Role of Microorganisms in Alleviating the Abiotic Stress Conditions Affecting Plant Growth

Abstract

Agriculture is one of the main sectors that participate in building up world economy, and offers the main source of food, income, and employment to their rural populations. Despite the necessity of doubling agricultural production, quantitatively and qualitatively, to cope with the worsening increase in the global population and to meet the increasing humanitarian needs, the agricultural sector faces many abiotic stress conditions. Additionally, the great climate changes lead to an increase in the negative impact of these stressors. There are many conventional and nonconventional ways that could directly or indirectly mitigate the adverse effects of these stressors, each of them has its advantages and disadvantages. The biological tool is one of the promising methods; it depends on the effective use of beneficial microorganisms to alleviate stress conditions that affect plant growth, development, and therefore productivity. This method is economically inexpensive and eco-friendly toward the environment. Beneficial soil microorganisms such as PGPRs and AMF colonize the root zone of many plant species and help to enhance plant growth and development. Thus, this chapter is aiming to highlight the role of microorganisms in alleviating the abiotic stress conditions affecting in plant growth.

1. Introduction

Agriculture is the backbone of developed and particularly developing countries, with more than 60% of the population of the developing countries depending on it for their livelihood. Increasing food production to fulfill the needs of increasing world population becomes a major concern. By the year 2050, it is expected that the human population will rise up to 10 billion. Hence, it is necessary to produce 70% more food for meeting the need of additional population. Furthermore, fighting poverty and hunger, consuming limited natural resources with more efficiencies, and acclimatizing to global warming must be taken into account to attain sustainable development [1]. Therefore, to make sure nourishment security, crop production will have to be doubled, and produced in more environmentally sustainable means [2]. However, improvements in the agriculture production process, land and water use are essential to realizing food security, poverty reduction, and total sustainable development. This can be realized by increasing cultivable land area and/or by increasing efficiently the productivity of land and water units. Really, several other factors cause a further reduction in crop productivity resulting in a lack of food security, particularly in developing countries. Of them, the availability of agricultural land, freshwater resources, ever-increasing abiotic and biotic stresses, and low economic activity in agricultural sector are the main factors. Moreover, Agriculture sector is categorized as one of the most exposed sectors to climate change. Plant productivity, principally in arid and semi-arid zones is fronting growing stresses triggered by natural and human’s activities issues. Augmented occurrence of both abiotic and biotic stresses has become the principal cause for declining productivity in main crops. There is evidence of yield drops in several crops in many parts of the world due to increasing drought, salinity stress, reduction in precipitation rate and elevated air temperature. Abiotic stresses can directly or indirectly disturb the physiological status of an organism by changing its metabolism, growth, and development. It is generally thought that abiotic stresses are considered to be the main source of yield reduction [3].

Abiotic stresses affect plants in various ways and are causes of reducing crop productivity (Figure 1). To enhance plant production, it necessities to apply cost-effective technologies to control stress conditions. Soil microorganisms, living in the soil under normal and harsh conditions, have shown great properties, which, if exploited can help agriculture for improving and sustaining crop productivity. Whereas it is well recognized that beneficial microbes can stimulate growth and increase productivity through mechanisms like increasing nutrient availability, hormone production and disease controlling, it is also becoming increasingly clear that their effects may be more far-reaching.

Figure 1.

Adverse effects of abiotic stress on plants and the role of PGPRs in alleviation of these stresses. This figure illustrates an overview of mechanisms in microbial phytohormone-mediated plant stress tolerance. Several root associated microbes produce cytokinin (CK), gibberellin (GB), indole-3-acetic acid (IAA), salicylic acid (SA), and abscisic acid (ABA), which help plants to cope with stress by improving its antioxidant potential, by up-regulation of the antioxidant system and by accumulation of compatible osmolytes therefore reducing oxidative stress-induced damage; improving photosynthetic capacity and membrane stability; promoting cell division and stomatal regulation; stimulating growth of root system, and acquisition of water and nutrients. (Adapted from [4]).

Soil microorganisms (SMs) are very important in naturally occurring populations that play a significant role in soil fertility, plant growth, and maintaining healthier environment. This microbial population may comprise number of microorganisms like bacteria, actinomycetes, cyanobacteria, and fungi. Some of these are considered efficient owing to their growth enhancing abilities. Among these naturally occurring populations, plant growth promoting rhizobacteria (PGPR) have been investigated widely due to their positive effect on plant growth and protecting the environment from various hazards. PGPR are free living bacteria that enhance plant growth by root colonization [5]. These are also noted as plant health promoting bacteria (PHPB) or nodule promoting bacteria (NPB) [6] and can be characterized as intracellular PGPR (iPGPR) and extracellular PGPR (ePGPR) on the basis of their proximity in related to the host plant [7]. Figure 2 shows the degree of nearness and influence of the plant-microbe interactions.

Figure 2.

The extent of proximity and influence of the plant-microbes interactions, small colored shapes (blue, green, red, purple and yellow) represent soil microbes. Diversity and density of microbes are variable according to soil organic contents and types, distance from plant roots, plant species, and plant tissue. (Adapted from [8]).

In the present chapter, we attempt an overview of current knowledge on how plant-PGPMs (Rhizobacteria, fungi, Arbuscular Mycorrhizal Fungi (AMF), Blue Green Algae or CyanoBacteria (BGA, CB), Actinomycetes or Actinobacteria, etc.) interactions help in alleviating abiotic stress conditions in different crop systems, which can be used for sustainable agriculture.

2. Stress definition and types

Stress conditions are a set of either abiotic or biotic factors that are unsuitable for plant growth of which the plant may be exposed during its various growth stages (one or more) from germination to fruiting, which may not only negatively affect its growth and productivity but may lead to entirety stopping its growth and thus its productivity. To which the plant may respond by making physiological and/or molecular and/or morphological changes or all of the previously. The plant stresses are defined as responses describing a suite of molecular and cellular processes prompted by the detection by a plant of some form of stress. These processes may be accompanied by the plant’s induces for a reduction or an increase in some plant metabolites leading to an increase in plant resistance or tolerance. These stresses can be abiotic stress such as nutrient deficit, drought (water deficit or salinity), water-logging or flooding, extreme cold, frost, heat, sodicity, and metal and metalloid toxicity or biotic stress which are responsible for the damage done to an organism by other living organisms like herbivores or pathogens, bacteria, viruses, fungi, parasites, beneficial and harmful insects, weeds, and cultivated or native plants.

3. Adverse effects of abiotic stress conditions on plant growth and productivity

Various abiotic stress conditions such as salinity, drought, flooding, temperature (heat, cold), nutrient elements deficiency, alkalinity, organic and inorganic pollutants and heavy metals adversely affect crop plants growth, development and productivity [9] as shown in Figure 3.

Figure 3.

Diverse abiotic stresses and the strategic defense mechanisms adopted by the plants. This figure shows diverse abiotic stresses and the strategic defense mechanisms adopted by the plants. although the consequences of salinity, heat, drought, and chilling are different, the biochemical responses seem more or less similar. High light intensity and heavy metal toxicity also generate similar impact, but submergence/flood situation leads to degenerative responses in plants where aerenchyma are developed to cope with anaerobiosis. It is, therefore, clear that adaptive strategies of plants against variety of abiotic stresses are analogous in nature. It may provide an important key for mounting strategic tolerance to combined abiotic stresses in crop plants. (Adapted from [10]).

3.1 Adverse effects of salinity stress conditions

Excessive salinity is one of the most important abiotic factors influencing the world’s agricultural lands [11]. Also, it is one of the principle reasons that limit agricultural productivity [12]. It delays plant development by shifting numerous physiological, biochemical, and metabolic processes. Excessive accumulation of sodium chloride (NaCl) and other salts persuades water-deficient conditions owing to uncontainable stomata closure causing osmotic stress to plant roots. It results in ionic inequity which causes reduction in shoot and leaf growth, untimely leaf death, and necrosis [13, 14]. Reduced water absorption and augmented salts accumulation like Na⁺, K⁺, Mg⁺₂, Ca⁺₂, and Cl⁻ inside the cell and as a result increased ion toxicity. The reduced growth of the plants under salinity is due to nutrient disturbances, affecting the availability, mobilization, and distribution of nutrients. This may be attributed to the competition of sodium (Na⁺) and chloride (Cl⁻) with nutrients such as potassium (K⁺), calcium (Ca⁺₂) and nitrate (NO⁻₃) [15]. Under higher accumulation of salts, the activity of nitrogenase enzyme encompassed in biological nitrogen fixation (BNF) is reduced then the nodulation process highly diminished [16, 17]. Currently, 50% of all irrigation patterns are impacted by salinity.

3.2 Adverse effects of drought stress conditions

Drought stress is one the greatest stressors for plants which can occur when the availability of water to the roots is insufficient or when the transpiration rate is too high. These two conditions regularly coincide with tropical (arid) and sub-tropical (semi–arid) climates. Water deficit restricted photosynthesis activity due to imbalance between light capture and its utilization as a consequence oxidative stress occurred [18]. Drought stress prompted a remarkable decreasing in photosynthesis, which is reliant on photosynthesizing tissue and photosynthetic pigments [19, 20]. Through stresses, active solute buildup (i.e., TSS, proteins, and FAAs) is claimed to be an effective stress tolerance mechanism [21]. Drought stress conditions lead to a decrease in the metabolic and physiological performance of plants and consequently the plant growth and productivity negatively affects. Additionally, drought stressor limits biological nitrogen fixation, and pigment content [13] as well as it reduces nutrients accessibility and their passage. Likewise, it greatly increases reactive oxygen species (ROS) concentration leading to an increase in oxidative stress, which take place because of an inequity created between the rate of electron transport and reducing power activity for metabolic consumption [22, 23]. Reactive oxygen species further prompt modifications in tissue construction and performance, enzyme stability, and lipid peroxidation [24].

3.3 Adverse effects of temperature stress conditions

Climatic changing conditions result in an increase of the intensity of heat and cold stress. The temperature stress causes alterations in membrane, water potential, and photosynthetic activity in plants. The optimum temperature for third carbon plants’ (C3 plants’) growth is stated 15–25°C by a number of scientists [25, 26, 27]. Up and down the optimum temperature, the plant performance was limited. Heat stress restricts cool-season plant development in summer in many positions of the world. Throughout the warm season, heat stress limited photosynthesis and carbohydrate buildup, augmented cell membrane damages triggered protein folding and even cell death in C3 plants [27]. The same damages have been recorded in warm-season plants, fourth carbon plants’ (C4 plant species), in the winter. Also, the C4 species uptake less water and needed to alter themselves to be able to absorb mineral elements with low solubility [28].

3.4 Adverse effects of nutrient element deficiency stress conditions

Nutrient elements are considered fundamental for plant growth, development, and survival. 17 essential elements are necessary to maintain plant growth and development. Three of them (C, H and O) are derived from the air and water whereas the rest (N, P, K, Ca, Mg, S, Fe, Mn, Cu, Zn, Cl, B, Mo, and Co) are supplied either from soil or by adding fertilizers. Each of them plays a special role in plant life cycle and their necessity varies with the plant species and growth phases. Both the shortage and surplus of these nutrients lead to negative impacts on plant growth and development (Figure 4). Further, to make sure the efficient utilization of the nutrients, the environmental factors should be satisfactory. The plants absorb these elements in ionic form and its ability to absorb them is related to their quantities and distribution in the soil.

Figure 4.

The signs of essential nutrient elements deficiency in plants.

3.5 Adverse effects of alkalinity stress conditions

Alkalinity achieves its specific negative effect characteristics on crop plants in alkaline soils and disturbs plants at biological and physiological level. In addition to sodium chloride (NaCl) stress, there are other salts like sodium carbonate (NaCO₃) and sodium hydrogen carbonate (NaHCO₃) which are harmful to crops at excessive accumulations. High pH (more than eight) in alkaline soils diminishes the nutrient availability of crucial macro- and micro-nutrients, such as phosphorus (P), manganese (Mn), zinc (Zn), copper (Cu), and iron (Fe) causing nutrient deficiency and osmotic stress [29].

3.6 Adverse effects of contaminants stress conditions

Organic and inorganic pollutants are repeatedly being used in our environment via human interfering comprising industrial effluent discharge and agricultural practices, e.g., unreasonable and undue application of mineral elements and plant protective materials (pesticides) to soil. These chemical pollutants are causing major dangers to human health and their environment and may be directly or indirectly affecting on crop growth, development and productivity

4. Plant behavior under stress conditions

A deficit of one or more of the vital nutrient elements caused several alterations that may be occurred at morphological, physiological, and also molecular levels of crop plants. The data presented in Table 1 summaries these changes and in addition the symptoms that result from the deficiency of these essential nutrient elements on plants.

ND	Plant responses at		Symptoms	References
	Physiological level	Morphological level
N	A decrease in the activity of nitrate reductase and RO scavenger enzymes like SOD and POD,; Decrease in chlorophyll content, and photosynthesis rate induces the chloroplast disintegration and loss of chlorophyll. An increase in production of phenolic compounds as secondary metabolites.	An elevated root shoot ratio with shortened lateral branches leaf area, High decreased in biomass production	Early, the older leaves show chlorosis comparing to the newer, Necrosis occurs. At later phases stunted growth and plant death if nitrogen deficiency continues.	[30, 31]
P	An increase in production of phenolic compounds as secondary metabolites and more organic acid was released.	A reduction in plant growth rate and remobilization of phosphorus happen	Optical disorders like red or purple color leaves occur because of anthocyanin accumulation.	[30, 32]
K	An increase in production of phenolic compounds as secondary metabolites.	A reduction in plant growth rate	Shortens inter nodes followed by bushy appearance, chlorosis and necrosis.	[30]
Ca	A significant decrease in chlorophyll content up to 50%, and protein, photosynthesis,; Limited in translocation of photosynthesis compounds from source to sink; significant increase in soluble nitrogen content of the plant.	Great reduction in growth rate,; Less protein–N, RNA and DNA,; A significant increase in soluble nitrogen content of the plant	A reduced amount of root and shoot branches.	[33, 34, 35]
Mg	Accumulation of sugar in source leaves was detected before reduction of photosynthesis and chlorophyll biosynthesis.		Leaf vines chlorosis.	[36, 37]
S			Habitually no visual symptoms,; Reduction in total crop yield. Leaves begin to develop chlorosis. The chlorosis started from the leaf’s edge and spread over intercostal area, but the zones beside the veins permanently remain green. Chlorosis happens, but it never turns into necrosis.	[38, 39]
Fe	Reduction in plant growth and even may stop some plant function; An efficient decrease in photosynthesis.		Chlorosis of young leaves; Reduction in crop production.
Zn		A decrease in biomass production	Initial early senescence of the old leaves or slight yellowing of the newer leaves to the formation of the yellow chlorotic or even necrotic areas on the leaves.
Mn	Necrotic spots or marginal necrosis may also develop. In dicotyledons the chlorosis develops first on the distal portions of the affected leaf blades, whereas in cereals, the leaf bases are first affected.	Diffuse interveinal chlorosis on the young, expanded leaf blades	Wheat leaves became mottled,; Decrease in chlorophyll content, plant appearance turned yellow.	[40, 41, 42]
Cu	A decrease in activity of the cytochrome oxidase. This enzyme has a role in plant root nodule cells recovery under low oxygen stress for nitrogen fixation.		New leaves margin necrosis, lateral shoot death, unformed leaf margin, bleeding in main node stem and low lignification value in vessels.	[43]
Mo	A decrease in nitrogen fixation,; Shoot and nodule dry weights.
B	Accumulation of the phenolic compound; A reduction in lignin biosynthesis.	Limitation of lateral bud growth in some plants	The inhibition or cessation of the roots and shoots elongations.	[44, 45, 46, 47, 48]
Cl		Less cluster formation and fewer yields	Reduction in leaf area and plant biomass. Leaves wilting, chlorotic mottling, bronzing, and tissue necrosis.	[49, 50]

Table 1.

Summaries the plant response at physiological and morphological levels and some symptoms under nutrient deficiency stress.

5. Role of microorganisms in mitigating abiotic stress conditions

The rhizosphere contains the tiny parts of soil inherent to roots of plants. The average count of microorganisms at the plant root region is very high as compared with the rest of the soil. So, it is clear that plant roots have an assortment of mineral, nutrient, and metabolite components, which are considered the principle factor for captivating microorganisms to assemble and link together. Root exudate of plants is a critical factor for microbial settlement in the rhizosphere. Shifting of microorganisms regarding the root exudates has an important role in pulling force of the microbial population to colonize the plant roots.

The interactions between microbial community and crop plants are vital to the modification and endurance of both in any abiotic environment. Induced Systemic Tolerance (IST) is the expression exploited for microbe-negotiated triggers of abiotic stress reactions. The duty of microorganisms in altering abiotic stresses in plants attracted the attention of several researchers [51, 52, 53]. The intrinsic metabolic of microbes and genetic aptitudes, participate to reduce abiotic environmental stresses in the plants [54]. The function of numerous rhizospheric microbes inhabitants with the genera Azospirillum [55], Azotobacter [56, 57], Bacillus [58, 59, 60], Bradyrhizobium [61], Burkholderia [62], Enterobacter [60], Methylobacterium [63], Rhizobium [60, 64], Pantoea [60, 65], Pseudomonas [60, 66], Trichoderma [67], and cyanobacteria [68] in elevation and control of growth in plant grown under different kinds of abiotic stresses has been reported.

In this regard, [69] reported that Streptomyces sp. strain PGPA39 alleviates salinity stress and stimulates the growth of “Micro-Tom” tomato plants and Arabidopsis [70]. Burkholderia phytofirmans strain PsJN overcome drought stress in maize [71] and wheat [72]. The data presented in Tables 2 and 3 outline some examples of beneficial microorganisms that play a pivotal role in alleviation the adverse effects of abiotic stresses.

Stress Type	PGPRs	Plant	References
Salt	Azospirillum brasilense	Hordeum vulgare, Lactuca sativa,Pisum sativum. Cicer arietinum	[55, 73, 74, 75]
Salt	Bacillus amylolequifaciens, B. insolitus Microbacterium sp. Pseudomonas syringae	Triticum aestivum	[76]
Salt	P. fluorescens	Arachis hypogea	[77]
Salt	B. subtilis	Arabidopsis thaliana	[78]
Salt, drought	Achromobacter piechaudii	Lycopersicon esculentum	[79, 80]
Drought	Azospirillum brasilense Pseudomonas spp.	Zea mays	[81, 82]
Drought	Rhizobium sp., P. putida P5	Helianthus annus	[83, 84]
Drought	Bacillus, P. mendocina	Lactuca sativa	[85, 86]
Drought	B. megaterium	Trifolium	[87]
Drought	Pseudomonas sp., Variovorax paradoxus	Pisum sativum	[88, 89]
Drought	Paenibacillus polymyxa, Rhizobium tropici	Vigna radiata	[90]
Drought	Pseudomonas spp.	Asparagus	[91]
Drought	Azospirillum sp., B. safensis, Ochrobactrum pseudogregnonense	Triticum aestivum	[92, 93]
Flooding	Enterobacter cloacae, P. putida	Lycopersicon esculentum	[94]
Heat	Pseudomonas sp. AMK-P6	Sorghum bicolor	[66]
Cold	P. putida	Brassica napus	[95]
Cold and heat	Burkholderia phytofirmans	Vitis vinifera	[96]
Heavy metals	Sanguibacter sp., Pseudomonas sp.	Nicotiana tabacum	[97]
Heavy metals	B. subtilis, Pantoea agglomerans	Avena sativa	[98]
Heavy metals	P. fluorescens, Microbacterium sp.	Brassica napus	[99]
Ni and Cd	Methylobacterium oryzae, Burkholderia sp.	Lycopersicon esculentum	[100]
Iron toxicity	B. subtilis, Bacillus sp., B. megaterium	Oryza sativa)	[101]

Table 2.

Soil microorganisms (endophyte or rhizobacteria acting as PGPR and conferring the plants’ abiotic stress tolerance.

Stress type	Arbuscular mycorrhizal fungi (AMF)	Plant	References
Drought	G. mosseae	Poncirus trifoliata	[102]
Drought	G. deserticola	Pepper	[103]
Drought	G. intraradices	Rosa hybrida L., Lactuca sativa, Cicer arietinum	[104, 105, 106]
Drought	G. etunicatum, G. versiform	Cicer arietinum	[106]
Salt	Glomus etunicatum	Carthamus tinctorius	[107]
Salt	G. intraradices	Zea mays,Trigonella foenum-graecum,; Fragaria ananassa	[108, 109, 110]
Salt	G. viscosum	Medicago sativa L.	[111]
Salt	G. etunicatum	Brachiaria humidicola	[112]
Nutrient deficiency, Heat	G. mosseae	Dalbergia sissoo, Acacia nilotica,; Poncirus trifoliata	[113, 114, 115]
Heat and cold	G. mosseae, G. sp. R10; G. aggregatum, G. fasciculatum; Gigaspora margarita	Fragaria ananassa	[116]
Heavy metals	G. mosseae	Piper nigrum	[117]
Heavy metals	G. mosseae, Aculaospora laevis	Zea mays	[118]
Heavy metals	G. intraradices	Thlaspi sp.	[119]
Heavy metals	G. etunicatum, G. intraradices	–	[120]
Heavy metals	G. macrocarpum	Zea mays	[121]

Table 3.

Arbuscular Mycorrhizal Fungi (AMF) that act as PGP and conferring the plants abiotic stress tolerance.

5.1 Role of microorganisms in mitigating salinity stress conditions

Endophytes and rhizobacteria as PGPB have potent in mitigating salinity stress. Their direct actions involve stimulation of phytohormones production, improvement of nutrient uptake, promotion of siderophore production, and nitrogen fixation. Some other indirect roles have resembled to actions in water-deficit stress as osmotic stability, which is pivotal in both conditions, such as accumulation of osmolytes (glycine betaine, proline, trehalose, EPS, and volatile organic compounds accumulation). These compounds elevate plant growth via perpetuate ion homeostasis. PGPR improves plant tolerance to salinity stress via induced systemic tolerance (IST) [16, 122]. In this connection, [123] proved that the application of plant growth-promoting bacteria, PGPB, producing ACC deaminase enzyme or transgenic plants revealed the corresponding acdS gene, growth evolution, seeds productivity, and enhancement of Camelina sativa quality on plants grown in marginal land which not suitable for cultivation due to high salinity.

5.2 Role of microorganisms in mitigating drought stress conditions

Plant Growth Promoting Bacteria (PGPB) supports the antioxidant apparatus of plants via managing antioxidant enzyme level, consequently, increasing the plant resistance to abiotic stresses [124]. Plant growth-promoting rhizobacteria mitigate the water deficit condition by altering several physiological and biochemical processes in plants via a rhizobacterial-induced drought endurance and resilience (RIDER). This procedure includes secretion of exo-polysaccharides (EPS), management of endogenous phytohormones and antioxidants, and coordinated organic solutes, e.g., sugars, amino acids, and polyamines, and/or fabricating of volatile organic constituents, dehydrins, and heat shock protein [125]. These techniques help plants to sustain water deficit by preserving plant growth, membrane stability, and enzyme constancy and effectively controlling the water and mineral uptake by increasing the surface area of root [16, 126].

5.3 Role of microorganisms in mitigating temperature stress conditions

Adapted microbes to high or low temperatures could alleviate their harmful effects. Microbes have explicit enzymatic structures that manage their metabolism to overcome the changing temperature and preserve their membrane and enzyme stability. Under these conditions, heat and cold shock proteins are established. These molecular chaperones contribute resistance to adjacent high-temperature stress [16, 127]. These severe conditions caused protein denaturation, which is handled with trehalose through formation of a gel-like web to save plants from dehydration [128]. Cold-adapted microbes found at high-altitude agro-ecosystem, have a vast prospect to assist plants in alleviating unfavorable climatic conditions. In cold desert of the Himalayas, India psychrophilic and psychro-tolerant bacteria exhibited plant growth-stimulating characteristics, including Arthrobacter, Aeromicrobium, Aeromonas, Bacillus, Bosea, Burkholderia, Brevundimonas, Citricoccus, Exiguobacter-ium, Janibacter, Janthinobacterium, Jeotgalicoccus, Kocuria, Methylobacterium, Pseudomonas, Providencia, Psychrobacter, Pantoea, Plantibacter, Rhodococcus, Sanguibacter, Sporosarcina, Staphylococcus, Sphingobacterium, and Variovorax [129]. Correspondingly, the isolation of bacteria associated with heat-tolerant plants from wheat exhibited improvement in traits of plant growth and development under heat stress. They encompassed bacterial genera like Alcaligenes, Arthrobacter, Bacillus, Delftia, Methylobacterium, and a number of pseudomonads [130].

5.4 Role of microorganisms in mitigating alkalinity stress conditions

Application of encouraging phytoremediation technology depends on the integrated effect of plants and associated microbes. It has a valuable strategy to clean up the biodegradation of organic pollutants and heavy metal-polluted soils.

5.5 Role of microorganisms in mitigating contaminants stress conditions

Application of encouraging phytoremediation technology depends on the integrated effect of plants and associated microbes. It has a valuable strategy to clean up biodegradable organic pollutants and heavy metal-polluted soils [131]. PGPB responds to heavy metal stress via different mechanisms involving bioaccumulation, enzymatic detoxification, metal mobilization, immobilization, volatilization, and EPS complexation as well as accumulation of phytohormone, solubilization of phosphate, siderophore, ACC-deaminase, and NF [132, 133]. Metal solubility and accessibility in the soil were influenced by microbes. Any metal pollutants cannot be easily degraded, so they must be either stabilized or extracted from the soil. Metal-chelating siderophores and enzyme mechanisms involved in phosphate solubilization expedite heavy metal uptake under stress conditions [134]. Growth-promoting microbes build up chelating compounds such as siderophores which may decrease soil pH and promote metal solubility via complex formation. Also, the production of organic acids, such as citric, gluconic, and oxalic, may promote metal mobilization, and uptake consequently, accumulation in plant shoots, by phytoextraction. Redox processes promote bioavailability of metals as reduction of Mn (IV) to Mn (III) and Fe (III) to Fe (II) so, become less toxic. Moreover, the bioavailability could increase using bio-surfactants and phyto-chelatins via formation of the complex with heavy metals [134, 135, 136, 137, 138]. Phyto-stablization through growth-enhancing bacteria and plant development may reduce metal availability in highly metal-polluted soils. This may occur via the formation of new specific metals, altered metal adsorption on plant cell walls, or ejection through downfall. Phyto-management is a combination of several phyto-technologies, a sustainable application and cost valid can contribute enormous assistance in repair of metal-polluted soils [139].

6. Mechanisms of microorganisms for alleviating abiotic stress conditions

The bio-fertilizers, bio-stimulators, and bio-control effects of PGPRs (Table 4) are contingent on their natural ability, as well as the interaction manner and militant endurance circumstances. GPB promotes plant proliferation with direct and/or indirect techniques [6, 145]. Concerning direct mechanisms, it involved the synthesis of compounds that expedite the uptake of crucial nutrients and micronutrients from the soil and accumulation of plant growth regulators, such as phosphorus and potassium solubilization, iron and zinc sequestration, siderophore and plant hormone accumulation, and atmospheric nitrogen fixation. Regarding the indirect techniques, it occurs through the accumulation of HCN and antifungal components, hostile activity regarding pathogenic organisms, and resistance to unfavorable stress conditions. Moreover, the bacteria can promote systemic resistance in plants via the accumulation of certain metabolites that provide extracellular signals and stimulate a series of internal processes. Ultimately, these signals are recognized by different plant cells responsible on the promotion of the defense system.

PGPR forms	Definition	Mechanism of action	References
Bio-fertilizer	An ingredient that has microbes (bacteria, fungi, AMF,BGA AB etc.) which, when applied on the seed, plant surface or soil, colonizes the environmental of roots and stimulate plant growth by various ways like, increased supply of primary nutrients for the host plant	Biological nitrogen fixation (BNF); Phosphate solubilizing microbes	[140, 141]
Bio-stimulator	Microorganisms that characterized by their ability to produce or synthesis phytohormones or other secondary metabolites that stimulate plant growth	Like indole acetic acid (IAA), gibberellic acid (GA), cytokinins and ethylene	[141, 142]
Bio-control agents	Microorganisms that protect plant against diseases by controlling phytopathogenic using different mechanisms	Synthesis of antibiotics, siderophores, HCN, hydrolytic enzymes,Acquired and Induced systemic resistance	[140, 141, 143]

Table 4.

Some mechanism of action of PGPRs that enhance the plant growth*.

*Adapted from [144].

In addition to bacteria, fungi especially mycorrhizae are considered pivotal plant growth stimulators. Mycorrhizae are mainly divided into mycorrhizal fungi (MF) and vesicular-arbuscular mycorrhizal (VAM) fungi. These types of fungi are either still connected externally with the host plant (ectomycorrhizae) or they may organize endosymbiotic associations (VAM). They form extended networking of fungal mycelium, so, maximize nutrient uptake via roots. In this connection, [146] concluded that the endophyte root fungal of Piriformos poraindica promoted salt and drought tolerance in Chinese cabbage and barley, respectively. These stimulatory effects were achieved by promoting the concentration and activity of antioxidants and stimulating many other processes [147]. The possibility of microbial connections with the plants has several aspects. It starts with the induction of local or systemic stress mitigation techniques in plants to resist unfavorable stress conditions. Then, they assist plants to protect their growth, proliferation, and development via fixation, mobilization and/or accumulation of nutrients, hormones and organic phytostimulant components. These multipronged roles of microorganisms or their populations demonstrate their strength, achievable and critical options for different alleviation techniques for abiotic stress in plant crops.

Various suggested techniques explain the effect of microbes in mitigation of abiotic stress. Soil-dwelling microbes can be classified into genera Achromobacter, Aeromonas, Azospirillum, Azotobacter, Bacillus, Enterobacter, Klebsiella, Pseudomonas, and Variovora which exhibited enhancement of plant growth under different stress conditions [60, 75, 89, 122, 125, 148]. Several publications concerned with the role of microbes for alleviating abiotic stresses indicate the importance of microbes in this field (Tables 5–9). All soil-inhabiting bacteria are organized as plant growth promoters (PGP) if they are able to promote plant growth even under different unfavorable physicochemical conditions. There are several tools by which microbes promote plant growth as indole acetic acid (IAA), which is synthesized in the shoot apical meristem and gathered in the active root apical meristems. The auxins have growth-promoting roles in plant-involved cell elongation, consequently root growth induction and lateral root formation. In contrast, the high auxins concentrations, promote retardant effects on root growth [60, 186]. The same result was recorded as a result of high ethylene synthesis [186]. Results also concluded that the rhizosphere colonizing bacteria promote plant growth via phytohormones production [187]. Generally, agricultural practices observed that the PGPRs not only assist in alleviation of environmental stresses, but also increase the yield of several crop plants including barley, maize, rice, and soybean [174, 188, 189]. In this regard, Pseudomonas sp. PMDzncd2003 enforces salt tolerance on rice germinates under salt stress. It also has a high ability to root colonizing parallel to the ability to accumulate exo-polysaccharides (EPS) that promote salinity tolerant [190]. Also, inoculation of rice with Bacillus pumilus mitigates salinity and high boron stresses [191]. The reported technique for cell protection under stress conditions was high antioxidant enzyme activity accompanied by the presence of bacterial inoculant. More studies are needed to investigate the communication between plant and bacterial colonizers at the molecular level.

Crop plants	Microorganisms	Effect/Mechanism	References
Maize (Zea mays)	Azospirillum lipoferum	Increase accumulation of TSS, FAAs, and proline; Enhance the growth parameters	[149]
	Bacillus Spp.	Increased accumulation of proline, TSS, FAAs,; Decrease electrolyte leakage, reduce the activity of antioxidants enzyme (CAL, GPX peroxidase)	[59]
Soybean	Pseudomonas putida H-2–3	Decrease the level of AB and SA, Increase the accumulation of JA. Modulated antioxidants by declining SOD, flavonoids, and RSA	[150]
Wheat (Triticum aestivum)	Bacillus amyloliquefaciens 5113 Azospirillum brasilense NO40	Bacterial-mediated plant attenuated transcript level and improves homeostasis.	[23]
	A. brasilense NO40,; R. leguminosarum (LR-30),; R. phaseoli (MR-2) Mesorhizobium ciceri (CR-30,39),	Improved the growth, biomass, and drought tolerance index throughout the production of CAL, EPS, and IAA	[151]
Lavandula dentate	Bacillus thuringiensis	IAA induced higher proline and K-content improved nutritional, physiological, and metabolic activities, Decreased the activity of: GR and APX	[152]
Cicer arietinum L.	Pseudomonas putida MTCC5279 (RA)	Increase: osmolyte accumulation, ROS scavenging ability, and stress-responsive gene expressions	[24]
Lettuce	Azospirillum sp.	Increased chlorophyll and ascorbic acid content, Promote air-part biomass, better overall visual quality, hue, chroma and antioxidant capacity, and a lower browning intensity	[153]
Arabidopsis	Azospirilum brasilense sp 245	Improved plants seed yield, plants survival, proline levels, and relative leaf water content; Decreased stomatal conductance, malondialdehyde, and relative soil water content	[154]
	Phyllobacterium brassicacearum strain STM196	Enhanced ABA content resulted in: Decreased leaf transpiration, Delay in reproductive development, Increased biomass and water use efficiency	[155]
Brassica oxyrrhina	Pseudomonas libanensis TR1 and Pseudomonas reactans Ph3R3	Enhanced plant growth, leaf relative water, and pigment content Decreased concentrations of proline and malondialdehyde in leaves	[133, 156]
Rice (Oryza sativa L.)	Trichoderma harzianum	Stimulate root growth independent of water status,; Delay drought response	[12]
Medicago truncatula	Sinorhizobium medicae	Improve root nodulation and nutrient acquisition during drought stress	[157]
Wheat	Bacillus spp., Enterobacter spp., Moraxella spp., Pseudomonas spp.	Auxin synthesis	[158]
Vigna mungo L. Pisum sativum L	Consortium (Ochrobactrum pseudogrignonense, Pseudomonas sp., Bacillus subtilis)	Enhance the production of ACC deaminase, RO scavenging enzymes, and osmolytes	[159]
Wheat	Pantoea agglomerans	Improving soil aggregation through (EPS)	[160]
Arabiodopsis	Paenibacillus polymyxa	Induction of stress-resistant gene ERD 15	[161]
Sunflower	Rhizobium sp.	Enhancing Soil aggregation through EPS	[83]
Wheat	Azospirillum sp.	Improved Water relations	[92]
Pea	Variovorax paradoxus	production of ACC-deaminase	[162]
Arabiodopsis	Paraphaeosphaeria quadriseptata )	Induction of HSP	[163]
Rice	Brome mosaic virus	-	[164]
Common bean	P. polymyxa and Rhizobium tropici	Change in hormone balance and stomatal conductance	[90]
Pea	Pseudomonas sp.	Decreased ethylene production	[88]
Lettuce	Pseudomonas mendocina, Glomus intraradices	Improved antioxidant status	[86]
Sunflower	Pseudomonas putida P45	Improved soil aggregation due to EPS production	[84, 165]
Trifolium	Bacillus megaterium, Glomus sp.	IAA and proline production	[87]
Tomato	Achromobacter piechaudii	Synthesis of ACC-deaminase	[79]
Sorghum	AM Fungi	Improved Water relation	[166]

Table 5.

List of some microorganisms that have the ability for mitigating drought stress condition through different mechanisms.

Crop plants	Microorganisms	Effect/Mechanism	References
Groundnut (Arachis hypogaea L.)	Brachybacterium saurashtrense (JG-06), Brevibacterium casei (JG-08), Haererohalobacter (JG-11)	Higher of K+/Na+ ratio, Ca2+, P, and N content.; Shoot and root contain a higher concentration of auxin	[12, 167]
Mung bean (Vigna radiate)	Rhizobium and Pseudomonas	Improving growth, nodulation and yield of mung bean under natural and salt-affected conditions throughout ACC-deaminase production	[168]
Barley and oats	Acinetobacter spp. , Pseudomonas sp.	Production of enzyme ACC deaminase,; lower ethylene and IAA promote plant growth	[169]
Wheat	Azospirillum sp.	Increased shoot dry weight and grain yield.; Plants accumulate some organic solutes as. Proline, TSS and inorganic ions to maintain osmotic adjustment
	Pseudomonas sp. Serratia sp.	Have ACC deaminase activity, Reduce ethylene level and enhance plant growth and yield	[170]
Maize (Zeya Mays)	Pseudomonas and Enterobacter	Enhance N, P, and K uptake and increase K+/Na+ ratios, Decrease triple response	[171]
Rice GJ-17	Pseudomonas pseudoalcaligenes; Bacillus pumilus	Reduced: the toxicity of ROS, the activity of lipid peroxidation, and SOD activity	[172]
Rice	Bacillus amyloliquefaciens NBRISN13 (SN13)	Modulating differential transcription in a set of at least 14 genes	[173]
Barley (Hordeum vulgare L.)	Hartmannibacter diazotrophicus E19	Increased: root and shoot dry weight. Enhance ACC-deaminase activity lower ethylene content	[174]
lettuce seeds	Azospirillum	Stimulated ascorbic acid content, antioxidant capacity, higher biomass, and a lower browning intensity	[153]
Brassica napus (canola) and Maize	Pseudomonas putida UW4	Modulation of plant protein differential expression and ACC deaminase activity	[175]
Oryza sativaL.Arabidopsis thaliana	Curtobacterium albidum	Modulation of osmolytes and antioxidative enzymes, and induction of systemic tolerance	[176]
Alfafa	Enterobacter sp.	Synthesis of 2-keto-4- methylthiobutyric acid (KMBA)	[177]
Barley	Piriformaspora indica	Increased antioxidative capacity	[178]
Wheat	B. amylolequifaciens; B. insolitus, Microbacterium sp. P. syringae	Restricted Na^+ influx	[76]
Groundnut	Pseudomonas fluorescens	production of ACC-deaminase	[77]
Rice	Scytonema	Production of GA and extracellular products	[179]
Tomato	Achromobacter piechaudii	Production of ACC-deaminase	[79]
Sorghum	AM Fungi	Amended Water relation	[166]

Table 6.

List of some microorganisms that have the ability for mitigating salinity stress condition through different mechanisms.

Temperature	Crop plants	Microorganisms	Mechanisms	Reference
Heat	Wheat	Pseudomonas putida	Phytohormone, HCN, ammonia, siderophore and P-solubilization, and accumulation of metabolites like proline, sugars, starch, amino acids, and proteins	[180]
Heat	Sorghum	Pseudomonas sp. AMK-P6	Induction of heat shock proteins and improved plant biochemical status	[66]
Low	Grapevine	Burkholderia phytofirmans PsJN	Synthesis of ACC-deaminase	[96]
Low	Canola	P. putida	Synthesis of ACC-deaminase	[95]

Table 7.

Some microorganisms that have the ability for mitigating temperature stress conditions through different mechanisms.

Water stress	plants	Microbes	Mechanisms	References
Flooding	Dragonblood (Pterocarpus officinalis)	AM fungi & Bradyrhizobium	Development of adv. roots, aerenchyma, and hyper trophied lenticels	[181]
Flooding	Tomato	Pseudomonas putida, Enterobacter cloacae	Synthesis of ACC-deaminase	[94]

Table 8.

List of some microorganisms that have the ability for mitigating flooding stress conditions through different mechanisms.

Heavy metal S	Crop plants	Microorganisms	Mechanisms	References
Cadmium and Iron toxicity	Hibiscus cannabinus	Enterobacter sp.	Metal immobilization Production:, IAA siderophore)	[182]
Lead toxicity	Sunflower	Pseudomonas gessardii, Pseudomonas fluorescens	Lead uptake (increase in APX, CAL, SOD, GR, and proline contents)	[183]
Arsenic toxicity	Rice	Achromobacter sp.	ACCD (Arsenic uptake)	[184]
Ni & Cd Toxicity	Tomato	Methylobacterium oryzae, Burkholderia sp	Reduced uptake and translocation	[100]
Metal toxicity	Chickpea	PGPR	Sequestration of metal ions	[185]

Table 9.

List of some microorganisms that have the ability for mitigating heavy metal stress conditions through different mechanisms

Finally, [192] have proved the duty of Trichoderma harzianum on alleviation of stress in different rice genotypes through adjustment of dehydrin, malonialdehyde and aquaporin, and genes parallel to several physiological traits. Rhizobacteria-promoted resistance to water deficit and resilience (RIDER) by altering the phytohormone levels, enzyme activities, defense-related proteins incorporation, antioxidant levels, and epoxypolysaccharide accumulation for plants. These strategies help plants to mitigate unfavorable conditions [122, 125]. Using stress tolerant microorganisms is a promising tool in improving the productivity of crop plants grown in stress-susceptible areas. Application of Trichoderma harzianum improved oil content in NaCl affected Indian mustard (Brassica juncea) via increasing the uptake of essential nutrients, promoting the accumulation of antioxidants and osmolytes, and decreasing NaCl uptake [67]. In addition to, up-regulation of monodehydroascorbate reductase in treated plants. It also alleviates salinity stress via accumulation of ACC-deaminase [193]. Moreover, inoculation of barley and oats, with Acinetobacter sp. and Pseudomonas sp. enhance the accumulation of IAA and ACC deaminase under saline soil [169].

7. Conclusion

Agriculture is the backbone of developed and particularly developing countries, with more than 60% of the population of the developing countries depending on it for their livelihood. Increasing food production to fulfill the needs of an increasing world population becomes of a major concern. Despite the necessity of doubling agricultural production, in terms of quantity and quality, to cope with the worsening increase in the global population and to meet the increasing humanitarian needs, the agricultural sector faces many abiotic and biotic stress conditions. Additionally, the great climate changes resulting from global warming lead to an increase in the negative impact of these stressors. Throughout this literature study, it is well established that the abiotic stress conditions (salinity, drought, high and low temperature, alkalinity, and organic and inorganic pollution have great side effects on plants (decreasing in plant growth and productivity, physiological changes, alteration in osmotic balance and ion cytotoxicity). Moreover, the side effects of abiotic stress conditions have been expected to be increased because of the bad or nonsustainable agricultural practices, water scarcity and reduced arable land, soil degradation, human activity, and the climate change (global warming of the planet). Hence, it has become a necessity to reduce the different causes behind the increasing abiotic stress conditions. On one hand, these can be achieved through good and sustainable agricultural practices such as agricultural rotation system, integrated crop management, integrated nutrient management, and integrated pest management re-mapping of agricultural map in the light of climate change, soil fertility, etc. On the other hand, in order to increase crop productivity, it becomes necessary to develop low-cost technologies for abiotic stress management. Soil microorganisms, surviving in the soil under extreme conditions, have shown high properties, which, if exploited can serve agriculture by increasing and maintaining crop productivity. Our literature study has indicated the paramount importance of these beneficial microorganisms in the mitigation of the negative consequences resulting from different abiotic stress conditions. Where, it is well established that beneficial soil microorganisms can promote growth and increase productivity through different mechanisms such as increasing the availability of essential nutrient elements and enhancement of their uptake, phyto-hormones production, ACC-deaminase production, biological control agents’ production, etc. Even though, more efforts should be given in this field like that, isolation and characterization worldwide benefit microbes from different biological niches and under various harsh conditions. Further researches will be required concerning the optimization of the mass production of these microorganisms, the best carrier that allow increasing the shelf life of beneficial microorganisms and par consequence increasing its storage ability, also, the better ways for its field application. The application of these beneficial microorganisms is still limited and how to increase their application rate should be taken into account.