Harnessing Bacterial Endophytes for Promotion of Plant Growth and Biotechnological Applications: An Overview

Endophytic bacteria colonize plants and live inside them for part of or throughout their life without causing any harm or disease to their hosts. The symbiotic relationship improves the physiology, fitness, and metabolite profile of the plants, while the plants provide food and shelter for the bacteria. The bacteria-induced alterations of the plants offer many possibilities for biotechnological, medicinal, and agricultural applications. The endophytes promote plant growth and fitness through the production of phytohormones or biofertilizers, or by alleviating abiotic and biotic stress tolerance. Strengthening of the plant immune system and suppression of disease are associated with the production of novel antibiotics, secondary metabolites, siderophores, and fertilizers such as nitrogenous or other industrially interesting chemical compounds. Endophytic bacteria can be used for phytoremediation of environmental pollutants or the control of fungal diseases by the production of lytic enzymes such as chitinases and cellulases, and their huge host range allows a broad spectrum of applications to agriculturally and pharmaceutically interesting plant species. More recently, endophytic bacteria have also been used to produce nanoparticles for medical and industrial applications. This review highlights the biotechnological possibilities for bacterial endophyte applications and proposes future goals for their application.


Introduction
Endophytes are fungal and bacterial organisms that inhabit the plant endosphere without harming their hosts. They live asymptomatically in the plant cellular environment and perform symbiosis-specific functions such as synthesis of secondary metabolites or signaling molecules that function as internal and external stimuli during the mutualistic interaction [1]. Endophytic microbes are sources of novel biomolecules for the biochemical and pharmaceutical industries [2]. They produce biologically active metabolites, including immune-suppressive compounds, anticancer agents, plant growth promotors, antimicrobial volatiles, insecticides, antioxidants, and antibiotics [3,4], with huge potential for for application in medicine, pharmaceutics industry, or agriculture ( Figure 1). Moreover, endophytic microbes can improve plant growth under harsh conditions such as nutrient stress, temperature stress, salinity, trace metal stress, or drought [5]. They can also help plants to grow in contaminated environments by degrading hazardous compounds. We describe the main concepts of the application of endophytes in agriculture and biotechnology.
Endophytic colonization can be local or systemic [9,10]. The plant endosphere represents a protective niche in which the endophytes are protected from biotic and abiotic stress. Moreover, endophytes can ecologically adapt to their environment and overcome plant defense responses [11].
Bacterial endophytes can also be classified as obligate or facultative endophytes. When endophytic bacteria rely on plant metabolites for survival and transfer between
Endophytic colonization can be local or systemic [9,10]. The plant endosphere represents a protective niche in which the endophytes are protected from biotic and abiotic stress. Moreover, endophytes can ecologically adapt to their environment and overcome plant defense responses [11].

Plant-Bacterial Endophyte Interactions
Interactions between bacteria and plants occur in many ways and at different levels ( Figure 2). All plant organs interact with microorganisms at a specific stage of their life, and these interactions are not necessarily harmful to the plant. Plants can also benefit directly or indirectly from the interaction [37,38]. An example includes the well-studied rhizobialegume interaction. Many endophytic bacteria form less specific symbiotic interactions with plants, although both partners adjust their metabolisms to the symbiotic conditions and can influence the biochemical properties of the partner [39]. This can result in promotion of the growth of the plant under normal and particularly harsh conditions [40,41].
Plants produce root exudates to attract beneficial bacteria, whereas bacterial endophytes recognize these compounds [42]. The bacteria in the root environment move towards the roots in response to the chemical attraction of the exudates [43]. After attachment to the root surface, they can enter the root, e.g., at lateral root emergence or openings caused by wounds or mechanical wounding [43]. Several bacterial structures are involved in their attachment to the plant surface, including fimbriae, flagella, bacterial surface polysaccharides, and lipopolysaccharides. For example, in Rhizobium spp., the surface polysaccharides are modified during the transition from free-living cells to the bacteroid form through the expression of surface antigens [44]. through the plant plasma membrane or by rhizophagy. Rhizophagy is a phenomenon in which many plants get microbes from the soil into their cells and digest them as a source of essential nutrients [50,51].
However, most endophytes reside in the intercellular spaces of their hosts, i.e., in sites that are rich in carbohydrates, inorganic nutrients, and amino acids [52]. Besides root colonization, endophytic bacteria can also occupy the intercellular spaces of stems, leaves, seeds, flowers, fruits, and xylem vessels [53][54][55][56][57]. Endophytes with intracellular colonization are difficult to study because they are often non-cultivable [58].

Plant Growth Promotion
Endophytic bacteria utilize the same mechanisms as rhizosphere bacteria for enhancing plant growth in silviculture, horticulture, and agriculture, as well as in phytoremediation [59]. The growth-promoting effect can be either direct or indirect ( Figure 3). Bacterial entrance and spread inside plant tissues require plant cell wall modification, which is achieved by the secretion of cell-wall-degrading enzymes like endoglucanases, xylanases, cellulases, and pectinases by the endophytic bacteria [45,46]. Penetration into the host can be active or passive. Active penetration is completed by proliferation and attachment tools involving pili, flagella, twitching motility, and lipopolysaccharides, whereas quorum sensing influences bacterial colonization and movement in the host plant [47]. Passive penetration occurs through cracks on root tips or root emergence zones or arising from the activities of harmful organisms [12].
Bacterial colonization often begins at the root surface. After successful entry, the bacteria can move to aerial parts by the transpiration stream and with the support of the bacterial flagella [48]. This colonization pattern begins with intracellular microbial access through root hairs [49]. Endophytes can pass through the plant cell wall and enter the root cell either directly by the secretion of plant cell-wall-degrading enzymes and passage through the plant plasma membrane or by rhizophagy. Rhizophagy is a phenomenon in which many plants get microbes from the soil into their cells and digest them as a source of essential nutrients [50,51].
However, most endophytes reside in the intercellular spaces of their hosts, i.e., in sites that are rich in carbohydrates, inorganic nutrients, and amino acids [52]. Besides root colonization, endophytic bacteria can also occupy the intercellular spaces of stems, leaves, seeds, flowers, fruits, and xylem vessels [53][54][55][56][57]. Endophytes with intracellular colonization are difficult to study because they are often non-cultivable [58].

Plant Growth Promotion
Endophytic bacteria utilize the same mechanisms as rhizosphere bacteria for enhancing plant growth in silviculture, horticulture, and agriculture, as well as in phytoremediation [59]. The growth-promoting effect can be either direct or indirect ( Figure 3).

Direct Plant Growth Promotion
A. Phytohormone production Plant growth regulators or phytohormones are organic substances that modify, inhibit, or promote plant growth and development at low concentrations (<1 mM) [60]. For agricultural applications, they are either chemically synthesized, extracted from plant materials, or produced by microbial fermentation. However, their complex chemical structures or low abundance in plants often prevent the application of these techniques [61]. Alternatively, the development of techniques for fermentative hormone production may decrease the production costs and increase productivity.
The plant defense hormone ethylene is involved in various stress responses, as well as developmental processes, including root development. In the rhizobia-legume symbiosis, it participates in the nodulation process [73]. Bacterial endophytes can possess a 1aminocyclopropane-1-carboxylate deaminase (ACC deaminase), which generates the nitrogen sources ammonia and α-ketobutyrate from the ethylene precursor ACC [74]. Therefore, these bacterial endophytes can promote plant growth under nitrogen-limitation conditions through the secretion of ACC deaminases. This also results in a stronger immune system and promotes tolerance against abiotic stress. For instance, Pseudomonas brassicacearum SVB6R1 increases salt stress tolerance in sorghum plants through the section of ACC deaminase [33]. Moreover, Paenibacillus polymyxa from the bulbs of Lilium

Direct Plant Growth Promotion
A. Phytohormone production Plant growth regulators or phytohormones are organic substances that modify, inhibit, or promote plant growth and development at low concentrations (<1 mM) [60]. For agricultural applications, they are either chemically synthesized, extracted from plant materials, or produced by microbial fermentation. However, their complex chemical structures or low abundance in plants often prevent the application of these techniques [61]. Alternatively, the development of techniques for fermentative hormone production may decrease the production costs and increase productivity.
The plant defense hormone ethylene is involved in various stress responses, as well as developmental processes, including root development. In the rhizobia-legume symbiosis, it participates in the nodulation process [73]. Bacterial endophytes can possess a 1aminocyclopropane-1-carboxylate deaminase (ACC deaminase), which generates the nitrogen sources ammonia and α-ketobutyrate from the ethylene precursor ACC [74]. Therefore, these bacterial endophytes can promote plant growth under nitrogen-limitation conditions through the secretion of ACC deaminases. This also results in a stronger immune system and promotes tolerance against abiotic stress. For instance, Pseudomonas brassicacearum SVB6R1 increases salt stress tolerance in sorghum plants through the section of ACC deaminase [33]. Moreover, Paenibacillus polymyxa from the bulbs of Lilium lancifolium promotes the growth of two Lilium varieties through secretion of ACC deaminase, among other effects [34].
Several studies reported endophytic bacterial species which produce gibberellins and cytokinins. Gibberellins control plant growth and development through enhanced seed germination, stem and leaf growth promotion, stimulation of flowering and fruit development, and delaying plant aging [75,76]. Cytokinin controls cell division and differentiation, increases resistance to biotic and abiotic stress, enhances phloem transport, and promotes flowering and axillary bud growth [77]. The endophytic Azospirillum lipoferum was inoculated in a maize plant previously treated by gibberellin inhibitor synthesis and subjected to drought stress. The inoculated maize plant performed better than the uninoculated controls, particularly under stress due to the bacterial gibberellin [78]. Moreover, endophytic bacterial strains including Pseudomonas resinovorans and Paenibacillus polymaxa isolated from Gynura procumbens exhibited an efficient ability to produce compounds similar to cytokinin in a broth extract [79]. These examples of endophytic bacteria-mediated biosynthesis of different phytohormones are illustrated in Table 2. Manufacturing nitrogenous fertilizers is costly, and their usage increases the pollution of groundwater with nitrate [90]. Interestingly, biological nitrogen fixation (BNF) accounts for about two-thirds of the globally fixed nitrogen [91]. Apart from photosynthesis, biological nitrogen fixation (BNF) is the most remarkable biological process, and this process is limited to prokaryotic organisms only. Bacterial endophytes can establish closed relations with certain crops. The plant endosphere contains excess carbon and a lack of oxygen, which presents suitable conditions for nitrogen fixation that can be then transported by endophytes to their host plant. Interestingly, endophytic bacteria can fix nitrogen within plants without forming nodule-like structures [92]. Some endophytic bacteria possess BNF genes that enable them to convert nitrogen gas (N 2 ) to other nitrogen forms such as nitrate and ammonium, which can be utilized by host plants [93,94]. In Brazil, it was observed that sugarcane plant (Saccharum officinarum L) cultivated without nitrogen fertilizers and infected with diazotrophic endophytes such as Herbaspirillum seropedicae and Acetobacter diazotrophicus were able to derive all their nitrogenous needs from atmospheric N 2 [95]. Regarding nitrogen fixation, endophytes do better than rhizosphere microbes in promoting plant growth and health, and help the plant thrive in nitrogen-restricted soil [96].
Bacterial endophyte inoculation has contributed to increased biomass over un-inoculated control plants, as noted by several authors (Table 3). Some endophytic strains of Enterobacter spp. and Klebsiella spp. have been reported to fix N 2 and promote the growth of sugarcane under gnotobiotic and natural conditions [97][98][99][100]. Wei et al. [101] isolated Klebsiella variicola DX120E, a nitrogen-fixing bacterium, from the roots of the ROC22 sugarcane cultivar. This strain was capable of fixing N 2 in association with sugarcane plants under gnotobiotic conditions, promoting GT21 cultivar growth and plant uptake of N, P, and K under greenhouse conditions. The total nitrogen content of Poa pratensis L. plants was increased by 37% after inoculation with the endophytic Burkholderia vietnamiensis WPB strain [102]. Significant increases in root and shoot biomass and flowers/fruits were obtained by the inoculation of cherry tomato Lycopersicon lycopericum cv 'Glacier', with Rahnella strain WP5, while an approximately twofold increase in total nitrogen content in root tissue of Lolium perenne was reported when the plant was inoculated with a multi-strain endophytic consortium (PTD1, WPB, WP19, WP1, and WW6) [103]. Andrade et al. [104] reported that about 40 endophytic bacterial strains were isolated from banana roots (Musa L.); out of these, 20 endophytic isolates had the capacity to grow in N-free media. Out of 20 isolates, four endophytic strains belonging to the Firmicutes (Bacillus spp.) showed the ability to fix nitrogen when assessed by the Kjeldahl and acetylene reduction assay methods. Moreover, these four isolates exhibit banana growth-promoting activities in vivo through nitrogen fixation, IAA production, and phosphate solubilization. The diazotrophic endophytic bacteria and their nitrogen-fixing capacity for plant growth promotion are summarized in Table 3.

b. Phosphate Solubilization
Plants take up monobasic (H 2 PO 4 − ) and dibasic phosphate (HPO 4 2− ) from the soil, whereas 95-99% of soil phosphorus is non-available for plants because it is present in precipitated, immobilized, and insoluble forms [119]. In agriculture, phosphate deficiency is compensated by applying chemical or organic phosphate fertilizers [120].
Endophytes increase phosphorus availability for plants, as they dissolve insoluble phosphate via secretion of organic acids, chelation, and/or ion exchange [121]. Furthermore, endophytes can secrete P-solubilizing enzymes, such as phosphatase, phytase, and C-P lyase (Figure 4) [122]. Secretion of organic acids such as citric, malonic, fumaric, tartaric, gluconic, acetic, or glycolic acid is considered the main mechanism involved in P solubilization. The P-solubilizing activity of the bacteria is usually correlated with a decrease in the pH value of the medium, which varies due to bacterial species (Figure 4). For example, the phosphate-solubilizing Bacillus spp. secretes itaconic, lactic, isobutyric, isovaleric, and acetic acid, and thus acidifies the medium and rhizosphere during sym-biosis [123]. Other P-solubilizing mechanisms are the secretion of exopolysaccharides ( Figure 4). [124] and the degradation of P-containing substances.

Ageratina adenophora
In vitro assay • Growth on nitrogen-free liquid medium [118] Although it is not clear how bacteria living in a plant can dissolve the insoluble phosphate that is located outside of the plant, 50% of the endophytes isolated from ginseng were able to dissolve phosphate [125]. Comparably high numbers of endophytes isolated from soybean, cactus, legumes, strawberry, and sunflower were effective phosphate solubilizers [126][127][128]. Very high phosphate-solubilizing activity was recorded for the Bacillus species of B. megaterium and B. amyloliquefasciens, which solubilized insoluble zinc and potassium salts [129].
The utilization of endophytic bacteria inoculants as microbial biofertilizer candidates would provide a promising alternative to chemical fertilizers and for commercial applications. Inoculation of peanut (Arachis hypogaea L.) with the P-solubilizing nodule endophyte Pantoea J49 increased the aerial dry weight in greenhouse experiments [130]. Pseudomonas letiola mobilized insoluble P and increased the shoot length and growth of the apple tree variety Ligol [131]. Moreover, inoculation of Rhodococcus sp. EC35, Pseudomonas sp. EAV, and Arthrobacter nicotinovorans EAPAA enhanced the Pavailability and plant growth of Zea mays in soils amended with tricalcium phosphate [132]. Oteino et al. [133] found that the endophytic Pseudomonas strains L111, L228, and L321 isolated from the leaves of Miscanthus giganteus showed high P solubilization activity. Pseudomonas fluorescens L321 inoculation resulted in gluconic acid accumulation in the medium and consequently larger P. sativum L. plants. Joe et al. [134] investigated the effect of two salt-tolerant and phosphate-solubilizing bacteria (Acinetobacter sp. and Bacillus sp.) on Phyllanthus amarus and showed that the endophytes were responsible for the better performance and faster growth of the plants due to the promotion of germination, better P uptake, and stimulation of the immune system by promoting the biosynthesis of phenolic compounds, the radical scavenging system, and antioxidative enzymes.  The utilization of endophytic bacteria inoculants as microbial biofertilizer candidates would provide a promising alternative to chemical fertilizers and for commercial applications. Inoculation of peanut (Arachis hypogaea L.) with the P-solubilizing nodule endophyte Pantoea J49 increased the aerial dry weight in greenhouse experiments [130]. Pseudomonas letiola mobilized insoluble P and increased the shoot length and growth of the apple tree variety Ligol [131]. Moreover, inoculation of Rhodococcus sp. EC35, Pseudomonas sp. EAV, and Arthrobacter nicotinovorans EAPAA enhanced the P-availability and plant growth of Zea mays in soils amended with tricalcium phosphate [132]. Oteino et al. [133] found that the endophytic Pseudomonas strains L111, L228, and L321 isolated from the leaves of Miscanthus giganteus showed high P solubilization activity. Pseudomonas fluorescens L321 inoculation resulted in gluconic acid accumulation in the medium and consequently larger P. sativum L. plants. Joe et al. [134] investigated the effect of two salttolerant and phosphate-solubilizing bacteria (Acinetobacter sp. and Bacillus sp.) on Phyllanthus amarus and showed that the endophytes were responsible for the better performance and faster growth of the plants due to the promotion of germination, better P uptake, and stimulation of the immune system by promoting the biosynthesis of phenolic compounds, the radical scavenging system, and antioxidative enzymes. Chen et al. [135] showed that the endophytic Pantoea dispersa promoted P uptake into cassava (Manihot esculenta Crantz) roots due to the secretion of salicylic and benzene acetic acids for more effective P solubilization. Root inoculation with P. dispersa also activated the natural soil microbial community in the rhizosphere. Such strains could be suitable for optimizing agro-microecological systems under P limitations. Finally, Castro et al. [136] used the mangrove endophytic Enterobacter sp. as an inoculum for the production of seedlings of A. polyphylla trees and found that the endophyte increased shoot dry mass and the fitness of the seedling.

c. Siderophore Production
Iron is essential for all life and is required as a co-factor of many essential enzymes, including the biochemical processes involved in nitrogen fixation in nodules. However, most soil iron is not available for plant absorption because it is present in extremely insoluble ferric (Fe 3+ ) forms of carbonates, hydroxides, oxides, and phosphates [137] in the soil. Under iron deficiency, many microorganisms can produce and secrete the low molecular weight siderophores, which bind Fe 3+ , Fe 2+ , and other divalent metal ions which are essential for plants [138]. Besides delivery to the plants, siderophores also participate in scavenging undesired metal ions in the rhizosphere to prevent uptake by the roots. These include Zn, Cd, Cr, Al, and Pb ions and, also radioactive ions such as U or Np to reduce toxicity for the plants [139]. Siderophores can also stimulate the plant-induced systematic resistant response to alleviate the toxicity of trace metals to plant growth [76].
Normally, endophytic bacteria produced siderophores only in soils with iron limitations [140]. Sabaté et al. [83] showed this for siderophores produced by two endophytic Bacillus spp. strains, which, in promoted the growth of common bean under iron limitation. Siderophores of the bacterial endophytes also outcompete phytopathogen by binding the essential elements required for their propagation, thereby protecting the plants [141]. For instance, endophytic Bacillus spp. inhibit the growth of Fusarium oxysporum by absorbing Fe 3+ from the environment through the secretion of siderophores. Lacava et al. [142] showed that the citrus endophyte Methylobacterium mesophilicum released hydroxamatetype siderophores into the medium. When the siderophore-containing supernatant was applied to Xylella fastidiosa subsp. pauca, it promoted the growth and chlorophyll content of the plants. Similar results were reported for various symbiotic interactions with different agriculturally relevant hosts in greenhouse experiments.

Indirect Plant Growth Promotion
A. Stress Tolerance Plants are exposed to various stresses [143], which are the result of antagonistic or toxic substances in their environment, nutrient or essential ion limitations, or biotic stress inducers [144]. Both biotic and abiotic stresses contribute about 30-50% of the agricultural loss worldwide [145]. Temperature, salinity, drought, trace metals, flooding, and nutrient deficiency are considered the major abiotic stresses ( Figure 5). Biotic stresses are induced by pathogenic microorganisms up to insects or nematodes. Therefore, future studies aim to develop eco-friendly technologies which increase plants' resistance to both abiotic and biotic stresses. A promising strategy is the generation of stronger and healthier plants with an improved immune system. Not surprisingly, endophytes have long been known to fulfill these criteria and provide excellent systems for agricultural application, as well as the identification of the molecular mechanisms by which they promote plant fitness. The microbial strategies range from the immediate activation of responsive systems which directly and specifically counteract the stress [146] and the production of anti-stress metabolites [147] that strengthens the plants, to a broad spectrum of immune responses which ultimately protect the plants better when exposed to different stresses. Understanding the mechanism behind these strategies may provide us with molecular and biochemical tools for agricultural applications. Endophytic bacteria support plants to combat drought stress via the production of volatile compounds, abscisic acid, ACC-deaminase, and IAA. Moreover, enhanced antioxidant activity and osmotic adjustment participate in the endophyte effects [148]. Razzaghi-Komaresofla et al. [149] introduced salinity-tolerant Staphylococcus sp. strains which improved the growth and salt tolerance of Salicornia sp. plants either individually or in combination. Endophyte-managed host resistance to pathogens also includes niche com- Endophytic bacteria support plants to combat drought stress via the production of volatile compounds, abscisic acid, ACC-deaminase, and IAA. Moreover, enhanced antioxidant activity and osmotic adjustment participate in the endophyte effects [148]. Razzaghi-Komaresofla et al. [149] introduced salinity-tolerant Staphylococcus sp. strains which improved the growth and salt tolerance of Salicornia sp. plants either individually or in combination. Endophyte-managed host resistance to pathogens also includes niche competition by the production of defensive metabolites such as antibiotics, antimicrobial, and structural compounds, as well as the induction of immunity or systemic resistance in the host plant [150].
Plants experiencing biotic and abiotic stress produce elevated concentrations of ethylene [151], which is are synthesized from ACC [152]. Production of the defense hormone ethylene restricts growth and hence affects the development of the plant in general [153]. Afridi et al. [154] reported the improved growth and stress tolerance of two wheat varieties inoculated with ACC-producing bacterial endophytes. An advantage of ethyleneproducing endophytes may be the local synthesis of the hormone in the symbiotic tissue, which might ensure that ethylene-induced defense occurs only in tissues that are exposed to stress. Endophyte-produced ACC-deaminase can alleviate the impact of elevated ethylene concentrations on stressful plants through the hydrolysis of ACC into α-ketobutyrate and ammonia. The stressed plant could utilize the ammonia and energy liberated from ACC decomposition for growth [155,156]. Multiple combinations of the beneficial features of endophytes, such as combinations of ethylene, siderophore, or exopolysaccharide production; nitrogen fixation; and phosphate solubilization are important to strengthen the plants under stress or nutrient limitations [148,157,158]. Interestingly, some endophytic bacteria possess sigma factors (Table 4), which are used to change the expression of some genes under unfavorable conditions to reduce negative impacts [106]. Data represented in Table 4 showed some examples of stresses and the mechanisms utilized by bacterial endophytes to alleviate these stresses.

B. Endophyte-Based Phytoremediation
Phytoremediation is a promising tool for cleaning soil, water and air of contaminants, and endophyte-assisted phytoremediation is used for metal bioremediation in the soil to allow or promote plant growth in previously contaminated soils [137]. Other investigations reported the use of endophytic remediation for contamination with organic contaminants [181], hydrocarbons [182], explosives [183], herbicides [184], tannery effluent [185], and uranium [186].
Eevers et al. [187] examined the effect of Enterobacter aerogenes UH1, Sphingomonas taxi UH1, and Methylobacterium radiotolerans UH1 on the growth of zucchini plants on 2,2-bis(pchlorophenyl)-1,1-dichloro-ethylene (DDE)-contaminated fields. Plants inoculated with the three strains separately or in combination showed an increased weight. Mitter et al. [188] planted sweet white clover plants on soils contaminated with diesel (up to 20 mg/kg). Plants inoculated with the hydrocarbon-degrading endophytes EA4-40 (Pantoea sp.), EA1-17 (Stenotrophomonas sp.), EA6-5 (Pseudomonas sp.), and EA2-30 (Flavobacterium sp.) showed increased biomass and successfully overcame the growth inhibition observed for noninoculated plants. Wu et al. [189] isolated the endophytic Bacillus safensis strain ZY16 from the roots of Chloris virgate. This strain exhibited multifunctional properties, including efficient degradation of the C 12 -C 32 n-alkanes of diesel oil and polycyclic aromatic hydrocarbons under hypersaline conditions, as well as production of biosurfactants, which resulted in stronger growth and biomass production in the inoculated plants compared with the controls. These studies indicated that bacterial endophytes have an important dynamic role in the management of abiotic stress and could efficiently be applied for environmental clean-up for sustainable agriculture development.

C. Disease Control
Currently, agrochemicals are considered the main method for combatting microbeinduced plant diseases; however, many of the applied substances have toxic effects on animals and humans. The application of endophytic bacteria is of great interest as an environmentally friendly alternative to agrochemicals [190].
Endophytes can restrict pathogen invasion into plants via direct and indirect mechanisms. The direct mechanism describes a competition between endophytes and phytopathogens in which the endophytes restrict pathogen growth, e.g., through the secretion of inhibitory metabolites. In the indirect mechanisms, the endophytes stimulate the plant's immune system or increase the plant's resistance toward the phytopathogens via upregulation of the defense genes [52]. Bacterial endophytes and phytopathogens have similar colonization patterns in the host plants and, consequently, they compete during invasion into host cells. Therefore, endophytes could be used as potential biocontrol agents to restrict pathogen entry into the host cell. The endophytic species Pseudomonas fluorescens and Pseudomonas aeruginosa produce 2, 4-diacetylphloroglucinol, penazine-1-carboxylic acid, pyoleutirin, pyrrolnitrin, or hydrogen cyanide, which suppress the growth of phytopathogenic fungi [191]. The most common endophytic bacterial species used in phytopathogen control are Bacillus species, since they produce lipopeptides, which hydrolyze fungal hyphal membranes [192,193]. The destabilization of the fungal membrane promotes nutrient leakage and hence reduces the virulence of fungi [191]. The indirect mechanisms include the stimulation of a jasmonate/ethylene-based defense response against necrotrophic microbes and a salicylic acid-based defense against biotrophic microorganisms [191,192].

D. Competition for Space and Nutrients
Niche competition means the competition of endophytes with deleterious pathogens for space and substrates. Blumenstein et al. [194] examined the competitive interaction between endophytes and the aggressive pathogen Ophiostoma novoulmi, which is the causative agent of the virulent Dutch elm disease. Based on the carbon utilization profiles, they showed that the endophytes showed extended niche overlap with the virulent pathogen; however, since the endophytes were more efficient at utilizing the applied carbon substrates, they were able to out-compete the pathogens. Another example described endophyte-produced siderophores that supplied sufficient iron to the endophytes but not the pathogen [195]. The chelated iron also became available to the host plant [52], which ultimately inhibited pathogen growth in the host plant by restricting mycelial growth and spore germination [196].

a. Antibiosis
Antibiosis is the synthesis and release of molecules that kill or inhibit the growth of the target phytopathogen [54], which results in plant disease control. The antibiotics and volatile organic compounds (VOCs) comprise ketones, alcohols, esters, terpenes, aldehydes, sulfur compounds, and lactones. VOCs, with their low molecular weights, can directly affect the growth of the phytopathogens at low concentrations, although the mechanisms are not well understood, since their perception systems are unknown [197,198]. Jasim et al. [199] reported the biosynthesis of iturin, surfactin, and fengycin by an endophyte Bacillus species from Bacopa monnieri. Besides toxic effects to pathogens, numerous endophytic bacterial VOCs control the symbiotic relationship in an extremely competitive environment for the host [200]. They might stimulate the propagation of the endophytes but not the pathogens.

b. Parasitism
Parasitism happens when one microbe feeds on another, e.g., a phytopathogen. This results in complete or partial lysis of its cellular structures. In particular, antagonistic bacteria feed on the fungal phytopathogen cell wall materials such as proteins, chitin, and glucans [201]. Bacteria form lipopolysaccharides and produce cell wall lytic enzymes for the infection of their hosts [202], and these cell wall lytic enzymes also cause hydrolysis of the cell wall of the fungal pathogen [203].

c. Induced Systemic Resistance (ISR)
Beneficial bacterial induce ISR in plants, which stimulates their local and systemic defensive responses, thus protecting the host against pathogen attacks. Besides the classical salicylic acid-based ISR, several endophytes also activate jasmonic acid-and ethyleneassisted immune responses [204]. An example of the latter mechanism includes the endophytic Bacillus velezensis YC7010, which confers systemic resistance in Arabidopsis seedlings against the insect pests Myzus persicae and the green peach aphid [205]. The different strategies are summarized in Table 5 and examples are provided in Figure 6. Table 5. Different strategies used by endophytic bacteria to resist phytopathogens.

Production of Bioactive Metabolites for Agricultural and Medical Applications
Endophytic bacteria produce diverse bioactive metabolites that can be used in medicine as well as in agriculture for plant growth promotion and pesticides. The following examples describe some of the metabolites with biotechnological relevance.

Pharmaceutical Applications
Newman and Cragg [217] argued that endophytes produced approximately half of the new drugs introduced in the market from 1981 to 2010. They are used as insecticides, antioxidants, antimicrobial agents, anticancer, and antidiabetic compounds, among others ( Figure 7) [218]. Many metabolites used as anticancer or antimicrobial agents have multiple targets in plants, animals, and human pathogens and offer many prospects in veterinary and medical therapy. Several of them are also considered eco-safe [219].
Medicinal plants have long been used to cure many diseases. More recently, it became obvious that many of their important chemical ingredients were derived from endophytes or the association of the medicinal plants with them. Alvin et al. [220] isolated endophytes from medicinal plants producing polyketides and small peptides, which displayed antituberculosis activity. The secondary metabolite profiles produced by Acinetobacter baumannii associated with Capsicum annuum L. uncovered phenolic compounds with peroxidant and antioxidant abilities [221]. Many peptides with antibacterial, antifungal, anticancer, immunosuppressive, and antimalarial properties have been identified, and several of them are interesting because of their target-specificities [222].

Production of Bioactive Metabolites for Agricultural and Medical Applications
Endophytic bacteria produce diverse bioactive metabolites that can be used in medicine as well as in agriculture for plant growth promotion and pesticides. The following examples describe some of the metabolites with biotechnological relevance.

Pharmaceutical Applications
Newman and Cragg [217] argued that endophytes produced approximately half of the new drugs introduced in the market from 1981 to 2010. They are used as insecticides, antioxidants, antimicrobial agents, anticancer, and antidiabetic compounds, among others ( Figure 7) [218]. Many metabolites used as anticancer or antimicrobial agents have multiple targets in plants, animals, and human pathogens and offer many prospects in veterinary and medical therapy. Several of them are also considered eco-safe [219].

Industrial Applications
The extracellular hydrolytic enzymes produced by bacterial endophytes are required for host cell infection and triggering ISR [223]. The osmoregulation and antioxidant enzymes of the bacteria are involved in mitigating salinity stress on the metabolism of the host plant [224]. Microbial synthesis of biologically active compounds such as enzymes and secondary metabolites have been used for the manufacture of industrial products, including food and food supplements [225], biofuels [226], pharmaceuticals [227], detergents [228], and biopesticides [229].
For example, Ntabo et al. [230] isolated endophytic bacteria from Kenyan mangrove plants and showed that they produce proteases, pectinases, cellulases, amylases, and chitinases with putative industrial value. The endophytic Pseudomonas aeruginosa L10, associated with the roots of Phragmites australis, efficiently degraded hydrocarbons and produced a biosurfactant [231]. Baker et al. [232] studied endophytic bacteria associated with Coffea arabica L. and found that they could degrade caffeine, which has potential use in the decaffeination of beverages.  Medicinal plants have long been used to cure many diseases. More recently, it became obvious that many of their important chemical ingredients were derived from endophytes or the association of the medicinal plants with them. Alvin et al. [220] isolated endophytes from medicinal plants producing polyketides and small peptides, which displayed antituberculosis activity. The secondary metabolite profiles produced by Acinetobacter baumannii associated with Capsicum annuum L. uncovered phenolic compounds with peroxidant and antioxidant abilities [221]. Many peptides with antibacterial, antifungal, anticancer, immunosuppressive, and antimalarial properties have been identified, and several of them are interesting because of their target-specificities [222].

Industrial Applications
The extracellular hydrolytic enzymes produced by bacterial endophytes are required for host cell infection and triggering ISR [223]. The osmoregulation and antioxidant enzymes of the bacteria are involved in mitigating salinity stress on the metabolism of the host plant [224]. Microbial synthesis of biologically active compounds such as enzymes and secondary metabolites have been used for the manufacture of industrial products,

Nano Biotechnology
Nanoparticles have numerous technological and industrial applications in electronics, the energy industry, medicine, catalysis, and biotechnology [233][234][235][236][237][238]. Biological methods for the synthesis of nanoparticles provide many advantages over physical and chemical methods, avoiding the need for high energy and the absence of any toxic waste, which makes it simple, economical, and environmentally friendly [239][240][241].

Conclusions and Future Prospective
Biotechnology has proven to be applicable in many medical, industrial, and agricultural fields, as it is inexpensive and eco-friendly. Endophytes are plant symbionts; unlike the rhizosphere and phyllosphere bacteria that live on the plant's surface, endophytes find their way into the plants' endosphere to become protected from inappropriate environmental conditions. Recently, different advanced techniques such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) have been used to explain the plant-microbe interaction. These advanced techniques develop ideal plants/microbes that are relevant for agricultural applications. Endophytes produce several active metabolites that have positive effects on plant growth, leading to increased crop yields. Compared with agrochemicals, the presence of endophytes inside the host plant puts them in direct contact with the plant and becomes more effective. Chemicals are applied outside the plant, and a large part of them do not benefit the plant and cause pollution of the environment. Apart from the biotechnological uses of endophytes in sustainable agriculture, bacterial metabolites include other compounds that can be used in many technological and industrial applications, as well as their ability to reduce metal ions to nanoparticles, which can be used in technological, industrial, medical, and electronic applications. In the future, nanoparticles will be helpful in the formation of new nano-drugs, nano-pestcides, and nano-fertilizers to suppress plant pathogens and to increase the fertility of soils and plants through providing essential elements. Therefore, the mechanisms of fabricating specific shapes and sizes using eco-friendly microbes, including endophytes, require more research. Moreover, the integration of bacterial endophytes into different biomedical and biotechnological applications is still limited; therefore, it is urgent to discover new compounds from endophytic bacteria that have biological activities. Much research is still needed to understand endophytic bacteria and their relationships with plants, and to optimize the use of their premium metabolic products and formulate them into products that can be marketed for economic benefit.

Data Availability Statement:
The data presented in this study are available on request from the corresponding author.

Conflicts of Interest:
The authors declare no conflict of interest.