Symbiosis under Abiotic Stress and Its Challenges

Abstract

Many abiotic factors have affected symbiosis effectiveness. However, the responses and interactions vary depending on the plant host, environmental factors, and symbiotic strains. The effect of various environmental factors on the competitiveness of rhizobial strains in host legumes has been examined, but many questions are still unresolved. For example, in the Rhizobia-legume symbiosis, the nitrogen fixation and nodulation processes are strongly related to the physiological state of the host plant. Therefore, a competitive and persistent rhizobial strain is not expected to express its total capacity for nitrogen fixation under limiting factors (e.g., salinity, unfavorable soil pH, nutrient deficiency, mineral toxicity, extreme temperatures, soil moisture problems, and inadequate photoperiods). Moreover, populations of rhizobial species vary in their tolerance to major environmental factors. Furthermore, this chapter emphasizes the studies on symbiosis under abiotic stress and its challenges. Additionally, this can help to understand and establish an effective biological process for improvement in agricultural productivity.

1. Introduction

In recent years, the effect of various environmental factors on the competitiveness of rhizobial strains for nodulation of host legumes has been examined. During the revision and search for an answer based on abiotic stress and symbiosis as the main topic, it was found that the progress of the studies has been advancing accordingly through the hard times for cultivation in different crops as time goes on. However, the type of manuscripts is based on 32.9% of published reviews of previous year’s studies and 6.1% of books. The remaining published articles were 61%, which indicated that the effect of various environmental factors on the cultivation plant host and their symbionts and the competitiveness of rhizobial strains with their host legumes had been examined (Figure 1). However, many questions still need to be solved, which is indicated by the low amount of studies based on the percentage of reported studies included in other such metabolism or mechanisms, inoculants, and interactions (Figure 1).

Figure 1.

Approximation of the total distribution of the main or critical topic of the studies during 2021 ~ 2022.

Furthermore, this chapter emphasizes the symbiosis under abiotic stress studies and its challenges. Additionally, this will help to lead future studies and to understand and establish an effective biological process for improving agricultural productivity or recovery of regions affected by contaminants, deforestations, or natural causes of losing their natural vegetation.

Foremost, the arid climate is characterized by hot, dry summers and cold winters, which limits the use of different species for soil revegetation [1, 2, 3, 4, 5]. Therefore, using native species for revegetation may be an interesting practice, especially in dry climatic conditions, where salinity and drought are often serious problems. About one-third of the world’s land area comprises arid and semiarid climates [2]. In the Rhizobium-legume symbiosis, the nitrogen fixation process is strongly related to the physiological state of the host plant. Therefore, a competitive and persistent rhizobial strain is not expected to express its total capacity for nitrogen fixation under limiting factors, such as salinity, unfavorable soil pH, nutrient deficiency, mineral toxicity, temperature extremes, insufficient or excessive soil moisture, inadequate photosynthesis, presence of other microorganisms in the rhizosphere [2, 3, 4, 5]. Several studies showed that the competition pattern between some strains might be affected by one or more factors mentioned above [2, 3, 4]. However, other factors, such as the host genotype, are also involved in determining the outcome of competition between strains of Rhizobium [3, 6] and, in recent years, between other rhizobia groups such as Microvirga, Paraburkholderia [7]. The most complex environments for rhizobia are marginal lands with low rainfall, extreme temperatures, acidic soils with low nutrient status, and poor water-holding capacity. Populations of rhizobial species vary in their tolerance to major environmental factors; consequently, screening for tolerant strains has been pursued (Figure 1, isolation). Biological processes (e.g., N₂-fixation) can improve agricultural productivity; however, minimizing soil loss and ameliorating adverse edaphic conditions are essential.

2. Symbiosis under different abiotic stress

In the years 2021 and 2022, approximately the main stress reported or described was salinity. In the revision, salinity stress was 22% of total studies reported (Figure 2, by Google Scholar as the main trusted tool of search), followed by metals such as Fe, Al, Ni, As, Cu, Cr, Cd, water-deficient or drought, and extreme temperature. In some cases, the combination of the interrelationship between several stresses was reported. Also, exceeding levels of pesticides and fertilizers were found in low percentages due to high dependence on utilization in crop production. The remaining studies are distributed between multiples stress which mean the combination of more than three kinds of abiotic stress, and other indicating different types of the main topic and collateral stress such as deficient of macro or micro-nutrients, the effect of manure of fertilization styles in combinations with symbionts under stress, individual strains studies for mechanisms, co-inoculations, and communities studies. Several of these abiotic stress mentioned will be described more deeply in the following sections.

Figure 2.

Distribution of the according to the type of abiotic stress described in 2021–2022.

2.1 Temperature tolerance

The temperature stress should be reported as high and low temperatures (or cold stress). First, the main report is the high temperature, which can cause different types of damage in the plant host, so reported as atmospheric or soil temperatures could be on good point from the new studies. Then, the soil temperature is a major problem for biological nitrogen fixation by legume crops [2, 3, 8, 9]. High root temperatures strongly affect rhizobia infection and N₂ fixation in several legumes, including soybean, peanut, cowpea, and beans [2, 3]. Critical temperatures reported for N₂-fixation are 30°C for Trifolium (clover) and Pisum (pea) species, and other crops such as soybean (Glycine max), peanut (Arachis sp.), Vigna sp. (cowpea, mungbean) are range between 35 and 40°C [10]. The optimal temperature for nodule functioning in common beans (Phaseolus sp.) is between 25 and 30°C and is vulnerable to soil temperatures around 30 and 33°C [11]. In addition, temperature affects root hair infection, cell differentiation, nodule structure, and the functioning of the root nodule [2]. For most rhizobia, the optimum temperature range for growth in culture is 28 to 31°C, but unable to grow at 37°C [12]. However, many rhizobial isolates have been recently described as heat-tolerant bacteria. For instance, Wei et al. [13] reported a temperature-tolerant strain of Mesorhizobium at 35°C. Furthermore, Bansal et al. [14] isolated rhizobia from Vigna radiata, and the isolates showed good growth at high temperatures.

High temperatures affect the plasmids’ transmission or induce large deletions and can result in modified modulation performance [15]. The large population of nodulation plasmids in soils could be seriously affected by high temperatures and the long-term effectiveness of rhizobia as a symbiont [2, 15]. Therefore, natural genetic tolerance is necessary, and their interaction with other symbionts could lead to plasmid replications and improve rhizobia’s performance in high temperatures. On the other hand, studies reported that exogenous melatonin and Rhizobium inoculation attenuated injuries and reduced plant oxidative damage [9]. The symbiotic relationship naturally establishes a balance between plant-symbiont under heat or cold stress; it would induce changes in the gene expressions related to cold or heat stress, affecting the oxidative stress in ROS production [9, 16, 17].

The temperature affects the response of both the roots and the shoots. However, the root temperature is more critical for symbiosis than the shoot temperature due to survival in soil by all rhizobia strains. Root hair formation is limited in some legume species, binding between symbiont and root cells, formation of infection threads, nodule initiation and growth, leghemoglobin content, and nitrogenase activity decreased [2, 8, 9]. As a consequence, low nitrogen fixation and low biomass.

For further inoculation, one possible solution is rhizobia coated with appropriate host lectin or suitable rhizobia to improve their symbiosis or interactions under extreme conditions [2, 3]. However, rhizobia as mass production and conservation pre-inoculation affect the effectiveness of the symbiosis such as low temperature 4°C conservation and inoculation in high temperatures such as >35°C leads to low effectiveness and weak competitiveness in front of native rhizobacteria [3, 16, 17].

Some studies suggest conserving after mass production inoculants at 25°C to apply in >35°C soil conditions; then, for cold or perm-frost soils, pre-cultivation in low temperatures should be better for applying in the field [3, 16, 17]. Cold stress is evidenced in soil and plants and affects the bacterial communities’ richness and diversity and their enzymatic activities or interactions with their hosts [16]. However, denitrifying bacteria may have a different mechanism to adapt to low temperatures [16, 17]. Some studies reported that cold stress could increase the production of exopolysaccharide (EPS), indirectly affecting cell survival by increasing cell density and biofilm production, and maybe some quorum sense [17, 18].

2.2 Moisture deficiency and drought

In the legume-rhizobia, the symbiotic nitrogen fixation is highly sensitive to drought, which results in decreased N accumulation and yield of legume crops. Both establishment and activity of the legume-Rhizobium symbiosis are extremely sensitive to drought stress [19, 20]. Moisture deficiency and drought are closely related to the occurrence of rhizobial populations in desert soils, and the effective nodulation of legumes growing [1, 21] emphasizes that rhizobia can exist in soils with limiting moisture levels. However, population densities tend to be low under the most desiccated conditions and to increase as the moisture stress is relieved [2]. It is well known that some free-living rhizobia (saprophytic) can survive under drought stress or low water potential [22]. In contrast, most legume crops are sensitive to drought stress.

The symbiotic association between rhizobia and legumes is also sensitive to soil water deficiency. The responses of root nodule bacteria to water stress have been widely investigated. For example, mild water stress reduces only the number of root nodules formed on soybean, while moderate and severe water stress reduces both the number and size of nodules; it is made by culturing some species in dry conditions and after inoculation and measuring water vapor exchange and others. [1, 2, 23, 24]. Rhizobium-legume symbioses are currently the most important nitrogen-fixing systems, which may potentially increase N input in arid lands. The leguminous plants include species or varieties that are extremely well adapted to the harsh conditions of arid lands. For example, Medicago sativa, Arachis hypogaea, Cyamposis tetragonoloba, and Melilotus spp.; these legumes are known to be adapted to conditions prevailing in arid regions.

Moreover, naturally occurring forage legumes (annuals and perennials) are well nodulated with antibiotic-resistant rhizobia, and their root nodules are active in fixing N₂ [2, 24]. These legumes can be found in deserts or cultivated lands as wild plants. Therefore, isolating effective rhizobia from those wild legumes to inoculate other legume crops is a new strategy to improve the efficiency of the Rhizobium-legume symbiosis in soil with moisture deficiency [3].

The rhizobia of wild legumes may have better traits than those of cultivated legumes and can contain a marker such as antibiotic resistance and their correlation with drought tolerance [24]. When rhizobial strains are inoculated into media containing an antibiotic, a few cells may exhibit resistance because of spontaneous genetic changes or mutations. The resistance of a rhizobial strain to an antibiotic is a useful marker for keeping track of the stress-tolerance, and every antibiotic has its mechanism of action for resistance [25, 26]. In addition, resistance cells will grow on the antibiotic media, and other bacteria will be suppressed in the field. Thus, it is important that antibiotic-resistant strains, which are selected for inoculation experiments, must not lose their infectiveness (ability to form nodules) nor their effectiveness (ability to fix nitrogen) in the symbiosis with the host plant. The resistance should be stable throughout infection, nodulation, nitrogen fixation, and subsequent re-isolation [24, 25, 26].

Drought is more likely to affect the growth and more severe if the soil profile has water limitation; the pore size of soil and its distribution that is unfavorable to water retention at the potential in the available range is most likely to become a severe drought such as Entisols [3, 8]; this condition impedes the root extension, water, and gas movement. They can aggravate the restriction in the symbiosis by limiting the movement of rhizobia and the root hair extensions and lead the poor communication between symbiont and host [8]. The long dry season can only be met through a continued search for drought-tolerant genotypes of host or symbiotic microorganisms that could provide forage for a long period as the possible and maximum nutritive value in dry conditions. However, a wide range of conditions, developing somewhat comparable intimacy with other plants, such as grass/legume mixtures balances, are indeed needed [3].

Recently, many reports have described the positive effect of using symbionts or rhizobacteria in plants. From the viewpoint of the symbiont, a common example is Bradyrhizobium japonicum, whose cells resist dehydration by decreasing energy consumption and increasing carbon accumulation, especially by up-regulating the genes involved in trehalose synthesis. When it rehydrated, the signaling downstream restarted [27]. More deeply, it is the exopolysaccharide (EPS, extracellular polymeric substance) and the production of biofilms protecting the cells. In this way, indirectly, the survival of symbionts and their releasing compounds, as mentioned, helps the plant cell endurance through accumulation and signaling for the synthesis of osmoprotectants such as trehalose, glycine, and flavonoids, as well increasing the plant-microbe communication [27, 28].

Climate change has harsh effects on plant growth and yield. In plants, the reactive oxygen species (ROS) generation, at the same time, decreases the plant defense system and other over-activating the dependent Fe-, Ca-enzymatic system, which leads to high energy production and utilization to end in oxidative damage cells or cell necrosis or death [28]. Lectins and recognition, no nodulation, specificity in nodulation, strains selection from the host side, enzymatic process affected by temperature, and toxic seed substances [3]. There are reports describing that ROS can be positively affected through rhizobia application by producing flavonoids necessary for plant-rhizobia communication and affecting some gene expression generating a plant response such as salicylic acid (SA) production and ROS mediation in the pathway like ROS-detoxification and avoiding ROS-homeostasis [29]. In addition, fixation-N₂ and chlorophyll content increase in the plant naturally, which could allow decreasing the irrigation time or amount of water calculated to apply in the field and even decrease the inorganic fertilizers used for cultivation.

Furthermore, the most neglected system or lacks of deep research is common in southern areas worldwide due to the small-scale crop farmer support or budget deficit for researchers to continue their studies [28]. Many of these reasons and other leads to farmers adding inorganic fertilizers affecting direct or indirect rhizobia communities and their interactions or symbiosis, besides that the high application of inorganic compounds affecting human and animal health [3], and the accumulation of these inorganic compounds leads to other problems described in next sections. Thus, understanding the inorganic compound application and nutrient supply economy is needed from a basic point of view. We can comprehend the biological role of legumes and their symbiosis in the context of soil nutrient transformations, both from the host view and symbiotic microbe sight.

2.3 Salinity stress

Salinity is a serious agricultural threat in different countries, principally in arid and semiarid regions. Nearly 40% of the world’s land surface has potential salinity problems [30]. Most of these areas are part of the Mediterranean and tropical regions [30]. As with most cultivated crops, the salinity response of legumes varies greatly and depends on climatic conditions, soil properties, and the growth stage. Legumes such as Vicia faba (broad or fava bean), P. vulgaris (common beans), and G. max (soybean) have been reported to be more salt tolerant than others, such as P. sativum (peas). Other legumes as Prosopis, Acacia, and Medicago sativa [2, 31, 32, 33], are salt tolerant, but those legumes are more susceptible to salt than their rhizobia.

The legume-Rhizobium symbioses and nodule formation on legumes are more sensitive to salt or osmotic stress than the rhizobia. For example, soybean showed little curling or deformation when inoculated with Bradyrhizobium japonicum in 170 mM NaCl, and nodulation was completely suppressed by 210 mM NaCl [2]. Salt stress had a negative effect on N₂ fixation by legumes, which is directly correlated to the decay of biomass and N content in the shoot induced by salt. The salt-induced distortions in nodule structure could also be the reason for the decline in the N₂-fixation rate by legumes subjected to salt stress. The reduction of photosynthetic activity might also affect the N₂ fixation under salt stress [2, 33]. Although the root nodule-colonizing bacteria are more salt tolerant than their legume hosts, they show marked variation in salt tolerance [2, 3, 33, 34]. Strains of Rhizobium leguminosarum have been reported to be tolerant to NaCl concentrations up to 350 mM NaCl in broth culture [34]. Thus, the rhizobia isolated from soybean and chickpea (Cicer sp.) were fast-growing tolerant strains, and the slow-growing rhizobia were sensitive at 340 mM NaCl [35]. Rhizobium strains from Vigna unguiculata were tolerant to NaCl up to 5.5%, equivalent to about 450 mM NaCl [36]. It has been found that slow-growing peanut rhizobia are more susceptible than fast-growing rhizobia [2]. Rhizobia from woody legumes also showed substantial salt tolerance: strains from Acacia, Prosopis, and Leucaena are tolerant to 500 to 850 mM NaCl [2, 3, 37, 38].

Successful Rhizobium-legume symbioses under salt stress require the selection of salt-tolerant rhizobia indigenous to saline soils. These salt-tolerant rhizobia usually show morphological and metabolic changes and structural modifications to cope with and adapt to salt stress. Effective salt-tolerant rhizobia were isolated from non-saline as well as saline environments. Recent reports support the finding that some rhizobia have the potential to form a successful symbiosis with legumes under salt stress, e.g., Rhizobium tropici, Sinorhizobium sp. [39, 40].

The salinity stress is closely related in soils from excessive natural accumulation or inorganic compound applications. The main salts are sodium-related compounds such as sodium chloride (NaCl), sodium nitrate (NaNO₃), sodium sulfate (Na₂SO₄), sodium carbonates (NaHCO₃, Na₂CO₃), and sulfate-related compounds such as potassium sulfate (K₂SO₄), calcium sulfate (CaSO₄), magnesium sulfate (MgSO₄) and other salts [3, 38]; the symbionts like rhizobia helps to increase the tolerance through releasing metabolites or compounds such as plant-hormones (auxins, gibberellins, cytokinins), organic acids such as succinic acid and SA [38, 41, 42, 43]. In addition, EPS accumulation helps the symbiont survival and the communication between microbe-microbe and microbe-host. These EPS indirectly helps to improve the soil structure and help the plant cell’s osmotic balance and ion homeostasis. Many reports show that B. japonicum may involve the up-regulated expression of NH₄, NO₃, Na^+, and Cl⁻ transporter-related genes in rhizobia and their host [41]. For Ensifer, it has been reported similar to B. japonicum in the trehalose synthesis for increased salt tolerance. In addition, regulation of methionine and inositol metabolisms [43]. In the case of other rhizobia, it has been found that flavonoid-accumulation improves the interaction under salinity stress, and these flavonoids could be salt-depend or salt-independent induction; then, the host-interaction continuing under salt stress due to the nodulation is not flavonoid-depend in some nod genes like happen in R. tropici CIA899 [38]. Thus, for the mitigation of salt stress, salt-tolerance rhizobia are necessary.

Rhizobia tolerate much higher salt concentrations than agricultural plants, selection for tolerance would be useful only to eliminate the sensitive strains [8]. Studies of coastal land areas will be useful to understand the capabilities of those strains and the mechanisms for their tolerance and their symbiosis under these conditions, as commonly happened in rice cultivated in coastal areas in Asian countries.

2.4 Alkaline pH stress

The case of alkaline pH is mainly from soil conditions and is another of the major problems affecting crop yield in arid and semiarid regions, especially in the tropics and the Mediterranean regions. Alkalinity appears to be the more severe, though less frequent, stress for legumes, and it goes in hand with salinity stress.

Most leguminous plants require a neutral or slightly acidic soil for growth, especially when they depend on symbiotic N₂ fixation. Legumes and their rhizobia exhibit varying responses to soil alkalinity. Legumes like alfalfa usually show growth restriction when the pH is below 5.5–6 or more than 8. On the other hand, the rhizobial species appear more tolerant to alkaline pH than their legume hosts [2]. For instance, some isolates from Argyrolobium uniflorum (a legume plant commonly found in Tunisian arid regions) belonging to Ensifer genera showed an alkali-tolerance tendency probably related to the basic pH that characterizes most soils in arid regions of Tunisia [44].

Similarly, some other isolates from Genista saharae (a spontaneous legume shrub found in Sahara) showed tolerance to pH 12 [44]. The Rhizobium-legume symbiosis is superior to other N₂-fixing systems concerning N₂-fixing potential and adaptation to severe conditions. Several symbiotic systems involving stress-tolerant partners (rhizobia and legumes) have been characterized [45]. These associations might have sufficient traits necessary to establish successful growth and N₂ fixation under the conditions prevailing in arid regions. Most of the reports indicated that those rhizobial strains isolated from alkaline conditions or alkali soils showed the best response under alkaline stress [45, 46, 47], and their mechanism to improve the tolerance during the symbiosis process is similar, or kind of related to salinity-stress reported up to date [41, 42, 43, 45, 46, 47]. The existence of Rhizobium-legume symbioses, which can fix the appreciable amount of N₂ under arid conditions, is fascinating. These symbioses represent the best source of the “ideal” fertilizer in arid regions and therefore command great interest as a subject of future research.

2.5 Acid soils

Soil acidity is associated with infertility and mineral toxicities and is a major constraint to agricultural production in several parts of the world. Acid soils are distributed over extensive areas, especially in tropical and subtropical soils such as Venezuela and Brazil [2, 3, 4, 5, 6, 48]. Acid soil infertility can be caused by toxic levels of hydrogen, Al, and Mg, as deficiencies of phosphorous and other minerals [8, 49]. These infertility factors have been shown to affect symbiotic nitrogen fixation through their effects on any stage of the symbiosis [2, 4, 8]. Soil acidity is an important factor in restricting the occurrence of rhizobia in soils, although there is considerable species variability in the degree of acid tolerance [6, 8]. An evaluation of Rhizobium meliloti indicated that the competitiveness of some of the strains was affected by soil acidity [6, 8]. In the case of B. japonicum associated with Glycine max and other crops were examined and selected for growth and survived in acid soil, also selected in vitro for being acid, Al, and Mn-tolerant [50]. Other cases, such as R. tropici and R. leguminosarum isolated from Amazonian soils, could survive and show high efficiency in nodulating P. vulgaris in acid soil with Al [45, 48, 51, 52]. Other authors showed that R. tropici can tolerate until 4% of Al concentration in vitro [48, 52]. The infection of legume root hairs by rhizobia included acid-sensitive steps, with infections significantly reduced below pH [8, 51, 52], a level of H⁺ that is common in acid soils. Studies about acid instability could affect root hair infection and lead to lectin binding proprieties affected.

Soil acidity is often associated with Al and Mn toxicity and Ca deficiency, as explained in the section below. All disorders are corrected by liming in traditional cropping. The symbiosis is affected by stooping rhizobia growth, nodule initiation, impairing nodule function, and slowing the plant’s growth. In this section, the importance of tolerance strain and the genetics of the host are key points. The plant’s sensitivity may cause symbiotic failure more often than the literature suggests; still, if there are acid tolerance rhizobia in an adequate amount, the acidity could inhibit the nodule imitation from the plant side [51, 52]. Some of the common acids responsible are carbonic, sulfuric, and nitric acids which generate by oxidation of another process.

2.6 Metals toxicity and tolerance

Many metals are commonly found in nature, though high amounts of metals and toxic elements have low mobility. Furthermore, they are a problem due to their low availability causing different kinds of problems, and sometimes it is necessary to remove them from the soil, water, and air. In this way, plants are the best way used until now; however, the beneficial organisms help the plants to grow and help the high biosorption or limiting their uptake. In this order, we can easily understand the negative effects of metal, and we can divide this chapter into heavy and light metals. Light metals with a low density are commonly found and used; their high accumulation or interaction with other factors is highly toxic, such as Aluminum (Al), Magnesium (Mg), Titanium (Ti), and copper (Cu). In contrast, heavy metals have high density, are less common, and are used in low amounts and their interactions are highly toxic such as Chromo (Cr), Cobalt (Co), Nickel (Ni), Zn (Zinc), Lead (Pb), Cadmium (Cd), Manganese (Mn), Arsenic (As). Furthermore, using microbes-plants metal tolerant can be worth applying in fields and therefore be crucial to promote detoxification, survival, or bioremediation of contaminated soil. However, their symbiosis or interaction is poorly investigated and reported leading to a lack of understanding and underestimation.

In this order, Al is the most abundant metal, becomes more soluble as acidity increases, and is often the major toxic element in acidic soils and water. Many hypotheses have been proposed for the mechanism of Al toxicity in animals and plants [52, 53, 54, 55]. However, Al-microorganism interactions have been receiving attention in recent years. Previous work on rhizobia has investigated direct and indirect mechanisms of Al-toxicity [53, 54, 55]. It has been shown that Rhizobium cells suggest that the repair mechanism used to overcome damage by Al to DNA in tolerant cells is quite different from that in sensitive cells, indicating that DNA is a possible site of action of Al in the common soil bacterium as Rhizobium [53]; this is an important factor for ecological applications. Many experiments demonstrated that using acid and Al-tolerant nitrogen-fixing bacteria is one alternative way to increase productivity in the field [53, 54, 55]. For example, soybean inoculated with B. japonicum strain BJ11 increased the production under acid-aluminum soil (pH 5.0–5.5) [56].

Al-toxicity is a major problem affecting soil fertility, microbial diversity, and nutrient uptake of plants. Rhizobia response and legume interaction under Al conditions are still unknown [54], and it is important to understand how to develop and improve legume cultivation under Al stress [55]. The rhizobia response was recorded under different Al concentrations, with decreasing rhizobial cell numbers as Al concentration increased. However, induced Al tolerance considerably depended on rhizobia types and their origins [53, 54, 55]. Accordingly, organic acids, biofilm, plant hormones, and EPS were correlated with growth rate, cell density, and improvement in plant growth [53, 54, 55, 56, 57]. Previous studies indicated that citric acid, GABA, and biofilm production might be a positive selective force for Al-tolerance in rhizobia tolerance [53, 57]. In addition, Al-toxicity delayed and interrupted the plant-rhizobia interaction. The effect was more pronounced under acidic conditions Bradyrhizobium, Paraburkholderia, and Rhizobium have been reported that significantly improve plant growth under acid-Al stress in combination with high Al concentration with soybean, alfalfa, and common bean and established an effective interaction, nodulation and N₂-fixation [54, 55, 56, 57]. Moreover, metabolic pathways have still been little known under Al-stress.

Al-toxicity limits plant production worldwide, particularly in acidic soils. In the Americas, 70% of tropical soils experience limitations related to acidic soil, Al- and Mn-toxicity, and the deficiency of other elements such as Ca, Mg, and P [48]. Thus, many types of plants are affected by different metal concentrations in soils. Furthermore, Al and low pH disrupt plants’ pathways and physiological functions, such as root elongation, root hair formation, and nutrient uptake (e.g., K, Ca, N) [58, 59]. The main symptom of Al-toxicity is the inhibition of root growth in the plant.

Moreover, Al can disrupt many other functions, including root hair elongation and nutrient uptake (especially Ca and K). Al can induce oxidative stress, disrupt cytoskeleton and apoplastic processes, and affect intracellular transport [60]. In previous studies, tolerance mechanisms were distinguished from resistance mechanisms. Exclusion mechanisms were predicted to depend on transport systems that export Al from the symplast or exudate ligands that bind Al and limit its uptake into the cytosol [60, 61]. In addition, Al and Mn toxicity are important inhibitors of the growth of rhizobia in soils; as mentioned before, this is truly affected by soil pH, and the Al toxicity has been found to stop legume growth in acid soils without inducing nodulation or by N starvation [51]. In some cases, Al toxicity happens because the Al is immobilized in humic chelates, such as in Histosols. In Mn, toxicity is more common in acid soil, where temporary or local anoxia results from wetness, high organic matter, impeding layers, or well-drained soils such as Oxisols [3, 8, 60, 61, 62].

Furthermore, heavy metals are important inorganic pollutants in recent years, such as Cu, Ni, Cd, Zn, Cr, and Pb. The studies of symbiosis with these heavy metals are more limited than light metals, mainly focused on Rhizobium and Ensifer species [60, 61, 62, 63, 64, 65, 66, 67]. Some studies indicate that the combination of Rhizobium and arbuscular mycorrhizal fungi (AM) induces plant tolerance under As stress [63]. Others showed that in Ni, Cu, Cr, Cd, and Zn, the symbiont tolerance varies according to the metal type, but the strain alleviates the effect of heavy metals in soybean [64]. Some Rhizobium species can nodulate species of Phaseolus, Trifolium, and Vicia under normal conditions but also can improve the seed germination, biomass, and chlorophyll content in these species under Cd-stress, and their response level depend more on the genotype of the plant associated with these rhizobia. For example, the application of R. leguminosarum and Rhizobium larrymoorei helps to decrease the negative effect on other crops, such as wheat [65] and rice [66]. The way these Rhizobium species survive under Cd-stress could be due to the glutathione accumulation, proline metabolic pathways, and its plant interaction could improve because of the accumulation of several compounds such as antioxidants and putrescine protecting the plant cell besides auxins production, N₂ fixation, and others [65, 66].

What we know about natural symbiosis under heavy metals stress is the induction or improvement of plant growth, protection of plant cells received from symbiont, pigment recovery, and increasing chlorophyll content and N₂ fixation. On the other hand, from a symbiont point of view is the high production of glutathione compounds, proline, antioxidants, biofilms, and EPS that help protect cells [67]. However, the further natural interactions and the mechanism or pathways are still unknown compared to non-symbiotic rhizobacteria.

2.7 Pesticides stress

Modern agricultural practices depended on agrochemicals, such as pesticides, for crop production. Pesticides, including herbicides, insecticides, and fungicides, are heavily utilized for high quantity and quality crop yield and reduce labor and energy input in crop production [68]. However, pesticide accumulation in the soil beyond the recommended levels due to repeated application or slow degradation process poses a threat to the environment. It affects the plant host by altering the root architecture, a number of root sites for infection, and the transformation of compounds for plant uptake, such as converting ammonia into nitrates [69]. On the other hand, it also influences the growth and activity of soil microbial communities such as free-living and endophytic nitrogen-fixing bacteria [70]. In particular, rhizobia are more susceptible to fungicides, herbicides, and then insecticides [71]. Fungicides such as captan and thiram significantly reduced survival and altered the phenotypic characteristics of Rhizobium leguminosarum bv. viceae [72]. Also, the legume nodulation and growth were affected at the highest concentration of captan. Similarly, chickpea seeds treated with captan or arrest decreased the number of viable Rhizobium ciceri, nodule dry weight, and nitrogen fixation [73]. On the other hand, Moorman [74] reported the direct effect of herbicide on the rhizobial symbiont and exerted indirect effects on the host legume. In parallel, herbicides had adverse effects on the nodulation and nitrogen fixation of peas inoculated with Rhizobium leguminosarum, not due to its influence on the rhizobia itself but on the host plant [75]. Lastly, insecticides, including methyl parathion and dichloro-diphenyl-trichloroethane (DDT), perhaps disrupt phytochemicals from alfalfa and nodD receptors of Sinorhizobium meliloti as the mechanism of action. Consequently, it significantly delays the specific timing and initiation of signals necessary for efficient symbiotic nitrogen fixation [76, 77]. On these accounts, abnormal concentrations of pesticides negatively impacted the legume-rhizobia symbiosis and disrupted the nitrogen fixation, leading to a decrease in plant yield. Although extensive studies on the effect of pesticides on legume-rhizobia symbiosis it is still limited to in vitro and greenhouse conditions. Studies regarding it under field conditions are scanty; thus, it is important to investigate and characterize rhizobia that can be employed in the field, considering the increasing pesticide residues currently.

2.8 Others

On a global scale, there are climate changes such as acid soils and long dry seasons; in tropical countries, mainly the soil type affected by infertility are Oxisols and Ultisols [3]. Their attendant problems include deficient or unavailable nutrients such as P, K, S, Ca, Mg, Zn, Mo, Bo, and Cu. Unfortunately, this is not the main topic in this chapter, but it is important to mention that the interaction between these essential life elements, whether with the host or symbiont, is also relevant. Accordingly, the research priorities have been done according to crop consumptions and their improvement in the field, subsequently with selection and, later, breeding of tolerant genotypes of legumes, a clearer definition of mineral nutrient requirements. Several reports described that the deficiency in nutrients in soils or environmental growth conditions of hosts or symbionts negatively affected the tolerance to different stress. For example, the improvement of Bo in media through the growth conditions of Ensifer meliloti leads the cell to increase the tolerance to salinity [78], and other studies state similar significance with other elements [3, 9, 48, 59].

3. Conclusions and future perspectives

In conclusion, many rhizobia can be classified into relatively tolerant and sensitive isolates to different stress conditions, suggesting the application of these isolates as effective inoculants to different legumes to obtain effective inoculants in environments with abiotic stress influence. Interestingly, the distribution of resistant or tolerant rhizobia to different abiotic stress is closely related to environmental conditions of their climate soil origins, mainly for salinity, temperature, and metal stress. Therefore, many studies suggested finding suitable inoculants with multi-tolerance for legumes; those strains must be isolated in the problematic areas where they will be applied. Research into these areas is currently underway in several research groups worldwide, and it is expected that this research will provide beneficial outcomes resulting in improved sustainability and productivity in agricultural systems. However, Tropical zones remain the most difficult zones to undertake studies of soil microorganisms. It has been suggested that tropical symbionts and wild hosts are poorly documented, although reports indicate that rhizobia diversity may be greater in tropical than in temperate regions. However, the communities’ interactions are still unknown in both tropical and temperate.

Many challenges need to be addressed for future studies as the expansion of worldwide distributed legumes is needed under different countries’ conditions, for example, beach bean, Mimosa species, and other non-common species, due to their capacity to adapt to each country’s conditions and their specificity or promiscuous symbiont and their pathways of survival or plant interaction, which can lead to the key for understanding the tolerance-mechanism under stress. Furthermore, there is a large number of rhizobia reported, but 98% of the well-described symbionts fall into the alpha-proteobacteria group during these revisions. Many rhizobia have been isolated, but their response under abiotic stress are unclarified such as Paraburkholderia, Microvirga, Phyllobacterium, Azorhizobium, Allorhizobium, and Cupriavidus.

As well as further studies are needed to screen isolates resistant to other compounds such as mercury (Hg), lithium (Li), and non-renewable elements commonly used in the new decade, and it is increasing their negative effect in crops such as soybean and other legumes, as a consequence of the revision of the articles published in 2021–2022. Last but not least, there are further studies in field conditions because 92% of the recent studies are only incubator or greenhouse experiments, and less than 20% of these studies used soil from field areas or in problematic areas. Furthermore, the studies of communities’ interactions can improve understanding of the changes in the enzymatic process and cycles, which can be done with new techniques such as qPCR, Next Generation Sequencing analysis (NGS), metagenomics, and metabolomics analysis. Also, the improvement of studies in another host, not only main crops such as soybean, which have been proven by the reports of symbionts applied in a non-natural host such as rice, wheat, and tomato under abiotic stress, showed improvement in the tolerance or crop production.

The symbiosis in legumes is well documented but poorly understood and known by farmers, principally in natural conditions or with wild legumes or strains. Also, many reports try to describe diversity, and many do not focus on communities or populations level. For example, a large number of studies involve soybean in which its focus from the host view as nodulation controlled by this legume. These reflect a delay in the onset of competition for energy and nutrients between the host-microbe, microbe-microbe, microbe-host-symbiont, and environment-host-microbe. Unfortunately, increasing studies on legume-rhizobia symbiosis are necessary; however, there is slow progress in detailed studies in situ, especially in the tropics. In addition, to develop sustainable agriculture in different ecological conditions, we need to obtain information on beneficial soil microorganisms showing nutrient accumulation, plant growth promoting, mobilizing potassium, phosphorous or iron, and nitrogen-fixing abilities associated with different legumes. New approaches are indeed needed to elucidate the mechanisms of different compounds production from symbionts, the host interactions with more than one symbiont per host or other rhizobacteria that interact in soils; these studies can be done through the research of the synergy microbe-plant, microbe-microbe, symbiont-plant-microbe. Also, the co-inoculation technology between symbionts, or symbiont and non-symbiotic bacteria, need to be investigated under different plant host.

It is necessary to strongly advocate and establish worldwide the application of natural symbionts in the field to mitigate climate change and abiotic stress as well as increase crop production globally and sustainably. In this order, the scientific work will be synergic and not need to become dead research. The global population is rapidly increasing, necessitating an increase in eco-friendly production. Climate change and its effects will be exacerbated in the coming decades, threatening plant and symbionts’ survival, causing negative changes such as lower growth, low yield, and more susceptibility to damage and diseases from plants. Governments and national and international agencies need to promote the utilization of biofertilizers, bio-compounds, and other eco-friendly alternatives for crop improvement and protect soil, also showing the farmers and consumers the benefits of its natural-based compounds from natural-symbiosis relationships. It is important to display that natural symbiosis and its interactions with the soil microbiome can protect plants from abiotic stress and improve plant health and soil fertility. Soil is the base for a non-ending game of dynamic and synergic between plants and microbes (not only their symbionts). As a result of their relationship, the plant microbes establish their symbiosis or interactions, and through time under different changes, including abiotic stresses, they co-exist and co-evolve for a better future.

Acknowledgments

We are grateful to Beijing Forestry University, the University of the Ryukyus, the University of the Philippines, and their staff for their kind support in accessing many kinds of literature.

Conflict of interest

The authors declare no conflict of interest.

Notes/thanks/other declarations

We thank Dr. Zhang Haolin for the support and revision in general of this manuscript. Also, Nika Karamatic from IntechOpen for her kind support throughout the process.