Skip to main content

Exploring the Benefits of Endophytic Fungi via Omics

  • Chapter
  • First Online:
Book cover Advances in Endophytic Fungal Research

Abstract

Endophytic fungi constitute a remarkably diverse, ubiquitous group of eukaryotes with the ability to synthesize secondary metabolites of clinical significance. Their presence has an advantageous effect on growth and health of host plants under duress. They have also been envisaged as a source of diverse medicinal compounds since the discovery of taxol, a prominent anti-cancer drug. In this chapter, we have discussed how resident endophytic fungi aids the host plant in tackling various forms of biotic and abiotic stresses. Their therapeutic potential, viz. cancer cytotoxicity, immunomodulatory, anti-parasitic and anti-pathogenic potential have also been reviewed here. This chapter also explores the plethora of literature available for genomics, metagenomics, transcriptomics, proteomics and metabolomics of endophytic fungi alongside their available web-resources. Applications of omics-based studies on these mutualistic biotrophs have been instrumental in discovery of many unanswered and novel aspects of their biosynthetic potential and overall biology. Data reservoir on fungal endophytes has been constantly growing over the past decades and this reservoir can pave the route of future exploration of these beneficial organisms in therapeutics, biology and evolution via emergent and evolving modes of analysis like machine learning and more.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adpressa DA, Loesgen S (2016) Bioprospecting chemical diversity and bioactivity in a marine derived Aspergillus terreus. Chem Biodivers 13(2):253–259

    Article  CAS  PubMed  Google Scholar 

  • Akiyama H, Fujii K, Yamasaki O, Oono T, Iwatsuki K (2001) Antibacterial action of several tannins against Staphylococcus aureus. J Antimicrob Chemother 48(4):487–491

    Article  CAS  PubMed  Google Scholar 

  • Ambrose KV, Belanger FC (2012) SOLiD-SAGE of endophyte-infected red fescue reveals numerous effects on host transcriptome and an abundance of highly expressed fungal secreted proteins. PLoS One 7(12):e53214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arnold AE, Mejía LC, Kyllo D, Rojas EI, Maynard Z, Robbins N et al (2003) Fungal endophytes limit pathogen damage in a tropical tree. Proc Natl Acad Sci U S A 100(26):15649–15654. http://www.ncbi.nlm.nih.gov/pubmed/14671327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Artanti N, Tachibana S, Kardono L, Sukiman H (2011) Screening of endophytic fungi having ability for antioxidative and α-glucosidase inhibitor activities isolated from Taxus sumatrana. Pak J Biol Sci 14(22):1019–1023

    Article  CAS  PubMed  Google Scholar 

  • Aschehoug ET, Callaway RM, Newcombe G, Tharayil N, Chen S (2014) Fungal endophyte increases the allelopathic effects of an invasive forb. Oecologia 175(1):285–291. https://doi.org/10.1007/s00442-014-2891-0

    Article  PubMed  Google Scholar 

  • Bacon CW, Porter JK, Robbins JD, Luttrell ES (1977) Epichloë typhina from toxic tall fescue grasses. Appl Environ Microbiol 34(5):576–581

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bacon CW, White JF, James F (2018) Biotechnology of endophytic fungi of grasses. CRC, Boca Raton

    Book  Google Scholar 

  • Bai Y, Chen B, Li M, Zhou Y, Ren S, Xu Q et al (2017) FPD: a comprehensive phosphorylation database in fungi. Fungal Biol 121(10):869–875

    Article  PubMed  Google Scholar 

  • Baltruschat H, Fodor J, Harrach BD, Niemczyk E, Barna B, Gullner G et al (2008) Salt tolerance of barley induced by the root endophyte Piriformospora indica is associated with a strong increase in antioxidants. New Phytol 180(2):501–510. http://www.ncbi.nlm.nih.gov/pubmed/18681935

    Article  CAS  PubMed  Google Scholar 

  • Bashyal BP, Wellensiek BP, Ramakrishnan R, Faeth SH, Ahmad N, Gunatilaka AAL (2014) Altertoxins with potent anti-HIV activity from Alternaria tenuissima QUE1Se, a fungal endophyte of Quercus emoryi. Bioorg Med Chem 22(21):6112–6116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bayat F, Mirlohi A, Khodambashi M (2009) Effects of endophytic fungi on some drought tolerance mechanisms of tall fescue in a hydroponics culture. Russ J Plant Physiol 56(4):510–516. https://doi.org/10.1134/S1021443709040104

    Article  CAS  Google Scholar 

  • Bonants P, Edema M, Robert V (2013) Q-bank, a database with information for identification of plant quarantine plant pest and diseases. EPPO Bull 43(2):211–215

    Article  Google Scholar 

  • Brakhage AA, Schuemann J, Bergmann S, Scherlach K, Schroeckh V, Hertweck C (2008) Activation of fungal silent gene clusters: a new avenue to drug discovery. In: Petersen F, Amstutz R (eds) Natural compounds as drugs. Progress in drug research, vol 66. Birkhäuser, Basel, pp 1–12

    Chapter  Google Scholar 

  • Channabasava, Govindappa M (2014) First report of anticancer agent, lapachol producing endophyte, Aspergillus niger of Tabebuia argentea and its in vitro cytotoxicity assays. Bangladesh J Pharmacol 9(1):129–139

    Article  Google Scholar 

  • Chaudhary VB, Rúa MA, Antoninka A, Bever JD, Cannon J, Craig A et al (2016) MycoDB, a global database of plant response to mycorrhizal fungi. Sci Data 3:160028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheplick GP, Clay K, Marks S (1989) Interactions between infection by endophytic fungi and nutrient limitation in the grasses Lolium perenne and Festuca arundinacea. New Phytol 111(1):89–97. https://doi.org/10.1111/j.1469-8137.1989.tb04222.x

    Article  Google Scholar 

  • Clay K (1987) Effects of fungal endophytes on the seed and seedling biology of Lolium perenne and Festuca arundinacea. Oecologia 73(3):358–362. https://doi.org/10.1007/BF00385251

    Article  CAS  PubMed  Google Scholar 

  • Clay K, Holah H (1999) Fungal endophyte symbiosis and plant diversity in successional fields. Forensic Sci Int 285(5434):1742–1745. http://www.ncbi.nlm.nih.gov/pubmed/10481011

    CAS  Google Scholar 

  • Crous PW, Gams W, Stalpers JA, Robert V, Stegehuis G (2004) MycoBank: an online initiative to launch mycology into the 21st century. Stud Mycol 50:19–22

    Google Scholar 

  • Cui J, Guo S, Xiao P (2011) Antitumor and antimicrobial activities of endophytic fungi from medicinal parts of Aquilaria sinensis. J Zhejiang Univ Sci B 12(5):385–392

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Fávaro LCL, de Sebastianes FLS, Araújo WL (2012) Epicoccum nigrum P16, a sugarcane endophyte, produces antifungal compounds and induces root growth. PLoS One 7(6):e36826

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Desale MG, Bodhankar MG (2013) Antimicrobial activity of endophytic fungi isolated from Vitex negundo Linn. Int J Curr Microbiol App Sci 2(12):389–395

    Google Scholar 

  • Deshmukh SK, Mishra PD, Kulkarni-Almeida A, Verekar S, Sahoo MR, Periyasamy G et al (2009) Anti-inflammatory and anticancer activity of ergoflavin isolated from an endophytic fungus. Chem Biodivers 6(5):784–789

    Article  CAS  PubMed  Google Scholar 

  • Dhankhar S, Dhankhar S, Parkash YJ (2013) Investigations towards new antidiabetic drugs from fungal endophytes associated with salvadora oleoides decne. Med Chem (Los Angeles) 9:624–632

    CAS  Google Scholar 

  • Du F-Y, Li X, Li X-M, Zhu L-W, Wang B-G (2017) Indolediketopiperazine alkaloids from Eurotium cristatum en-220, an endophytic fungus isolated from the marine alga Sargassum thunbergii. Mar Drugs 15(12):24

    Article  PubMed Central  CAS  Google Scholar 

  • Ekanayake PN, Rabinovich M, Guthridge KM, Spangenberg GC, Forster JW, Sawbridge TI (2013) Phylogenomics of fescue grass-derived fungal endophytes based on selected nuclear genes and the mitochondrial gene complement. BMC Evol Biol 13(1):270

    Article  PubMed  PubMed Central  Google Scholar 

  • Eyberger AL, Dondapati R, Porter JR (2006) Endophyte fungal isolates from Podophyllumpeltatum produce podophyllotoxin. J Nat Prod 69(8):1121–1124

    Article  CAS  PubMed  Google Scholar 

  • Firrincieli A, Otillar R, Salamov A, Schmutz J, Khan Z, Redman RS et al (2015) Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol 6:978

    Article  PubMed  PubMed Central  Google Scholar 

  • Gangadevi V, Muthumary J (2009) Taxol production by Pestalotiopsis terminaliae, an endophytic fungus of Terminalia arjuna (arjun tree). Biotechnol Appl Biochem 52(1):9–15

    Article  CAS  PubMed  Google Scholar 

  • Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J et al (2016) The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol 120(1):26–42

    Article  CAS  PubMed  Google Scholar 

  • Ghabooli M, Khatabi B, Ahmadi FS, Sepehri M, Mirzaei M, Amirkhani A et al (2013) Proteomics study reveals the molecular mechanisms underlying water stress tolerance induced by Piriformospora indica in barley. J Proteome 94:289–301

    Article  CAS  Google Scholar 

  • Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A et al (2012) Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PLoS Genet 8(3):e1002558

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Giridharan P, Verekar SA, Khanna A, Mishra PD, Deshmukh SK (2012) Anticancer activity of sclerotiorin, isolated from an endophytic fungus Cephalotheca faveolata Yaguchi, Nishim. and Udagawa. Indian J Exp Biol 50:464–468

    CAS  PubMed  Google Scholar 

  • Godstime O, Felix E, Jewo Augustina O, Christopher E (2014) Mechanisms of antimicrobial actions of phytochemicals against enteric pathogens – a review. J Pharm Chem Biol Sci 2(22):77–85

    Google Scholar 

  • Govindappa M, Sadananda TS, Channabasava, Ramachandra YL, Chandrappa CP, Padmalatha RS et al (2015) In vitro and in vivo antidiabetic activity of lectin (N-acetylgalactosamine, 64 kDa) isolated from endophytic fungi, Alternaria species from Viscum album on alloxan induced diabetic rats. Integr Obes Diabetes 1(1):11–19

    Google Scholar 

  • Gunatilaka AAL (2006) Natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence. J Nat Prod 69(3):509–526. http://www.ncbi.nlm.nih.gov/pubmed/16562864

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo B, Dai J-R, Ng S, Huang Y, Leong C, Ong W et al (2000) Cytonic acids A and B: novel tridepside inhibitors of hCMV protease from the endophytic fungus Cytonaema species. J Nat Prod 63(5):602–604

    Article  CAS  PubMed  Google Scholar 

  • Guo Z, Gai C, Cai C, Chen L, Liu S, Zeng Y et al (2017) Metabolites with insecticidal activity from Aspergillus fumigatus JRJ111048 isolated from mangrove plant acrostichum specioum endemic to hainan island. Mar Drugs 15(12):381

    Article  PubMed Central  CAS  Google Scholar 

  • Hua MDS, Senthil Kumar R, Shyur LF, Cheng Y Bin, Tian Z, Oelmüller R, et al (2017) Metabolomic compounds identified in Piriformospora indica-colonized chinese cabbage roots delineate symbiotic functions of the interaction. Sci Rep 7(1)

    Google Scholar 

  • Jalgaonwala RE, Mohite BV, Mahajan RT (2011) A review: natural products from plant associated endophytic fungi. J Microbiol Biotechnol Res 1(2):21–32

    Google Scholar 

  • Jogawat A, Vadassery J, Verma N, Oelmüller R, Dua M, Nevo E et al (2016) PiHOG1, a stress regulator MAP kinase from the root endophyte fungus Piriformospora indica, confers salinity stress tolerance in rice plants. Sci Rep 6(1):36765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson LJ, Johnson RD, Schardl CL, Panaccione DG (2003) Identification of differentially expressed genes in the mutualistic association of tall fescue with Neotyphodium coenophialum. Physiol Mol Plant Pathol 63(6):305–317. https://www.sciencedirect.com/science/article/pii/S0885576504000384

    Article  CAS  Google Scholar 

  • Joseph B, Priya RM (2011) Bioactive compounds from endophytes and their potential in pharmaceutical effect: a review. Am J Biochem Mol Biol 1(3):291–309

    Article  Google Scholar 

  • Kamal N, Viegelmann C, Clements C, Edrada-Ebel R (2016) Metabolomics-guided isolation of anti-trypanosomal metabolites from the endophytic fungus Lasiodiplodia theobromae. Planta Med 83(6):565–573

    Article  PubMed  CAS  Google Scholar 

  • Kang X, Liu C, Liu D, Zeng L, Shi Q, Qian K et al (2016) The complete mitochondrial genome of huperzine A-producing endophytic fungus Penicillium polonicum. Mitochondrial DNA B 1(1):202–203

    Article  Google Scholar 

  • Kaul S, Sharma T, Dhar MK (2016) Omics tools for better understanding the plant-endophyte interactions. Front Plant Sci 7:955. http://www.ncbi.nlm.nih.gov/pubmed/27446181

    Article  PubMed  PubMed Central  Google Scholar 

  • Kaur G, Asthir B (2015) Proline: a key player in plant abiotic stress tolerance. Biol Plant [Internet] 59(4):609–619. https://doi.org/10.1007/s10535-015-0549-3

    Article  CAS  Google Scholar 

  • Kemler M, Garnas J, Wingfield MJ, Gryzenhout M, Pillay K-A, Slippers B (2013) Ion torrent PGM as tool for fungal community analysis: a case study of endophytes in Eucalyptus grandis reveals high taxonomic diversity. PLoS One 8(12):e81718

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Khan AL, Hamayun M, Ahmad N, Hussain J, Kang S-M, Kim Y-H et al (2011) Salinity stress resistance offered by endophytic fungal interaction between Penicillium minioluteum LHL09 and Glycine max. L. J Microbiol Biotechnol 21(9):893–902. http://www.ncbi.nlm.nih.gov/pubmed/21952365

    Article  CAS  PubMed  Google Scholar 

  • Khan AL, Hamayun M, Kang S-M, Kim Y-H, Jung H-Y, Lee J-H et al (2012) Endophytic fungal association via gibberellins and indole acetic acid can improve plant growth under abiotic stress: an example of Paecilomyces formosus LHL10. BMC Microbiol 12:3. http://www.ncbi.nlm.nih.gov/pubmed/22235902

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khan AL, Waqas M, Hamayun M, Al-Harrasi A, Al-Rawahi A, Lee I-J (2013) Co-synergism of endophyte Penicillium resedanum LK6 with salicylic acid helped Capsicum annuum in biomass recovery and osmotic stress mitigation. BMC Microbiol 13(1):51. http://www.ncbi.nlm.nih.gov/pubmed/23452409

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kharwar RN, Mishra A, Gond SK, Stierle A, Stierle D (2011) Anticancer compounds derived from fungal endophytes: their importance and future challenges. Nat Prod Rep 28(7):1208

    Article  CAS  PubMed  Google Scholar 

  • Kim H-Y, Choi GJ, Lee HB, Lee S-W, Lim HK, Jang KS et al (2007) Some fungal endophytes from vegetable crops and their anti-oomycete activities against tomato late blight. Lett Appl Microbiol 44(3):332–337. http://www.ncbi.nlm.nih.gov/pubmed/17309513

    Article  PubMed  Google Scholar 

  • Kim JA, Jeon J, Kim K-T, Choi G, Park S-Y, Lee H-J et al (2017) Draft genome sequence of an endophytic fungus,Gaeumannomyces sp. strain JS-464, isolated from a reed plant, Phragmites communis. Genome Announc 5(31):e00734-17

    Article  PubMed  PubMed Central  Google Scholar 

  • Kim TY, Jang JY, Yu NH, Chi WJ, Bae C-H, Yeo JH et al (2018) Nematicidal activity of grammicin produced by Xylaria grammica KCTC 13121BP against Meloidogyne incognita. Pest Manag Sci 74(2):384–391

    Article  CAS  PubMed  Google Scholar 

  • Kodama Y, Shumway M, Leinonen R, International Nucleotide Sequence Database Collaboration (2012) The sequence read archive: Explosive growth of sequencing data. Nucleic Acids Res 40(D1):D54–D56

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Aharwal RP, Shukla H, Rajak RC, Sandhu SS (2014) Endophytic fungi: as a source of antimicrobials bioactive compounds. World J Pharm Pharm Sci 3(2):1179–1197

    Google Scholar 

  • Kusari S, Spiteller M (2012) Metabolomics of endophytic fungi producing associated plant secondary metabolites: progress, challenges and opportunities. In: Roessner U (ed) Metabolomics. InTech, London

    Google Scholar 

  • Kusari S, Lamshöft M, Zühlke S, Spiteller M (2008) An endophytic fungus from Hypericum perforatum that produces hypericin. J Nat Prod 71(2):159–162

    Article  CAS  PubMed  Google Scholar 

  • Kusari S, Lamshöft M, Spiteller M (2009a) Aspergillus fumigatus Fresenius, an endophytic fungus from Juniperus communis L. Horstmann as a novel source of the anticancer pro-drug deoxypodophyllotoxin. J Appl Microbiol 107(3):1019–1030

    Article  CAS  PubMed  Google Scholar 

  • Kusari S, Zühlke S, KoÅ¡uth J, ÄŒellárová E, Spiteller M (2009b) Light-independent metabolomics of endophytic Thielavia subthermophila provides insight into microbial hypericin biosynthesis. J Nat Prod 72(10):1825–1835

    Article  CAS  PubMed  Google Scholar 

  • Kusari S, Zühlke S, Spiteller M (2009c) An endophytic fungus from Camptotheca acuminata that produces camptothecin and analogues. J Nat Prod 72(1):2–7

    Article  CAS  PubMed  Google Scholar 

  • Kusari S, Zühlke S, Spiteller M (2011) Effect of artificial reconstitution of the interaction between the plant Camptotheca acuminata and the fungal endophyte Fusarium solani on camptothecin biosynthesis. J Nat Prod 74(4):764–775

    Article  CAS  PubMed  Google Scholar 

  • Kusari S, Verma VC, Lamshoeft M, Spiteller M (2012) An endophytic fungus from Azadirachta indica A. Juss. that produces azadirachtin. World J Microbiol Biotechnol 28(3):1287–1294

    Article  CAS  PubMed  Google Scholar 

  • Lata R, Chowdhury S, Gond SK, White JF (2018) Induction of abiotic stress tolerance in plants by endophytic microbes. Lett Appl Microbiol 66(4):268–276. https://doi.org/10.1111/lam.12855

    Article  CAS  PubMed  Google Scholar 

  • Lee C, Kim S, Li W, Bang S, Lee H, Lee HJ et al (2017) Bioactive secondary metabolites produced by an endophytic fungus Gaeumannomyces sp. JS0464 from a maritime halophyte Phragmites communis. J Antibiot (Tokyo) 70(6):737–742

    Article  CAS  Google Scholar 

  • Lehtonen PT, Helander M, Siddiqui SA, Lehto K, Saikkonen K (2006) Endophytic fungus decreases plant virus infections in meadow ryegrass (Lolium pratense). Biol Lett 2(4):620–623. http://www.ncbi.nlm.nih.gov/pubmed/17148304

    Article  PubMed  PubMed Central  Google Scholar 

  • Li B, Tang M, Tang K, Zhao L, Guo S (2012) Screening for differentially expressed genes in Anoectochilus roxburghii (Orchidaceae) during symbiosis with the mycorrhizal fungus Epulorhiza sp. Sci China Life Sci 55(2):164–171

    Article  CAS  PubMed  Google Scholar 

  • Lignanların A, Ve Bitkiler Ö, Dağılımı A, Konuklugil B (1995) The importance of aryltetralin (podophyllum) lignans and their distribution in the plant kingdom. J Fac Pharm Ankara 2422(13):301–302

    Google Scholar 

  • Lyons PC, Evans JJ, Bacon CW (1990) Effects of the fungal endophyte Acremonium coenophialum on nitrogen accumulation and metabolism in tall fescue. Plant Physiol 92(3):726–732. http://www.ncbi.nlm.nih.gov/pubmed/16667341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malinowski DP, Belesky DP (2000) Adaptations of endophyte-infected cool-season grasses to environmental stresses. Crop Sci 40(4):923. https://www.crops.org/publications/cs/abstracts/40/4/923

    Article  CAS  Google Scholar 

  • Malinowski DP, Brauer DK, Belesky DP (1999) The endophyte Neotyphodium coenophialum affects root morphology of tall fescue grown under phosphorus deficiency. J Agron Crop Sci 183(1):53–60. https://doi.org/10.1046/j.1439-037x.1999.00321.x

    Article  CAS  Google Scholar 

  • Marquez LM, Redman RS, Rodriguez RJ, Roossinck MJ (2007) A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science. 315(5811):513–515. http://www.ncbi.nlm.nih.gov/pubmed/17255511

    Article  CAS  PubMed  Google Scholar 

  • Miller AN, Bates ST (2017) The Mycology Collections Portal (MyCoPortal). IMA Fungus 8(2):65–66

    Google Scholar 

  • Mishra VK, Singh G, Passari AK, Yadav MK, Gupta VK, Singh BP (2016a) Distribution and antimicrobial potential of endophytic fungi associated with ethnomedicinal plant Melastoma malabathricum L. J Environ Biol 37(2):229–237

    CAS  PubMed  Google Scholar 

  • Mishra VK, Passari AK, Singh BP (2016b) In vitro antimycotic and biosynthetic potential of fungal endophytes associated with Schima Wallichii. In: Kumar P et al (eds) Current trends in disease diagnostics. Springer International, Basel, pp 367–381

    Chapter  Google Scholar 

  • Mishra VK, Passari AK, Chandra P, Leo VV, Kumar B, Gupta VK, Singh BP (2017a) Determination and production of antimicrobial compounds by Aspergillus clavatonanicus strain MJ31, an endophytic fungus from Mirabilis jalapa L. using UPLC-ESI-MS/MS and TD GC-MS. PLoS One 12(10):1–24. https://doi.org/10.1371/journal.pone.0186234

    Article  CAS  Google Scholar 

  • Mishra VK, Passari AK, Leo VV, Singh BP (2017b) Molecular diversity and detection of endophytic fungi based on their antimicrobial biosynthetic genes. In: Singh BP, Gupta VK (eds) Molecular markers in mycology, fungal biology. Springer International, Basel, pp 1–35. https://doi.org/10.1007/978-3-319-34106-4_1

    Chapter  Google Scholar 

  • Molina G, Pimentel MR, Bertucci TCP, Pastore GM (2012) Application of fungal endophytes in biotechnological processes. Chem Eng Trans 27:289–294

    Google Scholar 

  • Müller CB, Krauss J (2005) Symbiosis between grasses and asexual fungal endophytes. Curr Opin Plant Biol 8(4):450–456. https://www.sciencedirect.com/science/article/pii/S1369526605000683

    Article  PubMed  CAS  Google Scholar 

  • Na R, Jiajia L, Dongliang Y, Yingzi P, Juan H, Xiong L et al (2016) Indentification of vincamine indole alkaloids producing endophytic fungi isolated from Nerium indicum, Apocynaceae. Microbiol Res 192:114–121

    Article  PubMed  CAS  Google Scholar 

  • Nair DN, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J 2014:250693

    Article  Google Scholar 

  • Nicolás C, Hermosa R, Rubio B, Mukherjee PK, Monte E (2014) Trichoderma genes in plants for stress tolerance- status and prospects. Plant Sci 228:71–78

    Article  PubMed  CAS  Google Scholar 

  • Nicoletti R, Fiorentino A (2015) Plant bioactive metabolites and drugs produced by endophytic fungi of spermatophyta. Agriculture 5(4):918–970

    Article  CAS  Google Scholar 

  • Öpik M, Vanatoa A, Vanatoa E, Moora M, Davison J, Kalwij JM et al (2010) The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota). New Phytol 188(1):223–241

    Article  PubMed  CAS  Google Scholar 

  • Orr SP, Rudgers JA, Clay K (2005) Invasive plants can inhibit native tree seedlings: testing potential allelopathic mechanisms. Plant Ecol 181(2):153–165. https://doi.org/10.1007/s11258-005-5698-6

    Article  Google Scholar 

  • Osbourn A (2010) Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation. Trends Genet 26(10):449–457

    Article  CAS  PubMed  Google Scholar 

  • Pandi M, Manikandan R, Muthumary J (2010) Anticancer activity of fungal taxol derived from Botryodiplodia theobromae Pat., an endophytic fungus, against 7, 12 dimethyl benz(a)anthracene (DMBA)-induced mammary gland carcinogenesis in Sprague dawley rats. Biomed Pharmacother 64(1):48–53

    Article  CAS  PubMed  Google Scholar 

  • Passari AK, Mishra VK, Singh G, Singh P, Kumar B, Gupta VK, Sharma RK, Saikia R, Donovan A, Singh BP (2017) Insights into the functionality of endophytic actinobacteria with a focus on their biosynthetic potential and secondary metabolites production. Sci Rep 7(11809):1–17. https://doi.org/10.1038/s41598-017-12235-4

    Article  CAS  Google Scholar 

  • Philippe G (2016) Lolitrem B and indole diterpene alkaloids produced by endophytic fungi of the genus Epichloë and their toxic effects in livestock. Toxins (Basel) 8(2):47. http://www.mdpi.com/2072-6651/8/2/47

    Article  CAS  Google Scholar 

  • Phongpaichit S, Nikom J, Rungjindamai N, Sakayaroj J, Hutadilok-Towatana N, Rukachaisirikul V et al (2007) Biological activities of extracts from endophytic fungi isolated from Garcinia plants. FEMS Immunol Med Microbiol 51(3):517–525

    Article  CAS  PubMed  Google Scholar 

  • Powthong P, Jantrapanukorn B, Thongmee A, Suntornthiticharoen P (2013) Screening of antimicrobial activities of the endophytic fungi isolated from Sesbania grandiflora (L.) Pers. J Agric Sci Technol 15:1513–1522

    Google Scholar 

  • Prabavathy D, Valli Nachiyar C (2013) Antimicrobial and antidiabetic activity of an endophytic fungi isolated from Adathoda beddomei. Int J Pharm Pharm Sci 5(3):780–783

    Google Scholar 

  • Premalatha K, Kalra A (2013) Molecular phylogenetic identification of endophytic fungi isolated from resinous and healthy wood of Aquilaria malaccensis, a red listed and highly exploited medicinal tree. Fungal Ecol 6(3):205–211

    Article  Google Scholar 

  • Prestidge RA (1993) Causes and control of perennial ryegrass staggers in New Zealand. Agric Ecosyst Environ 44(1–4):283–300. https://www.sciencedirect.com/science/article/pii/016788099390051P

    Article  Google Scholar 

  • Pretsch A, Nagl M, Schwendinger K, Kreiseder B, Wiederstein M, Pretsch D et al (2014) Antimicrobial and anti-inflammatory activities of endophytic fungi Talaromyces wortmannii extracts against acne-inducing bacteria. PLoS One 9(6):e97929

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Puri SC, Verma V, Amna T, Qazi GN, Spiteller M (2005) An endophytic fungus from Nothapodytes foetida that produces camptothecin. J Nat Prod 68(12):1717–1719

    Article  CAS  PubMed  Google Scholar 

  • Puri SC, Nazir A, Chawla R, Arora R, Riyaz-ul-Hasan S, Amna T et al (2006) The endophytic fungus Trametes hirsuta as a novel alternative source of podophyllotoxin and related aryl tetralin lignans. J Biotechnol 122(4):494–510

    Article  CAS  PubMed  Google Scholar 

  • Ramos HP, Braun GH, Pupo MT, Said S (2010) Antimicrobial activity from endophytic fungi Arthrinium state of Apiospora montagnei Sacc. and Papulaspora immersa. Braz Arch Biol Technol 53(3):629–632

    Article  Google Scholar 

  • Ranadive K, Jagtap N, Khare H (2017) Fungifromindia: the first online initiative to document fungi from India. IMA Fungus 8(2):67–69. http://www.imafungus.org/Issue/82/MycoLens.pdf

    Google Scholar 

  • Rank C, Larsen TO, Frisvad JC (2010) Functional systems biology of Aspergillus. In: Aspergillus molecular biology and genomics. p 173–198

    Google Scholar 

  • Redondo-Gómez S (2013) Abiotic and biotic stress tolerance in plants. In: Rout GR, Das AB (eds) Molecular stress physiology of plants. Springer India, New Delhi, pp 1–20. https://doi.org/10.1007/978-81-322-0807-5_1

    Chapter  Google Scholar 

  • Richardson MD, Chapman GW, Hoveland CS, Bacon CW (1992) Sugar alcohols in endophyte-infected tall fescue under drought. Crop Sci 32(4):1060. https://www.crops.org/publications/cs/abstracts/32/4/CS0320041060

    Article  CAS  Google Scholar 

  • Rodriguez R, Redman R (2008) More than 400 million years of evolution and some plants still can’t make it on their own: plant stress tolerance via fungal symbiosis. J Exp Bot 59(5):1109–1114

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez RJ, White Jr JF, Arnold AE, Redman RS (2009). Fungal endophytes: diversity and functional roles. New Phytol 182(2):314–330. https://doi.org/10.1111/j.1469-8137.2009.02773.x

    Article  CAS  PubMed  Google Scholar 

  • Rouhier N, Koh CS, Gelhaye E, Corbier C, Favier F, Didierjean C et al (2008) Redox based anti-oxidant systems in plants: Biochemical and structural analyses. Biochim Biophys Acta 1780(11):1249–1260. https://www.sciencedirect.com/science/article/pii/S0304416507002991

    Article  CAS  PubMed  Google Scholar 

  • Rouxel T, Grandaubert J, Hane JK, Hoede C, Van De Wouw AP, Couloux A et al (2011) Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat-induced point mutations. Nat Commun 2(1)

    Google Scholar 

  • Rudgers JA, Orr S (2009) Non-native grass alters growth of native tree species via leaf and soil microbes. J Ecol 97(2):247–255. https://doi.org/10.1111/j.1365-2745.2008.01478.x

    Article  Google Scholar 

  • Saikkonen K, Young CA, Helander M, Schardl CL (2016) Endophytic Epichloë species and their grass hosts: from evolution to applications. Plant Mol Biol 90(6):665–675

    Article  CAS  PubMed  Google Scholar 

  • Sandhu SS, Kumar S, Aharwal RP (2014) Isolation and identification of endophytic fungi from Ricinus communis linn. and their antibacterial activity. Int J Res Pharm Chem 4(3):611–618

    Google Scholar 

  • Schardl CL, Leuchtmann A, Spiering MJ (2004) Symbioses of grasses with seedborne fungal endophytes. Annu Rev Plant Biol 55(1):315–340

    Article  CAS  PubMed  Google Scholar 

  • Schwarz M, Köpcke B, Weber RWS, Sterner O, Anke H (2004) 3-Hydroxypropionic acid as a nematicidal principle in endophytic fungi. Phytochemistry 65(15):2239–2245

    Article  CAS  PubMed  Google Scholar 

  • Seetharaman P, Gnanasekar S, Chandrasekaran R, Chandrakasan G, Syed A, Hodhod MS et al (2017) Isolation of limonoid compound (Hamisonine) from endophytic fungi Penicillium oxalicum LA-1 (KX622790) of Limonia acidissima L. for its larvicidal efficacy against LF vector, Culex quinquefasciatus (Diptera: Culicidae). Environ Sci Pollut Res 24(26):21272–21282

    Article  CAS  Google Scholar 

  • Shen M, Zhao DK, Qiao Q, Liu L, Wang JL, Cao GH et al (2015) Identification of glutathione S-transferase (GST) genes from a dark septate endophytic fungus (Exophiala pisciphila) and their expression patterns under varied metals stress. PLoS One 10(4):e0123418

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shinozuka H, Hettiarachchige IK, Shinozuka M, Cogan NOI, Spangenberg GC, Cocks BG et al (2017) Horizontal transfer of a ß-1,6-glucanase gene from an ancestral species of fungal endophyte to a cool-season grass host. Sci Rep 7(1):9024

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shukla ST, Habbu PV, Kulkarni VH, Jagadish KS, Pandey AR, Sutariya VN (2014) Endophytic microbes: a novel source for biologically/pharmacologically active secondary metabolites. Asian J Pharmacol Toxicol 2(3):1–16

    CAS  Google Scholar 

  • Shweta S, Zuehlke S, Ramesha BT, Priti V, Mohana Kumar P, Ravikanth G et al (2010) Endophytic fungal strains of Fusarium solani, from Apodytes dimidiata E. Mey. ex Arn (Icacinaceae) produce camptothecin, 10-hydroxycamptothecin and 9-methoxycamptothecin. Phytochemistry 71(1):117–122

    Article  CAS  PubMed  Google Scholar 

  • Singh R, Dubey AK (2015) Endophytic actinomycetes as emerging source for therapeutic compounds. Indo Glob J Pharm Sci 5(2):106–116

    CAS  Google Scholar 

  • Singh LP, Gill SS, Tuteja N (2011) Unraveling the role of fungal symbionts in plant abiotic stress tolerance. Plant Signal Behav 6(2):175–191. http://www.ncbi.nlm.nih.gov/pubmed/21512319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soliman SSM, Greenwood JS, Bombarely A, Mueller LA, Tsao R, Mosser DD et al (2015) An endophyte constructs fungicide-containing extracellular barriers for its host plant. Curr Biol 25(19):2570–2576. http://www.ncbi.nlm.nih.gov/pubmed/26412131

    Article  CAS  PubMed  Google Scholar 

  • Stajich JE, Harris T, Brunk BP, Brestelli J, Fischer S, Harb OS et al (2012) FungiDB: an integrated functional genomics database for fungi. Nucleic Acids Res 40(Database issue):D675–D681

    Article  CAS  PubMed  Google Scholar 

  • Staniek A, Woerdenbag HJ, Kayser O (2008) Endophytes: exploiting biodiversity for the improvement of natural product-based drug discovery. J Plant Interact 3(2):75–93

    Article  CAS  Google Scholar 

  • Stierle A, Strobel G, Stierle D (1993) Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. Science 260(5105):214–216

    Article  CAS  PubMed  Google Scholar 

  • Strobel GA, Pliam NB (1995) Immunosuppressant diterpene compound, p 24

    Google Scholar 

  • Strobel G, Daisy B (2003) Bioprospecting for microbial endophytes and their natural products. Microbiol Mol Biol Rev 67(4):491–502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strobel G, Ford E, Worapong J, Harper JK, Arif AM, Grant DM et al (2002) Isopestacin, an isobenzofuranone from Pestalotiopsis microspora, possessing antifungal and antioxidant activities. Phytochemistry 60(2):179–183

    Article  CAS  PubMed  Google Scholar 

  • Takeuchi S, Hirayama K, Ueda K, Sakai H, Yonehara H (1958) Blasticidin S, a new antibiotic. J Antibiot (Tokyo) 11(1):1–5. http://www.ncbi.nlm.nih.gov/pubmed/13525246

    CAS  Google Scholar 

  • Talbot NJ (2015) Plant immunity: a little help from fungal friends. Curr Biol 25(22):R1074–R1076. http://www.ncbi.nlm.nih.gov/pubmed/26583896

    Article  CAS  PubMed  Google Scholar 

  • Teles HL, Sordi R, Silva GH, Castro-Gamboa I, Bolzani Vda S, Pfenning LH et al (2006) Aromatic compounds produced by Periconia atropurpurea, an endophytic fungus associated with Xylopia aromatica. Phytochemistry 67(24):2686–2690

    Article  CAS  PubMed  Google Scholar 

  • Tian J, Liu XC, Liu ZL, Lai D, Zhou L (2016) Larvicidal spirobisnaphthalenes from the endophytic fungus Berkleasmium sp. against Aedes albopictus. Pest Manag Sci 72(5):961–965

    Article  CAS  PubMed  Google Scholar 

  • Toju H, Tanabe AS, Ishii HS (2016) Ericaceous plant-fungus network in a harsh alpine-subalpine environment. Mol Ecol 25(13):3242–3257

    Article  CAS  PubMed  Google Scholar 

  • Umashankar T, Govindappa M, Yarappa Lakshmikantha R, Padmalatha Channabasava, RS (2015). Isolation and characterization of coumarin isolated from endophyte, Alternaria species-1 of Crotalaria pallida and its apoptotic action on HeLa cancer cell line. Metabolomics, 5(4), 1–8.

    Google Scholar 

  • Uzma F, Hashem A, Murthy N, Mohan HD, Kamath PV, Singh BP, Venkataramana M, Gupta VK, Siddaiah CN, Chowdappa S, Alqaeawi AA, Abd Allah EF (2018) Endophytic fungi—alternative sources of cytotoxic compounds: a review. Front Pharmacol 9(309):1–37. https://doi.org/10.3389/fphar.2018.00309

  • Vasundhara M, Kumar A, Reddy MS (2016) Molecular approaches to screen bioactive compounds from endophytic fungi. Front Microbiol 7:1774

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Visalakchi S, Muthumary J (2010) Taxol (anticancer drug) producing endophytic fungi: an overview. Int J Pharma Bio Sci 1(3):1–9

    Google Scholar 

  • Wang X, Zhang X, Liu L, Xiang M, Wang W, Sun X et al (2015a) Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. BMC Genomics 16(1):28

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang X, Zhang X, Liu L, Xiang M, Wang W, Sun X et al (2015b) Genomic and transcriptomic analysis of the endophytic fungus reveals its lifestyle and high potential for synthesis of natural products. BMC Genomics 16:28

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wani ZA, Ashraf N, Mohiuddin T, Riyaz-Ul-Hassan S (2015) Plant-endophyte symbiosis, an ecological perspective. Appl Microbiol Biotechnol 99(7):2955–2965. https://doi.org/10.1007/s00253-015-6487-3

    Article  CAS  PubMed  Google Scholar 

  • Webber J (1981) A natural biological control of Dutch elm disease. Nature 292(5822):449–451. https://doi.org/10.1038/292449a0

    Article  Google Scholar 

  • Weig AR, PerÅ¡oh D, Werner S, Betzlbacher A, Rambold G (2013) Diagnostic assessment of mycodiversity in environmental samples by fungal ITS1 rDNA length polymorphism. Mycol Prog 12(4):719–725

    Article  Google Scholar 

  • Xu X-H, Su Z-Z, Wang C, Kubicek CP, Feng X-X, Mao L-J et al (2015) The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte. Sci Rep 4(1):5783

    Article  CAS  Google Scholar 

  • Yadav V, Kumar M, Deep AK, Kumar H, Sharma R, Tripathi T et al (2010) A phosphate transporter from the root endophytic fungus Piriformospora indica plays a role in phosphate transport to the host plant. J Biol Chem 285(34):26532–26544

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yadava P, Bhuyan SK, Bandyopadhyay P, Yadava PK (2015) Extraction of proteins for two-dimensional gel electrophoresis and proteomic analysis from an endophytic fungus. Protoc Exch. https://doi.org/10.1038/protex.2015.084

  • Yamaji K, Watanabe Y, Masuya H, Shigeto A, Yui H, Haruma T (2016) Root fungal endophytes enhance heavy-metal stress tolerance of clethra barbinervis growing naturally at mining sites via growth enhancement, promotion of nutrient uptake and decrease of heavy-metal concentration. PLoS One 11(12):e0169089. https://doi.org/10.1371/journal.pone.0169089

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang S (2010) Allelopathic effects of endophytic fungi of Achnatherum inebrians Keng on the seed and seedling of three turf grasses. Acta Agrestia Sinica. http://en.cnki.com.cn/Article_en/CJFDTOTAL-CDXU201001017.htm

  • Yang Y, Zhao H, Barrero RA, Zhang B, Sun G, Wilson IW et al (2014) Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431. BMC Genomics 15(1):69

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang P, Zhou P-P, Yu L-J (2009) An endophytic taxol-producing fungus from taxus media, Cladosporium cladosporioides MD2. Curr Microbiol 59(3):227–232

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Sun S, Zhu T, Lin Z, Gu J, Li D et al (2011) Antiviral isoindolone derivatives from an endophytic fungus Emericella sp. associated with Aegiceras corniculatum. Phytochemistry 72(11–12):1436–1442

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Han T, Ming Q, Wu L, Rahman K, Qin L (2012) Alkaloids produced by endophytic fungi: a review. Nat Prod Commun 7(7):963–968

    CAS  PubMed  Google Scholar 

  • Zhang H, Liu R, Yang J, Li H, Zhou F (2017a) Bioactive alkaloids of Aspergillus fumigatus, an endophytic fungus from Astragalus membranaceus. Chem Nat Compd 53(4):802–805

    Article  CAS  Google Scholar 

  • Zhang S, Wang XN, Zhang XL, Liu XZ, Zhang YJ (2017b) Complete mitochondrial genome of the endophytic fungus Pestalotiopsis fici: features and evolution. Appl Microbiol Biotechnol 101(4):1593–1604

    Article  CAS  PubMed  Google Scholar 

  • Zhao J, Mou Y, Shan T, Li Y, Zhou L, Wang M et al (2010) Antimicrobial metabolites from the endophytic fungus Pichia guilliermondii isolated from Paris polyphylla var. yunnanensis. Molecules 15(11):7961–7970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao J, Shan T, Mou Y, Zhou L (2011) Plant-derived bioactive compounds produced by endophytic fungi. Mini Rev Med Chem 11(2):159–168

    Article  CAS  PubMed  Google Scholar 

  • Zuccaro A, Lahrmann U, Güldener U, Langen G, Pfiffi S, Biedenkopf D et al (2011) Endophytic life strategies decoded by genome and transcriptome analyses of the mutualistic root symbiont Piriformospora indica. PLoS Pathog 7(10):e1002290

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Utpal Bora .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Chetia, H. et al. (2019). Exploring the Benefits of Endophytic Fungi via Omics. In: Singh, B. (eds) Advances in Endophytic Fungal Research. Fungal Biology. Springer, Cham. https://doi.org/10.1007/978-3-030-03589-1_4

Download citation

Publish with us

Policies and ethics