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Kamran, M.;  Imran, Q.M.;  Ahmed, M.B.;  Falak, N.;  Khatoon, A.;  Yun, B. Endophytes and Abiotic Stresses. Encyclopedia. Available online: https://encyclopedia.pub/entry/39866 (accessed on 15 July 2025).
Kamran M,  Imran QM,  Ahmed MB,  Falak N,  Khatoon A,  Yun B. Endophytes and Abiotic Stresses. Encyclopedia. Available at: https://encyclopedia.pub/entry/39866. Accessed July 15, 2025.
Kamran, Muhammad, Qari Muhammad Imran, Muhammad Bilal Ahmed, Noreen Falak, Amna Khatoon, Byung-Wook Yun. "Endophytes and Abiotic Stresses" Encyclopedia, https://encyclopedia.pub/entry/39866 (accessed July 15, 2025).
Kamran, M.,  Imran, Q.M.,  Ahmed, M.B.,  Falak, N.,  Khatoon, A., & Yun, B. (2023, January 07). Endophytes and Abiotic Stresses. In Encyclopedia. https://encyclopedia.pub/entry/39866
Kamran, Muhammad, et al. "Endophytes and Abiotic Stresses." Encyclopedia. Web. 07 January, 2023.
Endophytes and Abiotic Stresses
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This entry is adapted from the peer-reviewed paper 10.3390/cells11203292

Biotic and abiotic stresses severely affect agriculture by affecting crop productivity, soil fertility, and health. These stresses may have significant financial repercussions, necessitating a practical, cost-effective, and ecologically friendly approach to lessen their negative impacts on plants. Endophytes are microorganisms that inhabit plants. Endophytes are known to promote the growth of host plants in several ways, including detoxification of toxic compounds, defense against pathogens, and production of plant growth-promoting hormones. The most common abiotic stressors include temperature, drought, salinity, and nutrient deficiency. These stresses may cause alterations in metabolomics and transcriptomics, which change the exudates from the roots and leaves and, in turn, influence the microbial community associated with plants. In the soil ecosystem, plant-associated microbes play a central role, working as natural partners that facilitate local and systemic mechanisms in plants to defend against adverse environmental conditions. 

endophytes plant defense drought salinity

1. Temperature

Temperature is the most common stress experienced by plants. The average global temperature and the frequency of extreme weather events have increased considerably over the past several decades owing to climate change. According to the results of several climate model simulations, the average temperature of the world is predicted to be between 1.1 and 5.4 °C warmer in 2100 than it is today [1]. The main effects of temperature stress include alterations in plasma membrane activity, transpiration, reduced photosynthesis, enzymatic dysfunction, cell division, plant growth, and development [2]. Previous studies have shown that plant response to heat stress may be influenced by microbe interactions [3][4][5].
Reports suggest that the endophytic bacteria Burkholderia phytofirmans strain PsJN can alter photosynthesis and the carbohydrate metabolism involved in chilling stress, thereby enhancing the cold tolerance of grapevine plants [6][7]. Bacterial endophytes induce adaptation to chilling, resulting in reduced cell damage, increased photosynthesis, and accumulation of chilling stress-associated metabolites, such as proline, starch, and phenolic compounds [8].
Some microbes can protect themselves from extreme temperature conditions by enhancing the production of heat- and cold-tolerant proteins. Molecular chaperones have been reported to play essential roles in heat stress tolerance in microbes [9][10]. For example, the DnaK gene encoding heat shock protein (Hsp70), a well-known chaperone in heat stress tolerance, was found to be highly expressed in Alicyclobacillus acidocaldarius during heat and cold stress [11]. Microbes adapted to low or high temperatures could alleviate the negative impacts of extreme temperatures and expand the host plant’s ability to survive these conditions. Khan et al. reported that thermotolerant Bacillus cereus strain SA1 alleviated heat stress in soybean plants by enhancing antioxidant defense enzymes and altering hormonal profiles [12]. Several other studies have reported a similar mechanism of heat stress tolerance in host plants mediated by thermotolerant endophytes and rhizobacteria, such as Bacillus amyloliquefaciens in rice [13], Pseudomonas putida strain AKMP7 in wheat [14], and Pseudomonas sp. strain AKMP6 in sorghum [15]. In some cases, the relationship between plants and microbes is important for both partners. The symbiosis between the fungus Curvularia protuberata and panic grass is interesting, as this relationship allows both organisms to survive high soil temperatures. However, neither the host plant nor the fungus can individually tolerate high-temperature conditions [16]. Furthermore, C. protuberata is required to be infected by Curvularia, a thermal-tolerant virus (CThTV), to confer heat tolerance to the host plant [16]. Moreover, C. protuberate-mediated heat tolerance has been observed in tomatoes [17], indicating that the underlying process may have a wide range of applications to help plants survive at elevated temperatures [18].

2. Salinity

Salinity is a global issue that affects agricultural productivity. The regions affected by salinity are gradually expanding owing to insufficient precipitation, poor irrigation systems, salt deposition, water pollution, and other environmental factors [19]. Although the development of salt-tolerant crops has been an important scientific aim, there has not been much progress in this direction because not many of the key genetic traits that affect salt tolerance have been identified [20][21][22]. Introducing salt-tolerant microorganisms that promote plant growth is a potential alternative to increase crop tolerance to salinity stress [23].
Plants exhibit a two-stage response to salinity stress. During the first phase, growth slows drastically, and stomata close in response to decreased water potential. Sodium ions are built up in the second phase, increasing oxidative stress, which in turn damages photosynthetic components [21]. In addition to harmful stress by-products, reactive oxygen species (ROS) may also function as signal molecules to initiate defense mechanisms against salt and other stressors [24].
Multiple mechanisms have been implicated in endophyte-mediated salinity tolerance. One approach is to produce large quantities of organic osmolytes such as trehalose, proline, glycine, and betaine, which offer an adaptive response to salinity stress [19]. Some endophytes help plants tolerate salinity stress by reprogramming the antioxidant defense system and hormonal profiles. For example, Khan et al. [25] reported that bacterial endophytes Bacillus cereus, Micrococcus yunnanensis, Enterobacter tabaci, Curtobacterium oceanosedimentum, Curtobacterium luteum, and Enterobacter ludwigii isolated from halotolerant plants enhanced the salt stress tolerance of rice by altering defense enzymes, indole-3-acetic acid, abscisic acid (ABA), and gibberellin levels. Similar mechanisms have been observed for soybean [26], tomato [27], cucumber [28], and maize [29].
Some endophytes enhance the ability of the host plant to alleviate salt stress by improving key transcripts that are required for salinity tolerance. For example, the bacterial endophyte Bacillus subtilis has been reported to enhance salinity tolerance in Arabidopsis by simultaneously downregulating high-affinity K+ transporter 1 (HKT1) expression in roots and upregulating it in shoots. The induction of HKT1-dependent shoot-to-root recirculation was likely to result in a 50% reduction in plant-wide Na accumulation [30]. Another study reported that auxins produced by Bacillus amyloliquefaciens alleviate salt stress by upregulating the expression of ethylene-responsive element binding protein (EREBP), betaine aldehyde dehydrogenase (BADH), salt overly sensitive 1 (SOS1), and catalase genes in rice [31]. Another endophytic bacterium, Pseudomonas pseudoalcaligenes, was shown to enhance salt tolerance in rice by accumulating high concentrations of glycine betaine-like compounds [32]. Some endophytes secrete exopolysaccharides that bind cations in the roots (particularly Na+) and inhibit their transport to leaves, thereby reducing salt stress [31]. They proposed that roots from inoculated seedlings had a larger proportion of soil sheaths covering them, which could slow down the passage of apoplastic Na+ into the stele.

3. Drought

Without water, life on Earth is not possible. Too little water (drought) or too much water (flood) can have a considerable influence on several aspects of plant and microbial life. A drought is described as a period when there is insufficient water available for an organism or environment to function at its best [33][34][35]. Drought stress may occur at any plant developmental stage and can affect growth and development to varying degrees based on the onset time, duration, and severity. At the reproductive stage of the plant, drought stress may directly reduce more than 50% of the yield [13][36]. Plant breeders have made remarkable progress in creating drought-tolerant crops, but despite this, they are still unable to satisfy the needs of food security in the face of a rising global population, climate change, and water scarcity [35]. Traditional breeding, however, requires much work from the breeder, takes a long time, and may result in the loss of other desirable features [37][38]. Endophytic microorganisms have been reported to alter plant responses to drought and can be used as an alternative and rapid way to enhance crop productivity.
Plants alter phytohormone abscisic acid (ABA) production in response to drought stress. When ABA concentration rises, it sets off a chain reaction that causes the plant to undergo extensive physiological and transcriptional changes, such as the closing of stomata to decrease water loss via transpiration [39]. Furthermore, cell size and membrane integrity are reduced, ROS are produced, and leaf senescence is promoted, all of which contribute to a reduction in agricultural productivity [40].
Under water-deficient conditions, endophytic microorganisms colonize the rhizosphere and promote plant growth and development through a variety of direct and indirect mechanisms. Plant endophytes can produce plant hormones that promote plant growth and development. Mahest et al. reported that the endophytic actinobacteria S. olivaceus strain DE10 enhanced wheat growth via auxin production under drought conditions [41]. Azospirillum brasilense improves drought tolerance in Arabidopsis thaliana by increasing ABA levels [42]. Endophyte-facilitated drought tolerance via alteration of hormonal profiles has been reported in soybean [43], wheat [44], Lavandula dentata [45], cucumber [46], sugar cane [47], and soybean [48].
Additionally, in certain instances, Rhizophagus irregularis reduced drought stress in tomatoes and lettuce by colonizing the roots [49]. Interestingly, both drought and colonization by R. irregularis increased the synthesis of the phytohormone strigolactone. Since strigolactones are known as host identification signals for arbuscular mycorrhiza (AM) fungi, this implies that they operate as a “call for help” signal and start a positive feedback loop of R. irregularis colonization that increases host plant tolerance to drought conditions [50]. A similar positive effect of bacterial endophytes has also been reported in wheat, where endophytes played a key role in metabolite balance and the reduced effects of drought stress [51].
Some endophytes help the host plant survive drought-induced oxidative stress by enhancing antioxidant defense enzymes. Moghaddam et al. [52] reported that endophytic fungi Neocamarosporium goegapense, Neocamarosporium chichastianum, and Periconia macrospinosa isolated from a desert plant alleviated drought stress in wheat and cucumber by boosting antioxidant defense enzymes. The endophytic bacteria Bacillus safensis and Ochrobactrum pseudogregnonense increased antioxidant activity and enhanced wheat growth under drought conditions [53]. Similar mechanisms of endophyte-mediated drought tolerance have been reported in maize [54][55], wheat [44], Chinese cabbage [56], and other popular crops [57].
Drought also affects the microbial diversity in the host plant rhizosphere. Xu et al. [58] showed that drought drastically lowered bacterial diversity in the rhizosphere and root endosphere, whereas the bacterial community diversity in the surrounding soil remained mostly unchanged. Furthermore, the authors reported that drought enhanced the abundance of actinobacteria, which in turn resulted in the enrichment of metabolites required for drought tolerance. However, it is still unclear how these drought-enhanced metabolites reconfigure the root microbiome makeup to improve plant stress responses. Nonetheless, this intriguing association raises the possibility that plants, and their associated microbiomes engage in molecular dialogues during drought to change the root microbiota to better tolerate drought stress. Understanding this molecular exchange will help us obtain foundational information regarding the use of microbiota to improve agricultural productivity under drought conditions [18].

4. Nutrient Deficiency

Nutrient stress, characterized as either suboptimal availability of necessary nutrients or excessive and toxic amounts of essential and non-essential macronutrients, is considered a major stress that has significantly affected crop productivity worldwide. Extracting insoluble nutrients from soils is one of the biggest challenges in the evolution of terrestrial plants; as a result, they may have formed symbiotic relationships with mobile microbes and have flagella or hyphae that can extend into the soil to provide plants with nutrients [59]. Many studies have shown that endophytes can assist plants by transforming and solubilizing nutrients such as N, P, K, and other microminerals, thus making them conveniently accessible to plants [60][61]. For example, Pseudomonas sp., as described by Choi et al., mediates phosphate solubilization in rice and wheat by altering gibberellic acid production [62]. Abadi and Sepehri [63] reported that the ability of wheat to absorb mineral nutrients, particularly zinc, was aided by the presence of the endophytes Azotobacter chroococcum and Piriformospora indica. The bacterial endophyte Enterobacter sp. has been reported to help plants adapt to various environmental conditions by improving nutrient acquisition, including nitrogen fixation [64]. Yamaji et al. [65] reported that Phialocephala fortinii, Rhizodermea veluwensis, and Rhizoscyphus sp. isolated from mining site soil enhanced the growth of C. barbinervis seedlings by increasing K uptake in shoots and reducing the concentrations of Cu, Ni, Zn, Cd, and Pb in roots. This suggests that isolating and characterizing endophytes from mining sites may help discover novel endophyte species that can assist in crop improvement under heavy metal stress. Some other examples in Table 1 represent endophytes, their host sand, and their role in various abiotic stresses.
Table 1. List of endophytes mediating abiotic stress tolerance in plants.
Endophyte Host Plant Stress Mechanism Reference
Mucilaginibacter stain K Arabidopsis thaliana Salinity Increase in anti-oxidative defense machinery [66]
Pantoea agglomerans Zea mays Salinity Upregulation of aquaporins [67]
Arthrobacter endophyticus,
Nocardiopsis alba		 A. thaliana Salinity Enhancing the expression of genes responsible for water, potassium ion uptake, carotenoid biosynthesis, phenylalanine metabolism, phenylpropanoid biosynthesis, glycerolipid and nitrogen metabolism [68]
Penicillium brevicompactum and P. chrysogenum Solanum lycopersicum Lactuca sativa Salinity Enhanced energy production and Na+ sequestration [69]
Alternaria chlamydospora Triticum aestivum Salinity Inducing the physiological and biochemical responses [70]
Trichoderma harzianum TH-56 Oryza sativa Drought Upregulation of aquaporin, dehydrin, and malonialdehyde genes [71]
Pseudomonas putida Cicer arietinum Drought miRNAs and their target genes indicated the involvement in the stress regulatory pathways, which control/regulate drought stress response [72]
Bacillus cereus, Pseudomonas otitidis and Pseudomonas sp. Glycine max Drought Improving plant growth, membrane integrity, water status, accumulation of compatible solutes, and osmolytes [73]
Gluconacetobacter diazotrophicus Saccharum officinarum Drought IAA and proline production [47]
Paraphoma sp., Embellisia chlamydospora, and Cladosporium oxysporum Zea mays Drought Altered root development [74]
Pseudomonas aeruginosa strain 2CpS1 T. aestivum Heat Reducing heat and drought–induced oxidative stress [75]
Bacillus amyloliquefaciens subsp. plantarum UCMB5113 T. aestivum Heat by molecular modifications in wheat leaf transcript patterns [76]
Bacillus velezensis T. aestivum Heat (1) express several proteins related to stress defense and energy supply
(2) modulate several metabolic pathways of amino acids
(3) increase the accumulation of GABA in the leaves		 [77]
Burkholderia phytofirmans PsJN A. thaliana Cold Pigment accumulation and cold response pathway induction [78]
Bacillus sp. and Lysinibacillus sp. Argentine screwbean Nutrient deficiency Increase in antioxidant defense enzyme, photosynthetic pigments and low lipid peroxidation siderophore, and alteration in IAA, gibberellic acid content [79]
Bacillus amyloliquefaciens Oryza sativa Nutrient deficiency Modulates carbohydrate metabolism [80]
Pseudomonas sp. Pisum sativum Nutrient deficiency Gluconic acid used by bacteria to solubilize phosphate [80]

5. Negative Effects of Endophytes: the Other Side of the Picture

Although endophytes promote the host plants’ growth in several ways [81], these endorsing effects are sensitive to changes in the abiotic environment and may shift from positive to negative when the tolerance range of either symbiont is compromised [82]. The shift in this unstable symbiotic relationship between endophytes and host plants to pathogenicity may be due to variations in abiotic environments, such as nutrient shortages or prolonged extreme weather. Despite a good understanding of the behavior and mechanism of endophyte-host plants using high-throughput techniques, there are still substantial gaps regarding microbial lifestyle and their function in host plants [83]. It is therefore inferred that endophytic status cannot be assumed to be certain, as these co-evolved relationships are plastic/dynamic and can be anticipated to destabilize under severe environmental change scenarios [84].
In addition, one should consider the compatibility of endophytes, especially when used as a consortium of endophytes in field conditions. Reports suggested that co-inoculation of chickpea with compatible endophytes such as Mesorhizobium, Serratia marcescence, and Serratia spp. have synergetic effects on plant growth in terms of nodule number and dry weight, the number of pods per plant, etc. [85]. Similar results were reported by Oliveira et al. [86], where inoculation with a consortium of five diazotrophic bacteria (Gluconacetobacter diazotrophicus, Herbaspirillum seropedicae, Herbaspirillum rubrisubalbicans, Azospirillum amazonense, and Paraburkholderia tropica) resulted in higher stem production in sugarcane as compared to single endophyte inoculated plants. On the contrary, applying a consortium of incompatible bacteria may have damaging effects on crop growth and production. Co-inoculation of nitrogen-fixing bacteria Herbaspirillum seropedicae and H. rubrisubalbicans with sugarcane did not increase the overall yield of sugarcane [86]. Therefore, it is highly recommended to do a compatibility test for the endophytes before their application [87].

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Subjects: Plant Sciences
Contributors MDPI registered users' name will be linked to their SciProfiles pages. To register with us, please refer to https://encyclopedia.pub/register :
Muhammad Kamran
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Qari Muhammad Imran
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Muhammad Bilal Ahmed
,
Noreen Falak
,
Amna Khatoon
,
Byung-Wook Yun
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Update Date: 09 Jan 2023
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