Endophytic fungi mediates production of bioactive secondary metabolites via modulation of genes involved in key metabolic pathways and their contribution in different biotechnological sector

Abstract

Endophytic fungi stimulate the production of an enormous number of bioactive metabolites in medicinal plants and affect the different steps of biosynthetic pathways of these secondary metabolites. Endophytic fungi possess a number of biosynthetic gene clusters that possess genes for various enzymes, transcription factors, etc., in their genome responsible for the production of secondary metabolites. Additionally, endophytic fungi also modulate the expression of various genes responsible for the synthesis of key enzymes involved in metabolic pathways of such as HMGR, DXR, etc. involved in the production of a large number of phenolic compounds as well as regulate the expression of genes involved in the production of alkaloids and terpenoids in different plants. This review aims to provide a comprehensive overview of gene expression related to endophytes and their impact on metabolic pathways. Additionally, this review will emphasize the studies done to isolate these secondary metabolites from endophytic fungi in large quantities and assess their bioactivity. Due to ease in synthesis of secondary metabolites and their huge application in the medical industry, these bioactive metabolites are now being extracted from strains of these endophytic fungi commercially. Apart from their application in the pharmaceutical industry, most of these metabolites extracted from endophytic fungi also possess plant growth-promoting ability, bioremediation potential, novel bio control agents, sources of anti-oxidants, etc. The review will comprehensively shed a light on the biotechnological application of these fungal metabolites at the industrial level.

Introduction

Endophytic fungi are among the most diverse group of endophytes that colonize a large number of medicinal plants and have been shown to alter secondary metabolite production (Das et al. 2012; Bajaj et al. 2018). Most of these secondary metabolites are responsible for imparting pharmaceutical properties to medicinal plants (Gupta and Chaturvedi 2019; Hussain et al. 2021a, b). Extensive literature is now available that depicts the role of endophytic fungi associated with medicinal plants in the augmentation of these secondary metabolites (Erb and Kliebenstein 2020; Kong et al. 2021; Yang et al. 2020a, b; Ravi et al. 2022). Endophytic fungi affect the different steps of biosynthetic pathways of these secondary metabolites by modulation of various genes responsible for the synthesis of key enzymes involved in these pathways. Some reports have shown that endophytic fungi modulate the expression of genes HMGR (3-hydroxy-3-methyl-glutaryl-CoA reductase), DXR ((1-deoxy-d-xylulose 5-phosphate reductoisomerase), etc., involved in the production of a large number of phenolic compounds (Ming et al. 2013; Zhai et al. 2018). Furthermore, endophytic fungi also regulate the expression of genes involved in the production of alkaloids and terpenoids (Pandey et al. 2016a, b; Singh et al. 2020a). The present review will give detailed information regarding the endophyte-mediated gene expression of these metabolic pathways.

Endophytic fungi stimulate the production of an enormous number of bioactive metabolites as evident from studies carried out in previous years (Nischitha and Shivanna 2022; Han et al. 2022; Mohamed et al. 2022; Siebatcheu et al. 2022; Kalimuthu et al. 2022). Studies have been carried out for the isolation of these secondary metabolites from these endophytic fungi at a large scale and for analyzing their bioactivity (Zhu et al. 2022; Siebatcheu et al. 2022). Substantial reports of bioactivity of these metabolites have been observed such as anti-microbial, anti-cancerous, anti-inflammatory, anti-viral, anti-oxidative, etc. (Jayasekara et al. 2022; Bedi et al. 2018; Maharjan et al. 2020). Due to the ease of synthesis and their huge application in the medical industry, a number of bioactive metabolites such as Fumitremorgin D, Penochalasin I, 3-O-methylfunicone, Herquline B, Ferrirubin, Peniproline A, Saponins (Liang et al. 2015; Huang et al. 2016; Wang et al. 2017; Jin et al. 2017) are now being extracted from various endophytic fungi such as Aspergillus, Trichoderma, Penicillium, Fusarium, Phomopsis etc. and are are being commercially utilized for their applications in the biomedicine, agriculture, food, and biotechnology industries (El-Sayed et al. 2020; Torres-Mendoza et al. 2020; Devi et al. 2023a).

Fungal endophytes have emerged as a key player in the biotechnological sector apart from their application in the pharmaceutical industry, most of these endophytes have been shown to bear plant growth-promoting ability, bioremediation potential, as well as novel biocontrol agents (Wang et al. 2021; d’Errico et al. 2021). The present review will elaborate on all these aspects of endophytic fungi and discuss their modern-day application in the biotechnology sector.

Most of the previous articles published concerning endophytic fungi have not shown the effect of the endophytic fungi on the host at the molecular level that leads to secondary metabolite production. This review will be the first of its kind that comprehensively discusses the endophytic-mediated secondary metabolites and their molecular mechanism for this increased concentration of secondary metabolites.

Plant secondary metabolites

Plant secondary metabolites have been classified according to their chemical structure into several major classes viz.-terpenoids, phenylpropanoids (phenolic substances), nitrogen-containing compounds (alkaloids, non-protein amino acids, and cyanogenic glycosides), sulfur-containing compounds (phytoalexins, glucosinolates, and defensin) and phytohormones (Erb and Kliebenstein 2020). Phenolics impart significant contributions to pharmacological activities (anti-microbial, anti-inflammatory, anti-diabetic, insecticidal, anti-septic, anti-oxidant, hepatoprotective, anti-coagulant, anti-cancer, etc.) of several medicinal plants (Hussein and El-Anssary 2019). Alkaloids are nitrogen-containing organic compounds that serve as nitrogen reservoirs during environmental stress and actively participate in stress signaling (Bhambhani et al. 2021). Many alkaloids also showed promising anti-microbial (protoberberine from Berberis aristate, tomatidine from tomato piperine from Piper), insecticidal (nicotine from Nicotiana, colchicine from Colchicum autumnale), antiherbivoral (solasonine and solamargine from Solanum tuberosum, swainsonine from Astragalus and Oxytropis), anticarcinogenic (berberine, evodiamine from Evodia rutaecarpa), neuroprotective (rescinnamine from Rauvolfia reflexa, harmaline from Peganum harmala) and other pharmacological properties (Wang et al. 2010; Cretton et al. 2016; Yang et al. 2015; Kong et al. 2021).

Terpenoids or isoprenoids contribute to aroma, fragrance, flavor, and pigments and exert a wide range of pharmacological activities- anti-tumor and anti-cancer (geraniol from Geranium, ursolic bioactive acid from Rosmarinus, cucurbitacin from Cucurbita), anti-inflammatory (paeoniflorin from Paeonia lactiflora, Triptolidenol from Tripterygium wilfordii), anti-microbial (menthol from Mentha, oleanolic acid from Syzygium), antiviral (andrographolide from Andrographis paniculata, betulinic acid from Syzygium claviforum), cardioprotective (Tanshinone from Salvia miltiorrhiza, ginsenoside from Panax ginseng), anti-diabetic (stevioside from Stevia rebaudiana, artimisinin from Artemisia annua), etc. (Yang et al. 2020a, b; Galle et al. 2014; Das 2015; Kim et al. 2017). Non-protein amino acids such as γ-aminobutyric acid (GABA), β-aminobutyric acid (BABA), l-mimosine (from Mimosa pudica), l-DOPA, l-canavanine (from Canavalia ensiformis), etc., showed significant anti-microbial and anti-oxidant activities (Rodrigues-Correa and Fett-Nato 2019). Glucosinolates are abundant in cruciferous plants and play important role in regulating oxidative stress, inhibiting angiogenesis and metastasis, and preventing inflammation along with anti-cancer and anti-bacterial properties (Traka 2016). Venieraki et al. (2017) has reviewed upon the list of well known medicinal plants that are found associated with endophytic fungi and have been employed for the extraction of bioactive secondary metabolites similar to that of medicinal plants.

Endophytic fungi and medicinal plants

Endophytes that are found associated with medicinal plants have been proven to be a source of a large number of bioactive compounds, enzymes, biostimulants, etc. Additionally, these endophytes carry out a versatile role in the production of secondary metabolites in medicinal plants as evidenced by the reports of previous studies (Fig. 1). Several fungal endophytes were isolated from the leaf and stem of a medicinal herb (Ocimum sanctum) collected from three different geographical locations in India and Worldwide. Among the different isolates, Macrophomina phaseolina showed the highest anti-fungal activity against phytopathogenic fungi Sclerotinia sclerotiorum, Rhizoctonia solani, and Fusarium oxysporum (Chowdhary and Kaushik 2015). In a similar type of study, endophytes that have been isolated from four medicinal plants Rheum emodi, Hypericum perforatum, Dioscorea deltoidea, and Artemisia annua in the Jammu and Kashmir region, India showed significant anti-fungal and anti-bacterial activity (Dar et al. 2017). Substantial anti-microbial activity was also observed from the endophytes isolated from the leaves and bark of the traditional endemic medicinal plant Litsea cubeba in the Northeast region of India. The isolates were identified as Nigrospora sphaerica, Acremonium falciforme, Penicillium, chrysogenum, and Allomyces arbuscula. However, A. falciforme was the most prevailing and demonstrate the highest anti-microbial (Deka and Jha 2018). Several fungal endophytes isolated from leaves, flowers, and fruits of Monarda citriodora, an important medicinal and aromatic herb revealed biocontrol potential against many phytopathogenic fungi (Katoch and Pull 2017). Phytopathogenic strains of endophytic fungi viz. Colletotrichum, Eupenicillium, Fusarium, Hypoxylon, Penicillium, Phomopsis, Trametes, Trichoderma, Umbelopsis, Verticillium, and Xylaria that possess anti-microbial activity were isolated from medicinal plant Kadsura angustifolia (Huang et al. 2015).

Fig. 1.

Schematic representation of a procedure for isolation and identification of the endophytic fungi from different parts of medicinal plants. Endophytic fungi act as bioinoculant for augmenting the growth and development of plants and modulate the transcript expression of genes involved in the biosynthetic pathway of secondary metabolite production. (ANR- Anthocyanidin reductase; HDR- 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase; HMGR- 3-Hydroxy-3-Methylglutaryl-CoA Reductase; HMGS- 3-Hydroxy-3-methylglutaryl-CoA synthase; 4CL- 4-coumarate:Co1-ligase; C4H- Cinnamate-4-hydroxylase; CHI- Chalcone isomerase; CHS-Chalcone synthase; CMK- 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DFR- Dihydroflavonol 4-reductase; DXR- 1-deoxy-D-xylulose 5-phosphate reductor isomerase; DXS- 1-deoxy-D-xylulose-5-phosphate synthase; F3H:Flavonoid 3-hydroxylase;H6H- Hyoscyamine 6β-hydroxylase PAL- Phenylalanine ammonia lyase; PMK- Phosphomevalonate kinase; ODC- Ornithine decarboxylases; PMT- Putrescine N-methyltransferase; QPT- Quinolinic acid phosphoribosyl Transferase; SMT1- C-24 sterol methyltransferase 1; SMT2- C-24 sterol methyltransferase 2; TR 1- Tropinone reductase 1)

Besides that, it has been reported that endophytic fungi (Alternaria alternata and Fusarium sp.) isolated from the medicinal plant Mappia foetida possess potent anti-cancerous activity (Ravi et al. 2022). GC–MS analysis confirmed the presence of two important anti-cancerous compounds triruthenium dodecacarbonyl and molybdenum in fungal extracts synthesized from the above endophytic fungi (Ravi et al. 2022). Similarly, endophytic fungi isolated from different medicinal plants in their extract showed the presence of different phenolic substances like catechol, p-OH benzoic, ferulic, protocatechuic acids, and cinnamic acid (Hassane et al. 2022). Additionally, different flavonoids were also detected such as chrysin, rutin, apigenin, luteolin, acacetin, luteolin, and quercetin (Hassane et al. 2022). Similarly, endophytic fungi Nigrospora sphaerica isolated from the medicinal plant Euphorbia hirta (dudhi) L. revealed the occurrence of 2,4-Di-tert-butylphenol in the ethyl acetate fungal extract which is a phenolic compound liable for the anti-oxidative potential (Gautam et al. 2022). Concomitantly, the endophytes under culture showed the presence of tannins, phenols, ascorbic acid, flavonoids, etc. which indicated their potential for extraction of bioactive compounds (Kumaresan et al. 2015). Several different endophytic fungi were isolated from different parts of the medicinal tree Aegle marmelos grown in the Western Ghats of India. Some endophytic fungi were pigmented and were identified as Cladosporium cladosporioides FC75A, Aspergillus niger FC30AGr, Alternaria alternate FC39BY, Curvularia australiensis FC2AP, Alternaria citrimacularis FC8ABr. Bioactive metabolites extracted from this fungus showed noteworthy anti-oxidant and anti-microbial activity against many bacterial and fungal pathogens under in-vitro assays (Mani et al. 2015). Another study by Sheik and Chandrashekar (2018) also reported anti-microbial and free radical scavenging activity from the endophytic fungi isolated from the endemic plant of Humboldtia brunonis. The study also showed variation in endophyte frequency over different seasons. An endophytic fungus Curvularia geniculata isolated from the medicinal plant Phyllanthus niruri was assessed for anti-oxidant potential and anti-cancer activity (Kalimuthu et al. 2022). In another work, the endophytic fungus Aspergillus fumigatus isolated from traditional Chinese medicine, Crocus sativus showed the presence of thirty-two different chemical compounds that were reported to be secondary metabolites namely, anthraquinones, emodin, physcion, carviolin, endocrocin, alkaloids, pseurotin A, fumiquinazoline C, two benzoate derivatives, methyl asterrate, and asterric acid (Jiang et al. 2022).

Studies have also shown that the endophytic fungi isolated from medicinal plants improve the growth of the host plants by producing ammonia, solubilizing phosphates, siderophore production as well as indole acetic acid (IAA) production (Toppo et al. 2022; Huang et al. 2022; Zhu et al. 2022; Madasi et al. 2021). Chen et al. (2021a) reported in their study that endophytic fungi Byssochlamys spectabilis 1-N2, Chaetomium nigricolor 3-G7, and Phomopsis sp.1-G1 isolated from medicinal plant Bletilla striata were capable of producing IAA, siderophore and cellulolytic enzymes that significantly increased the growth of the host plants. Furthermore, from the leaves of medicinal plants Ephedra pachyclada, fifteen fungal endophytes belonging to the genera Penicillium, Alternaria, and Aspergillus sp. were isolated and tested for their plant growth promotion activity, enzyme production as well as anti-microbial activity (Khalil et al. 2021). In a different study, Khan et al. (2021) isolated the fungal endophyte Acremonium sp. Ld-03 from the bulbs of the Chinese medicinal plant Lilium davidii. The endophytic fungal strain Ld-03 showed significant production of IAA, siderophore, and phosphate solubilization activity. Further, in vitro analysis of the growth of Allium tuberosum was assessed in presence of endophytic fungal strain Ld-03 and it was observed that plants tend to increase in root and shoot length. A study showed that endophytic fungi (Colletotrichum sp. SXS649, Pestalotiopsis sp. SXS650, Diaporthe sp. SXS652, and Botryosphaeriales SXS651) isolated from a native medicinal plant of the Brazilian savanna, i.e., Palicourea rigida exhibited substantial production of amylase, cellulase, protease, and tannase (Dos Santos et al. 2021). Moreover, the thirty-two fungal endophytes isolated from the stem and bark of Albizia lebbeck showed a positive result for the extracellular production of all enzymes such as amylase, protease, lipase, laccase, cellulase, and gelatinase (Mathur et al. 2022). Additionally, the utilization of these enzymes in the biodegradation of vegetable oil, dye decolourization, saccharification of bagasse and paper, and wastewater treatment was also observed (Mathur et al. 2022). A large endophytic fungal diversity has been isolated from the leaves of the medicinal plants of Brazil Myracrodruon urundeuva. Among the different isolates, the isolate Diaporthe was unique in the sense that it produces the important amino acid l-asparagine (Pádua et al. 2019). Several studies showing the number of endophytic fungi isolated from different medicinal plants have been summarized in Table 1.

Table 1.

A list of endophytic fungi with potential bioactivity isolated from different parts of medicinal plants

Medicinal plant	Host tissue	Endophytic fungi	Bioactivity	References
Bauhinia forficata	Leaves Sepals Stems Seeds	Acremonium curvulum Aspergillus ochraceus Gibberella fujikuroi Myrothecium verrucaria Trichoderma piluliferum	Anti-biotic Enzyme source	Bezerra et al. (2015)
Ocimum sanctum	Leaves Stems	Fusarium verticillioides Hypocrea sp. Bipolaris maydis Macrophomina phaseolina Meyerozyma guilliermondii Chaetomium coarctatum Rhizoctonia bataticola Hypoxylon sp. Diaporthe phaseolorum Alternaria tenuissima A. alternate	Anti-phytopathogenic	Chowdhary and Kaushik (2015)
Asclepias sinaica	Leaves	Penicillium chrysogenum Alternaria alternata	Anti-microbial Enzyme source	Fouda et al. (2015)
Calotropis procera, Catharanthus roseus Euphorbia prostrate Vernonia amygdalina Trigonella foenum-graecum	Leaves Stems Seeds	Alternaria sp. Bipolaris sp. Curvularia sp. Chaetomium sp. Drechslera sp. Emericella sp. Aspergillus sp. Cladosporium sp. Paecilomyces sp. Phoma sp.	Anti-oxidant	Khiralla et al. (2015)
Azadirachta indica	Leaves	Chaetomium sp. Curvularia sp. Colletotrichum sp. Trichoderma sp.		Kumaresan et al. (2015)
Aegle marmelos	Barks, Branches Leaves Roots	Alternaria alternata, Alternaria citrimacularis Curvularia australiensis	Anti-microbial	Mani et al. (2015)
Rauwolfia serpentine	Leaves Stems	Colletotrichum gloeosporioides Penicillium sp. Aspergillus sp.	Anti-microbial Anti-oxidant Hypocholestraemic	Nath et al. (2015)
Solanum xanthocarpum	Leaves	Phomopsis vexans	Drug-Lovastin	Parthasarathy and Sathiyabama (2015)
Crescentia cujete	Leaves	Nigrospora sphaerica Fusarium oxysporum Gibberella moniliformis Beauveria bassiana	Anti-bacterial Anti-cancerous Anti-oxidant	Prabukumar et al. (2015)
Ocimum sanctum Aloe vera	Leaves Stems Roots	18 endophytic fungi were isolated	Anti-fungal Enzyme source	Yadav et al. (2016)
Anthocleista djalonensis Fagara zanthoxyloides	Leaves	Colletotrichum gloeosporioides Pestalotiopsis thea	Anti-Respiratory Syncytial Virus Compounds	Uzor et al. (2016)
Calotropis procera Trigonella foenum-graecum Vernonia amygdalina Catharanthus roseus Euphorbia prostrata	Leaves Stems Seeds	Alternaria alternata Aspergillus terreus Cladosporium cladosporioides Trametes versicolor Chaetomium globosum Aspergillus terreus Hansfordia sinuosae Curvularia aeria Pleosporales sp. Phoma multirostrata Curvularia australiensis Alternaria sp. Byssochlamys spectabilis	Cytotoxic Antibiotic	Khiralla et al. (2016)
Nothapodytes foetida Hypericum mysorense H. japonicum	Leaves Stems	Penicillium sp. Aspergillus sp. Fusarium sp. Gliocladium sp. Cladosporium sp. Trichoderma sp. Colletotrichum sp. Pestalotiopsis sp.	Anti-oxidant Free radical scavenging	Samaga and Rai (2016)
Combretum lanceolatum	Roots	Trichoderma spirale Penicillium verruculosum Penicillium simplicissimum Fusarium oxysporum Diaporthe phaseolorum Leptosphaerulina chartarum Cladosporium perangustum	Anti-microbial Anti-oxidant	de Siqueira et al. (2017)
Monarda citriodora	Leaves Roots Flowers	Fusarium sp. Aspergillus sp. Cladosporium sp.	Biocontrol	Katoch and Pull (2017)
Mirabilis jalapa	Roots	Aspergillus clavatonanicu	Anti-microbial	Mishra et al. (2017)
Elaeocarpus sylvestris	Leaves Stems	Pestalotiopsis sp. Diaporthales sp. Meyerozyma sp. Diaporthales sp. Pestalotiopsis sp. Pseudocercospora sp.	Anti-oxidants	Prihantini and Tachibana (2017)
Glycyrrhiza glabra	Rhizomes	Diaporthe terebinthifolii	Diapolic acid A–B Cytotoxic Anti-microbial activity	Yedukondalu et al. (2017)
Humboldtia brunonis	Leaves Stems	Aspergillus sp. Curvularia clavata Curvularia pallescens Debaromyces hansenii Guignardia sp. Hypoxylon anthochroum Meyerozyma caribbica Paecilomyces lilacinus Alternaria alternate Cunninghamella echinulata Fusarium fusarioides Fusarium oxysporum Phanerochaete sp.	Anti-microbial Free radical scavenging	Sheik and Chandrashekar (2018)
18 medicinal plants	Leaves Stems	Aspergillus flavus A. niger A. sydowii A. versicolor Aspergillus sp.	Anti-viral Anti-oxidant	Selim et al. (2018)
Terminalia pallida Rhynchosia beddomei Pterocarpus santalinus	Leaves Stems	Cladosporium delicatulum	Plumbagin-Anti-microbial	Venkateswarulu et al. (2018)
Hypericum perforatum	Leaves Stems Roots Flowers	Epicoccum nigrum Alternaria sp. Trichoderma harzianum	Anti-microbial	Vigneshwari et al. (2019)
Zingiber officinale Salix sp.	Leaves	Epicoccum nigrum	Anti-fungal Anti-bacterial Cytotoxic potential	Harwoko et al. (2019)
Aloe dhufarensis Lavranos	Leaves	Sarocladium kiliense Penicillium oxalicum	Anti-phytopathogenic	Al-Rashdi et al. (2020)
Cotyledon orbiculata Psychotria zombamontana, Tecomaria capensis Catha edulis Melianthus comosus	Leaves Stems Roots	Diaporthe sp. Talaromyces funiculosus Penicillium commune Cochliobolus sp. Phomopsis sp. Clonostachys rosea	Anti-microbial Enzyme source Presence of type I polyketide synthases (PKS)	Abdalla et al. (2020)
Papaver somniferum Cassia fistula Catharanthus roseus	Roots Leaves	Aspergillus sp. Curvularia sp.	Anti-bacterial Anti-fungal	Khattak et al. (2020)
Aquilaria malaccensis	Stem Leaves	Alternaria sp. Curvularia sp. Rhizopus sp. Sterilia sp.	Anti-microbial	Mochahari et al. (2020)
Lafoensia pacari Guazuma ulmifolia Campomanesia xanthocarpa Siparuna guianensis	Leaves	Colletotrichum sp. Diaporthe sp. Bjerkandera sp. Talaromyces sp. Cochliobolus sp. Phaeophlebiopsis sp. Curvularia sp.	Anti-oxidants Anti-inflammatory	Santos et al. (2020)
Memecylon umbellatum	Leaves Bark Fruits	Endomelanconiopsis endophytica Lasiodiplodia iranensis L. theobromae Phyllosticta capitalensis Aspergillus niger Cochlibolus lunatus Pestalotiopsis guepinii	Anti-bacterial	Suryavamshi and Shivanna (2020)
Euphorbia geniculate	Leaves Stems Roots	Aspergillus favus A. ochraceus A. terreus Emercilla nidulans var. acristata Macrophomina phaseolina	Anti-fungal	Kamel et al. (2020)
Taxus baccata	Bark	Acremonium Colletotrichum Fusarium sp. Nodulisporium sp. Paecilomyces Periconia sp.	Paclitaxel Cytotoxic	El-Bialy and El-Bastawisy (2020)
Euphorbia larica	Roots	Neocosmospora sp. Alternaria alternata	Anti-fungal	Khuseib et al. (2020)
Siraitia grosvenorii	Roots Stems Leaves Fruits	Diaporthe angelica Fusarium solani	Mogroside V	Bin et al. (2020)

Endophytic fungi and bioactive metabolite production

Endophytes play a key role in the production of a large number of bioactive metabolites and bioprospecting of endophytes in search of novel metabolites has gained considerable attention all over the World (Gouda et al. 2016). Endophytes are the source of new natural compounds including polyketides, alkaloids, phenylpropanoids, terpenoids, and phenols (Fig. 1). Yang et al. (2019) reported the production of a completely new sesquiterpenoid colletotrichine A, a potent inhibitor of acetylcholinesterase (AChE) from endophytic fungus Colletotrichum gloeosporioides GT-7 isolated from the healthy tissues of Uncaria rhynchophylla. The endophytic fungus, Neosartorya fischeri JS0553 is a rich source of new secondary metabolites meroditerpenoid named sartorypyrone E and fischerin compounds and these compounds possess significant neuroprotective activity (Bang et al. 2019). Furthermore, isolated endophytic fungi Eurotium rubrum from the roots and shoots of the mangrove plant Suaeda salsa produces many anthraquinones (such as catenarin, rubrocristin, emodin, and 2-methyleurotinone) that have anti-bacterial, anti-fungal, anti-mycobacterial, anti-malarial and cytotoxic activities (Zhang et al. 2017). Another study reported that an endophytic fungus Mucor irregularis QEN-189, isolated from the fresh inner tissue of the stems of the marine mangrove plant Rhizophora stylosa has potent unique compounds rhizovarins A–F and indole-diterpenes (Gao et al. 2016). These organic compounds hold anti-tumor activity against HL-60 and A-549 cell lines. A fungal endophyte Campylocarpon sp. HDN13-307 associated with the roots of Sonneratia caseolaris exhibited production of a new family of secondary metabolites such as 4-hydroxy-2-pyridone alkaloids, campyridones A and B and campyridones C and D that have strong cytotoxic activity against cancerous cells (Zhu et al. 2016).

An endophytic fungus Neofusicoccum luteum isolated from the plant Kigelia africana led to the formation of a bioactive secondary metabolite C16-terpene dilactole. This metabolite exhibited anti-bacterial activity against Pseudomonas aeruginosa (Bodede et al. 2022). Elkhouly et al. (2021a) reported that the endophytic fungus Aspergillus terreus AH1 isolated from the tissues of Ipomoea carnea produced significant bioactive compounds namely, butyrolactone I, pariplanamide B, pyranterrone D, arenarin A, asterrelenin. These compounds showed anti-microbial activities against several pathogenic microbes such as Staphylococcus aureus and Bacillus subtilis which were gram-positive bacteria as well as the gram-negative bacteria Pseudomonas aeruginosa and Escherichia coli. Among all the compounds produced, butyrolactone and periplanamide B showed anti-biofilm activity to a great extent. Periplanamide B also showed effective activity against cancer cell lines such as HCT116, HepG2 and MCF7. Similarly, another study from Elkhouly et al. (2021b) showed that the endophytic fungus Aspergillus tubenginsis ASH4 which was extracted from the plant Hyoscyamus muticus produced the bioactive metabolite afonic acid. This afonic acid showed acute anti-microbial activity against several bacteria like Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, and Bacillus subtilis which are very much pathogenic against humans. It also hinders biofilm formation and had anti-oxidant and anti-cancer activities against HCT116, HepG2, and MCF7. GC–MS analysis of fungal extract of endophytic fungi Cladosporium cladosporioides and C. tenuissimum showed the presence of 1-octen-3-ol, 3-methyl-1-butanol, hexanol, trans-2-octanol and hexadecanol. These compounds were cloasely related to the compounds found in host extract, i.e., leaf of Cymbopogon martini and have significant anti-oxidant, anti-cancer and anti-microbial activities (Jayaram et al. 2021). Furthermore, an endophytic fungus Talaromyces assiutensis JTY2 isolated from the leaves of the host plant Ceriops tagal produced secondary metabolite helicascolide F, talaromydine that exhibited both anti-fungal and cytotoxic activities against many phytopathogenic fungi (Li et al. 2021). Another study by Zou et al. (2021) reported that an endophytic fungus Aspergillus fumigatus HQD24 isolated from the flower of Rhizophora mucronata, a Chinese mangrove plant led to the production of 8 alkaloids namely pyripyropene A, 1,11dideacetyl-pyripyropene A, pyripyropene E, chaetominine, tryptoquivaline J, fumitremorgan C, 1-acetyl β-carboline and nicotinic acid. These compounds correspondingly exhibited cytotoxic activity. Among the nine fungal isolates from the pulp of the plant Chaenomeles speciosa, 7 were those of Penicillium spp., one Aspergillus spp., and one Mucor spp. Out of the three fungi, Penicillium spp. produced various bioactive metabolites such as 3-furanacetic acid, 4-hexyl-2,5-dihydro-2,5-dioxo, diisooctyl phthalate, 11-hexadecyn-1-ol and propanedioic acid, dihydroxy that showed anti-microbial activity against Alternaria alternata, Fusarium culmorum and F. oxysporum. Cao et al. (2021) revealed that a natural bioactive product huperzine A produced by the endophytic fungi Penicillium sp. and Colletotrichum gloeosporeoids was found to be a significant remedy against the Alzheimer’s disease. The fungus was isolated from the host plant Huperzia serrata belonging to the family Lycopodiace. Silva et al. (2021) demonstrated the presence of bioactive compounds Mellein and β-orcinaldehyde as the major compound. These were produced from the endophytic fungus Botryossphaeria fabicerciana which was isolated from the leaves of the host plant Morus nigra. These two compounds showed activities against gram-positive bacteria and also possessed anti-oxidative properties. A bis-indole alkaloid, vinblastine was produced by the endophytic fungus Fusarium solani RN1 and Chaetomium funicola RN3 which were isolated from the plant Catharanthus roseus and showed mild anti-cancer activity. The endophytic fungus Alternaria sp. isolated from the plant species Papuacedrus papuana produces tenuazonic acid which is a bioactive metabolite that showed active anti-bacterial activities against Escherichia coli and also showed anti-oxidant activities (Praptiwi et al. 2021). Likewise, Elfita et al. (2022) demonstrated the production of the bioactive compounds 3-hydroxy-4-(hydroxy(4-hydroxyphenyl) methyl) dihyfrofuran-2-on by the fungus Fusarium verticillioides which was isolated from the bark of the host plant Syzygium jambos. The bioactive compound showed anti-bacterial activity against gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis) and gram-negative bacteria (Escherichia coli, Salmonella typhi). The fungal isolate Phyllostica sp. from the medicinal plant Hippobroma longiflora produced useful secondary metabolites such as alkaloids, flavonoids and terpenoids which showed anti-oxidant activities (Widjajanti et al. 2022). A number of studies that summarize the significant role of endophytes in the production of bioactive metabolites have been shown in Table 2.

Table 2.

A list of studies summarizing the fungal endophyte-mediated bioactive secondary metabolite production

Host plant	Endophytic fungi	Secondary metabolite	Bioactivity	References
Fritillaria unibracteata var. wabuensis	Fusarium redolens 6WBY3	Peimisine Imperialine-3b-d-glucoside	Anti-tumor	Pan et al. (2015)
Hevea brasiliensis	Eutypella scoparia	Scoparasin C	Cytotoxic	Kongprapan et al. (2015)
Diphylleia sinensis	Aspergillus fumigatus	Fumitremorgin D	Cytotoxic	Liang et al. (2015)
Myoporum bontioides	Penicillium chrysogenum	Penochalasin I	Cytotoxic	Huang et al. (2016)
Arbutus unedo	Talaromyces pinophilus	3-O-methylfunicone, Herquline B Ferrirubin	Insecticidal	Vinale et al. (2017b)
Cucumeropsis mannii	Penicillium decumbens	Peniproline A	Cytotoxic	Wang et al. (2017)
Panax notoginseng	Fusarium sp. Aspergillus sp.	Saponins	Anti-microbial	Jin et al. (2017)
Uncaria rhynchophylla	Colletotrichum gloeosporioides	Colletotrichine A	Acetylcholinesterase inhibitor	Chen et al. (2018)
Ficus elastic	Penicillium funiculosum Trichoderma harzianum	Isocoumarin	Anti-microbial	Ding et al. (2019)
Vitex negundo	Alternaria alternata	Alternariol methyl ether (AME)	Anti-tumor and anti-cancer	Palanichamy et al. (2019)
Glehnia littoralis	Neosartorya fischeri JS0553	Sartorypyrone E	Neuroprotective	Bang et al. (2019)
Uvaria grandiflora	Nigrospora spp. Colletotrichum spp.	Flavonoids Sterols Phenols Terpenoids	Anti-bacterial Anti-oxidant	Notarte et al. (2019)
Uncaria rhynchophylla	Colletotrichum gloeosporioides	4-Epi-14-hydroxy-10, 23-dihydro-24,25-dehydroaflavinine 10, 23-Dihydro-24,25 -dehydro-21–oxoaflavinine Ergosterol Ergosterol peroxide Mellein 4,5-dihydroblumenol A Colletotrichine A Cyclo (L-leucyl-L leucyl) Brevianamide F	Anti-tumor	Yang et al. (2019)
Bruguiera sexangula	Phyllosticta capitalensis	Guignardone A 12- hydroxylated guignardone A Guignardone J Guignardone M Xenofuranone B 6,8-dihydroxy-5- methoxy-3-methyl-1H-isochromen-1-one Regiolone 3,4-dihydroxybenzoic acid	Anti-microbial Cytotoxic	Xu et al. (2009)
Huperzia serrata	Fusarium sp. Rsp5.2	Huperzine A	Alzheimer disease	Le et al. (2020)
Achyranthes bidentata	Phomopsis sp.	Chromanones	Cytotoxic	Yang et al. (2020b)
Phlegmariurus taxifolius	Fusarium sp.	Huperzine A	Alzheimer disease, Acetylcholinesterase inhibition	Cruz-Miranda et al. (2020)
Camptotheca acuminate	Penicillium polonicum	β-lactone polonicin A Enoic acid Polonicin B	Anti-HCC (HepG2 hepatocelluar carcinoma), GLUT4 translocatioGlucose uptake	Wen et al. (2020)
Vitex negundo	Nigrospora oryzae	Phenol 2,4bis(1,1-dimethylethyl) 3-hexadecyloxycarbonyl-5-(2-hydroxyethyl)-4-methylimidazolium ion Naphthalene 1,2-benzenedicarboxylic acid diisooctyl ester Eicosene	Anti-bacterial	Suradkar and Hande (2020)
Kigelia africana	Neofusicoccum luteum	C16-terpene dilactone	Anti-bacterial	Bodede et al. (2022)
Ipomoea carnea	Aspergillus terreus AH1	Butyrolactone I Pariplanamide B Pyranterrone D Arenarin A Asterrelenin	Anti-microbial, Cytotoxic Anti-biofilm	Elkhouly et al. (2021a)
Hyoscyanus muticus	Aspergillus tubenginses ASH4	Anofinic acid	Anti-microbial Anti-biofilm Anti-oxidant Anti-cancer	Elkhouly et al. (2021b)
Cymbopogon martini	Cladosporium clasdosporioides, Cladosporium tenuissimum	Terpenoid Alkaloids Flavonoids Phenols Tannins	Anti-oxidant Anti-cancer Anti-microbial	Jayaram et al. (2021)
Ceriops tagal	Talaromyces assiutensis JTY2	Helicascolide F Talaromydine	Anti-fungal Cytotoxic	Li et al. (2021)
Rhizophora mucronata	Aspergillus fumigatus HQD24	Pyripyropene A 1,11dideacetyl-pyripyropene A Pyripyropene E Chaetominine Tryptoquivaline J Fumitremorgan C 1-acety β-carboline Nicotinic acid	Cytotoxic	Zou et al. (2021)
Chaenomeles speciosa	Penicillium spp. Aspergillus spp. Mucor spp.	3-Furanacetic acid 4-hexyl-2,5-dihydro-2,5-dioxo Diisooctyl phthalate, 11-Hexadecyn-1-ol Propanedioic acid dihydroxy	Anti-microbial	Lykholat et al. (2021)
Huperzia serrata	Penicillium sp. Colletotrichum sp. Gloeosporeoids	Huperzine A	Treatment for Alzheimer’s disease	Cao et al. (2021)
Morus nigra	Botryosphaeria fabicerciana	Mellein, β-orcinaldehyde	Anti-microbial Anti-oxidant	Silva et al. (2021)
Catharanthus roseus	Fusarium solani RN1 Chaetomium funicola	Alkaloid Vinblastine Vincristine	Anti-cancer	Linh et al. (2021)
Lilium davidii	Acremonium sp.	Xanthurenic acid Valyl aspartic acid Gancidin W Peptides Cyclic dipeptides Valylarginine Cyclo-[l-(4-hydroxy-Prp)-l-Leu], Cyclo(pro-phe) (3s,6s)-3-benzyl-6-(4-hydroxybenzyl) piperazine-2,5-dione	Anti-fungal	Khan et al. (2021)
Syzygium zeylancium	Penicillium brefeldianum	p-hydroxybenzaldehyde	Anti-bacterial	Syarifah et al. (2021)
Papuacedrus papuana	Alternaria sp.	Tenuazonic acid	Anti-bacterial Anti-oxidant	Praptiwi et al. (2021)
Eichhornia crassipes	Fusarium sp.	Altersolanol 4-hydroxydihydromorjavanicin 5-hydroxy-7-methoxy-2-isopropylchromone Fusaraichromenone	Anti-microbial	Hiranrat et al. (2021)
Acanthus ilicifolius	Penicillium sp.	Benzophenones	Anti-bacterial	Bai et al. (2021)
Syzygium jambos	Fusarium verticillioides	3-hydroxy-4-(hydroxy(4-hydroxyphenyl) methyl) dihyfrofuran-2-on	Anti-bacterial	Elfita et al. (2022)
Hippobroma longiflora	Phyllosticta sp.	Alkaloid Flavonoid Terpenoid	Anti-oxidant	Widjajanti et al. (2022)

Endophytic fungi and regulation of key secondary metabolite genes in plants

Ren and Dai (2012) revealed that the endophytic fungus Gilmaniella sp. isolated from the host plant Atractylodes lancea induced the production of jasmonic acid (JA) which acts as a downstream signaling molecule in the NO and H₂O₂-mediated volatile oil accumulation induced by the endophytic fungi. It was also seen that JA also had interconnection with the salicylic acid (SA) signaling pathway and the expression of the gene HMGR was restored by the JA alongside sesquiterpenoids, which was significantly increased by fungal endophyte. A group of abietanoid diterpenes (tanshinone) were significantly enhanced by the endophytic fungus Trichoderma atroviride D16 found in the host plant Salvia miltiorrhiza due to increased transcript expression of genes HMGR, DXR and GGPPS (geranylgeranyl diphosphate synthase) that plays a major role in the synthesis of tanshinones (Ming et al. 2013) (Fig. 1). Subsequent studies by Chen et al. (2021b), also revealed the up-regulation of the genes HMGR, DXS, DXR, GGPPS, CPS, KSL, and CYP76AHI helped in the biosynthesis of secondary metabolite tanshinone which was produced by the endophytic fungus Cladosporium tenuissimum extracted from the host plant Salvia mitiorrhiza. Similar studies were seen by Zhai et al. (2018), where it was reported that the fungus Chaetomium globosum D38 found in the host plant Salvia mitiorrhiza triggered tanshinones production, a major bioactive compound that was markedly up-regulated by the expression level of the fundamental genes such as HMGR, DXR, GGPPS while CPS and KSL were downregulated. Apart from these, some experimental reports by Verma et al. (2014) showed the biosynthesis of the bioactive secondary metabolites sanguinarin by the increased transcript expression of genes—cheilanthifoline synthase (CFS), stylopine synthase (STS), tetrahydroprotoberberine cis-N-methyltransferase (TNMT), and protopine 6-hydroxylase (P6H). Pandey et al. (2016b) experimentally demonstrated that the fungal endophytes namely Culvularia sp., Choanephora infundibulifera associated with host plant Catharanthus roseus escalated the vindoline content by the upregulation of the genes (geraniol 10-hydroxylase (G10H), tryptophan decarboxylase (TDC), strictosidine synthase (STR), 16-hydoxytabersonine-Omethyltransferase (16OMT), desacetoxyvindoline-4-hydroxylase (D4H), deacetylvindoline-4-Oacetyltransferase (DAT), octadecanoid-responsive Catharanthus AP2-domain protein (ORCA3) (Fig. 1). The gene PRX1 (the gene for vascular class III peroxidase) was also upregulated by the endophyte which is in charge of coupling vindoline and cathranthine and Cys2/His2-type zinc finger protein family transcriptional repressors (ZCTs) were downregulated. Similar reports were made by Magotra et al. (2017) that showed the formation of seven secondary metabolites pseurotin F2, fumagillin, tryprostatin C, pseurotin D, pseurotin A, bis (dimethylthio) gliotoxin, and gliotoxin by the endophytic fungus Aspergillus fumigatus (GA-L7) isolated from the host plant Grewia asiatica of Malvaceae family. There was significant up-regulation in transcript expression of genes Afua_6g 12040, Afua_6g 12050, Afua_6g 12060, Afua_6g 12070, Afua_6g 12080 involved in the biosynthesis of fumiquinazoline C and the presence of valproic acid, an epigenetic modifier upregulated the above genes. Likewise, Yuan et al. (2016) demonstrated increased production of sesquiterpenoids from the ethylene signaling mechanism brought about by the endophytic fungus Gilmaniella sp. AL12 within the host plant Atractylodes lancea via activation of gene TPS21 and TPS11. The endophytic fungus Aspergillus niger CSR3 isolated from the host plant Cannabis sativa modulated the expression of genes P450-1, P450-3, P450-4 which are part of GA biosynthesis pathway and led to increased accumulation of gibberellins (Lubna et al. 2018). Increased transcript of the gene PHGPX by polysaccharide fraction (PSF) induced tanshinones were seen in the case of the endophytic fungus Trichoderma atroviride D16 isolated from the plant Salvia miltiorrhiza belonging to the family Lamiaceae Peng et al. (2019). Several endophytic fungi Culvularia sp., Choamphora infludibulifera, Aspergillus japonicus showed extensive production of root alkaloids ajmalicine and serpentine by modulating the terpenoid indole alkaloid (TIA) pathway in the roots of the plant Catharanthus roseus (Singh et al. 2020a) There was upregulation of the key genes G10H, TDC, and strictosidine synthase and also octadecanoid-derivative responsive Catharanthus AP2/ERF domain transcription activators like ORCA3, while the downregulation of the ZCTs (Cys2/His2-type zinc finger protein family). Ding et al. (2020) reported an active production of a bioactive indole alkaloid meleagrin on the deletion of hdaA (histone deacetylase) an epigenetic regulator in the endophytic fungus isolated from the leaves of Ficus elastic. Therein, there was upregulation of roqO gene which also functioned as the key catalyst in the bioactive secondary metabolite biosynthesis. Table 3 depicts the key genes responsible for the increased production of bioactive metabolites influenced due to endophytic fungi.

Table 3.

A list of studies summarizing the effect of fungal endophyte on bioactive metabolite and regulation of key genes

Name of endophyte	Host plant	Bioactive metabolites	Name of genes	Effects of gene	References
Gilmaniella sp.	Atractylodes lancea	Jasmonic acid	HMGR	Upregulation	Ren and Dai. (2012)
Verticillium longisporium	Arabidopsis sp.	Tryptophan	CYP71A12 CYP71A13 CYP71B15	Upregulation	Iven et al. (2012)
Trichoderma atroviride D16	Salvia mitiorrhiza	Tanshinone	HMGR DXR GGPPS CPS KSL	Upregulation-HMGR, DXR, GGPPS Downregulation- CPS, KSL	Ming et al. (2013)
Chaetomium globosum, Aspergillus niveoglaucus, Paecilomyces lilacinus, Trichoderma harzianum	Papaver somniferum	Sanguinarine, Shikimate	CFS STS TMNT P6H	Upregulation	Verma et al. (2014)
Curvularia sp., Choanephora infundibulifera	Catharanthus roseus	Vindoline	TDC, STR, 16OMT, D4H, DAT, ORAC3, ZTCs, PRX1		Pandey et al. (2016b)
Aspergillus fumigatus (GA-L7)	Grewia asiatica	Pseurotin F2, Fumagillin, Tryprostatin C, Pseurotin D, Pseurotin A, Bis(dimethylthio)gliotoxin Gliotoxin	Afua_6g 12040 Afua_6g 12050 Afua_6g 12060 Afua_6g 12070 Afua_6g 12080	Upregulation	Magotra et al. (2017)
Gilmaniella sp.	Atractylodes lancea	Sesquiterpenoids	TPS21, TPS11		Yuan et al (2016)
Chaetomium globosum D38	Salvia miltiorrhiza	Tanshinones, Salvianolic acid	HMGR, DXR, GGPPS, CPS, KSL	Upregulation-HMGR, DXR Downregulation-GGPPS, CPS, KSL	Zhai et al. (2018)
Aspergillus fumigatusTS1, Fusarium proliferatum BRL1	Oxalis corniculata	Indole acetic acid, Gibberellins	P50-1, P450-3, P450-4, ggs2, des	Upregulation	Bilal et al. (2018)
Aspergillus nidulans	Rhizophora stylosa	Abscisic acid	TBP, TAF14, XBP, CDK7, CCNH	Upregulation	Xu et al. (2018)
Aspergillus niger CSR3	Cannabis sativa	Gibberellins, Indoleacetic acid	P450-1, P450-3, P450-4, ggs2, des	Upgregulation-P450-4	Lubna et al. (2018)
Trichoderma atroviride D16	Salvia miltiorrhiza	Tanshinones	PHGPX	Upregulation	Peng et al. (2019)
Acetinobacter sp. Marmoricola sp.	Papaver somniferum	Benzylisoquinoline	T60D, CODM, COR	Upregulation by (SM3B)- T60DM, CODM, COR	Ray et al. (2019)
Culvularia sp., Choanphora influndibulifera, Aspergillus japonicus	Cathranthus roseus	Ajmalicine, Serpentine	ORACA3, ZCTs	Upregulation-ORACA3 Downregulation-ZCTs	Singh et al. (2020b)
Penicillium chrysogeum	Ficus elastica	Meleagrin	roqO	Upregulation	Ding et al. (2020)
Mucor circinelloides	Salvia mitiorrhiza	Tanshinone	DF20		Chen et al. (2021b)
Pyricularia oryzae	Oryza sativa	Melanin, Tenuazonic acid, Nectriapyroles, Pyriculols	NRPS-PKS		Motayama et al. (2021)
Cladosporium tenuisssimum DF11	Salvia mitiorrhiza	Tanshinone	HMGR, DXS, DXR, GGPPS, CPS, KSL, CYP76AHI	Upregulation	Chen et al. (2022)

HMGR- 3-Hydroxy-3-Methylglutaryl-CoA Reductase;CYP71A12-Cytochrome P450 71A12; CYP71A13-Cytochrome P450 71A13; CYP71B15- Bifunctional dihydrocamalexate synthase/camalexin synthase; DXR- 1-deoxy-D-xylulose 5-phosphate reductor isomerase; GPPS- geranylgeranyl diphosphate synthase; CPS-Capsule polysaccharide locus; KSL-Kaurene synthase-like; CLS-Cardiolipin synthase; STS- Steroid sulfatase; TMNT-; P6H-Protopine 6-hydroxylase; TDC- Tryptophan decarboxylase; STR-Short tandem repeat; 16OMT-Tabersonine 16-O-methyltransferase; D4H-Deacetoxyvindoline 4-hydroxylase; DAT- Dopamine transporter; ORAC3-; ZTCs-; PRX1-Parired related homeobox 1; T60DM-Thebaine 6-O-demethylase; CODM-Codeine O-demethylase; Afua_6g 12,040-; TPS21-Terpene synthase 21;TPS11-Trihalos phosphatase/synthase 11; ggs2-Geranylgeranyl pyrophosphate synthase2; des-Desmin; PHGPX-Glutathione peroxidase; COR-Cold regulated; roqO-Cytochrome P450 monooxygenase roqO; NRPS-Non ribosomal peptide synthetase; PKS-Polyketide synthase; CYP76AHI- Cytochrome P450 enzyme 76AH1

Biosynthetic gene clusters and secondary metabolite production in fungi

It has been reported that there are a set of defined genes regularly clustered together in specified regions of fungal genome referred to as biosynthetic gene clusters (BGCs) that mediates the production of a large number of secondary metabolites in medicinal plants as well as in fungi (Chakraborty and Chakraborty 2021).

The genes located in these BGCs regions encode for various structural parts of the enzyme(s), and transport genes that take part in the biosynthesis of secondary metabolites that are co-regulated. Additionally, these genes are responsible for maintaining the operational integrity of various transcription factors (TFs) involved in the secondary metabolite production pathway (Fig. 2). Interestingly, the physical clustering of these BGCs augments the expression and regulation of genes involved in the formation of various substrates, and transport products, as well as alter the chemical scaffold of enzymes of key metabolic pathways of secondary metabolite synthesis (Kwon et al. 2021) (Fig. 2). Broadly fungal BGCs include genes for the synthesis of core enzymes like polyketide synthases (PKSs), non-ribosomal peptide synthetases (NRPSs), hybrids (PKS-NRPS), terpene synthases (TPS), and prenyltransferases (PTs) that alone or in combination directs the synthesis of the first product of biosynthesis pathway of fungal secondary metabolites (Avalos and Limón 2021; Sagita et al. 2021) (Fig. 2). Additionally, Sagita et al. (2021) showed that phenotype of secondary metabolite from endophyte fungi can be successfully linked to genotype by performing various experimental tools. Extensive variation has been seen in relation of the number of BGCs for different secondary metabolites among different fungal orders like Ascomycota, Basidiomycota, etc. (Mózsik et al. 2021).

Fig. 2.

Global regulatory network for augmenting endophytic fungi mediated bioactive secondary metabolite production. Biosynthetic gene clusters (BGCs) are responsible for the production of enzymes, transcription factors, and transport genes involved in major metabolic biosynthesis pathways. These BGCs can be studied and analyzed through both conventional biology approaches as well as synthetic biology approaches. [Polyketide synthases (PKSs); non-ribosomal peptide synthetases (NRPSs); hybrids (PKS-NRPS), terpene synthases (TPS); prenyltransferases (PTs); one strain many compounds (OSMAC)]

A study by Kjærbølling et al. (2018) demonstrated the presence of a secondary metabolite cluster for aflatoxin, chlorflavonin, and ochrindol that are linked to three different Aspergillus species, i.e., A. ochraceoroseus, A. campestris, and A. steynii. Simultaneously, work also revealed clusters for secondary metabolite novofumigatonin, ent-cycloechinulin, and epi-aszonalenins in A. novofumigatus. Concomitantly, there are specific BGCs accountable for particular bioactive metabolites like cyclosporin produced by the fungus Tolypocladium inflatum has been shown to be encoded by 14 BGCs (Bushley et al. 2013). Metabolic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 showed the presence of 65 BGCs responsible for the production of secondary metabolites like sordarin, aculeacin A, citreoviridin, alternariol, copalyl_diphosphate, etc. Among them, 23 gene clusters were encoding for PKS genes, 12 gene clusters of (NRPSs) along with some terpenes, and the remaining were PKS/NRPS hybrids gene clusters. Cheng et al. (2020) showed that the key secondary metabolite compound aurovertin, which is a polyketide-derived structure was mainly composed of seven genes, including aurA (these genes encode a PKS), aurB (a SAM-dependent methyltransferase), aurC (a FAD-dependent monooxygenase), aurD, aurE, aurF, and aurG (an acetyltransferase). In the fungus, Aspergillus flavus the BGCs comprise of hybrid PKS-NRPS cluster necessary for the synthesis of secondary metabolites 2-pyridones and leporins (Cary et al. 2015). Likewise, Wang et al. (2015a) reported the involvement of 27 PKSs, 12 NRPSs, five dimethylallyl tryptophan synthases, 15 terpenoid synthases, seven terpenoid cyclases, seven fatty-acid synthases, and five hybrids of PKS-NRPS for the synthesis of secondary metabolites in endophytic fungus Pestalotiopsis fici. In a different study, gene cluster encoding for two polyketide synthase enzyme (VdtA and VdtG) were identified in Paecilomyces variotii and Aspergillus viridinutans that are involved in biosynthesis of anti-bacterial compound viriditoxin (Urquhart et al. 2019). Whole-genome transcriptomic analysis of endophytic fungi, Alternaria sp. SPS-2 isolated from Echrysantha chrysantha showed that the protein-coding genes harbored 22 secondary metabolites BGCs including 7 PKSs, 10 NRPSs, 4 Terpenes, and 1 fungal-RiPP, and 14 of the BGCs are unknown (Tao et al. 2022). Recently, Yuan et al. (2022) identified 39 BGCs linked to 208 strains of A. oryzae using high end genome mining tools for 185 distinct terpenoid biosynthesis. Some of the examples of BGCs that have been studied in different endophytic fungi have been listed in Table 4. These BGCs mimic the gene clusters present in plants for the production of specialized metabolites (Polturak and Osbourn 2021). Due to recent advancement in genomics and other related tools, predicting the BGCs in endophytic fungi has become somewhat easy and as BGCse code of similar kind of secondary metabolites as that of plants, research efforts are being made to isolate secondary metabolites from endophytic fungi.

Table 4.

List of recent studies carried out for the identification of biosynthetic gene clusters (BGCs) in relation to bioactive secondary metabolite

Fungal strains	Secondary metabolites	Biosynthetic gene clusters	References
Penicillium decumbens, Aspergillus aculeatus, Aspergillus versicolor	Azaterrilone A	PKS	Grijseels et al. (2018)
Aspergillus flavus	Aspergillic acid	NRPS	Lebar et al. (2018)
Colletotrichum gloeosporioides Cg01, Penicillium polonicum hy4	Huperzine A	Epigenetic modification by histone methylation (HMTs), histone acetyltransferases (HATs), and histone deacetylase (HDACs)	Kang et al. (2019)
Cochliobolus lunatus (TA26-46)	Cochliobopyrones A and B, along with three isocoumarins and one chromone	Chemical epigenetic manipulation by DNA methyltransferase inhibitor 5-azacytidine	Wu et al. (2019)
Calcarisporium arbuscula NRRL 3705	Predominant metabolite aurovertins	65 BGCs including 23 PKS, 12 NRPS, 11 terpenes, seven PKS/NRPS hybrids,11 indoles and one other types	Cheng et al. 2020
Aspergillus terreus	Azaphilones	Four BGCs, two nonreducing PKSs, one highly reducing PKS, and one NRPS-like	Huang et al. (2020)
Penicillium brasilianum	Brasiliamide A	Epigenetic modulators such as suberoylanilide hydroxamic acid (SAHA) and nicotinamide (NAA) responsible for HDAC inhibition	Akiyama et al. (2020)
Grammothele lineata SDL-CO-2015-1	Paclitaxel, taxol	One NRPS, six Type I PKSs, 12 terpene and 10 NRPS-like	Ehsan et al. (2020)
Aspergillus calidoustus, Aspergillus westerdijkiae	Emericellamide A, emericellamide B, phenylahistin	Epigenetic modification through histone deacetylase (HDAC) inhibition by vorinostat	Aldholmi et al. (2020)
Penicillium dangeardii	Azaphilones, Dangelone A-F, Dangelone G, Dangelone H, Dangeloside A-B, Didangelone A-E, Didangelone H, Didangelone F, Didangelone G, Tridangelone A-E	43 BGCs including 22 PKSs, eight NRPSs, eight PKSs/NRPSs hybrids, and five terpene synthases	Wei et al. (2021)
Alternaria sp. SPS-2	Equisetin, Betaenones A–C, Alternariol, Dimethylcoprogen, Melanin	22 BGCs including 10 NRPSs, seven PKSs, four terpenes, and one fungal-RiPP	Tao et al. (2022)
Helotiales sp. BL73	Cochlioquinone B and D, Isofusidienol A	77 BGCs including 26 PKS type I, three PKS type III, 25 NRPSs, six PKS/NRPS hybrids, and 13 terpene and four indole gene clusters	Oberhofer et al. (2022)
Alternaria dauci	Aldaulactone	NRPS, PKS	Courtial et al. (2022)
Sarocladium zeae	Pyrrocidine	PKS-NRPS hybrid	Liu et al. (2022)
A. oryzae	185 distinct terpenoids	39 BGCs linked to 208 strains of A. oryzae	Yuan et al. (2022)

Regulation of biosynthetic gene clusters by different stimuli and secondary metabolite production

Secondary metabolites produced by endophytic fungi are often regulated by stimuli that switch on inactivated BGCs of fungi and stimulate the production of particular bioactive metabolites (Mózsik et al. 2022) (Fig. 2). Additionally, some studies demonstrated activation of similar BGCs by different stimuli for various unrelated secondary metabolites thereby hinting towards the existence of cross-talk of multiple gene clusters. There are several approaches to switch on the multiple silent gene clusters responsible for encoding secondary metabolites. Stroe et al. (2020) showed that bacteria Streptomyces rapamycinicus during its interaction with the fungus Aspergillus fumigatus activates its previously silent BGCs and stimulate the production of fumigermin encoded by gene FgnA (a PKS synthase). This fumigermin has been shown to inhibit spores of bacteria and provide a competitive advantage to fungi. Interestingly, the production of secondary metabolites in fungi is extensively transcriptionally regulated and is being activated by different methods (Mózsik et al. 2022).

El Hajj Assaf et al. (2020) deciphered in their review that the production of secondary metabolite in Penicillium is regulated by various transcription factors as well as environmental stimuli. Transcription factors like basic leucine zipper (bZIP) are well known for their role in the regulation of secondary metabolite production. Endophytic fungus Pestalotiopsis fici CGMCC3.15140 present bZIP transcription factor PfZipA that regulates the production of isosulochrin, RES1214-1, and pestheic acid that are resistant to the oxidative reagents tert-butylhydroperoxide (tBOOH), diamide, and menadione sodium bisulfite (MSB) (Wang et al. 2015b). Various other transcription factors like Zn(II)₂Cys₆, Cys₂His₂, helix turn helix also regulate the production of key secondary metabolite in Aspergillus nidulans, Collettrichum lagenarium, and Acremonium chrysogenum (Rashmi and Venkateswara 2019).

Transcript expression of BGCs is often controlled by epigenetic regulation mediated by enzymes such as histone deacetylases (HDACs) and histone acetyltransferases (HATs) which are responsible for eliminating, establishing, silencing biosynthetic gene clusters, thereby resulting in the production or enhancement of a variety of secondary metabolites (Cichewicz 2010; Albright et al. 2015). A group of scientists, Magotra et al. (2017) reported in their study that epigenetic modifiers like valproic acid-induced tenfold enhancement of the production of secondary metabolites fumiquinazoline C in an endophytic fungus Aspergillus fumigatus (GA‑L7) isolated from Grewia asiatica. Various genes including Afua_6g 12040, Afua_6g 12050, Afua_6g 12060, Afua_6g 12070, and Afua_6g 12080 were involved in the biosynthesis of fumiquinazoline C and these were upregulated in the presence of epigenetic modifier, valproic acid. Further evidence of differential expression has been recently reported by Qadri et al. (2017), where small-molecule epigenetic modifiers induce the expression of secondary metabolism-related genes from an endophytic fungus, Muscodor yucatanensis Ni30. The researchers observed that in the Ni30 strain, small-molecule epigenetic modifiers such as suberoylanilide hydroxamic acid (SAHA) and 5-azacytidine were used for the over-expression of PKS genes. In this regard, bioactive extrolite brefeldin A was isolated from the wild variant of Ni30, and the production of ergosterol and xylaguaianol C was done from the epigenetic variant of endophytic fungus M. yucatanensis EV1.

Modern approaches for enhancing secondary metabolite production and analyzing biosynthetic gene clusters

Synthetic biology has significantly provided a new era of research in the production of secondary metabolite from endophytic fungi by manipulating BGCs (Fig. 2). Baral et al. (2018) comprehensively explained the various advanced methods like pleiotropic approaches, targeted genome-wide and, BGCs specific approaches that can be adopted to improve secondary metabolite production through endophytic fungi. Retro biosynthesis has also emerged one of the interesting way to for augmenting secondary metabolite production by exploring enzymes of particular secondary metabolite through studying enzymes of known s biosynthetic pathway of structurally similar secondary metabolites (Sagita et al 2021). One of the most common and long terms followed approaches that have been extensively utilized for producing a wide range of secondary metabolites is the OSMAC approach, i.e., “one strain many compounds” in which cultural conditions are being manipulated like aeration, light, temperature, etc. for the isolation of novel secondary metabolites (Fig. 2) (Ramírez-Villalobos et al. 2023; Staropoli et al. 2023) Remarkably, previous literature has also shown that certain chemical inducers and environmental cues also stimulate the production of secondary metabolites (Xue et al. 2023) Apart from this, co-cultivation using different bacteria or different microbial partners also stimulates the production of fungal metabolites (Akone et al. 2016; Vinale et al. 2017a; Wakefield et al. 2017; Abdelwahab et al. 2018; Xue et al. 2023).

It has been established that co-culture with microbes for the augmentation of plant secondary metabolite concentration is very momentous approach and will drastically improve secondary metabolite composition of plants (Zhi-lin et al. 2007). These fungal endophytes acts as a elicitor molecule during co-culture for escalating the production of secondary metabolite in plants (Hussain et al. 2021a, b). A study by Ding et al. (2018) demonstrated significantly improved bioactive secondary metabolite production in tissue cultured Rumex gmelini seedlings when co-cultured with endophyte Aspergillus sp. An interesting research by Li et al. (2009) demonstrated increased production of important anti-cancerous drug paclitaxel in a co-bioreactor where cell suspension cultures of Taxus plant and an endophytic fungi Fusarium mairei were co-cultured. It has been observed that co-culture to cell suspension with endophytic fungus led to increased activity of enzymes responsible for production of secondary metabolites as evident from the work of Tang et al. (2011) where activity of enzymes phenylalanine ammonia lyase (PAL) and TDC were found to be increased in cell suspension cultures of Cathranthus roseus on inoculation with Fusarium oxysporum under in-vitro conditions. Increase biosynthesis of tanshinone was observed in seedlings of medicinal plant Salvia miltiorrhiza root co-cultured with an endophytic fungus Mucor circinelloides DF20 (Chen et al. 2021a, b, c). Similar, beneficial effects of co-culturing of endophytic fungi for improving secondary metabolite concentration were seen in the recent work of Devi et al. (2023b) where inoculation of Stevia rebaudiana with endophytic fungi Fusarium fujikuroi promoted substantial increase of polyphenols and rutin in comparison to control plants without any inoculation. Overall fungal endophytes has great potential in regulating the production of secondary metabolite concentration in plants and elicitation is one of the major approach that has tremendous benefit for increasing large-scale production of secondary metabolite during cell or plant culture (Isah et al. 2018). One of the major advantage of using fungal endophytes for the extraction of secondary metabolite is the yield and it was observed that there eightfold increase in taxol production by the endophytic fungus Paraconiothyrium SSM001 when co-cultured with Alternaria and Phomopsis isolated from the bark of the same host plant (Soliman and Raizada 2013a, b). Similarly, Bhalkar et al. (2016) demonstrated that co-culture of two endophytic fungi isolated from Nothapodytes nimmoniana Colletotrichum fructicola SUK1 and Corynespora cassiicola 25 SUK2 escalated the production of camptothecine an important anti-cancer drug. The study revealed that using response surface methodology (RSM) and mixed fermentation with two fungi there was increased production of camptothecine (146 mg l⁻¹) in comparison to their monocultures (Bhalkar et al. 2016).

Several other methodologies that can be regulated for the extraction of novel secondary metabolites from fungi are heterologous expression, chromatin remodeling, cluster-specific regulation, etc. With the advent of genomic advancement, target specific, i.e., promoter modification of BGCs has been carried out to augment secondary metabolite production. Keller (2019) depicted the presence of an extensive number of BGCs that may account for only a few secondary metabolites, although there are a plethora of BGCs that are still being explored and may lead way to the discovery of new bioactive metabolites that might have application in agriculture, pharmaceutical, etc.

Kjærbølling et al. (2019) reviewed the application of various molecular and genomic tools for understanding these BGCs and secondary metabolite production. Next-generation sequencing has played a pivotal role in the identification and correlation of BGCs with different secondary metabolite production among different fungal species as reviewed by Cacho et al. (2015). By analyzing these BGCs, biosynthesis of novel metabolites useful for human and animal health can be carried out as well as production of important metabolites responsible for providing defense to plants against various abiotic and biotic stress can be strategically enhanced using genetic manipulation techniques (Fig. 2). Subsequently, Ren et al. (2020) also reviewed the application of various bioinformatics tools such as AntiSMASH, PlantiSMASH, NP.searcher, SMURF, ClustScan, eSNaPD, Cluster Finder, EvoMining for the identification of BGCs responsible for the production of bioactive natural product in different plant and microbes (Fig. 2). By analyzing these BGCs, one can predict chemo diversity based evolutionary lineage among fungi as reviewed by Rokas et al. (2020). Theobald et al. (2018) carried out extensive genome mining using SMURF and antiSMASH for the identification of BGCs of Aspergillus section Nigri responsible for the malformin biosynthesis, an important secondary metabolite. Simultaneously, phylogenetic studies were completed to categorize different Aspergillus species based on BGCs of malformin biosynthesis in different clades. Deep learning has also been emerged as a new technology to understand the endophyte and bioactive secondary metabolite production gene network and bioprospection a evident from the study of Aghdam and Brown (2021)

Endophytic fungi mediated gene expression for growth, nutrient acquisition, and defense

Endophytic fungi in various plants augment plant biomass, seed production, and tolerance against different abiotic and biotic stresses (Vahabi et al. 2013; Toppo et al. 2022). Many studies have shown the positive effects of endophytic fungi on plant growth (Baron and Rigobelo 2022), nutrient acquisition (Verma et al. 2021), and stress alleviation (Karimi et al. 2022) due to which these endophytic fungi have now been utilized as biostimulants in modern agriculture under climate change conditions. Concomitantly, molecular studies have confirmed that these endophytic fungi affect the expression of various genes involved in various growth and metabolic pathways as well as defense (Rauf et al. 2022). The colonization of the endophytic fungus Piriformospora indica in the roots of trifoliate orange manifested effective results on plant growth and nutrient accession, especially P. There was up-regulation in the expression of the PtPT3, PtPT5, PtPT6 genes mainly in the epidermal cells and outer cortex of the root by a single inoculation of the endophytic fungus P. indica resulting in the better uptake of P at the root-soil configuration (Yang et al. 2021). Endophytic fungus Bipolaris sp. CSl-1 when inoculated in the soybean plant remarkably improves the root length, shoot and root fresh and dry weight, chlorophyll content, and concentration of SA under NaCl stress (Lubna et al. 2022). At the same time, inoculation of Bipolaris sp. CSl-1 enhanced soybean resistance towards NaCl stress and down-regulated the expression of the genes GmFDL19, GmNARK, and GmSIN1 and intensifies plant growth under salt stress (Lubna et al. 2022).

A study by Camehl et al. (2011) showed that growth promotion by Piriformospora indica in Arabidopsis was mediated by gene (OXI1) (Oxidative Signal Inducible 1). It was seen that P. indica upregulated transcript expression of OXI1 and PDK1 while downregulated the expression of the defense genes. In a different study, inoculation of endophytic fungus Fusarium oxysporum strain F047 induced resistance against Fusarium wilt in tomato by increasing transcript expression of three genes CH31, GLUA, and PR-1-a (Aimé et al. 2013). Endophytic fungus Trichoderma asperelloides T203 colonized in the roots of the plant Arabidopsis thaliana enhanced the expression level of the genes WRKY18 and WRKY40, which energized the expression of the defense genes FM01, PAD3 and CYP1A13. The wrky18/wrky40 double mutant line had reduced root colonization while over-expression of WRKY40 resulted in the partial phenotypic complexion. It has been observed that Trichoderma inoculated plants increased the expression of MDAR gene resulting in plant growth, osmo-protection as well as tolerance towards general oxidative stress in the root of the plant (Brotman et al. 2013). Defense-related genes were discriminatively expressed on the tomato plants colonized with the endophytic fungus Fusarium solani strain K (FsK) after spider mite affliction in comparison to those of the spider mite-infested un-colonized plants. The genes GLU-A and CHI9 were predominantly induced against the pathogens that were upregulated in the FsK-colonized plant. Substantially, upregulation of the genes PI-IIc and PR-1A and downregulation of the gene PPO-F occurred on the FsK-colonized plants. Furthermore, a remarkable further increase in the transcript levels of WIPI-II was led by FsK-colonization (Pappas et al 2018). Rondot and Reineke (2019) demonstrated upregulation in transcript expression of genes PR-2 (β-1,3-glucanases), PR-3 (chitinases), PR-5 (thaumatin-like proteins), and the PR protein 10.3 with inoculation of the endophytic fungus Beauveria bassiana against the infections by grapevine downy mildew Plasmopara viticola. Additionally the study also showed genes related to the stilbene synthesis and other related genes that were also upregulated that were involved in the plant pathogen interaction and defense of grapevine against the pathogen (Rondot and Reineke 2019). The genes LOX1 and OPR7 in the JA biosynthesis were upregulated by the inoculation of the endophytic fungus Metarhizium robertsii in the maize plant and led to improved plant defense mechanisms (Ahmad et al. 2020). Similarly, in the SA response pathway, PR5 was upregulated along with chitinase gene ECH A, whereas, the PR4 was downregulated in the leaf tissue isolated from the plants grown from M. robertsii -inoculated seeds (Ahmad et al. 2020). The wheat spikes treated by the endophytic fungus Penicillium oslonii ML37 showed faster and stronger expression of the defense metabolism against the Fusarium head blight in wheat (caused by Fusarium graminearum). The transcriptional activation of WRKY transcriptional factors was seen as a response to the fungal colonization which lowered the metabolites 15-acetyl-DON and culmorin of the pathogen F. graminearum (Rojas et al. 2022).

Emerging applications of endophytic fungi in different biotechnological sectors

Novel bioactive compounds produced by various endophytic fungi are of biotechnological attention as they can be potentially utilized as a source of secondary metabolites, anti-microbial agents, biological control agents, immune-suppressant, antiviral compounds, anti-tumor compounds, anti-diabetic, antihypertensive, anti-inflammatory, anti-atherogenic, anti-thrombotic, cardioprotective, vasodilatory and anti-allergic agents, antibiotics, a natural anti-oxidant, and much more (Yadav 2018; Yan et al. 2018). Thus, bioactive compounds from endophytic fungi can principally be exploited in multifaceted arenas, ranging from biomedicine, pharmaceutical drugs, agriculture, and industrial uses to biofuel and biocatalytic developments (Liu et al. 2017; Pan et al. 2017). In this direction, a prospective strategy can be to develop strain improvement methods using genetic engineering, optimization of culture conditions/media for cultivation, and co-culturing of different endophytic strains. Recent advances in high-throughput technologies and the “genomic revolution” have contributed considerably to natural product research and the discovery of biosynthetic gene clusters (Zazopoulos et al. 2003; Lautru et al. 2005). Genetic engineering of endophytes is still in its infancy and is often regarded as a progenitor of system biology and functional genomics strategies (Tyo et al. 2007) with the potential for long-term translational success. Studies have suggested the inclusion of metabolic pathways and genes in endophytes via genetic recombination between plant hosts and endophytes. In addition, horizontal gene transfer, an evolutionary mechanism, has been suggested as an adaptive mechanism for endophytes, and it confers novel traits to the associated microbes (Kumari et al 2016; Tiwari and Bae 2020).

Recently, harnessing microbial resources via biotechnological means has been promising; with vast applications in agricultural and environmental studies. Current research on plant growth-promoting endophytic fungi has revealed more insights into their biotechnological importance in the synthesis of biofertilizers and biopesticides in developing agriculturally friendly chemicals to ensure maximum food security in a sustainable and safe manner (Igiehon and Babalola 2017). The culture-dependent approach has been used to isolate various microorganisms from different environments, however only a small proportion of total microbes can be cultured; hence, the large microbial population can be assessed using culture-independent metagenomics approaches (focused on gene sequencing, and further computational analysis of sequence data from microbial DNA to detect structural, functional, and metabolic pathways) (Dissanayake et al. 2018; Fadiji and Babalola 2020).

Metagenomic analysis of endophytes from various plant organs allows to determine the structural, functional, and phylogenetic construction of genetic relatedness (from a metagenomic library) in the microbial genome from long reads of metagenome sequence data. Next-generation sequencing approaches such as 454 pyrosequencing (Roche) and Illumina sequencing have been employed in the study of whole microbial communities with novel traits responsible for growth promotion, cellular metabolism, phytohormone synthesis, and nitrogen fixation from the internal tissues of plant roots. At the gene level, the analysis of gene prediction, taxonomic profiling, and molecular functions of plant growth-promoting microorganisms are permissible using metagenomic analysis (Hardoim et al. 2015).

Recently, in-vitro preparation of the Cas9-gRNA ribonucleoprotein complex and transformation into protoplasts of filamentous fungi has become available (Pohl et al. 2016; Al Abdallah et al. 2017; Wang et al. 2018). Although it has not been applied in endophytic fungi, this is a promising strategy to advance not only in gene editing, but it also advances the development of gene expression for biotechnological purposes using the recently developed CRISPR interference and CRISPR activation systems which offer novel strategies to regulate gene expression (Zheng et al. 2019). To a large extent, the use of omics technology has advanced microbial studies to a level of genomics, proteomics, and transcriptomics (Akinola and Babalola 2020). However, there are challenges like diffusion of plant DNA compared to microbial DNA (making it difficult to separate fungal metagenome), the inability to manage and conduct automation classification of large sequence datasets, and the unattainability of functional gene annotations in the gene library for fungal genomes under examination. Due to the abundance of plant DNA compared to fungal DNA, it is difficult to successfully sequence only microbial DNA at high coverage. Very recently, the enrichment of fungal DNA from the stems and leaves of maize, rice, and soybean (Mehmood et al. 2019) and the internal tissue of potato tubers has been reported (Krell et al. 2018). With the current ongoing metagenomics research of the microbial world, scientists could efficiently engineer fungal endophytes and harness their possible biological resources to formulate bio-inoculants in promoting plant growth for improved agricultural productivity.

Biocontrol agents

Extensive and irrational usage of chemical pesticides to regulate phytopathogens has caused environmental deterioration, residue complications, resistance to pathogens, and diverse threats to the health of living organisms (Liu et al. 2016). However, various bioactive secondary metabolites being produced by endophytic fungi act as biocontrol agents and have been extensively described to help hosts by improving resistance to pathogenic invaders (Yu et al. 2017). Based on this, few studies on efficient endophytes as the biocontrol agents of phytopathogens have been illustrated in Table 5. Endophytic fungi can suppress pathogens by inducing morphological changes and overexpression of endogenic anti-microbial compounds in hosts, competition for niche utilization, anti-biotics production, egg parasitic (breakdown of the shell integrity), hatching inhibition, (Ownley et al. 2008; Siddaiah et al. 2017). Besides providing resistance to stresses, these fungi can also augment plant development by stimulating nutrient availability (e.g. solubilizing different sources of phosphorus, improving plant–endophyte–herbivore communications for nitrogen cycling), and transferring rhizospheric nutrients to their plant hosts, by decomposing soil organic compounds and/or by stimulating growth hormones like indole acetic acid in host plants (Kiers et al. 2011; Priyadharsini and Muthukumar 2017). Fungal-derived polysaccharides especially exopolysaccharides may aid these fungi to resist various abiotic stresses, assist in the establishment of biofilms for colonizing the host, turn into bio-elicitors to stimulate efficient metabolite to build up in plant partners, and/or employ many other biological activities (Liu et al. 2017). These microbial polysaccharides can be applied for the production of many bioproducts, e.g., coverings in wound shock healing, suspension stabilizers, tablet granulation tissue and coating, and many more (Freitas et al. 2011; Moscovici 2015).

Table 5.

A list of endophytic fungi with application in various other biotechnology sectors

Name of endophyte	Host plant	Consequence	Reference
Biocontrol agent
Fusarium solani TRX-34–1,  Rhexocercosporidium sp.	Sophora tonkinensis Gapnep	Biocontrol agents against phytopathogens of Panax notoginseng	Yao et al. (2017)
Fusarium verticillioides	Zea mays	Biocontrol—Restrict Ustilago maydis growth	Rodriguez et al. (2012)
Penicillium sp.,  Guignardia mangiferae,  Hypocrea sp.,  Neurospora sp.,  Eupenicillium javanicum, Lasiodiplodia theobromae	Cucumis sativus	Biocontrol of Fusarium oxysporum f. sp. cucumerinum	Abro et al. (2019)
Alternaria alternata	Grapevine leaves	Production of three anti-fungal metabolites • Three diketopiperazines: cyclo (l-phenylalanine-trans-4-hydroxy-l-proline) • Cyclo (l-leucine-trans4-hydroxy-l-proline) • Cyclo (l-alanine-trans-4-hydroxy-l-proline) Effective against Plasmopara viticola	Musetti et al. (2006)
Cryptosporiopsis sp. and Phialocephala sphareoides	Norway spruce (Picea abies)	Inhibit phytopathogen (anti-fungal)—Heterobasidion parviporum, Phytophtora pini, and Botrytis cinerea	Terhonen et al. (2016)
Root-knot nematode (Meloidogyne spp.)	Roots of almost all cultivated plants	Biocontrol effect against Meloidogyne incognita	Yao et al. (2015)
Xylaria	Pinus strobus	Production of secondary metabolite including terpenoids, cytochalasins, mellein, alkaloids, and polyketides—promising herbicide, biopesticide, and biocontrol agents	Macías-Rubalcava and Sánchez-Fernández (2017)
Fusarium proliferatum	Macleaya cordata (plume poppy), Sanguinaria canadensis (bloodroot), and Chelidonium majus (swallowwort poppy)	Sanguinarine—Anti-bacterial Anti-inflammatory Anti-helminthic	Wang et al. (2014)
Guignardia mangiferae	Citrus sp.	Can synthesize 5–30-nm-sized, spherical-shaped AgNps of Anti-bacterial Anti-fungal and Anti-proliferative activity	Balakumaran et al. (2015)
Pestalotia sp.	Leaves of Syzygium cumini	AgNps with anti-microbial activity can be increased by combination with antibiotics such as gentamycin and sulphamethizole. Together they can inhibit the growth of the human pathogens Staphylococcus aureus and Salmonella typhi	Raheman et al. (2011)
Eupenicillium parvum	Azadirachta indica	Azadirachtin A and B and their structural analogs—bioinsecticides with antifeedant and insect growth-regulating properties	Kusari et al. (2012)
Guignardia mangiferae,  Fusarium proliferatum,  Colletotrichum gloeosporioides	Taxus x media	Taxol—Fungicide	Xiong et al. (2013)
Stress tolerance/ Bioremediation/Biosorption
Piriformospora indica	Hordeum vulgare, Brassica rapa	Biotic/abiotic stress tolerance especially Drought stress tolerance	Sun et al. (2010), Johnson et al. (2013) and Ghaffari et al. (2019)
Mucor sp. MHR-7	Brassica campestris	Metal toxicity reduction	Zahoor et al. (2017)
Rhizopus sp. CUC23, A. fumigatus ML43  Penicillum radicum PL17	Lactuca sativa	Chromium detoxification	Bibi et al. (2018)
Neotyphodium coenophialum, N. uncinatum	Festuca arundinacea, Festuca pratensis	Bioaugmentation, total petroleum hydrocarbons (TPH) and polycyclic aromatic hydrocarbons (PAHs) removal from the soil	Soleimani et al. (2010)
Verticillium sp., Xylaria sp.	Plants from Ecuadorian Amazon	Degradation of Petroleum hydrocarbon	Marín et al. (2018)
Curvularia sp., Neusartorya sp.	Mangrove sp.	Heavy metal biosorption	Onn et al. (2016)
Bjerkandera adusta SWUSI4	Sinosenecio oldhamianus	Detoxification of triphenylmethane dyes	Gao et al. (2020)
Lasiodiplodia theobromae	Boswellia ovalifoliolata	Heavy metal tolerance	Aishwarya et al. (2017)
Lindgomycetaceae P87, Aspergillus sp. A31	Aeschynomene fluminensis	Heavy metal resistance, bioremediation	Pietro-Souza et al. (2020)
An endophytic fungus,  Lasiodiplodia sp. MXSF31	Stem of Portulaca oleracea	Fungi have the potential in promoting the growth of Portulaca in metal-contaminated soils. The biosorption process of MXSF31 was attributed to the functional groups of hydroxyl, amino, carbonyl, and benzene ring on the cell wall	Deng et al. (2014)
Fusarium sp.	Mangroves	Tailored Biosorption—Endophytic fungi were dried and powdered and then chemically modified by formaldehyde, methanol, and acetic acid to augment their affinity for uranium from polluted wastewater	Chen et al. (2014)
Plant growth promotion/Biofertilizers
Penicillium sp. 21,  Penicillium sp. 2,  Aspergillus sp. MNF	Camellia sinensis	Mineral-solubilizing function (Ca3(PO4)2 and rock phosphate)	Gupta et al. (2007) and Nath et al. (2012)
Trichoderma gamsii (NFCCI 2177)	Lens esculenta	Solubilization of Tricalcium phosphate	Rinu et al. (2014)
Trichoderma peudokoningi, Chaetomium globosum, Fusarium oxysporum	Solanum lycopersicum	Siderophore production, HCN and ammonia production	Neha et al. (2015)
Ophiosphaerella sp., Cochliobolus sp.	Triticum aestivum	PGP activities	Spagnoletti et al. (2017)
Cladosporium sphaerospermum	Glycine max	Solubilize calcium phosphate	Hamayun et al. (2009)
Fusarium tricinctum RSF-4L, Alternaria alternata RSF-6L	S. nigrum	Production of phytohormones (gibberellins)	Khan et al. (2015)
Coniothyrium aleuritis 42, Pichia guilliermondii F15, Fusarium oxysporum NSF2,  F. proliferatum AF04, Aspergillus nidulans FH5, Trichoderma spirale YIMPH30310	Lycopersicon esculentum	Plant biomass increase, fruit yield	Xia et al. (2019)
Phialocephala fortinii	Chamaecyparis obtuse, Rubus sp.	Promote Asparagus officinalis growth	Surono and Narisawa (2017)
Phomopsis liquidambari	Arachis hypogaea	Increase nodulation and N2 fixation by enhancing hydrogen peroxide and nitric oxide signaling	Xie et al. (2017)
Metarhizium robertsii	Phaseolus vulgaris Glycine max Panicum virgatum Triticum aestivum	The insect-pathogenic fungus Metarhizium robertsii couple root association and insect (Galleria mellonella) pathogenicity so that it acts as a conduit to provide insect-derived nitrogen to plant hosts	Behie and Bidochka (2014a, b)
Penicillium chrysogenum Pc_25 Alternaria alternata Aa_27	Asclepias sinaica	Produces ammonia, indole acetic acid (IAA), and phytohormone to improve the growth parameters of plant	Fouda et al. (2015)
Alternaria sp.,  Fusarium tricinctum RSF-4L, Alternaria alternata RSF-6L	Brassica napus, Crocus sativus Linn., Solanum nigrum	Growth-promoting—Indole-3-acetic acid	Shi et al. (2017), Wani et al. (2016) and Khan et al. (2017)
Acremonium curvulum, Aspergillus niger,  Cochliobolus lunatus,  Gibberella baccata, Myrmecridium schul zeri, Myrothecium verrucaria,  P. commune,  Phoma putaminum,  Pithomyces atro-olivaceus, Trichoderma piluliferum	Bauhinia	Forficate for the production of cellulase, lipase, protease, and xylanase	Bezerra et al. (2015)
Pharmaceutical industry
Taxomyces andreanae, T. brevifolia	Pacific yew	Paclitaxel—Anti-cancer	Stierle et al. (1993)
Fusarium subglutinans	Tripterygium wilfordii	Subglutinol A—Immuno-suppressant	Strobel and Pliam (1997)
Trametes hirsuta	Podophyllum hexandrum	Podophyllotoxin—Antiviral, Radio-protective	Puri et al. (2006)
Rhizoctonia bataticola	Coleus forskohlii	Forskolin—Anti-HIV, Anti-tumor	Mir et al. (2015)
Fusarium proliferatum	Macleaya cordata	Sanguinarine—Antihelmintic	Wang et al. (2014)
Alternaria sp.	Digitalis lanata	Digoxin—Cardiotonic	Kaul et al. (2013)
Phomopsis sp.	Cinchona ledgeriana	Quinine—Antimalarial	Maehara et al. (2010)
Alternaria alternata	Capsicum annuum	Capsaicin—Cardio-protective	Devari et al. (2014)
Fusarium solani	Rheum palmatum L	Rhein—Anti-microbial, Anti-tumor and Anti-inflammatory	You et al. (2013)
Taxomyces andreanae, Cladosporium cladosporioides, Paraconiothyrium SSM001, Guignardia mangiferae,  Fusarium proliferatum,  Colletotrichum gloeosporioides	Phloem (inner bark) of the Pacific yew, Taxus brevifolia or Taxus media	Taxol, a diterpenoid anti-cancer drug, originally been extracted from Taxus brevifolia or Taxus media. Taxol-producing fungal endophytes, like Taxomyces andreanae, Cladosporium cladosporioides, Paraconiothyrium SSM001, Guignardia mangiferae, Fusarium proliferatum, Colletotrichum gloeosporioides are being actively developed as alternative means for the production of taxol	Zhang et al. (2009); Soliman and Raizada (2013a, b); Xiong et al. (2013) and Soliman et al. (2015)
Chaetomium globosum	Polysiphonia urceolata	Chaetopyranin—benzaldehyde derivative isolated from fungal endophytes has anti-cancerous and anti-oxidant properties	Wang et al. (2006)
Pestalotiopsis fici	Camellia sinensis	Novel chromone Pestalotiopsone F 22 reported from the culture filtrate of fungal endophyte exhibit adequate cytotoxic effect against the murine cancer cell line L5178Y	Xu et al. (2009) and Liu et al. (2009)
Fusarium oxysporum	Ephedra fasciculata	Beauvericin—a depsipeptide isolated from the fungal endophyte repress movement of the metastatic prostate cancer (PC-3M) and breast cancer (MDA-MB-231) cells	Zhan et al. (2007)
Trichoderma atroviride, Fusarium solani,  Fomitopsis sp.,  Alternaria alternata,  Phomopsis sp.	Catharanthus roseus acuminata, Miquelia dentata	Camptothecin (CPT) is a monoterpenoid indole alkaloid and its derivatives (inhibit DNA topoisomerase I) are anti-cancer agents targeting small lung and refractory ovarian cancers. CPT and its derivatives were originally extracted from Camptotheca acuminata and Miquelia dentata	Pu et al. (2013); Kusari et al. (2011) and Shweta et al. (2013)
Endophyte	Mimosops elengi	Ergoflavin (anti-cancer compound), a pigment isolated from endophyte inhibit the production of TNF-α and IL-6	Deshmukh et al. (2009)
Nigrospora sphaerica,  Talaromyces radicus	Catharanthus roseus	Vinca alkaloids (Vas) are naturally found in Catharanthus roseus. Well-known anti-cancer compounds (used in the treatment of leukemia, and Hodgkin’s disease) include vinorelbine, vindesine, vincristine, and vinblastine	Ayob et al. (2017) and Palem et al. (2015)
Penicillium oxalicum	Gymnema sylvestre	Gymnemagenin—Antidiabetic	Parthasarathy and Sathiyabama (2014)
F. oxysporum SYP0056	Ginkgo biloba	produces Ginkgolide B, which used in the treatment of cardiovascular diseases	Cui et al. (2012)
Chloridium species	Azadirachta indica	Javanicin (naphthaquinone), with anti-microbial properties, extracted from endophytic fungus	Kharwar et al. (2009)
Chaetomium	leaves of Sapium ellipticum	Produce chaetocochin A-C having anti-cancer properties	Akone et al. (2016)
Exserohilum rostratum	Amazon Plant (Bauhinia guianensis)	Polyketide monocerin has antagonist activity against E. coli (ATCC 25922), Pseudomonas aeruginosa (ATCC 27853), Staphylococcus aureus (ATCC 25923), Bacillus subtilis (ATCC 6633), and Salmonella typhimurium (ATCC 14028)	Pinheiro et al. (2017)
Phomopsis sp. XP-8	Eucommia ulmoides Oliver	Antihypertensive—Pinoresinol diglucoside, Pinoresinol monoglucoside, Pinoresinol	Shi et al. (2012) and Yan et al. (2015)
Fusarium solani SD5	Alstonia scholaris (devil tree)	Produce PS-I (capsular polysaccharide) with anti-inflammatory activities	Mahapatra and Banerjee (2012, 2013)
Diaporthe sp. JF766998, Diaporthe sp. JF767007	Piper hispidum Sw	Antiproliferative activity against human breast carcinoma (MCF7) and hepatocellular carcinoma (HepG2-C) cell	Orlandelli et al. (2017)
Penicillium chrysogenum MTCC 5108	Mangroves	Source of non-ribosomal peptides (NRP) and Penicillin (antibiotic)	Devi et al. (2012)
Anti-oxidants
Pestalotiopsis microspora VJ1/VS1	Gymnema sylvestre	AgNPs—Anti-oxidant and Anti-cancer	Netala et al. (2016a)
Mucorfragilis fresen, Eupenicillium parvum	Sinopodophyllum hexandrum	Kaempferol—Anti-oxidant and anti-microbial activity	Huang et al. (2014)
Fusarium sp. JZ-Z6,  F. sp. JZ-Z7,  F. redolens Sz1_1 H,  F. tricinctum WS11790	Fritillaria unibracteata	Anti-oxidants with anti-cancerous activity—Gallic acid, Phlorizin and Rutin	Pan et al. (2017)
Arthrinium sp. 0042,  Colletotrichum sp. 0047/0048,  Diaporthe sp. 0051	Aquilaria subintegra	Anti-oxidants—oxo-Agarospirol, α-Agarofuran, β-Agarofuran, δ-Eudesmol and β-Dihydro agarofuran	Monggoot et al. (2017)
Sordariomycete sp. B5	Eucommia ulmoides Oliver (Du-Zhong)	Chlorogenic acid (phenolic ester of caffeic and quinic acids)—Anti-bacterial Anti-oxidant, Anti-tumor and Anti-fungal	Chen et al. (2010)
Berkleasmium sp. Dzf12	Dioscorea zingiberensis (yellow ginger)	Produce Exopolysaccharide, with anti-oxidant activities	Li et al. (2012a)
Fusarium oxysporum Dzf17	Dioscorea zingiberensis	Produce water-soluble polysaccharides (WPS) with anti-oxidant activities	Li et al. (2011, 2012b)
Aspergillus sp. Y16	Mangrove	As1-1, an exopolysaccharide with anti-oxidant properties	Chen et al. (2011)
Aspergillus versicolor ENT7	Centella asiatica	AgNPs—Anti-bacterial, Anti-fungal and Anti-oxidant activity	Netala et al. (2016b)
Dabaryomyces hansenii	–	The fermentation of black tea with endophytes has resulted in the addition of major vitamins such as A, B1, B2, B12, and C, which are sufficient to fulfill the recommended dietary allowance. It also resulted in the reduction of tannins and caffeine in an effective amount. Moreover, the compound theophylline, which accumulates due to fermentation, imparted a bronchodilatory effect to the tea	Pasha and Reddy (2005)
Biofuels
Gliocladium roseum NRRL 50072	Eucryphia cordifolia (ulmo)	Produce a series of volatile hydrocarbons and their derivatives on oatmeal-based agar and cellulose-based media in a species-specific manner	Strobel et al. (2008) and Griffin et al. (2010)
Penicillium brasillianum, Penicillium griseoroseum,  Xylaria sp. (NICl3),  Xylaria sp. (NICL5),  Penicillium sp. (PAOE),  Trichoderma spp.	From several different species of tropical plants	Produce high concentrations of a lipid matrix that may serve as promising sources of biofuel precursors	Santosfo et al. (2011)
Nigrograna mackinnonii	–	Produces a series of volatile natural products, including terpenes and odd chain polyenes—a source of biofuel	Shaw et al. (2015)
Gliocladium sp.	Eucryphia cordifolia (ulmo)	Degrade plant cellulose and synthesize complex hydrocarbons under microaerophilic conditions. This fungus could produce hydrocarbons ranging from C6 to C19 (i.e., hexane, heptane, as well as benzene) directly from cellulosic biomass	Ahamed and Ahring (2011)
Hypoxylon sp.,  Daldinia eschscholzii	–	Sources of biomass deconstructing carbohydrate-active enzymes (for conversion of lignocellulose into advanced biofuels)	Wu et al. (2017)
Periconia sp.	Torreya grandifolia	Produces thermotolerant β-glucosidase, a thermotolerant secondary metabolite which has high activity toward cellobiose and carboxymethylcellulose. The enzymes can convert lignocellulosic biomass into biofuels and chemicals	Harnpicharnchai et al. (2009)

Bioremediation

Continued industrial development in the world is leading to the accelerated emission of various pollutants including heavy metals (HMs), anti-biotics, and pesticides (Ma et al. 2011; Zouiten et al. 2016; Vignaroli et al. 2018). These pollutants leak from industrial surpluses and aquatic resources into soils and cause environmental pollution, adversely affect plant growth and raise toxic food chain concerns (Deng and Cao 2017; Hassan et al. 2017). Remediation strategies available for reducing the damaging effects at HMs-contaminated sites include physicochemical approaches such as filtration treatment, excavation, on-site metal stabilization, and phytoremediation. All these strategies have their limitations (beyond the scope of this chapter), thus, recent research indicates that bioremediation like the utilization of endophytic fungi (a few studies mentioned in Table 5) has emerged as an eco-friendly technique to clean metal-contaminated areas (Xiao et al. 2010; Deng et al. 2014; Khan et al. 2017; Zahoor et al. 2017). The fungi can eliminate rhizospheric HMs by biotransformation, biosorption on the fungal cell wall, and/or their buildup in fungal hyphae, thus dropping their disposal and harmfulness to host plants (Khan et al. 2017; Zahoor et al. 2017). Since bio-adsorption efficiency can be improved by modulating the density of the functional groups on a fungal cell wall, endophytic fungi can be tailored into a significantly efficient biosorbent (with improved biosorption efficiency for metal ions) by making chemical modifications. Other aspects comprise interaction time, pH, solid/liquid ratio, and original HMs levels in the polluted areas (Chen et al. 2014). It was observed that endophyte fungus can also be exploited for the commercial production of enzymes as evident from studies by Toghueo et al. (2017) that showed remarkable production of extracellular enzymes such as cellulases, amylases, lipases, and laccases from fungal endophytes. Recently, Abdalla et al. (2020) also showed the production of cellulases and xylanases from the endophytic fungus isolated from medicinal plants of South Africa. The study depicted the presence of the polyketide synthase type 1 (PKS1) gene that will be utilized for the production of bioactive metabolites in future. Several endophytes isolated from the medicinal plant Kadsura angustifolia were found to have degradative activity (Huang et al. 2015).

Secondary metabolite

Plants are a potential synthesizer of functional secondary metabolites—the source of crude natural drugs (Venugopalan and Srivastava 2015), but dependency on the plant growth rate, little quantities of drug yield/plant, laborious extraction, and over-harvesting lead to extinction distress in some rare medicinal plants (Huang et al. 2014) make plants inappropriate source of drugs. In this direction, many studies have provided key insights into the existing and emerging significance of fungal endophytes in drug discovery and research (Tiwari and Bae 2022). In contrast, endophytic microorganisms also exhibit competence to yield associated plant secondary metabolites with therapeutic and cosmetics values (Budhiraja et al. 2013; Kaushik et al. 2014). Cultivation of such fungal endophytes has been exploited as more efficient large-scale production systems for valued metabolites as they are fast-growing with reduced space utilization, and can be easily modified as per requirement (Palem et al. 2015).

The rising mandate for fuels and ecological complications triggered by the emission of greenhouse gases have directed towards a convincing necessity of sustainable alternate energy sources like biological organisms (Wu et al. 2017). Endophytic fungi could yield volatile organic compounds (VOCs—mainly hydrocarbons and other oxygenated compounds) and lignocellulolytic enzymes while growing on plant and agricultural residues. VOCs are being measured as promising alternatives to fossil as they look like fossil fuels and are known as mycodiesel (Strobel et al. 2008; Suryanarayanan et al. 2012; Wu et al. 2016). Endophytic fungi absorb nutrients from the plant as well as from the surrounding environment and hence secrete enzymes to catabolize complex organic matter (Thirunavukkarasu et al. 2015). Endophytes secreted enzymes can be exploited for biotechnological purposes by various industries (agriculture, pulp, pharmaceutical, paper, and industries) for example glutaminase-free l-asparaginase is used for the treatment of lymphoblastic leukemia (Nagarajan et al. 2014). Chitin-modifying enzymes secreted by fungal endophytes isolated from leaves of various Western Ghats trees can acetylate chitosan to diverse degrees (Rajulu et al. 2011). Compared with crustacean chitosans, the fungal enzymes are of low molecular weight, have higher polydispersity, and act on substrates with a lower degree of acetylation (Nwe et al. 2009). Therefore, screening for the diversity of such endophytic fungal enzymes is a novel but promising method to be utilized in food and environmental industries (Suryanarayanan et al. 2012) for example the fungal enzyme laccase can be exploited for the biosensor formation, biodegradation of dyes, phenols, and pesticides (Senthivelan et al. 2016). Pigment secreted by Penicillium aculeatum can be used in the soft drink because of its stability at neutral pH (Mapari et al. 2009) and pigment from Monascus purpureus is stable at higher pH (Huang et al. 2011). Natural colorants fungal endophytes have wide applications in cosmetics, foods, pharma, and textiles industries for example glucoamylase from Aspergillus niger and A. oryzae is exploited by the sugar and starch industry to harvest glucose (Devi et al. 2020). Due to increasing health consciousness, the use of fungal food like mycoproteins has risen globally as nutraceuticals, especially among vegetarian folks (Ghorai et al. 2009). Besides the food industry, traditional Chinese medicine has been using shiitake mushrooms for example Ganoderma lucidum is a promising anti-cancer agent, stress reducer, and potent immune system regulator (Devi et al. 2020).

A few examples of endophytic fungi involved in agriculture, bioremediation, biomedicine, pharmaceutical, biofuel, biocatalyst, and in the production of functional secondary metabolites, polysaccharides, are mentioned in Table 5.

Conclusion

Fungal endophytes oblige as “biosynthetic platforms” of significant secondary metabolites with huge biotechnological applications. However, partial knowledge of endophyte biology and reduced production of secondary metabolites in recurring sub-cultures of endophytic strains necessitates the requirement to adopt a comprehensive and systematic approach toward the exploitation of endophytes in various industries and research. In this direction, a forthcoming strategy is to use high-throughput technologies and the “genomic revolution” to develop strain improvement methods (Lautru et al. 2005). One such approach is the inclusion of metabolic pathways and genes in endophytes via genetic recombination between plant hosts and endophytes since endophytes mimic their host plant in the self-governing biosynthesis of secondary metabolites (Tiwari and Bae 2020). Scientific tools and approaches are intended to employ the co-integration of bioprocess techniques and genetic/metabolomics approaches to study the dynamics of plant–endophyte interactions and produce high yields of industrially important metabolites.

Author contributions

PT—writing, editing, formatting; LLK and AG—writing, formatting, preparation of figures and tables; PG—writing, editing; RC—writing; SR—editing, PM—conceptualization, drafting, editing, formatting, corrections.

Funding

This work was supported by the University of North Bengal with research project Ref. No. 2225/R-2021 granted to Dr. Piyush Mathur.

Availability of data and materials

Not applicable.

Declarations

Conflict of interest

All the authors declare that there is no conflict of interest.