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CHAPTER 4

Signalome: Communication between crops and microbiomes 4.1 Signaling in the microbiome Rhizosphere signaling studies have focused on closely interacting plants with symbiotic microorganisms. However, this focus is likely to be extended to other microorganisms as the rhizomicrobiome is important for plant health and influences the structure of the microbial community. Rhizomicrobiome shaping is divided into three classes: (i) from plant to microorganism, (ii) between microbes, and (iii) from microorganism to plants with regard to signaling. Different organisms in soil, including the plant, receive signals. The key role of mycorrhizal-and rhizobial interkingdom signals in the formation of associations has been revealed and the recent discovery of signage by nonsymbiotic microorganisms shows that communication is an important part in the forming of rhizomicrobiome [1]. With secretion and detection of signals compounds, the plant and the rhizomicrobiome have strong influence on each other [1–5]. Signals have mainly been investigated between plants and rhizosphere microorganisms in intimate symbiosis, including mycorrhizal and rhizobial fungi. This is now obvious, as well as the nonsymbiotic microorganisms, as a more widely spread phenomenon. The rhizomicrobiome is a very rich and complex microbial community that is signaled both within and between species. The plant signaling molecules include flavonoids, strigolactones, monomers, or some low molecular compounds. Microorganisms generate signals, mainly via a process called priming, affecting plant growth and inducing systemic resilience in plants [4–12]. Microorganisms, which are known as phytomicrobiome, including bacteria, archaea and fungi, colonize almost every part of the plant. Microorganisms are a key plant component that is often host-complicated and the plant is considered a metaorganism [3]. Over the past few decades, it has been learnt that plants and microbes can communicate through molecular signals, as is well established for legume rhizobic syndrome or for mycorrhizal associations. Quorum sensing and other mechanisms communicate bacteria in the phytomicrobiome. Plants are also able to detect and activate Sustainable Agriculture: Advances in Plant Metabolome and Microbiome https://doi.org/10.1016/B978-0-12-817109-7.00004-3

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pathogen-reaction systems for materials produced by potential pathogens. This intercommunication dictates the development, architecture, and productivity of plants [5]. Close relationships are now evident and established over decades between all higher organisms and the microbial community. The microbial communities associated with plants must also be examined detailing the role of human microbiome in human metabolism and health. Since the plants colonized the ground about 0.5 billion years ago [1], plants have been associated with the microbiome, and more plants have developed intimate, complex, subtle and relatively constant relations with a series of phytomicrobiomas. The phytomicrobiome genomes expand the plant’s genetic repertoire. Microbes are linked to every plant structure, but the roots are always in touch with wet, microbe-packed soils in general and are, therefore, associated with the highest number of microbes. A fossils showing mycorrhizae relations from almost 400 million years ago [2–4] is the earliest indication of plant-microbe interactions. This association has resulted in the redefinition of Karl August Mobius’ concept of biocenosis into the concept holobiont [3–5]. This increase in agricultural productivity must be obtained from existing arable soil and water in harsher climate conditions. Furthermore, we need to protect our agriculture from pests and pathogens new, emerging, and endemic. The most effective approach for sustainable improvement of farm productivity and food quality is proposed for the harnessing of natural resources including phytomicrobiome, and it could also encourage constructive environmental and social outcomes [7]. The excessive and indiscriminate use of agrichemicals has resulted in contamination of food, negative effects on the environment, and resistance to disease, which together has a significant impact on human health and food safety. This environmental impact can be minimized through microbiome technology and at the same time the quality and quantity of agricultural products with less resource-based inputs can sustainably be improved [5, 9]. Plants and associated microbiota have evolved together and have developed a reciprocal relationship for all. However, this association was inadvertently broken up by plant breeding programs, which caused the loss of key beneficial members of the plant microbiome [2]. The regulatory activity of the plant is through the availability of metabolites; however, signals between the plants and members of their phytomicrobiome are also becoming increasingly evident. In phytomicrobiome activity, for example, quorum sensing [2, 4] and other less well characterized signaling systems [5] are also regulated by the signaling system [2]. Like establishing specific plant

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phytomicrobiomas such as willows, they can better tolerate soil contamination and thus make phytoremediation more effective [6, 7]. Certain soil nutrients such as P and Zn, and some microbes are relatively immobile. AMF enables these nutrients to be uptaken by increasing their effective root surface. Similarly, the mobilization of plant nutrients by other microbes uses chelators and other molecular procedures. The N-fixation in the atmosphere is another key role of the phytomicrobiome. The nutrients of N are the major plant nutrient, but are very mobile in soils and can be depleted quickly. Furthermore, the use of the plant microbiome is obviously capable of revolutionizing agriculture and the food industry by: • combining crop health with better management practices to develop productivity and quality for specific climatic conditions; • use of environmentally friendly pest and pathogens control methods to lessen the use of chemical pesticides with environmental and health consequences; • consideration of more intelligent and effective methods of using natural resources; • making food with less chemical contamination and improved quality; and • minimizing losses by improving crop fitness in severe conditions [8–11]. Plants also detect potential pathogenic materials and activate pathogen response systems. This interconnection dictates the development, architecture, and productivity aspects of the plant. Comprehension by biochemical, genomic, proteomic, and metabolomic studies has provided valuable insight into the development of effective, low cost, eco-friendly inputs for crops to reduce intensive inputs of fossil fuels. This knowledge strengthens the engineering of phyto-microbiomes by manipulating the profitable consortia, which produce signals, or products, which enhance the phytomicrobiome community’s capacity to address various environmental requirements, which increase crops’ overall productivity [1]. Between leguminous plants and associated nitrogen fixing rhizobia, the best understood example of signalization between plant and phytomicrobiome elements is documented [2, 9, 10]. Plant-secreted isoflavonoids guide root rhizobic cells into the cells and activate important genes in the rhizobial cells, including the lipo-citoo-saccharides encoding genes that signal to the plant. A specific suite of isoflavonoids is produced by each legume species and only the correct rhizobia usually responds to them [1]. Taking advantage of the interactions of soil microbial communities and plants in the current global change scenario is a relevant method of increasing food production

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at the lowest environmental cost for the growing global population. Basically two important soil microbiome management strategies are based on either microbial development or manipulation of natural microbial populations. Applied microbial biotechnology in agriculture has rhizosphere bacteria and fungi, either saprophytic or endophytic symbionts. The formulation, quality control and method of use of microbial inoculants are particularly important. Many of the mechanisms underlying plantmicrobial interactions are still misunderstood in the rhizosphere. Efforts mainly depend on the need to profile the wide range of processes in which large and diverse microbial groups, consisting mainly of uncultivable microbes, are involved. An abundance of culture-independent molecular techniques are being developed and used to decipher the hidden diversity or the molecular foundations for plant-microbiome interactions of microorganisms in soil and the rhizosphere environment. Various types of stress factors, including salinity, drought, nutrient shortfalls, contamination, diseases, and pests, adversely affect the functionality and productivity of agricultural systems. A network of orchestrated interactions between plant and microbiome are necessary to thrive and survive in stressful environments. Understanding this signal crosstalk is fundamental to the development of biotechnological strategies to optimize mechanisms of plant adaptation and improve the capability of soil microbes to alleviate crop stress. Several approaches are being taken to determine if the rhizosphere can be engineered to stimulate positive organisms while preventing pathogens from occurring. Many successes have been achieved in general by the use of microbial biotechnology in agriculture but numerous challenges and opportunities for future sustainable agricultural developments need to be explored [11].

4.2 Microbial signal: Crop growth and growth Soil microorganisms play fundamental roles in agriculture, mainly through the enhancement of plant nutrition and health and soil quality [12, 13] for sustainable and healthy cultivation. Agricultural practices are now carried out at a global scale and different approaches are addressed with the final objectives of delivering yield while conserving the biosphere. The quality of the soil as a nonrenewable resource, which has a number of environmental and social functions, some driven by soil microbes [14], is an essential question in a sustainable environment. The aim is to find effective methods of nutrient recycling, control of pests and pathogens, and to alleviate the

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negative impact of abiotic stress factors; key issues for human and global ecosystem life. The objective is to achieve sustainable development. These activities are typical microbial services that can be used after proper management and functional management of beneficial microorganisms [15]. Soil microbiomes are documented as relevant components within the diverse environmental quality factors required for sustainable healthy food production. The rhizo-deposit pools attract and preserve microorganisms in rhizosphere microhabitats [16]. A variety of organisms are included in the soil microbiome but in soil microbiology studies bacteria, fungi, and archaea have received far greater focus [17]. Some 109 microbial cells per gram of soil show a high level of diversity, reaching approximately 106 taxa. In the standard culture media, however, only 1% of microorganisms living in large soils and 10% of plant-influenced areas can grow, while the rest remain as noncultural microbes, which can be detected by using molecular approaches, according to discussions later [18]. The prokaryotic bacteria associated with plants and the eukaryotic fungi have a wide range of trophic and living habits that could be either harmful or beneficial in their spinal or symbiotic relationships with the plant. Most of them remain in the rhizosphere soil or rhizoplane, but small subpopulations of endophytes can penetrate and live in the tissue of plants [19–23]. The endophytes escape immune responses and colonize in different parts of the plant and, in some cases, within cells, without causing symptoms of disease in various plant parts. Some endophytes affect the growth of plants and plants, or produce important secondary metabolites to respond to disease, herbivores, and environmental changes. Most endophytes cannot be cultivated; therefore, the analysis of their diversity and the molecular basis of their interactions with the plant are revealed by using molecular approaches [11]. In addition, the beneficial saprophytic microbes of the saprophytic rhizoid improve the activity of the plants by acting as detrivores or plant growth promoting rhizobacteria (PGPR). In many important processes of the ecosystem, such as biocontrol of plant pathogens and nutrient cycling, PGPR is well known. PGPR must at least be able to survive and multiply in the time needed to express their beneficial plant growth promotion activities in rhizosphere microhabitats and in competition with local microbiota [24]. PGPR nutrient cycling processes include N-fixation, P-mobilization, and the release of other nutrients into soil [11, 25]. Various methods are currently used to understand the molecular basis of plant and microbial rhizosphere interactions. A fundamental view here is that the selection of microbial diversity in the target plant in its rhizosphere is driven by plant

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specific rhizodeposition, including root exudation [16]. The feedback loop between plant and microbial organisms is created because the associated root micros, which are stimulated by rhizodeposition, perform specific activities that impact plant nutrition and health [14]. These authors point out that plant functioning affected by microbial community activity can be analyzed through high-performance plant phenotyping, while plant genotype effects can be analyzed through molecular ecology tools on the diversity and functioning of microbial communities. In the same way, in interkingdom communications with the establishment of plant assemblies, the application of new technology has allowed the detection and operation of signal molecules and signaling processes. Drogue et al. [26] divided these signal molecules according to whether they are produced by plants affecting gene expression by PGPR, or PGPRs affecting the plant architecture that affect others as well. Small signal molycles produced by PGPR that can directly affect plant growth and stress relief include the different classic phytohormones, AHLs, and DAPGs. These molecules are used in controlling root architecture, phytostimulation, systemic resistance induction (ISR), root exudation stimulation, and so forth [26–28]. The mutualistic symbionts of the beneficial plant include N2-fixing bacteria, and AMF [29, 30]. In addition, Actinomycetes make N2-fixing nodules, which have a high ecological significance, on the root of the so-called actinorhizal plant species [31]. The AMF of Phylum Glomeromycota, which is known to establish mycorrhizal associations with roots of most plant species, is the second major group of mutualistic microbial simbionts [32–34]. Arbuscular mycorrhizal formation can also be considered an adaptive strategy, giving the plant increased capability to absorb nutrients and cycle to soils with low availability of nutrients, which leads to increased tolerance for environmental stress, both biotic and abiotic (drought, salinity, heavy metals, organic pollutants). The AM symbiosis, therefore, is an important factor in helping the plant to be productive in sustainable agriculture under adversity [35]. AMF has significant functions in forest ecosystems in connection with that [36]. As a biotechnological feasible to AM-colonization, the chemical composition of root exudates changes while an AM-soil mycelium itself incorporates physical modifications into the environment that surround the root and affects the microbial structure and diversity forming the mycorrhizosphere. Many co-inoculation experiments have been described using selected AMF and microbiological rhizospheres, including as-symbiotic N-fixation, mobilization of phosphates, heavy-metal phytoremediation of contaminated soils, biological control

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of root, and soil quality control [12]. In addition to sustainable agriculture, the scenarios for the use of microbial technology also cover other ecosystem issues, including ecosystem restoration, recovery of endangered plants, improved plant resilience, adaptive strategies to diversity conservation, etc. [37].

4.3 Bacterial quorum sensing Quorum-sensing (QS) systems are used in several artificial systems that require cell to cell communication in order that bacterial organisms co-ordinate their behavior in accordance with their local population density. Bacteria that affect the gene expression of their behavior will detect the accumulation of optimized stimulative levels of auto-inducers. These selfinductors are the chemical signals or substances released by QS bacteria and their external concenter. QS bacteria delay virulence production, leading to infection leading to the host immune system activating by secreting virulence factors capable of production infections, until the cell count reaches optimum levels. The technique is successful in coordinating the gene expression of the organizations’ groups. The QS system is also known to modulate the production of antibiotics, siderophores, and secondary metabolites, and the development of biofilms. The induction of systemically resistance with leaf pathogens seems to be also a part of microbial QS molecules like AHLs [18]. The accumulation of minimal auto-inducer stimulation affects the behavioral reaction by changing gene expression [38]. As the signal reaction system functions as multicellular organisms, bacteria coordination specific activities of the entire population. The similarities of these systems may be caused by the inherent communication capacity of bacteria when system differences arise, because in a particular niche, every system must be optimized for its survival. In crux, various types of signal receivers imitate the unique ecology performed by a particular bacterial species by means of their signal transduction mechanism and target outputs for each QS system [39].

4.3.1 Communication between cells Different promising studies on cell-cell communication are currently under way, in which both intra- and intertype QS are analyzed to predict bacterial survival and workplace division in an entire community. In both plant and human pathogens, QS regulates virulence, since it has a peculiar property of delaying the production of the virulence factor by preventing the activation

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and secretion of the host immune system, causing productive infection [40, 41]. Moreover, auto inducers produced by various S. aureus vary from strain to strain particularly with reference to Agr-mediated quorum sensing [42]. However, QS via HSL auto-inducer signaling has been shown to play a critical role in the proper development of bacterial biofilms [43]. Likewise, in biofilms, bacteria are organized into elaborate structures composed of either single or different species possessing aqueous channels promoting the transport of nutrients and hence preventing desiccation; each bacterial strain having unique patterns for gene expression and differentiation [44]. These biofilm characteristics show that the bacteria within them are more likely to live and spread. Likewise, the QS monitor the production, as Pseudomonas aureofaciens is a part of the interspecies communication, of antibiotics such as phennazin in the plant pathogens. The documented production of antibiotics is also monitored by other bacterial species other than the autoinducer P. aureofaciens HSL [45]. This may be because of P. aureofaciens sensitivity during intense competition in nutrients.

4.3.2 QS in Gram-positive bacteria Gram-positive bacteria are a common feature of two component membrane systems using signals of modifiable oligopeptides and histidine kinase sensor receptors. The phosphorylation cascade mediates cell signaling, which in its turn regulates reaction regulator activity, in particular the transcriptional factors that are binding on DNA. Since Gram-negative bacteria (GNB) use Lux IR quorum sensing systems, Gram-positive bacteria are equally sensitive to signal structures by using cognitive receptors. Therefore, intra species communication confers peptide quorum-sensing circuits as in LuxIR systems. Although, the peptide signals do not spread across the membrane, henceforth to mediate cell signaling by committed oligopeptide exporters. Signals of peptide QS are reported to be derived from larger precursor peptides that are later adapted to contain lactone and thiolactone rings, lanthionines, and isoprenyl groups, though biochemical processes leading to these events are not clearly comprehended [43, 46–48]. Moreover, in combination with other types of QS signals, Gram-positive bacteria communicate with multiple peptides, e.g., S. aureus is an enthusing example for the sensing of peptide quorum. It is normally a benign human commensal, but it becomes a deadly pathogen [49] by open penetration in host tissues. S. aureus is used for biphasic strategy for the transmission of the disease. When cell counts are small, however, as cell density increases, the bacterium suppresses these

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features to produce proteins that facilitate attachment viz-a`-viz colonization and then induce toxin and protease production, which eventually results in dissemination [50]. This switch to gene expression programs is regulated in Agr QS system. S. aureus are classified according to the AIP thiolactone sequence [41]. Every AIP leads remarkably to the activation of the AgrC receiver and blocks the expression by competitive binding of all other noncognized receivers [51]. Thus, in all three other groups, S. aureus inhibits virulence cascade activation. Competition of intra-species exists when two different S. aureus are co-infected [43]. Hence QS in S. aureus inhibits the spread of nonkin progeny while allowing the spread of closely related offspring. This means that the communication between cells was instrumental in setting up a specific niche for each strain [52]. Signal-receptor pair divergence in these bacteria could be part of the molecular mechanisms underlying the development of new bacterial species. Streptomycetes has an important clinical importance as it is a reservoir of secondary metabolites, many of which are used as antibiotics, of the diverse family of Gram-positive soil dwelling bacteria [53]. Streptomycetes control morphological differentiation with quorum sensing and secondary production of metabolites. They utilize γ-butyrolactones as auto inducers. These signals are interesting because they are structurally linked to autoinducers from AHL. No reports of cross-communication between Streptomycetes and other Gram-positive bacteria that communicate with AHLs are yet available.

4.3.3 QS in Gram-negative bacteria In most GNB, the bioluminescent marine bacterium Vibrio fischeri [54] is a model of quorum sensing. It inhibits the light organ of Hawaiian squid Euprymna when it grows and increases cell density, leading to gene expression of bioluminescence. This light provided by bacteria is used by Euprymna scolopes to cover their shadow for preventing predation [55]. On the other hand, the bacteria also benefit from the light organ nutrients. In light production, two LuxI and LuxR proteins are used for the expression of luciferase operon [LuxICDaBE]. The auto-inducer synthase (AHL) [56, 57] is LuxI and the auto-inducer cytoplasmic receptor (DNA) is LuxR [58]. The DNA is a transcriptional activator [58]. AHL spreads freely in and out of cells, whereas the cell density increases there [59]. After reaching the signal threshold, the signal becomes LuxR bound, completing the operon encoding luciferase transcription in turn [60]. LuxR-AHL, in particular, induces LuxI expression via luciferase operons. This regulatory setup

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generates a positive feedback, which causes the whole population to switch to “quorum sensing mode” and to create light. There have been reports that a number of other GNBs have LuxIR proteins and communicate with the AHL signals [61]. The LuxR proteins and their cognate AHL signals are extremely specific, and these are mainly used for communication within intra-species systems. In addition to its linkage with specific acyl fatty chains on acyl-acyl carrier proteins, the protein-type LUI plays an important role in lactonizing the S-adenosyl methionine (SAM) mode [62, 63]. Diverse lengths of side chains of the fatty acyl groups keep the signal specificity [64]. Structural analyzes of LuxI-type proteins have shown that they have acyl binding pockets that fit in side-chain movement specifically [65, 66]. LuxI proteins, therefore, produce high fidelity signaling molecules [67]. Structural analysis of LuxR proteins also reveals that they have certain pockets of acyl binding, which enable their cognitive signal to be activated [68, 69]. There are, therefore, mixed species environments where there are several AHL signals and each species only reacts to its own signal build-up afterwards. Bacteria are not often used on one LuxIR quorum sensing system, but often in conjunction with other types of circuits it uses many LuxIR systems. Mechanisms that ensure that both the signal and the detector are synthesized and interact in the cytoplasm preventing premature activation of quorum circuits type LuxIR. LuxR homolog TraR shows that in Agrobacterium tumefaciens, such a mechanism is used to increase the stability of LuxR proteins when binding AI. In presence of a self-inducer, TraR increases its half-life to over 30 min, while it has a half-life of some minutes in its absence [70]. In addition, TraR’s radiolabeled TraR indicates that its cognate AHL is stabilized only if the binding of its incipient polypeptide AHL is added before the protein labeling [69, 71]. Thus, TraR only accumulates AHL at a significant concentration in the quorum sensor cascade. Another mechanism preventing “shortcircuiting” of LuxIR systems is active export of AHL signals [72]. Once the signal is accumulated, the high cell density dispersal indicator in the cell will overwhelm export and thus engage the circuit. AHLs with long acyl sides need active export to cross the bacterial membrane [72].

4.3.4 Quorum sensing genetic regulation An example of QS is the prevalence of community behavior among different bacterial species. The ability of a microorganism, through production and subsequent reaction to diffuse molecules, to perceive and react to the density

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of the microbial population are known as QS. Acyl-HSLs are generated for the majority of GNB, which function as signaling molecules. The physiological processes regulated by QS vary from bio-light to swarming motility, depending on the bacterial species. Much research has been done over the past decade that has led to a significant understanding of many aspects of QS, including the synthesis of acyl-HSLs, the receptors that recognize the acylHSL signal and transmit this information to the level of gene expression, and the interaction. QS in bacteria are dependent on population density for the gene expression. QS gene expression in bacteria depends on population density. Two components of the QS systems are mandatory: the regulatory receptor protein interacting with a regulation system and an autonomous regulator that can be easily diffused via the cytoplasm membrane. QS systems include two components. The critical density of the bacterial population achieves the rapid activation of certain genes and operons, with selfinduction at the required threshold value. In order to identify inherent stress-resistant and metabolomic products, and their application in the bioremediation of various industrial and environmental pollutants, quorum sensing has been used effectively in environmental biosanitation. Advanced GM in QS can help senses of environmental pollutants that could be used in various bioremediation technologies (Fig. 4.1). Bacteria can create a new platform for ecometabolomics by integrating quorum sensing with Biofilms [39].

Bacteria cell 2

Bacteria cell 1

Fig. 4.1 Engineered cell consortium of two different bacterial strains. Gray cells are sensitive to molecules produced by light gray cells and vice versa, depicting interdependent chemical response via quorum sensing.

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4.4 Concept of signal molecules The population of the world has been predicted by the UN Food and Agriculture Organization (FAO) to rise alarmingly to between 8 and 9 billion by 2030 [73]. As a result of increasing urbanization and industrialization, environmental threats have increased and agricultural land has shrunk on the one hand, and crop growth has declined significantly on the other. Abiotic stress can reduce crop plant growth significantly, resulting in substantial yield losses and posing a potential threat to global food security [74, 75]. Plants undergo different abiotic stresses, i.e., drought, flooding, extreme temperatures, salinity, and xenobiotics. It has also been reported that about 25% of the world’s agricultural land is being deteriorated by drought and that salt affects approximately 5%–7% [76]. Abiotic stresses have a negative impact on plant physiology and morphology due to defects in cellular pathway genetic regulation. Plants use multiple tolerance mechanisms and pathways to avoid stress effects that are triggered whenever metabolism changes occur. Phytohormones are among the most important growth regulators as well as playing a vital role in stimulating plant defense response mechanisms against stress; they are known to have a prominent impact on plant metabolism. Better knowledge of the multiple methods of tolerances to preserve plant efficiency can assist to preserve much of the necessary genetic capacity of plants through manipulation of environmental circumstances. Phytohormones are major development regulators synthetized in specified crop species, which have a prominent position and have an important effect on crop metabolism in the mitigation of abiotic stress [77, 78]. However, abiotic pressure alters endogenous amounts of phytohormone like auxins, gibberellins, abscisic acid, jasmonic acid (JA), and salicylic acid (SA), causing a perturbation in crop growth [79–81]. Drought and salt stress have also inhibited plant tissue phytohormone levels. Microbes are known to defend plants against certain pathogens as well as providing resistance to stress conditions. Endophytic microbes of the rhizosphere and the root, including PGPR, Trichoderma spp., and AM fungi, protect plants from pathogens by space and nutrient competition, antibiotics, mycoparasitism, and induction of mechanisms for plant protection [12]. The precondition for immunity induced with microbial colonization is defense priming, which is essential for effective pathogens protection. The symbiosis protects plants from harmful organisms, including microbial pathogens, herbivores, and parasites. Colonization of AMs can enhance the

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plant’s immunity to respond to pathogens where JA is of key importance. Furthermore, PGPR, Trichoderma spp., and NPF strains also provide prime resistance and SIS, because they create MAMPs that trigger immune reactions and further activate the JA signaling pathway to support protection systems in plants [82, 83]. In this way PGPR is also used in plants with high resistance and ISR. The following sections discuss the detailed account of numerous signaling molecules that are prevalent in plant microbe systems..

4.4.1 Phytohormones Plant hormones are a group of organic substances that occur naturally and influence low concentration physiological processes. Processes affected mainly include growth, differentiation, and development, but can also be affected by other processes, such as stomach movement [84]. Plant hormones are also called phytohormones. Auxin, the first plant hormone identified, generates a growth response at a distance to its synthesis site and, therefore, fits the definition of a chemical messenger transported. Recent research has shown that root-related microbes can produce phytohormones as key goals in metabolic engineering that lead to abiotic stress tolerance [85]. The phytohormone biosynthetic pathways of several genetic and biochemical methods have been identified and a detailed list of phytohormones is given in Fig. 4.2 and discussed in the following subsections.

N2 fixation

Siderophore production

P solubilization

Biofertilization PGPR

Biocontrol Rhizosphere Antibiosis

Lytic enzyme production

ISR

Increased plant growth

Fig. 4.2 PGPR-mediated plant growth promotion by the alteration of the whole microbial community in the rhizosphere niche through the production of various substances.

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4.4.2 Auxins IAA is the primary auxin for plant life, and in order to stimulate the cell prolife and improve host use of minerals and nutrients in soils, IAA can synthesize IAA colonized seed or root surfaces in combinations with endogenous IAA in plants [86]. IAA is synthesized in the primordias of leaf and young leaves and the development of seeds from tryptophan or indole. The IAA’s biosynthesis by the PGPR is based upon the most common mechanism in bacteria such as Pseudomona, Rhizobium, Bradyrhizobium, Agrobacterium, Enterobacter, and Klebsiella, indole-3-pyruvic acid, and indole-3-acetic Aldehyde [69]. Auxin supports several growth and developmental events like cell enlargement and stem growth, division of cells, differentiation of vascular tissues, initiation of the root, tropical responses, apical domination, leaf and fruit abscissions, fruit development and growth, and fruit maturation [87]. Ljung [88] has reported strong evidence to encourage auxin-mediated growth and control of development through changes in the pattern of gene expression. There are numerous reports showing various modulations of synthesis, transport, metabolism, and auxin activity following plant stress exposure [88] however, many reports advocate the role of auxins in the mediation and improvement of plant toleration of abiotic stress [89]. After exposure to salinity stress, rice plants showed a significant decrease in IAA. Moreover, this variance in IAA can lead to growth modulation by increasing other phytohormones, as reported, such as ABA [90]. Jung and Park [91] found a close association between auxin signaling and salt stress that developed through the involvement of auxins in determining the NTM2 membrane-bound transcription factor [92]. Auxins play a significant role, either directly or indirectly, in promoting heavy metal tolerances. Hu et al. [78] also indicated that the biosynthesis of auxins is negatively affected by heavy metals. The low IAA concentration, which stimulated increase in root volume, area, and diameter [10–98], alleviated the toxic effect of lead on sunflower plant growth. In Iqbal and Ashraf [99], the ionic homeostasis and the induction of SA biosynthesis were reported to have a significant mitigation of the salt stress-induced hostile effects on wheat following IAA priming, suggesting the possibility of a crosstalk that mediates tolerance responses in plants between auxin and SA. However, the salinity limiting the IAA synthesis has shown that the exogenous application of SA inhibits significantly to mitigate hostile effects [100].

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4.4.3 Cytokinins Cytokinin is also an important additional body of plant hormones that contribute to the maintenance and differentiation of the cellular proliferation and prevent senescence, thus inhibiting premature leaf senescence [101]. Many plant growth promoters, such as Azotobacter sp., Rhizobium sp., Pantoea agglomerans, Pseudomonas fluorescens, Pseudomonas subtilis, and Paenibacillus polymyxa, can make cytokinins or gibberellin, or either produce cytokine or gibberellin or the two can promote plant growth [102]. However, it was observed that stay-green genotype types may show increased tolerance under stress conditions, in particular water stress in the grain-filling stage, which was attributed to a higher concentration of cytokinin in xylem sap [103]. Zhang et al. [104] demonstrated a higher tolerance to drought compared to wild-type vegetables for cytokinin overexpressing transgenic manioc. The genes involved in cytokinin’s biosynthesis were overexpressed and their role has been validated in stress tolerance. In field analysis, for instance, the ipt gene was validated [105]. Reduced cytokinin leads to stomatal closure due to the induction of ABA and thereby reduces carbon uptake and assimilation and, under stressful circumstances, cytokinin oxidase upregulation can also reduce carbon metabolism. Mohapatra et al. [106] have shown that the filling of grain improves cytokinin. Cytokinin is used for exogenous use to optimize cytokinin’s internal concentrations. It was also found that the seedling development of chickpea has become severely impaired through the inhibition of the levels of GA3 and Z in plant tissue by heavy metals such as zinc and lead [107]. Kinetin has stimulated the growth and the development of salt plants in earlier reports [108], as well as in another report by enhancing its antioxidant potential [108], in which eggplant stress was reduced by kinetin.

4.4.4 Abscisic acid ABA is well known for its important role in plants, like other phytohormones, through the improvement of stress and adaptation. It is a sesquiterpenoid naturally occurring, which is a group of key growth control phytohormones. Many reports have supported ABA’s role to integrate the signaling of stress exposure with subsequent downstream response control [109]. There are several reports. Under abiotic stress, the expression of ABA-induced and mediated ABA-regulating stress-responsive genes leading to better tolerance response elicitation [110]. Furthermore, ABA has been

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reported in dry stress conditions for control of root growth and water content [111]. A sharp rise in ABA levels during stresses may, however, cause growth delay and can modulate stress tolerance responses [87]. However, there have been reports that exogenous ABA has a positive effect on the reverse effects of stresses such as salinity [112], chilling [113], drought [114], and cold stress [115]. The exogenous application of ABA has shown that the antioxidant system and its relative water content are protected from drought-induced damage by Bano et al. [114]. The exogenous ABA application for improving stress tolerance was proposed as an effective tool for stress mitigation. Zhou et al. [115, 116] reported substantial alterations to tea proteome in the context of an exogenous application of ABA during drought conditions, including changes in transportation proteins, carbon metabolism, and stress tolerance. ABA was suggested to maintain other levels of hormones, including ethylene, resulting in Zea maize shoot and root growth [117]. ABA synthesis and build-up in plant tissues increase when stress is affected. In addition to its role in signaling, the most important role of ABA is its ability to act as an antitranspirant following stomach closure and canopy expansion reduction [118]. Exogenous application of ABA to rice seedlings exposed to drought has resulted in photosynthesis protection by upregulating the expression of the genes OsPsbD1, OsPsbD2, OsNCED2, OsNCED3, OsNCED4, and OsNCED5, leading to improved photosynthesis capacity and stomata regulation under normal and stressed conditions, suggesting that these genes are involved in photosystem II induction after exogenous application. Cabot et al. [119] reported that in citrus plants ABA exogenously inhibited the accumulation of sodium and chloride. In another study, in the common bean under salt stress, ABA treatment increased plant growth, nutrient absorption, and nitrogen fixation [120].

4.4.5 Gibberellic acid The literature available clearly shows the improvements to the salinity of gibberellic acid (GA). GA was found in several abiotic stress conditions to encourage plant growth and development [121, 122]. Improved uptake of plant water and decreased stomata resistance were observed in GA-treated tomato plants grown under saline conditions [123]. GA induces efficient uptake and partitioning of ions within the plant system, resulting in increased growth and maintenance of plant metabolism under normal and stressful conditions [90]. Several studies [122–125] reported improved germination and growth due to GA under salt stress conditions. Additionally,

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gibberellins may exhibit crosstalk with other phytohormones, resulting in significant responses and mediating mechanisms of tolerance to enhance stress tolerance. It is also possible to promote gibberellin synthesis by applying other hormones, such as auxin [126]. Enhanced GA synthesis leads to increased catabolism of ABA. In addition, GA has a direct impact on growth, yield, and mineral nutrition, as well as the metabolism of nitrogen. There has also been an increase in fruit yield, leaf area, and nitrogen, phosphorus, and potassium intake in tomatoes due to exogenous application of GA [127]. An increase in osmotic components was reported in plants exposed to salt stress and their content was further increased through treatment with GA. The endogenous application of GA has caused osmotic stress in plants to be modified and the water content of the tissue maintained [122]. Manjili et al. [125] for wheat and Tuna et al. [124] for maize have observed such effects. GA further increased the activity of antioxidant enzymes by decreasing reactive oxygen (ROS) levels that helped to improve stress growth [125]. In addition, GA exogenous application mitigates salinity effects on Arabidopsis thaliana germination and growth through the use of enriched SA syntheses that lead to increased isochorismat synthase activity [128]. The same study shows that overexpression of the Fagus sylvatica gibberellin reactant gene has enhanced Arabidopsis salt tolerance.

4.4.6 Salicylic acid SA is another phenolic phytohormone and functions in plant stress tolerance by modulating antioxidant enzyme activity [129, 130]. SA plays a major role in pathogen resistance by inducing the production of pathogenesis-related proteins and participating in the systemically acquired resistance response (SAR), in which a pathogenic attack on older leaves causes the development of resistance in younger leaves, although it is debatable whether SA is the signal transmitted. SA is the calorigenic substance that causes thermogenesis in Arum flowers. It has also been reported to improve flower longevity, inhibit ethylene biosynthesis and germination of seeds, block wound response, and reverse ABA effects. Senaratna et al. [131] for water stress, Azooz et al. [132] for salt stress, and Ahmad et al. [129] for heavy metal stress reported the relief of different abiotic stresses by application of SA. SA modulates various physiological processes involving stress tolerance in plants through signal pathways under stress and response mechanisms [81, 129–133]. The relief effect of SA on plants, i.e., beans [132], maize [134], and wheat [135], is reported in several

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reports. In terms of accumulation of biomass, promotion of the divide, and increased photosynthesis and antioxidant enzyme activity, SA-treated plants showed better increases [81, 130–141].

4.4.7 Ethylene A vital phytohormone that has various biological activities, including the promotion of root initiations, the inhibition of root elongation, the promotion of fruit maturation, the promotion of low wilting, the stimulation of germination of seed, and the promotion of leaf abscission [142]. High ethylene concentration leads to defoliation and other cellular processes leading to a decrease in crop performance [143]. Carboxylic acid (ACC) enzyme (1aminocyclopropane-1) is a precondition for ethylene production and has ACC oxidase catalyzing properties. Iqbal et al. [144] reported improved nodule number, dry weight nodule, fresh biomass, grain yield, straw yield and nitrogen content in lentil grains as a result of reduced ethylene production through inoculation with plant growth supporting Pseudomonas sp. strains. Bacterial strains with ACC deaminase activity have currently been identified in a wide range of genera such as Acinetobacter, Achromobacter, Agrobacterium, Alcaligenes, Azospirillum, Bacillus, Burkholderia, Enterobacter, Pseudomonas, Ralstonia, Serratia, and Rhizobium, etc. [102]. As mentioned earlier, soils are sources of different organisms, including fungi, bacteria, and plants [145]. The root-exudates or rich nutrient component [146, 147] is strongly colonized with microorganisms. Rhizosphere is a nutrient-rich environment with amino acids, sugars, fatty acids, and other organic compounds that attract the various root nutrients [148]. Microbes synthesize biologically active compounds like phytohormones and compatible solutes, antimicrobial compounds, enzymes, etc. The plants’ nutrition and developments play a key role in these microbial metabolites [76, 85, 149]. They can stimulate the development of plant growth, resist various abiotic and biotic stress factors, improve the acquisition of nutrients, and protect plants from various soil-borne pathogens [150, 151]. The beneficial interactions of plant microbes, their positive effect on plant growth, and their improvement in stress tolerance under extreme environmental conditions [152] as well as the mechanisms used by PGPR are well established [153]. There are several mechanisms for stimulating plant growth, protecting plants, and alleviating PGPR salt stress, such as fixing nitrogen, synthesizing osmoprotectants, exopolysaccharides, 1-aminocyclopropane-1-carboxylate [ACC] deaminase, cell wall

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degrading enzymes and phytohormones, and modulating antioxidant enzymes or nutrients and solubilizing minerals, i.e., P and K [154–156]. Microbes mitigate stress responses by regulating plant nutritional and hormonal equilibrium and inducing systemic stress tolerance [157]. Microbial phytohormones affect the metabolism of plant tissue endogenous growth regulators [147] and play a major role in changing root morphology following exposure to drought, salinity, extreme temperature, and heavy metal toxicity [158, 159].

4.4.8 N-Acyl-L-homoserine lactones QS is an intercellular signaling mechanism that allows bacteria to coordinate cell-dependent group behavior. Small molecule or peptide signals called auto-inducers are used for this signaling process. Bioluminescence, forming of biofilm, motility, sporulation, root nodulation, and the production of the virulence factor are broadly differentiated between bacterial species and their environment. These bacterial population behaviors have profound effects on the associated host eukaryotes. QS allows a sufficiently high number of bacteria to grow before starting a coordinated attack on the host and overwhelming its defenses in pathogenic bacteria [160]. In contrast, symbiotic bacteria use QS to establish mutually beneficial relationships with their hosts at high cell densities. GNB typically use AHL signals and their cognate LuxR-type receptors for QS [161]. The interactions between plant and bacteria are driven by the presence of QS molecules. For the model plant Arabidopsis thaliana, most knowledge has been gathered about the effects of AHL, the major group of QS-signaling molecules in GNB on plants. The perception and effects of short carbon chain [C4-,C6-, C8-] and long carbon chain [C12 and C14] AHLs must be distinguished in this plant [4, 162]. While the G-protein coupling receptor (GPCR) in Arabidopsis is perceived as the short carbon chain AHL [163], the receptor mechanism of the long carbon lipophilic chain AHL is still unclear. Of course, the long carbon chain AHLs, such as the 3-oxo-C14-HSL, are generally the prime plants for improved resistance; they have been called AHL priming [164] and are based on oxylipine and SA signal pathways. In addition to perceiving the plant-born molecules through the QS receptors of bacteria, plants can perceive AHLs in a very specific way. For example, the impact on the nodulation of the potential host plant Medicago truncatula of 3-oxo-C14-HSL, an AHL produced by Sinorhizobium meliloti [165]; the fact that the increased number of nodules was observed only

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after treatment with 3-oxo-C14-HLS, whereas other AHLs or the use of another leguminous plant had no effect, was very striking. These results indicate a very precise system of legumes perception. The report by Zhao et al. [166] shows a central role of calcium signaling and calmodulin in Arabidopsis response to short carbon chain AHLs. In addition, mutants did not respond to the treatment in the AtCaM genes. This strongly indicates that calmodulin plays a significant role in the perception of short carbon chain AHLs. AHL treatment seems to affect the metabolism of the host and even the systems of reproduction on a different scale [167]. This difference may be due to reduced transport of AHLs in yam bean due to lactonase degradation [140]. Obviously, plant-associated microbiomas can play a central role in developing new strategies to improve our food supply and food quality.

4.4.9 Volatile organic compounds Plants that are sessile cannot change places; consequently, they are easy targets for organisms that want to feed on them. Plants have developed a wide range of defense characteristics, reducing their foes effectiveness [168]. Plants need a way to interact without physical touch and volatile organic compounds (VOCs) are the “words” that form the “vocabulary” of crops. In the envelope issued from crops, the quantity and relative ratios of VOC enable the plant to transmit complicated signals, which can be defined as sentences using the language analogy. Plants generate a wide variety of chemicals including a variety of vocabulary products, produced by flowers, foil, peel, radicals, and specialist constructions. Plant compounds that are far greater than other crop species, not commonly discovered in the greater crops but limited to certain seed species, are described as secondary crop composition [168]. Plant volatility accounts for 1% of known seed plant submissive metabolites. Plants are constitutively emitting volatiles; the production of constituent isoprene and monoterpenes in chloroplasts is known to be associated with heat stress protection [169]. The toxic, repellent, and deterrent properties [169–171] of some constitutive VOCs can have a direct influence on the physiology and behavior of herbivores. Generalist herbivores have VOCs which may be repulsive, but plants’ specific volatile signals reveal plant identity and increase food damage and reduce plant fitness when perceived by specialist herbivores [170]. A number of different stress levels contribute to the secretion of plants to a vast array of volatile compounds and their mechanisms are very complicated

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as well [171]. The circumstances include abiotic variables, including precipitation, thermal stress and oxygen [169], pathogens [172], herbivores [173, 174], and biotic stressors. The effects of herbivorous creatures on the instability of a multitude of crops in a multitude of species are regarded as profound and variable. When herbivores start to eat, plants have two kinds of unstable reaction. The first reaction is the rapid emission of stored compounds released by damage to plant tissues. The second answer is the de novo compound synthesis, which is not saved but released as it is produced [175]. These two mechanisms may overlap compounds with volatile substantially emitted compounds and often increase in quantities by herbivorous feeding [171]. Additional compounds are exclusively used for herbivore plant damage. For example, only pinene and limonene are emitted by Phaseolus lunatus if they are intact; but seven other VOCs are released after 48 h of feeding from spider mites [176]. The natural enemies of plant-feeding insects—and this can be shown in laboratory [177], seminatural [178], and natural conditions [179]—are the inducible herbivore compounds or the relative odor-relief ratios in damaged plants. It can be concluded that the particular VOC signals from the herbivores following the damage are important signals that enhance the fitness of the plant by causing behavioral answers in herbivores’ natural enemies and thus increase the predation rate which leads to a reduction in plant harm. This reply was often described as a cry for assistance due to the natural enemies of herbivores who use these volatile signals as a sign during the foraging process. However, the recipient of signal could be interpreted as a “cry” [180] while it could be considered a much more eloquent monologue [181] in the complex nature of the signal.. The plants can benefit by detecting such fluids and changing their depths accordingly as the herbivore-induced volatiles are reliable indicators for the presence of herbivores. The communication of plants was previously reported in 1983 [182] and there was sufficient evidence of interspecific communication [183–185], intraspecific communication [186–188], and communication of plants [189]. Interspecific communication was observed [182–185], with wild tobacco plants shown to experience less foliar damage when exposed to clipped sagebrush neighbors than plants exposed to unclipped sagebrush [184,186]. Sagebrush [185] also proved intraspecific interaction, which resulted in considerably fewer damages to unspoilt Sagebrush with brushed sagebrush neighbors than to the Sagebrush with uncluttered ones. This interaction took place at intervals from the cut crops of up to

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60 cm [186]. Methyl jasmonate is produced by sagebrush constitutively. Methyl jasmonate was therefore projected to be a significant message mediating interaction between plants [189]. Methyl jasmonate is an essential part of crop defense reactions to insect feeder, an unstable form of JA. The most important group of secondary compounds, comprising about 40,000 compounds, are also terpenoids with at least 1000 monoterpenes and 6500 sesquiterpenes [168]. Certain terpenoids are vital oils and resins, which are made and deposited in special constructions such as glandular trichomes or resin ducts. These structures will be crushed and the compounds produced after harm by herbivores. Herbivorous foods can induce the de novo biosynthesis of terpenoids locally and systemically. Therefore, terpenoids as a collective can provide the received crops with fast, but also herbivoresrelated harm signals. Likewise Methyl salicylate is synthesized from SA, it is a phenolic compound and plays an important role in plant defense. This is produced in important quantities from crops as a result of aphid feed harm and in reaction to tobacco mosaic virus (TMV) disease is produced by smoking. The resistance of tobacco crops subjected to methyl salicylate to tobacco mosaic disease was improved. Plant breeding in corn showed that the green leaf volatile [Z] 3-hexen-1-ol is controlled, and that the impact is synergized with ethylene [190, 191]. In order to promote our understanding of ourselves and self-knowledge in plants, VOCs signalizing in plants is a potentially relevant discovery. However, the accumulated evidence for communication between various plant species within the plant suggests that the plant itself is likely to emit. In a tree, hybrid poplars [192] and two woody shrubs, sagebrush [185] and blueberries [193], communication with plants was also demonstrated in Lima bean. Branches have decreased or absent vascular interactions in all of these species, which means that it is impossible to regulate systemic response via internal signals. External volatile indicators, therefore, provide a means of avoiding these limitations. The hexenyl acetate green leaf cis 3 was shown to be a crucial element in plant communication in both Lima bean and hybrid poplar [194]. Blueberry [193] and sagebrush [195] also produce this compound and within 5 min after the beginning of herbivore feeding [41], which makes it a good candidate to signal quickly from harmed to undamaged parts of a plant. Nevertheless, it is rather an overall signal, which can be found by multiple types and induced by multiple stimuli that is apparently freed by cis 3, and which is released both as a response to mechanical damage and as a result of herbivore feed.

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4.4.10 Bacteriocins Bacteria generate and excrete products in their surroundings, primarily to control microbial population dynamics and are called a “never ending arms race” against microbial competitors [196]. The bacterial compounds excreted include a variety of widespread ribosomal-based synthesized antibiotic products, lytic enzymes, metabolic products of particular importance in bacterial defense such as organic acids, protein exotoxins, as well as chromosomal and ribosomal antimicrobial peptides generated defense like organic acids. Bacteriocins are extra cellular substances generated by organisms of unique morphological and biochemical features from extremely small to big molecular complex weights, which are primarily connected during exercise with a protein. Most of these plasmids are synthesized, but they also have chromosome origins and are synthesized at different phases of the development of bacteria and under different environmental conditions [197]. The bacteriocins are categorized into four separate groups that are based on protein properties such as posttranslation changes, side-chains, thermal stabilization, N-terminal homology of the structure, and molecular weight [198]. In 1976, bacteriocins were produced for the first time [199] by bacillus organisms. The bactericidal activity of Gram-positive bacteria’s lowmolecular-weight bacteriocins has been shown [200]. Colicin from Enterobacteriaceae [201] is the most widely researched bacteriocin. These antimicrobial peptides have been an important region of science studies because of their business significance as nature preservatives and as therapeutic agents for pathogenic fungi [200–203]. Nisin, produced by Lactococcus lactis is the only usually considered secure bacteriocine for human intake. However, it is only of restricted use as it is GNB ineffective [204], requiring earlier bacteriocins to be investigated. The evaluation therefore refers to the bacteriocins generated by colonizer plants and to plant pathogens that could be used in forestry, veterinary, or human health. Bacteriocin cerein 7, originating from Bacillus cereus, was the first to be isolated from this species [27] although other species of Bacillus such as B. thuringiensis, B. stearothermophilus, B. megaterium, B. licheniformis, and Bacteriocin-like products, of which subtilin from B. subtilis were previously produced by cereus. Bacteriocin [BacGM17] from Ononis angustissima rhizosphere bacteria Bacillus clausii is a single-sequence monomer protein (5158 kDa) with a bactericidal effect on Agrobacterium tumefaciens C58 and a fungistatic effect on Candida tropicalis R2 CIP203 [205]. Bacteriocin putidacin, isolated from the banana root, produced by Pseudomonas putida strain is very similar to mannose binding plant

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lectins [206]. Amylocyclicin, a Bacillus amyloliquefaciens FZB42 6381 kDa peptide, is a novel circular, ribosomally synthesized bacteriocin with high antibacterial activity closely related to GPB [207–209]. Due to its interesting array of excreted proteins, Bacillus thuringiensis (Bt) is the most widely studied Bacillus species. B. thuringiensis is a Gram-positive spore-forming bacterium characterized by its ability to synthesize the characters of diptera, coleopteran, and lepidoptera larvae [210–212] and represents approximately 90% of the biopesticides produced on the market [213], apart from the incorporation of Bt in seven genetic groups. Sixteen strains of B. thuringiensis have been identified for their capability to protect plants from phyto-pathogens. The lowest cytotoxic and hence possibly appropriate for the food sector and farm plant applications for defense against deleterious organisms were BtHD868 Tochigiensi and BtHD9 entomocidi species. This alignment was based on the concentrations and antibiotic Zwittermicin A actions of autolysins, bacteriocins, and AHL lactonases. Moreover, fungal disorders induced by Aspergillus niger, Aspergillus fumigatus, Aspergillus flavus, Cryphonectria parasitica, Fusarium oxysporum, Monilia sitophila, Monilia hiemalis, Penicillium digitatum, and Rhizopus sp. [214–218] have also been involved in these disorders [214–218]. A bacteriocin separated from B. thuringiensis NEB17 is now known as Thuricin 17 (Th17) [214–220]. Thuricin 17 is a low-weight, 3162 kDa molecular protein stabilized over a 1.0–9.24 pH spectrum, extremely heat-resistant and inactivated through proteolytic enzyme therapy. Th17 also has a beneficial effect on soya bean and maize and enhanced development [220–229], which confirm the first account of crop development inhibition by bacteriocin. The world’s leading challenges for scientists are indiscriminate use of fertilizers and other chemicals in agriculture and multidrug-resistant microbes. The bacteriocins, considered as being the promoter of plant growth and disease suppressors, provide a viable alternative to use of fertilizers and chemical products, such as fungicides and insecticides, efficiently in agriculture. With respect to multidrug resistance, both veterinary and human health bacteriocins may be useful as a target protein, as well as for their use in food preservation, to substitute effective antibiotics or for combinatorial therapy [222–224].

4.5 Expression of protective genes under abiotic stress in plant crops Drought and heat can decrease crop productivity and lower farm income. The yield decrease was observed by up to 40% for maize and 21% for wheat

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[225]. The effects of climate change will exacerbate further reductions in crop productivity. The IPCC report concludes with clear evidence of warming of air and ocean temperatures and an increased level of greenhouse gases [226]. Both have direct influences on crop and plant growth [227, 228]. Changes in climate affect the Earth’s crust, leading to rare and erratic precipitation, high temperatures, and expansion in flooded or water deficit regions of affected land. These adverse conditions help develop droughtprone areas and thus crop growth and productivity but plants have developed dynamic responses to manage these abiotic stresses at the morphological and phytosanitary levels so that they survive in variable environmental conditions [229]. Physiologically, plants can be categorized under two separate processes for dryness and hot stress. Evasive processes include morphological and physiological changes, including an increasing root scheme, reduced stomach numbers, reduced bloom region, enhanced plant space, and flower flip to reduce evapo-transpiration, which lead to an exhaust from or thermal pressure [230, 231]. Likewise, all living organisms have a prevalent signal understanding characteristic through cell surface receptors. Under pressure circumstances, signaling cascades are activated as an initial phase of reaction when signaled from the setting [232]. Different receptor kinds interpret different environmental signals and stimuli. The first receptor-like kinase protein in crops was defined at the beginning of the 1990s: receptor-like kinase (RLK). Stress understanding is accompanied by systemic cascades activation. Research shows that aquaporin proteins are managed by environmental stimulation, including alteration of the pH cytoplasm, phosphorylation [233], and pH-Ca [234, 235], or intracellular relocation [236], at a biochemical stage as main drivers of hydric conductivity. Plant hormones were shown to involve long-distance signaling and hydraulic conductivity monitoring of the root and shoot. In controlling abiotic stress tolerance, such as dripping, salinity, cold temperature, ABA is the most critical hormone [237, 238]. ABA is engaged in the development of abiotic cellular answers to the synthesis or catabolism of several other development inhibitors, including auxin, cytokine, ethylene, gibberellin, brassinoid, JA, and other variables shown to be engaged in regulating the physiological process. ABA involves the regulation of abiotic cellular reactions Increased Ca2+ intracellular concentrations are also inducing multisignal modules under pressure circumstances, including inositol trisphosphate, hexaphosphate inositol, diacyl glycerol, and ROS [239]. Ca binding enzymes that act as Ca2+ detectors detect high concentrations of Ca2+ [240] that can cause calcium-dependent protein kinases to activate.

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The rates of expression of stress-responsive genes can, therefore, be regulated by activated kinases or phosphatase [241] using phosphorylate or dephosphorylate particular transcription variables. Capable of interacting with the DNA-bounding protein regulating these genes, leading to its activation or suppression, the activated Ca2+ sensors can also connect with the cis elements of major stress-response gene promoters [240, 241]. Huge cell injury or loss may occur after long-term exposure or following extremely short-term exposure to very high temperatures at moderately high temperatures [242]. This can decrease ion flow and lead to ROS and other toxic compounds, which have a severe effect on plant growth [243]. The expression of heat shock proteins and other proteins is a good adjustment strategy under conditions of exposure to high temperatures, where the proteins are often related to stress tolerance [242] and WU [244], membrane stability [245], and cellular hydration maintenance [246]. Different abiotic stresses cause ROS surges, which are extremely reactive and toxic, leading to harmful and ultimately oxidative stresses to protein, lipid, carbohydrogen, and DNA [247–249]. Recently, new retrograde signals such as 30 -phosphoadenosin 50 phosphate metabolite have been reported, which have been shown to accumulate from chloroplast to the nucleus during high light and drought, to regulate ABA signals and stomatological closures during oximal stress. This leads to drought tolerance and highlights transcriptome activation [250] and shows an indispensable part in stress tolerance. An amount of abiotic genes and TFs linked to stress in transgenic crop organisms have been isolated and overexpressed to enhance stress tolerance. For example, cycling overexpression Dof Factor 3 in Arabidopsis increased drought, cold, and salt tolerance [251, 252] as well as the increased control of cell osmoprotection genes and ROS homeostasis [252, 253].

4.5.1 Genetics and genomics approaches The impact on crop efficiency of abiotic pressure is restricted to traditional reproduction of vegetable crops. This could be ascribable to the nature of the features regulated in a set of genes in various discrete characteristics loci (QTL) [254]. However, success for improved heat and drought tolerance traits can be seen in conventional breeding. Haley et al. [255] have developed a drought-tolerant wheat variety called Ripper and in Colorado they have achieved an excellent ranch with superior grain yields. In breeding

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programs with marker-assisted backcrossing and recurrent marker-assisted selection strategy, the use of quantitative characteristics locus markers has produced positive results also [256]. In order to enhance drought resistance in elite durums (T. turgidum ssp. hardum) and baked (T. aestivum) wheat cultures, QTLs of wild emmer wheat are introduced through a marker-assisted selection [257]. In the genome sequence, annotation, and functionality of major proteins, significant advancement was achieved, notwithstanding difficulties arising from the chromosome size and the polyploidism of cultivars such as wheat [258]. The fresh wheat full-genome sequence assortment of shotgun sequences, using combines of optimized information kinds and an assembly algorithm to address large and complicated genomes, have lately been produced by Clavijo et al. [259]. 104,091 protein-coding genes were recognized as reliable and 10,156 RNA genes were not coding. The genome sequence data of both wheat and Aegilops should identify structural variants and help to annotate gene models that include those involving complex characteristics such as heat and drought. In order to control drought stress, in addition to protein coding genes, miRNAs are functionally conserved across some crops. In drought-resistant wild emmer wheat MIR166 was controlled [260]. Huang et al. [261] have also recognized a long miRNA gene that is not encoding and regulates the development of β-diketone wax, which is highly efficient in reducing water loss in drought tolerance. These findings suggest the ability to enhance the drought tolerance in grain plants with directed miRNA-based genetic modifications [262]. The design of plants with enhanced dryland tolerance can serve as models for genome study for species extremely tolerant to drought, such as tolerant desiccation or resurrection plants [263]. Although seed and other organisms are often tolerant of desiccation, only some angiosperm species have an advancing tolerance to vegetative desiccation caused by environmental constraints [263]. A species of monocotyledonous plants closely related to cereals is Xerophyta viscosa. It is, therefore, an ideal model to understand extreme cereal dehydration. Vegetative DT reactivation is based on the presence in reproductive structures of DT-associated genes such as seeds, and therefore DT genomic information is re-directed to vegetative tissues [264]. Costa et al. [264] demonstrated that ABI5, which is an important element for the longevity of X, could be an expression regulator of the LEA4 family, dry state viscosa. These researchers also identified two structural orthologies for ABI3, a key seed maturation regulator and DT, together with most of the blood-regulated ABI3 genes.

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4.6 Conclusion and future perspectives Plants have developed sophisticated mechanisms for adapting to various and complex abiotic stresses. New technologies like genomics and genetic transformation have made considerable progress in the comprehension of these complex characteristics in higher plants. But further validation of products or prototypes in the field is necessary for the commercial application of positive research outcomes. Research from new, emerging fronts, epigenetics, and interactions between plants and the microbiome of the soil, also has opportunities. In the field of soil microbiome research, for example, biotic stress and abiotic stress can be improved in crops. Plant mechanisms to escape dryness or heat stress can be mediated by the microbes around a plant, especially the roots, and are linked with different phases of plant development, physiological cascades, and biochemical or molecular reactions occurring at cellular or whole organism levels. Advances produced through the use of the latest instruments and methods for molecular and genomic diseases have opened up study possibilities for crop microbiota, so that a variety of microorganisms are explored biologically in and outside the recipient cells. Significant developments in the field of plant genome characterization and genome editing technology optimization in culture have improved our knowledge and ability to grow plant stress tolerant crops. In the final analysis, genome modification and transgenic approaches must be combined with efforts to achieve the desired improved varieties using conventional and marker-assisted breeding activities. In order to guide breeding programs in target traits to select and identify newly adapted germplasm it is also necessary to consider geographically different climate change models. These initiatives will produce tangible practical results, which can help to alleviate the effects of climate change, in particular in relation to drought and heat stress, and help to enhance crop productivity and food security, particularly in areas like Africa.

References [1] D.L. Smith, S. Subramanian, J.L. Lamont, M.B. Ekegard, Signaling in the phytomicrobiome: breadth and potential, Front. Plant Sci. 6 (2015)709. [2] D.L. Smith, V. Gravel, E. Yergeau, Editorial: signaling in the phytomicrobiome, Front. Microbiol. 8 (2017)611. [3] K.R. Theis, N.M. Dheilly, J.L. Klassen, R.M. Brucker, J.F. Baines, T.C.G. Bosch, et al., Getting the hologenome concept right: an eco-evolutionary framework for hosts and their microbiomes. mSystems 1 (2016), e00028–16 https://doi.org/ 10.1128/mSystems.00028-16.

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