneficial systemic changes in plants' gene expression that are surprisingly similar. For example, all induce gene expression that produces proteins which detoxify reactive oxygen species (ROS). ROS are increased by environmental stresses on plants or by overexcitation of photosynthetic pigments. Gene overexpression results in a cellular environment where ROS levels are controlled and made more compatible with plants' metabolic processes. EPHs also frequently exhibit increased rates of photosynthesis that contribute to greater plant growth and other capabilities. Soil organic matter (SOM) is augmented when plant root growth is increased and roots remain in the soil. The combination of enhanced photosynthesis, increasing sequestration of CO2 from the air, and elevation of SOM removes C from the atmosphere and stores it in the soil. Reductions in global greenhouse gas levels can be accelerated by incentives for carbon farming and carbon cap-and-trade programs that reward such climate-friendly agriculture. The development and spread of EPHs as part of such initiatives has potential both to enhance farm productivity and incomes and to decelerate global warming.

Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica

Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.

Transcriptional responses of soybean roots to colonization with the root endophytic fungus Piriformospora indica reveals altered phenylpropanoid and secondary metabolism

Piriformospora indica, a root endophytic fungus, has been shown to enhance biomass production and confer tolerance to various abiotic and biotic stresses in many plant hosts. A growth chamber experiment of soybean (Glycine max) colonized by P. indica compared to uninoculated control plants showed that the fungus significantly increased shoot dry weight, nutrient content, and rhizobial biomass. RNA-Seq analyses of root tissue showed upregulation of 61 genes and downregulation of 238 genes in colonized plants. Gene Ontology (GO) enrichment analyses demonstrated that upregulated genes were most significantly enriched in GO categories related to lignin biosynthesis and regulation of iron transport and metabolism but also mapped to categories of nutrient acquisition, hormone signaling, and response to drought stress. Metabolic pathway analysis revealed upregulation of genes within the phenylpropanoid and derivative pathways such as biosynthesis of monolignol subunits, flavonoids and flavonols (luteolin and quercetin), and iron scavenging siderophores. Highly enriched downregulated GO categories included heat shock proteins involved in response to heat, high-light intensity, hydrogen peroxide, and several related to plant defense. Overall, these results suggest that soybean maintains an association with this root endosymbiotic fungus that improves plant growth and nutrient acquisition, modulates abiotic stress, and promotes synergistic interactions with rhizobia.

Proteomic approach to understand the molecular physiology of symbiotic interaction between Piriformospora indica and Brassica napus

Many studies have been now focused on the promising approach of fungal endophytes to protect the plant from nutrient deficiency and environmental stresses along with better development and productivity. Quantitative and qualitative protein characteristics are regulated at genomic, transcriptomic, and posttranscriptional levels. Here, we used integrated in-depth proteome analyses to characterize the relationship between endophyte Piriformospora indica and Brassica napus plant highlighting its potential involvement in symbiosis and overall growth and development of the plant. An LC-MS/MS based label-free quantitative technique was used to evaluate the differential proteomics under P. indica treatment vs. control plants. In this study, 8,123 proteins were assessed, of which 46 showed significant abundance (34 downregulated and 12 upregulated) under high confidence conditions (p-value ≤ 0.05, fold change ≥2, confidence level 95%). Mapping of identified differentially expressed proteins with bioinformatics tools such as GO and KEGG pathway analysis showed significant enrichment of gene sets involves in metabolic processes, symbiotic signaling, stress/defense responses, energy production, nutrient acquisition, biosynthesis of essential metabolites. These proteins are responsible for root's architectural modification, cell remodeling, and cellular homeostasis during the symbiotic growth phase of plant's life. We tried to enhance our knowledge that how the biological pathways modulate during symbiosis?

Do Endophytes Promote Growth of Host Plants Under Stress? A Meta-Analysis on Plant Stress Mitigation by Endophytes

Endophytes are microbial symbionts living inside plants and have been extensively researched in recent decades for their functions associated with plant responses to environmental stress. We conducted a meta-analysis of endophyte effects on host plants' growth and fitness in response to three abiotic stress factors: drought, nitrogen deficiency, and excessive salinity. Ninety-four endophyte strains and 42 host plant species from the literature were evaluated in the analysis. Endophytes increased biomass accumulation of host plants under all three stress conditions. The stress mitigation effects by endophytes were similar among different plant taxa or functional groups with few exceptions; eudicots and C₄ species gained more biomass than monocots and C₃ species with endophytes, respectively, under drought conditions. Our analysis supports the effectiveness of endophytes in mitigating drought, nitrogen deficiency, and salinity stress in a wide range of host species with little evidence of plant-endophyte specificity.

The endophytic fungus Piriformospora indica enhances Arabidopsis thaliana growth and modulates Na+/K+ homeostasis under salt stress conditions

The mutualistic, endophytic fungus Piriformospora indica has been shown to confer biotic and abiotic stress tolerance to host plants. In this study, we investigated the impact of P. indica on the growth of Arabidopsis plants under normal and salt stress conditions. Our results demonstrate that P. indica colonization increases plant biomass, lateral roots density, and chlorophyll content under both conditions. Colonization with P. indica under salt stress was accompanied by a lower Na⁺/K⁺ ratio and less pronounced accumulation of anthocyanin, compared to control plants. Moreover, P. indica colonized roots under salt stress showed enhanced transcript levels of the genes encoding the high Affinity Potassium Transporter 1 (HKT1) and the inward-rectifying K⁺ channels KAT1 and KAT2, which play key roles in regulating Na⁺ and K⁺ homeostasis. The effect of P. indica colonization on AtHKT1;1 expression was also confirmed in the Arabidopsis line gl1-HKT:AtHKT1;1 that expresses an additional AtHKT1;1 copy driven by the native promoter. Colonization of the gl1-HKT:AtHKT1;1 by P. indica also increased lateral roots density and led to a better Na⁺/K⁺ ratio, which may be attributed to the observed increase in KAT1 and KAT2 transcript levels. Our findings demonstrate that P. indica colonization promotes Arabidopsis growth under salt stress conditions and that this effect is likely caused by modulation of the expression levels of the major Na⁺ and K⁺ ion channels, which allows establishing a balanced ion homeostasis of Na⁺/K⁺ under salt stress conditions.

Metabolic and transcriptional response of central metabolism affected by root endophytic fungus Piriformospora indica under salinity in barley

The root endophytic fungus Piriformospora indica enhances plant adaptation to environmental stress based on general and non-specific plant species mechanisms. In the present study, we integrated the ionomics, metabolomics, and transcriptomics data to identify the genes and metabolic regulatory networks conferring salt tolerance in P. indica-colonized barley plants. To this end, leaf samples were harvested at control (0 mM NaCl) and severe salt stress (300 mM NaCl) in P. indica-colonized and non-inoculated barley plants 4 weeks after fungal inoculation. The metabolome analysis resulted in an identification of a signature containing 14 metabolites and ions conferring tolerance to salt stress. Gene expression analysis has led to the identification of 254 differentially expressed genes at 0 mM NaCl and 391 genes at 300 mM NaCl in P. indica-colonized compared to non-inoculated samples. The integration of metabolome and transcriptome analysis indicated that the major and minor carbohydrate metabolism, nitrogen metabolism, and ethylene biosynthesis pathway might play a role in systemic salt-tolerance in leaf tissue induced by the root-colonized fungus.

Piriformospora indica: Potential and Significance in Plant Stress Tolerance

Owing to its exceptional ability to efficiently promote plant growth, protection and stress tolerance, a mycorrhiza like endophytic Agaricomycetes fungus Piriformospora indica has received a great attention over the last few decades. P. indica is an axenically cultiviable fungus which exhibits its versatility for colonizing/hosting a broad range of plant species through directly manipulating plant hormone-signaling pathway during the course of mutualism. P. indica-root colonization leads to a better plant performance in all respect, including enhanced root proliferation by indole-3-acetic acid production which in turn results into better nutrient-acquisition and subsequently to improved crop growth and productivity. Additionally, P. indica can induce both local and systemic resistance to fungal and viral plant diseases through signal transduction. P. indica-mediated stimulation in antioxidant defense system components and expressing stress-related genes can confer crop/plant stress tolerance. Therefore, P. indica can biotize micropropagated plantlets and also help these plants to overcome transplantation shock. Nevertheless, it can also be involved in a more complex symbiotic relationship, such as tripartite symbiosis and can enhance population dynamic of plant growth promoting rhizobacteria. In brief, P. indica can be utilized as a plant promoter, bio-fertilizer, bioprotector, bioregulator, and biotization agent. The outcome of the recent literature appraised herein will help us to understand the physiological and molecular bases of mechanisms underlying P. indica-crop plant mutual relationship. Together, the discussion will be functional to comprehend the usefulness of crop plant-P. indica association in both achieving new insights into crop protection/improvement as well as in sustainable agriculture production.

The effect of Piriformospora indica on the root development of maize (Zea mays L.) and remediation of petroleum contaminated soil

As the depth of soil petroleum contamination can vary substantially under field conditions, a rhizotron experiment was performed to investigate the influence of endophyte, P. indica, on maize growth and degradation of petroleum components in a shallow and a deep-reaching subsurface layer of a soil. For control, a treatment without soil contamination was also included. The degree in contamination and the depth to which it extended had a strong effect on the growth of the plant roots. Contaminated soil layers severely inhibited root growth thus many roots preferred to bypass the shallow contaminated layer and grow in the uncontaminated soil. While the length and branching pattern of these roots were similar to those of uncontaminated treatment. Inoculation of maize with P. indica could improve root distribution and root and shoot growth in all three contamination treatments. This inoculation also enhanced petroleum degradation in soil, especially in the treatment with deep-reaching contamination, consequently the accumulation of petroleum hydrocarbons (PAHs) in the plant tissues were increased.

Sustained exposure to abscisic acid enhances the colonization potential of the mutualist fungus Piriformospora indica on Arabidopsis thaliana roots

Root colonization by the beneficial fungus Piriformospora indica is controlled by plant innate immunity, but factors that channel this interaction into a mutualistic relationship are not known. We have explored the impact of abscisic acid (ABA) and osmotic stress on the P. indica interaction with Arabidopsis thaliana. The activation of plant innate immunity in roots was determined by measuring the concentration of the phytoalexin camalexin and expression of transcription factors regulating the biosynthesis of tryptophan-related defence metabolites. Furthermore, the impact of the fungus on the content of ABA, salicylic acid, jasmonic acid (JA) and JA-related metabolites was examined. We demonstrated that treatment with exogenous ABA or the ABA analogue pyrabactin increased fungal colonization efficiency without impairment of plant fitness. Concomitantly, ABA-deficient mutants of A. thaliana (aba1-6 and aba2-1) were less colonized, while plants exposed to moderate stress were more colonized than corresponding controls. Sustained exposure to ABA attenuated expression of transcription factors MYB51, MYB122 and WRKY33 in roots upon P. indica challenge or chitin treatment, and prevented an increase in camalexin content. The results indicate that ABA can strengthen the interaction with P. indica as a consequence of its impact on plant innate immunity. Consequently, ABA will be relevant for the establishment and outcome of the symbiosis under stress conditions.