Introduction

Extreme climatic events tend to cause the global crop damage due to increased frequency of climatic change (Fedoroff et al. 2010). The goal of achieving global food security will be severely hampered by these changing environmental patterns, which could pose serious threats to the crops (Porfirio et al. 2018; Ali et al. 2022). Most abiotic stresses that affect plant machinery includes drought, flooding, extreme temperature, salinity and nutrient deficiency. These abiotic stresses tend to hinder plant development, growth and productivity (Bailey-Serres and Voesenek 2008; Khan et al. 2019). The extremity of abiotic stress response depends on exposure of particular stressor or in combination, duration of exposure, growing stage and the susceptible of plant cultivar (Sorty et al. 2018). Stress alleviating approaches to the adverse nature of abiotic stresses are important global agriculture drivers to optimize the crop productivity under detrimental environmental conditions (Nutan et al. 2020). Execution of different intrinsic combating mechanisms tend to cease the negative consequences of abiotic stressors which includes accumulation of osmolytes, antioxidant enzyme expression, heat shock proteins etc. (Scarpeci et al. 2008; Prasch and Sonnewald 2013; Kumawat et al. 2022; Singh et al. 2022b). Microbes can help plants to cope with abiotic challenges by modifying their physiology (De Zelicourt et al. 2013; Maheshwari et al. 2021; Chandwani and Amaresan 2022). Under abiotic circumstances plant growth promoting microorganisms (PGPM) act as potent candidates to actively increase the level of antioxidants enzymes, osmolytes and stress based expression of genes (Hayat et al. 2010; Wang et al. 2012; Farrar et al. 2014; Notununu et al. 2022). So, these PGPMs have biochemical, molecular as well as physiological based response against stressor in plants imparting integral function of plant surveillance mechanisms and immunity (Hacquard et al. 2017). PGPM includes plant growth promoting bacteria/rhizobacteria (PGPR), plant growth stimulating fungi, actinomyctes, and bacteria involved in nitrogen fixing (Wani et al. 2015; Hassen et al. 2016; Elhindi et al. 2017; Jiménez-Mejía et al. 2022). These PGPM provides improved progression of crops and imparts tolerance against numerous environmental stresses (Bano and Fatima 2009; Lugtenberg and Kamilova 2009). Plant growth promoting bacteria (PGPB) induces the plant immune response so as to resist various infections (van Hulten et al. 2006). Moreover, these plant linked microbes support development of crops by synthesizing secondary metabolites, phytochemicals and hormone production (Mendes et al. 2011; Hardoim et al. 2015; Egamberdieva et al. 2017; Srinivasa et al. 2022). A deeper understanding regarding the interaction of microbes with plants under changing climatic conditions as well as the approaches employed by them to combat the negative effects of stress will ease out to predict the impact of climate change on primary productivity. This will also help to develop management and policy tools to increase the resilience of plant systems (Trivedi et al. 2022). A systems-based approach that takes into account the ecology of microbial communities may aid in improving the reliability of existing technologies while encouraging innovation and wider implementation (Jurburg et al. 2022). In current review, we thoroughly explored the impact of microorganisms in enhancing stress tolerance to a wide variety of abiotic stress factors for growth and development attributes plant. A special emphasis was put on enlisting the role of plant growth promoting microbes in activating antioxidant enzymes systems, sequestration of metal ions and combating the nutritional deficiencies. Moreover, we have detailed the mechanism of stress tolerance aided by plant growth promoting microbes through the production of siderophores, by several physiological adaptations, production of volatile organic substances (VOCs) and maintaining the higher K+/Na+ ratio.

Plant metabolite insights related to abiotic stress tolerance

The deeper knowledge of the many tolerance approaches for preserving agricultural yield through management of environmental variables might be beneficial in ensuring that crops retain their optimum genetic potential (Brooker et al. 2022). Phytohormones are plant growth factors that are produced in specific organs and have a significant influence on plant metabolism (Singh et al. 2022a). They also aid in the mitigation of abiotic stressors. Auxins are key phytohormones, and the auxin indole-3-acetic acid (IAA) has been found to induce cell division, elongation, and differentiation, among other growth and developmental processes along with mediating abiotic stress tolerance. Cytokinins (CK), a class of plant hormones, are involved in sustaining cellular proliferation and differentiation as well as preventing senescence, which results in the avoidance of early leaf senescence (Tariq and Ahmed 2022). Overexpression of genes involved in cytokinin production has been confirmed, as has their significance in stress tolerance. Under abiotic stress, ABA-induced and -mediated signaling regulates the expression of stress-responsive genes, resulting in greater elicitation of tolerance responses (Sah et al. 2016). Plant growth and development were discovered to be stimulated by gibberellic acid under a variety of abiotic stress situations (Waadt et al. 2022). Gibberellic acid promotes effective absorption and ion allocation in plants, resulting in increased growth and the maintenance of plant metabolism under normal and stressful conditions (Sherin et al. 2022). Through stress-activated signal pathways and response mechanisms, phytohormones affects various physiological processes involved in plant stress tolerance.

Plants have evolved a variety of defences at the phytochemical, biochemical, morphological, and molecular levels to deal with a wide range of environmental challenges. The buildup of numerous osmoprotectants such as polyamines (PAs), proline, glycine betaine (GB), and sugars is one of the key adaptive stress responses for improving stress in plants (Ramazan et al. 2022). All of these solutes contribute to the maintenance of homeostasis, the maintenance of cell turgor and water uptake, the scavenging of excess reactive oxygen species (ROS), and the re-establishment of cellular redox balance, all of which protect the cellular machinery from oxidative damage and osmotic stress (Ghosh et al. 2019). PAs are small polycations that are involved in growth, and development and are well documented for their anti-senescence and anti-stress characteristics due to their acid balancing and antioxidant properties (Choudhary et al. 2022). PAs have been suggested to have a role in modifying plant defense responses to a variety of environmental stresses, such as salinity, oxidative stress, drought, chilling stress and metal toxicity (Sinha and Mishra 2022). GB is an essential osmolyte that helps plants grow and function properly. Plant species, on the other hand, differ in their ability to naturally accumulate GB. Plants accumulate diverse proportions of GB; GB accumulators naturally accumulate GB under normal and stress conditions (Ayub et al. 2022). Proline also appears to be promising in genetics and genomics techniques for improving plant adaptation responses to changing climatic circumstances (Ghosh et al. 2022).

Microbe facilitated abiotic stress tolerance mechanisms adopted by plants

Wide range of stress tolerance mechanism are adopted by plants in abiotic stress conditions depending upon the microbial variability and diversity (Elhindi et al. 2017; Van Oosten et al. 2017). Plant root rhizosphere is usually a site rich in nutrients such as, sugars, amino acids, fatty acids and secondary metabolites to act as strong chemoattractant for microbes. These microbes utilize plant metabolites to flourish in rhizosphere and in turn synthesize important biological chemicals, such as, compatible solutes, antifungal compounds, enzymes, gibberellins, cytokinins, auxins, and ABA (Figure 1). PGPM enhance growth and metabolism of crop through induction of wide range of metabolites such as, phytohormones synthesis, growth inducing metabolites, osmoprotectants, heavy metal sequestration, induction of siderophores, morpho-anatomic changes, modulating physiological attributes through induction of volatile compounds and positive modulation of nutrient profile (Kazan 2013). Positive modulations through PGPM to regulate plant growth and metabolism are further discussed in the proceeding sections of this review.

Fig. 1
figure 1

Plant Growth Promoting Microorganisms mediated tolerance mechanisms adopted by crop plants to combat abiotic stresses. Micro-organisms thrive in the rhizosphere by consuming plant metabolites and produce vital biological substances such suitable solutes, antifungal compounds, enzymes, gibberllins, cytokinins, auxins, and ABA

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Microbe derived plant growth hormone production

Plant development and metabolism are controlled by plant hormones including auxin, cytokinin, gibberellins, JA, abscisic acids and ethylene (Kazan 2013; da Silva et al. 2022). In addition, they are central elements in the fight against environment based stress in plants (Hu et al. 2013). Growth of plant is altered by abiotic stress via altered phytohormones production (Khan et al. 2014; Sati et al. 2022). However, the root associated microbes tend to promote the biosynthesis of metabolically active substances and regulators of growth in plants (Kudoyarova et al. 2014; Pereira et al. 2016; Asaf et al. 2017). The microbial metabolites modulate the growth of plants through induction of hormones almost prototypical to the application of exogenous hormonal treatments (Shahzad et al. 2016). Root associated bacteria like Sinorhizobium sp., Marinobacterium sp., Rhizobium sp., Pseudomonas sp., have remarkable role in indole-3-acetic-acid (IAA) production (Hayat et al. 2010). This bacterial IAA results in activation of 1-aminocyclopropane-1- carboxylate (ACC) deaminase that mediates degradation of ACC that acts as initiator molecule for ethylene synthesis (Glick 2005). In a study on the relationship between Trichoderma and plants, it was found that genotypic traits of plants can influence the way microbes and plants interact, which in turn affects plant growth and reduces stress. Degradation of IAA in the rhizosphere and ACC deaminase activity on tomato show the growth-promoting and stress-relieving activities of T. atroviride (Gravel et al., 2007). Through RNA interference, a potential ACC-deaminase sequence discovered in the Trichoderma genome was identified (Viterbo et al., 2010; Kubicek et al., 2011). Two types of ACC-deaminase genes (acdS) comparable to those of Pseudomonas fluorescens for reducing stress were discovered using PCR analysis in a study on potato endophytes. The whole acdS operon from an uncultivated endophyte was identified by analysis of clones found in metagenomic libraries, and the transcriptional regulator gene acdR was found to be located upstream of acdS. Burkholderia, a major member of the genus, included this operon (Nikolic et al., 2011). Induction of stress response genes was discovered in Sinorhizobium meliloti by next-generation RNA sequencing in IAA overproducing strains (Defez et al., 2016). In addition, it is reported that overall growth and improvement of plant under stressful conditions is promoted via decreased ethylene formation and relieving the ethylene based repression on synthesis of auxin based response factor (Kang et al., 2010). Several physiological parameters involving cell differentiation, seed germination, root elongation and photosynthesis etc. are influenced by the auxin homeostasis (Ahemad and Kibret 2014; Khedr et al. 2022; Mousavi et al. 2022; Rolón-Cárdenas et al. 2022) .

Root associated PGPR have remarkable role in inducing the synthesis of auxin to mediate plant growth and development. These auxin producing microbes include Rhizobium sp., Psuedomonas sp. etc., which are colonized positively by auxin (Suzuki et al. 2003; Chang et al. 2014; Cai et al. 2022; Mathur et al. 2022). Cytokinin is another phytohormone synthesized under the influence of microbes such as, Bacillus, Azospirillum and Arthobacters (Gray and Smith 2005; Naz et al. 2009). While Arthrobacter koreensis produces auxin, gibberellic acid (GA), abssisic acid (ABA) and jasmonates (JA) (Piccoli et al. 2011). GA is produced in plants by Aspergillus fumigatus and Azospirillum lipoferum against abiotic stress (Creus et al. 2004; Khan et al. 2011). Endophytic Phoma glomerata fungi also produces GA, improves plants abiotic stress resilience (Waqas et al. 2012). Fungal inoculations tend to decrease the levels of ABA, but modifying levels of salicylic acid (SA) and JA that act as vital plant defense hormones under stress conditions (Shinozaki and Yamaguchi-Shinozaki 2007). Psuedomonas putida helps Arabidopsis thaliana to combat water stress by enhancing the endogenous levels of hormones involving GA, auxin, cytokinin and ABA (Ghosh et al. 2019). In addition this strain helps soyabean plants to ameliorate the drought and salt stress by enhancing GA production Sphingomonas sp. and Paecilomyces formosus provides combating ways against metal stress in soyabean plants via increased production of endogenous hormone concentrations including IAA, JA and GB (Bilal et al. 2018). So, microorganisms have a tendency for building up plant hormones, which enhance plant development and confer tolerance to abiotic stimuli, reducing abiotic stress in plants (Liu et al. 2013; Latef et al. 2016; Tiwari et al. 2020; Iqbal et al. 2022; Shah et al. 2022).

Plant growth inducing metabolites

The differential metabolic regulations of prime and secondary plant metabolites occurs in responses to abiotic stresses. Plant primary metabolites like carbohydrates and amino acids are fundamental requirements for plant growth and overall development. While other metabolites of secondary fate like flavonoids and alkaloids are consumed for plant protection and some allied functions depending on plant species (Akula and Ravishankar 2011; Yadav et al. 2021). PGPR has been seen to have capability of promoting productivity and growth of plants by metabolic modulation (Lugtenberg and Kamilova 2009). Metabolic and proteomic studies of crop plants under stress have shown differential protein expression and metabolite expression as that of non-stressed plants (Meena et al. 2017; Dissanayake et al. 2022; Patel et al. 2022; Wang et al. 2022). Differential metabolite accumulation of L-proline, L-glutamine, γ-aminobutyric acid (GABA) succinic acid, uridine − 5-diphosphate, pyruvic acid ascorbic acid, citric acid, glutathione etc. was reported by Bacillus velezensis treatment under different abiotic stress circumstances (Abd El-Daim et al. 2019). GABA is involved in the metabolism of amino acids, carbohydrates as well as the carbon-nitrogen balance and plant growth control (Shelp et al. 2017). Some plant-associated bacteria have a role in purine and pyrimidine metabolism, which might affect the quantity of plant metabolites (Izaguirre-Mayoral et al. 2018). The composition of plant phenolic compounds has been acknowledged to be affected by Pseudomonas, Bacillus, Streptomyces, and Azospirillum spp. (Walker et al. 2011). The accumulation of monoterpenes such as, sabine hydrate, thymol, -terpinene and carvacrol took place in shoots of oregano roots with the inoculation of Azospirillum brasilense and Pseudomonas fluorescens (Banchio et al. 2010). Rhizophagus irregularis inoculation increased phosphorus levels and showed changes in the leaf metabolome in plants belonging to the Poaceae, Plantaginaceae and Fabaceae families (Schweiger et al. 2014). Moreover, as per recent reports endophytes augmentation can promote the medicinal plant species in storing potentially important secondary metabolites even under different abiotic stress conditions (Ogbe et al. 2020; Elnahal et al. 2022).

Osmoprotectants

Abiotic stress induced circumstances cause the modification of cellular functions of plant that involves the formation and buildup of osmolytes (Wang et al. 2018; Riaz et al. 2019; Hossain et al. 2022). The osmolytes have pivotal protective role in plants at cellular level against any damage. These osmolytes prevent protein denaturation thereby maintaining cellular integrity of plant without interfering with the normal physiology (Nahar et al. 2016). Depending upon chemical composition, osmolytes are divided into three types that includes amino acids, sugars (reducing and non-reducing) and betaines (Slama et al. 2015). According to study, plant osmolyte content and concentration vary depending on species and environmental stress (Lugan et al. 2010). Differential osmolyte concentration has been reported to be enhanced in crop plants upon inoculation by different strains of PGPR under abiotic stress environments. A plant growth-promoting rhizobacterium was inoculated into Vitis vinifera. At a low temperature, Burkholderia phytofirmans boosted grapevine physiological activity along with growth (Barka et al. 2006). The concentration of glycine betaine-based quaternary entities was greater in plants infected with Pseudomonas pseudoalcaligenes (Jha et al. 2011). Furthermore, in drought stress, seed priming of maize with bacteria Pseudomonas spp. strains resulted in greater amounts of carbohydrates, proline, and free amino acids (Vardharajula et al. 2011; Ibrahim and El-Sawah 2022). Report based on Trichoderma-plant interaction, established the effects of genotypic features of plants on the modification of microbe plant interaction (Trichoderma atroviride and Trichoderma harzianum) and ectoine for salt tolerance in Halomonas elongata OUT30018. Some of its genes involved in ectoine synthesis were cloned and inserted into the tobacco plant Nicotiana tabacum L. cv Bright Yellow 2 (BY2), which grew normally under these conditions and boosted resistance to osmotic shock by accumulating ectoine (Lucena and Wang 2022). As per several studies PGPM have vital function in imparting resistance against abiotic stressors through increased osmolyte and other metabolite accumulation. The desirable characteristic of Miscanthus grass that frequently differs among cultivars is chilling tolerance. Variation among its cultivars for chilling tolerance exists and is confirmed by the molecular expression of relevant genes for the accumulation of carbohydrates. The molecular marker of sensitive genes, expressed in sensitive genotypes, can be used to predict the loss of tolerance among variety (Purdy et al. 2013).

Antioxidant enzymes

Abiotic stress causes a significant rise in reactive oxygen species (ROS) that causes oxidative damage (Mittler 2002). There is need to equilibrate the ROS production to maintain growth of plant and physiology (Noctor et al. 2018). Under constant abiotic stress, the growth of plants is highly effected until complete halt of metabolism, leading to complete death. One strategy to lessen oxidative stress in plants is to supplement them with beneficial microbes that have a tendency to produce high amounts of antioxidant enzymes that can help diminish oxidative stress. The PGPM inoculants boosts antioxidant levels and minimizes ROS and oxidative stress that makes plant more resilient to abiotic challenges. The cellular homeostasis is disturbed by changes in water availability, pH, temperature, heavy metals and UV-B radiation. This results in increase in ROS like hydroxyl radical, superoxide anion, singlet oxygen and hydrogen peroxide (Khoshru et al. 2020). Microbial inoculants protect the plants from cellular damage imparted by ROS by increasing the production of antioxidants such superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), ascorbate peroxidase (AsA), tocopherols and carotenoids (Arora et al. 2020; Lopes et al. 2021). Bacterial inoculants increase the antioxidant propensity of drought-stressed plants. Leaves of Lactuca sativa L. (Lettuce) were given Pseudomonas mendocina Palleroni, and Glomus mosseae or Glomus intraradices or alone. P. mendocina inoculated cultivars growing under extreme stress showed the highest levels of CAT activity. Under intermediate drought circumstances, fungal and bacterial inoculation increased total CAT and peroxidase activity. It is reported in the lettuce study, these beneficial microorganisms can be employed to eradicate plant oxidative stress (Kohler et al. 2008). The Proteobacterium Xanthomonas citri, on the other hand, has increased production of catalase (KatG), allowing to battle the task of oxidative burst by citrus plants during leaf infection. (Tondo et al. 2016). The SOD and CAT were increased but the H2O2 and lipid peroxidation levels diminished in the nodules of plants co-inoculated with Bradyrhizobium and Paenibacillus graminis or Actinomandura (Santos et al. 2018). Under saline stress plants inoculated with Pseudomonas mendocina showed very less oxidative damage (drying, necrosis and reduced chlorosis) related with non- inoculated salt-stressed plants. These effects were evident because of improved antioxidant enzyme activity (Bianco and Defez 2009). According to Koussevitzky et al. (2008), the cytosolic ascorbate peroxidase 1 gene Apx1 is especially needed for Arabidopsis to be tolerant of drought and heat stress. Also different antioxidant enzymes, including CAT, SOD, GR and peroxidase (POD), are produced by arbuscular mycorrhizal fungus (AMF) species to help reduce the impact of ROS produced under salinity stress (Kumar et al. 2022).

Biocontrol

Combination of different inoculant mixtures that are having synergetic approach of interaction, tend to improve the functioning of beneficial microbes. Different bacterial strains like Bacillus, Rhizobium and Psuedomonas improved plant development and growth as compared to single inoculant (Figueiredo et al. 2010). Rhizobium- Azospirillum combination was capable to rise the expression of nod genes. It also led to formation of nodulation factors in Rhizobium etli and Rhizobium tropici under absence or presence of 50mM saline conditions (Dardanelli et al. 2008). Moreover, co-inoculation of Rhizobium with Bacillus megaterium or Pseudomonas striata led to gain in crop yield, dry matter, and phosphorus assimilation considerably over the non-inoculated in legume plants (Elkoca et al. 2010). These also enhanced the tolerance level of plants to drought, salt by implementing stress adaptive mechanisms (Marulanda et al. 2010; Zhou et al. 2016; Seleiman et al. 2021; Kaur et al. 2022).

Combating nutrient deficiency

Plants that experience abiotic stresses are resilient on their capability to avoid or tolerate adverse abiotic stresses by developing adaptive mechanisms of productivity and survival. The mineral and nutritional status of plants are greatly affected due lack sufficient water status as seen in drought, saline kind of stresses due to which nutrients become unavailable to plant. This seems to cause further intensification of adversity due to prevailing stressful condition thereby eventually leading to decrease in crop productivity (Munns and Tester 2008). However, it is reported that soil microorganisms have a crucial part in the management of nutrients (Adhya et al. 2015). Nitrogen fixation has pivotal function in augmenting soil fertility, nitrogen-fixing bacteria aids the atmospheric nitrogen conversion for the plant to synthesize amino acids (Lata et al. 2018). Solubilization of phosphate is also an important aspect of plant. Microorganisms involved in Phosphorus solubilizing (PSMs) have an essential role in its mineralization and solubilization of phosphorus. The PSM’s are largely composed of bacteria, fungi and serve as substitutes to fulfil the phosphate demands of plants (Mokrani et al. 2020). Among bacteria Pseudomonas, Rhizobium and Bacillus, while in fungi Penicillium and Aspergillus are most efficient phosphate solubilizers (Sharma et al. 2013). In addition, some microorganisms such as, Pseudomonas sp., Azotobacter sp., Bacillus mucilaginosus, Klebsiella sp., Rhizobium sp. and Paenibacillus sp., play a very fundamental role in potassium solubilization in plants that also accounts its place among the most important minerals for overall functioning and development of plant (Liu et al. 2012; Mazahar and Umar 2022; Rawat et al. 2022).

Sequestration of heavy metals

Metal contamination is one among the different pollutions that prevail worldwide in water, soils, and air. Anthropogenic sources like mining, industries, waste disposal, metal smelting, corrosion of metals in use etc. are the main causes of metal pollution (Ahemad 2012). The release of metallic sewage have harmful effect on plant and animal health (Ma et al. 2016). Heavy metals disrupt the homeostasis and nutritional metabolism of plants and it is pertinent to investigate their accumulation and effect for assuring safety and sustainability of environment (Glick 2010; Asati et al. 2016). Bioremediation is a new technology for removing heavy metal pollution from soil that relies on plant associated bacteria (Ojuederie and Babalola 2017). Microbes have a higher level of complexity than other living species, and they can serve as a reliable indication of heavy metal stress (Praveen Kumar et al. 2014). The plant endophytes aid their host to tolerate heavy metals and reduce metal toxicity, particularly the root-associated endophytes. In the mangrove palm species Nypa fruticans, several strains of Pestalotiopsis spp. conferred notable tolerance against heavy metals like copper (Cu), lead (Pb), zinc (Zn), and chromium (Cr). It is reported that 1 among the 93 endophytic isolates of Nypa fruticans could tolerate heavy metal adulterations to a level of 1000 ppm due to which nipa palm is having significant metallic stress combating strategies (Choo et al. 2015). Boehmeria nivea is having endophyte rich rhizosphere like Bacillus, Pseudomonas and Cupriavidus that protects it from excessive concentration of Pb, Cu and Cu (Jiang et al. 2017). Penicillium funiculosum, Exophiala pisciphila, Gigapora spp. and Pseudomonas spp. endophytes effectively overcome the metal stress exhibited by plants by employing metal chelation, improving antioxidant enzyme machinery, altering hormonal status (Friesen et al. 2013; Khan and Lee 2013; Wang et al. 2016; Ma et al. 2019). According to reports, Penicillium funiculosum LHL06 secretes gibberellin, which reduces metal toxicity and reprograms the 26 Endophyte-Mediated Host Stress tolerance as a strategy of crop improvement under Cu and Cd stress in soya bean (Khan and Lee 2013). Likewise, endophytes like Gigaspora and Pseudomonas spp. species can modify the endogenous ethylene levels to increase plant resistance to harmful metals. Exophiala pisciphila, a fungal endophyte associated with maize roots, was found to provide resistance to soil cadmium (Cd) toxicity (Friesen et al. 2013). The E. pisciphila inoculated plants showed higher expression of genes involved in uptake and translocation of metal mediating chelating in maize. So, increased Cd deposition on maize cell walls, transformation of Cd to less toxic form and antioxidant enzyme activity in response to Cd stress. Furthermore, compared to maize plants devoid endophytes, the plants containing endophytes exhibited excellent growth characteristics and a considerable reduction in Cd-induced phototoxicity levels (Wang et al. 2016). Pseudomonas stulzeri produces silver-based crystallic structures that circumvents the toxic effect of metals (Klaus-Joerger et al. 2001).

Moreover, The PGPM have significant role in phytoremediation. They can enhance phytoremediation by plant via fixing of atmospheric nitrogen, mineral solubilization, producing phytohormones and nutrient translocation (Stępniewska and Kuźniar 2013). P. aeruginosa inoculation to Brassica juncea and Cucurbita pepo decreased the Cd uptake, while in chickpea increased plant growth and reduced Ni uptake plants (Sinha and Mukherjee 2008; Tank and Saraf 2009). Thus, communications between PGPM and plants can also compliment the process of metal sequestration by increasing the phyto-remedial capabilities of plants under normal as well as under heavy metal stress.

Enhanced ion production via siderophores

Siderophore producing microorganisms can produce secondary metabolites that encourage plant growth, such as hormones, phosphate solubilization, secondary metabolites, etc. They can pave the way to encourage plant growth in stress conditions such as drought (Breitkreuz et al. 2021). Oxidation states heavy metals are altered by siderophore, rendering them less hazardous in nature (Schalk et al. 2011). Iron is a dynamic supplement for all living organisms. Naturally iron is available as Fe3+ and possibly forms insoluble hydroxides which cannot be usable by plants and microbial entities (Rajkumar et al. 2010) Microorganisms discharge iron-binding ligands called ‘‘siderophores,’’ that have high affinity for Fe3+ complexes (Gupta and Gopal 2008; Agrawal et al. 2022). B. subtilis produces iron-chelating chemicals that increase the amount of nutrients in the soil mediating growth of wheat plant under drought stress (Lastochkina et al. 2020). Under drought conditions, siderophore-producing microorganisms like Pseudomonas, improve soil nutrients and other soil activities, such as phosphate and potassium solubilization and siderophore formation (Breitkreuz et al. 2021). Rhizobacteria forms a complex of Fe3+ converts it into Fe2+ which gets across the cell (Rajkumar et al. 2010). Therefore, under iron-stressed conditions, siderophores producing microorganisms can play the part as iron-solubilizing entity from natural forms (Dimkpa et al. 2009). Microbe based siderophores assist in relieving metal induced stress in plants due to presence of increased metal concentration in the soil (Diels et al. 2002; Schmidt et al. 2005). Streptomyces tendae F4 is a Cd-resistant bacterium that produces a number of Cd-binding hydroxamate siderophores. In the absence or presence of (minimum) iron (Fe) concentrations, its production is increased by the metal (Schmidt et al. 2005; Dimkpa et al. 2008). Azospirillum brasilense and Gluconactobacter diazotrophicus are plant growth promoting bacteria and are reported to produce hydroxamate and catechol siderophore, respectively provides iron nutrition to plants under iron deficiency (Delaporte-Quintana et al. 2020). Toxic heavy metals are trapped by siderophores, which prevents them from impeding the effectiveness of plant cells. Siderophore producing microorganisms can alleviate an iron deficiency. Siderophores tend to maintain iron levels in iron deprived (Braud et al. 2009; Sayyed et al. 2019).

Changes in morphology of root and shoot

Under abiotic stress environments disruption of plant homeostasis occurs that results in decreased plant metabolic functioning, reduced yield, decreased morphological characteristics (Athar and Ahmad 2002; Glick et al. 2007; Bianco and Defez 2009). Formation of phytohormones by microorganisms like gibberellins, indole acetic acid by unknown PGPR’s and ACC deaminase-producing Klebsiella spp. in wheat in salt stress and high activity of antioxidant enzyme was reported in Medicago plants inoculated by PGPR Sinorhizobium meliloti strain as a result of increasing surface area, root length and root surface area that improved nutrient uptake (Bianco et al. 2009; Egamberdieva and Kucharova 2009; Singh et al. 2015; Li et al. 2022a; Neshat et al. 2022). Pseudomonas extremorientalis, Pseudomonas putida, Pseudomonas aurantiaca and Pseudomonas chlororaphis produced indole acetic acid under saline conditions in wheat plant (Egamberdieva and Kucharova 2009). Inoculation with Streptomyces and saline-adapted Azospirillum strains considerably developed enhanced the germination rate, dry weight, shoot length and P, Fe, Mn, and N concentrations in wheat plants with saline stress (Nia et al. 2012; Sadeghi et al. 2012). Tomato seeds that have been infected with Azospirillum brasilens FT326 considerably enhanced the shoot, root weight, and length of root hairs, due to higher production of phytohormones depending on host specificity (Vaikuntapu et al. 2014). Pseudomonas fluorescens have been reported to promote same influence induced by familiar PGPB Azospirillum brasilens (Gupta et al. 2015). So, under stressful conditions, ethylene regulates plant homeostasis and leads to growth inhibition including chlorosis, senescence and abscission (Glick et al. 2007; Chen et al. 2022; Liu et al. 2022). But bacterial ACC-deaminase mediated decline of ethylene precursor ACC depresses the concentration of ethylene in roots of plant, thereby relieving its repression and promoting plant growth (Kang et al. 2010).

Volatile organic substances

Volatile organic compounds (VOCs) are small molecular weight (< 300 g mol− 1) signaling based molecules that modulates physiological processes of plants and diffuse through the air, water and soil (Audrain et al. 2015; Kanchiswamy et al. 2015; Fincheira et al. 2021; Song et al. 2022). VOCs released from microorganisms in a certain range of scales depending on the living environment and heterogeneity of soil that can act as stimuli to activate the cascade of signals, which controls the physiological processes of plant (Bailly and Weisskopf 2012; Kai et al. 2016; Maheshwari et al. 2021). From past few years, PGPR’s role have been deciphered in abiotic stress tolerance (Kumar et al. 2021; Lazazzara et al. 2022). Bacillus subtilis based VOCs are known to impart alkaline tolerance in Arabidopsis thaliana (Zhang et al. 2010). Wheat seeds treated with Bacillus thuringiensis and Paenibacillus polymyxa B demonstrated adequate drought resistance. Geranyl acetone, b-pinene and Benzaldehyde like VOCs were produced from these wheat seedlings that tend to mitigate different phases of stress manifestation (Timmusk et al. 2014). Moreover, bacterial VOCs have role in formation of biofilm, which contain exopolysaccharides as main constituent and in turn help to maintain soil moisture content thereby, increasing tolerance against drought in plants (Grover et al. 2011; Naseem and Bano 2014).

Role of different kinds of microbes that are associated with mediating various physiological effects in plants pertaining to abiotic stress tolerance is elucidated in Supplementary Table 1.

Higher K+/Na+ ratio

PGPRs have role mediating ion homeostasis in plants under abiotic stress commonly seen under salt stress conditions. Ionic stress causes plants to generate an excessive quantity of Na+ in the cytosol, which has a deleterious influence on plant cellular physiology in a variety of ways (Hernández et al. 2001; Zhu 2001). PGPR-inoculated plants when grown under salinity conditions have advanced concentration of K+ ion and there by higher ratio of K+/Na+ than non- inoculated plants (Kasotia et al. 2015). Potassium shows a vital part in water stress tolerance, stomatal movements and leaf water status. PGPR may help to prevent salinity-prompted closure of stomata by increasing K+ concentration (Caravaca et al. 2004). The downregulated K+ transporter HKT1 expression in roots and upregulation in shoots in Arabidopsis was reported by inoculation of Bacillus subtilis microbe (Zhang et al. 2010). Glomus clarum and Glomus etunicatum microbes inoculated mungbean and pepper plants, resulting in increased K+ in the root and reduced Na+ in the root and shoot. (Rabie 2005; Kaya et al. 2009).

Brief insights on current scenario of abiotic stress alleviation using multi-omics approaches

The information regarding multi-omics, which is linked to bioinformatics breakthroughs, has increased our knowledge of microbial diversity and its functional aspect in complex ecosystems where microbial community interactions govern plant responses to stressors (Dukare et al. 2022). Meta-omics methods have developed possible tools for delving into microbiota and their behavior in a specific environment (Parray et al. 2022). Abiotic stress management by agricultural genetic modification is critical, yet it is a challenging topic that demands extensive breeding programmes (Tay Fernandez et al. 2022). Marker-aided selection requires knowledge of the genetic areas that influence tolerance qualities, as well as the presence of molecular markers that are intimately linked to them (Mir et al. 2022). Omics approaches help researchers to acquire a better knowledge of well-known plant–microbe relationships (Gupta et al. 2022). These investigations need to be integrated with advanced technologies such as metagenomics, metatranscriptomics, and temporal-spatial mapping of plant responses and microbes colonizing plants. There are several pioneering works in animal microbiota research (Shi et al. 2020) but technological development is still needed for plant microbiota research. For a better knowledge of PGP rhizobacterial populations, metagenomic sequencing at high throughput has also proved to be a very beneficial technique (Kalam et al. 2022). Metagenomics-based diversity profiling and colonization studies can potentially indicate quantitative colonization of a specific host under stress. When combined with meta-transcriptomic analysis, this can provide useful information on stressor-induced changes at functional and taxonomic level of the invading population (Zhou et al. 2022). Plants have been widely investigated in terms of proteomic studies for stress responses (Dong and Chen 2022). Metabolomics is being utilized more and more to get deeper insights into abiotic stress responses. Metabolomics research has benefited from recent high-throughput breakthroughs in the field of molecular identifying methods (Mashabela et al. 2022). Complex connections in the agroecosystem were revealed by multi-omics and integrated informatics, which showed numerous network modules represented by plant attributes that were heterogeneously related with soil metabolites, minerals, and microbes (Figure 2) (Ichihashi et al. 2020). So, implementation of omics strategies in future to plants as well as its associated microbiome can be the efficient way to tackle the abiotic stresses by them.

Fig. 2
figure 2

Demonstration of utilizing omics approaches viz., epigenomics, transcriptomics and genomics for unraveling the resilient genes against the abiotic stressors triggered by plant growth promoting microorganisms and their use to develop stress tolerant crop plants using genome editing technologies

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Epigenomics

Due to interactions with their environment, plants acquire an epigenetic memory that they pass on to their progeny. Programs for crop development can thus take use of the trans-generational inheritance of epimarks. Epialleles, epigenetic quantitative trait loci and recombinant inbred lines are used in this process to breed for abiotic stress resistance (Gahlaut et al. 2022; Singh et al. 2022c). The prolonged abiotic stress induced the epigenome changes via DNA demethylation and histone remodeling in cold-tolerant genotypes of chickpea and soyabean under cold and salt stress, respectively (Akhter et al. 2021; Sun et al. 2022). Long term exposure of stress leads to methylation of DNA in tolerant cultivar of soybean by inducing expression of some genes like repressor of silencing 1 or by inducing different crosstalk between acetylation and methylation of histones (Liang et al. 2019). Species-specific or conserved epigenetic mechanisms of gene regulation under abiotic stress may exist. By comparing epimarks between species, comparative epigenetics helps us understand the mechanism of epigenetic regulation of biological processes (Zhong 2016). Utilizing naturally occurring epialleles will accelerate the development of alternative plant germplasms with less genetic information.

Transcriptomics

The appropriate model of the gene expression in a target cell or tissue can be provided by transcriptomics, a potent method for quantifying gene expression. The molecular mechanism behind the complicated biological process of a plant response to stress has not yet been fully understood (Wang et al. 2020). Transcriptomics can be used to identify novel genes associated with plant resistance, highlight the complex regulatory network and expression at the entire genome level under stress, and quantitatively quantify changes in plant gene expression at a specific time point in a particular condition (Li et al. 2021). Serial analysis of gene expression (SAGE) and microarrays can now be used to derive comprehensive transcriptome data because of the advancement of high-throughput technologies. Ribonucleic acid sequencing (RNA-seq) data can be used to detect the differential expression of genes. It is also possible to employ a recently developed method for quantitatively estimating gene expression termed differential gene expression (DGE) (Million and Feyissa 2022). A cost-effective, high-throughput sequencing method called RNA-seq analysis makes it possible to examine a considerable quantity of transcriptome data. In order to comprehend the relevant regulatory mechanisms of plant adaptation to drought, or to increase drought resistance, as well as to clarify the mechanism of plant drought response, transcriptome sequencing is used to study the expression of the entire genome under drought stress (Mishra et al. 2022). After PEG6000 treatment, a total of 11,359 differentially expressed genes (DEGs) were found in sweet potato, of which 7666 were upregulated and 3693 were downregulated (Zhu et al. 2021). Analysis of the leaf and root RNA-sequencing data of Eucalyptus globulus revealed a total of 51 EglWRKY genes under the condition of cold acclimation with an activation of the expression of numerous EglWRKY genes. In the leaf tissues, 11 EglWRKY genes were modulated during cold alleviation (Aguayo et al. 2019). Comparative transcriptome study of anthers in rice grown in cold climates under cold stress revealed sucrose and starch metabolism were significant pathways (containing 47 DEGs) (Guo et al. 2019). The common sulphur metabolic pathway is activated under extreme heavy metal stress like aluminium, copper and cadmium according to transcriptome analysis of root toxicity stress in Arabidopsis thaliana depending on severity of these stresses (Kusunoki et al. 2018). Both drought-tolerant and drought-sensitive types of soybean have transcriptional alterations that have been documented by comparative transcriptome analysis (Prince et al. 2015). In a transcriptome investigation, Singh et al. discovered potential candidate genes expressed during drought stress in lentil seedlings whereas Pandey et al. discovered dehydration-responsive proteins in chickpea (Pandey et al. 2008; Singh et al. 2017). Using SuperSAGE and deep SuperSAGE, the transcriptomes of chickpeas under drought stress and discovered 80,238 tags representing 17,493 distinct transcripts (Molina et al. 2008). A study of the chickpea root transcriptome revealed the exciting activation of jasmonate in roots under drought conditions (De Domenico et al. 2012).

RNomics

Non-coding RNAs, such as micro ribonucleic acids (miRNAs) and long non-coding RNAs (lncRNAs), are the focus of a novel omics method known as RNomics (Micheel et al. 2021). The miRNAs are thought to be involved in plant related regulation of the stress response. Multiple miRNAs responded to biotic and abiotic stressors, indicating that stress-responsive mechanisms interact with one another (Yung et al. 2022). These miRNAs have a role to develop and react to biotic and abiotic challenges by controlling complex regulatory networks and being involved in a wide variety of biological activities in eukaryotic cells (Šečić et al. 2021). Plant miRNAs are essential regulators of gene expression or silence because they bind to complementary regions on the target messenger RNA (mRNA) to suppress translation or degrade transcripts (Rani and Sengar 2022). These miRNAs are associated with abiotic stress response mechanisms with respect to oxidative stress and impact on DNA in various plant species. Some miRNAs are also activated by a number of conditions in plants, including high temperature, cold, drought, high salt, oxidation, and heavy metals. Upregulating or downregulating the expression of corresponding miRNAs relies on various stimuli and are stress specific in nature (Pagano et al. 2021). The miRNA based response to single or many environmental cues can be as varied like their reactions to plant growth and development. These are known to regulate various aspects of growth and development (Chand Jha et al. 2021). Aux/IAA14 is reported to modulate the miRNA-mediated cold stress response in Arabidopsis. Next-generation sequencing discovered 71 new and 180 known cold-responsive miRNAs (Perea-García et al. 2021). The regulation of maize growth and development under low temperature stress is regulated by miRNA and their potential targets (Aydinoglu 2020). By controlling the GA and ABA signal transduction network, miRNAs demonstrate a substantial superposition or coordinating role in preventing the effects of cold stress (Legnaioli 2013). The first miRNA found in plants includes miR156, which helps plants tolerate high temperatures, is strongly stimulated (Stief et al. 2014). However, miRNAs may have pivotal role in conferring tolerance to drought stress in plants (Singroha et al. 2021). Under salt and wilt stress, several conserved and novel miRNAs linked to gene regulation in chickpea (Kohli et al. 2014). The antioxidant defense system in plants improved their tolerance to salt. The miRNAs might control the scavenging of ROS produced by salinity stress. The miR172 is a confirmed positive regulator of salt tolerance. One of the downstream targets of miR172 is IDS1, which binds to the promoters of ROS scavenging genes to suppress transcription. Thus, during salt stress in cereal crops like rice and wheat, miR172-IDS1 reveals clear regulatory interactions in maintaining ROS homeostasis (Cheng et al. 2021). Long non coding RNA (LncRNAs) are involved in a range of biological processes involving stress tolerance make up a significant share of non-coding RNAs (Jha et al. 2020). Using transcriptome data and the innovative tool plant long non coding RNA prediction (PLncPRO), lncRNAs in plants were reported, and the results showed that the chickpea plant contains a total of 3714 (for drought) and 3457 (for salinity) high-confidence lncRNAs. This tool is based on Machine Learning and utilizes random forest algorithms to classify coding and long non-coding transcripts. The tool is suitable for plants and has better prediction accuracy compared with existing tools (Li et al. 2022b).

Genomics

The study of the structural, functional, and evolutionary components of an organism’s genome is referred to as genomics. It means evaluating an organism’s complete DNA sequence and thorough genomic mapping (Irion and Nüsslein-Volhard 2022). Whole-genome sequencing helps to find genomic variants and genes related to climate adaptability in wild species of crop plants. It may be directly applicable for using breeding techniques to create crops that are environmentally friendly (Zenda et al. 2021). The development of molecular biology tools has resulted in a plethora of genomic information on legumes. Several species of legumes, including Medicago truncatula, Glycine max, and Lotus japonicus, already had their genomes sequenced. These comparative genomics of legume crops have uncovered important regulatory networks for genes involved in stress adaption and crop productivity (Young et al. 2005; Young and Bharti 2012). The function of protein glycosylation in pulses under stress can be revealed via glycoproteomics. It was discovered that flood stress had a detrimental effect on the N-glycosylation of functional proteins involved in stress control in the case of soybean (Mustafa and Komatsu 2014). An important signaling mechanism in the plant response to abiotic stress is protein phosphorylation. Studies involving phosphoproteomic and glycoproteomic modifications in chickpea and soybean under stress were used (Subba et al. 2013; Showalter et al. 2016). The importance of integrating different omics techniques for abiotic stress tolerance in the model legume crop, soybean, is highlighted by Deshmukh et al. (2014). In terms of the availability of molecular markers, QTL mapping, genome-wide association studies (GWAS), genomic selection (GS) techniques, and transcriptome profiling, significant genomic advancements have been made for abiotic stress tolerance in soybean (Deshmukh et al. 2014). To understand stress responses, microarray studies have been widely used in crop species as well as less-emphasized but nonetheless significant industrially and agriculturally plant species (Ergen et al. 2009; Luo et al. 2010; Loukehaich et al. 2012). High-throughput study of many mutants is made possible by Targeting Induced Local Lesions IN Genomes (TILLING) (McCallum et al. 2000). Salt stress response in legume species was evaluated using TILLING mutants for a particular kinase (De Lorenzo et al. 2009). In order to produce improved varieties with desired features, such as disease resistance, abiotic stress tolerance, or high yield, a process known as marker- assisted selection is used (Collard and Mackill 2008). Genome editing technologies offer a way to introduce precise sequence change, insertion/deletion (indel), and targeted mutation into a range of organisms. The most popular genome editing techniques are clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 (CRISPR-associated nuclease 9), transcriptional activator-like effector nucleases (TALENs), and zinc finger nucleases (ZFNs) (Satheesh et al. 2019).

Method

Literature survey was done by peer-reviewing the international journals and web sources such as Google Scholar/ Academic, pubmed central and Science Direct. In this review, the data pertaining to only various approaches adopted by microbes to mediate abiotic stresses alleviation by microbes is focused.

Conclusion

Microorganisms associated with plants produce different metabolites for combating abiotic stresses and promoting plant growth. Comprehensive understanding of plant–microbe mediated mechanisms for abiotic stress tolerance is necessary to translate the practical use of microbes for plant survival under extreme conditions. This will pave the way for climate-smart agricultural research, which will lead to the advancement and manipulation of beneficial bacteria as the basis of crop bio-fertilizers in the face of changing climatic circumstances, allowing agriculture to become more sustainable. Isolation and characterization of abiotic stress-tolerant microbial variations can help plants cope with stress and might be a viable technique for improving agricultural output in difficult conditions. The extent of microbial stress modification can be dignified as the better proportional effect of beneficial microbes on performance of plant under stressful milieus. However, implementation of genetic techniques serve as signpost in alleviating abiotic stresses via microbial interaction. Numerous omics-based methods, including transcriptomics, proteomics, genomics, phenomics and metabolomics have a vast potential involving the plant‐associated microbiome and their collaboration with host plants. It is important to unravel the mechanism and utilization of crop associated beneficial stress tolerant microbes that can be critical to improve food security on global scale. To summarize, we feel that in-depth research on the identification, trait categorization, compatibility evaluation, delivery methods, and impact of introducing microorganisms isolated from varied environmental conditions to agricultural plants for the reduction of abiotic stressors should receive greater attention. Microbiome plant interactions have been proven to have a role in stress reduction across a variety of climatic and edaphic circumstances, thus we need to figure out new functions for microbial metabolites produced in stressed environments.