Abstract
Although heeding and leading in the application perspective, we are lagging to address the variegated cross-talks involved in plant-endophyte interactions, the basis for the pertinence of endophytes. Endophytism represents the phenomenon in which a microbe resides asymptomatically within the plant tissues. The competency of the endophytes to penetrate, colonize, and flourish inside the plant premises by exhibiting complex multivariate interactions with the host, makes them unique. An endophyte, besides dealing with the host has to deal with the existing endospheric microbiota to make its colonization successful. However, we are at the beginning to appreciate the involvement of complex crosstalks between a plant and its endophytic microbiome and among the endophytic microbes associated with the plant. In this review, conglomerate cross-talks existing between plants and endophytes to maintain an ecological balance has been emphasized. Endophytic fungi have developed a palette of strategies to make their subsistence asymptomatic within the host. However, it is still a concern of exploration to unravel all the strategies employed by the endophytes, especially at the molecular level to accomplish this complex cross-kingdom association and making an asymptomatic existence inside the host. In recent years, the bioprospection of endophytes has received much attention, however, the differential survival strategies developed by them are poorly understood. This review summarizes currently available knowledge about the mechanisms behind the endophytic fungal colonization emphasizing the strategies employed by them in maintaining endophytism with special reference to quorum sensing and quorum quenching.
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Abdelwahab MF, Kurtán T, Mándi A, Müller WEG, Fouad MA, Kamel MS, Liu Z, Ebrahim W, Daletos G, Proksch P (2018) Induced secondary metabolites from the endophytic fungus Aspergillus versicolor through bacterial co-culture and OSMAC approaches. Tetrahedron Lett 59(27):2647–2652. https://doi.org/10.1016/j.tetlet.2018.05.067
Affeldt KJ, Brodhagen M, Keller NP (2012) Aspergillus oxylipin signalling and quorum sensing pathways depend on G protein-coupled receptors. Toxins 4(9):695–717. https://doi.org/10.3390/toxins4090695
Ahmad A, Viljoen AM, Chenia HY (2014) The impact of plant volatiles on bacterial quorum sensing. Lett Appl Microbiol 60(1):8–19. https://doi.org/10.1111/Iam.12343
Akone SH, Mándi A, Kurtán T et al (2016) Inducing secondary metabolite production by the endophytic fungus Chaetomium sp. through fungal–bacterial co-culture and epigenetic modification. Tetrahedron 72:6340–6347. https://doi.org/10.1016/j.tet.2016.08.022
Akum FN, Steinbrenner J, Biedenkopf D, Imani J, Kogel KH (2015) The Piriformospora indica effector PIIN_08944 promotes the mutualistic Sebacinalean symbiosis. Front Plant Sci 6:906. https://doi.org/10.3389/fpls.2015.00906
Alagarasan G, Aswathy KS, Madhaiyan M (2017) Shoot the message, not the messenger – combating pathogenic virulence in plants by inhibiting quorum sensing mediated signalling molecules. Front Plant Sci 8:556. https://doi.org/10.3389/fpls.2017.00556
Alvarez-Loayza P, White JF Jr, Torres MS, Balslev H, Kristiansen T, Evenning J-C, Gil N (2011) Light converts endosymbiotic fungus to pathogen, influencing seedling survival and niche-space filling of a common tropical tree, Iriartea deltoidea. PLoS One 6(1):e16386. https://doi.org/10.1371/journal.pone.0016386
Aly AH, Debbab A, Kjer J, Proksch P (2010) Fungal endophytes from higher plants: a prolific source of phytochemicals and other bioactive natural products. Fungal Divers 41(1):1–16. https://doi.org/10.1007/s13225-010-0034-4
Antico CJ, Colon C, Banks T, Ramonell KM (2012) Insights into the role of jasmonic acid-mediated defences against necrotrophic and biotrophic fungal pathogens. Front Biol 7(1):48–56. https://doi.org/10.1007/s11515-011-1171-1
Antunes LC, Ferreira RB, Buckner MM, Finlay BB (2010) Quorum sensing in bacterial virulence. Microbiology 156(8):2271–2282. https://doi.org/10.1099/mic.0.038794-0
Arnold AE (2007) Understanding the diversity of foliar endophytic fungi: progress, challenges, and frontiers. Fungal Biol Rev 21(2–3):51–66. https://doi.org/10.1016/j.fbr.2007.05.003
Arora P, Riyaz-Ul-Hassan S (2018) Endohyphal bacteria; the prokaryotic modulators of host fungal biology. Fungal Biol Rev 33:72–81. https://doi.org/10.1016/j.fbr.2018.08.003
Ayob FW, Simarani K (2016) Endophytic filamentous fungi from a Catharanthus roseus: identification and its hydrolytic enzymes. Saudi Pharmaceut J 24(3):273–278. https://doi.org/10.1016/j.jsps.2016.04.019
Bacon CW, White J (2000) Physiological adaptations in the evolution of endophytism in the Clavicipitaceae. In: Bacon CW, White J (eds) Microbial endophytes. Marcel Dekker, New York, pp 237–263
Bai X, Todd CD, Desikan R, Yang Y, Hu X (2012) N-3-oxo-decanoyl-L-homoserine-lactone activates auxin-induced adventitious root formation via hydrogen peroxide-and nitric oxide-dependent cyclic GMP signaling in mungbean. Plant Physiol 158(2):725–736. https://doi.org/10.1104/pp.111.185769
Baltrus DA, Dougherty K, Arendt KR, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D et al (2017) Absence of genome reduction in diverse, facultative endohyphal bacteria. Microb Genomics 3(2):e000101. https://doi.org/10.1099/mgen.0.000101
Bamsile BS, Akutse KS, Dash CK, Qasim M, Anguila LCR, Ashraf HJ, Huang W, Hussain M, Chen S, Wang L (2020) Effects of seedling age on colonization patterns of Citrus limon plants by endophytic Beauveria bassiana and Metarhizium anisopliae and their influence on seedlings growth. Journal of Fungi 6(1):29. https://doi.org/10.3390/jof6010029
Bartsch M, Bednarek P, Vivancos PD, Schneider B, von Roepenack-Lahaye E, Foyer CH, Kombrink E, Scheel D, Parker J (2010) Accumulation of isochorismate-derived 2,3- dihydroxybenzoic 3-O-β-D-xyloside in Arabidopsis resistance to pathogens and ageing of leaves. J Biol Chem 285(33):25654–25665. https://doi.org/10.1074/jbc.M109.092569
Bastías DA, Johnson LJ, Card SD (2020) Symbiotic bacteria of plant-associated fungi: friends or foes? Curr Opin Plant Biol 56:1–8. https://doi.org/10.1016/j.pbi.2019.10.010
Becker Y, Eaton CJ, Brasell E, May KJ, Becker M, Hassing B, Cartwright GM, Reinhold L, Scott B (2015) The fungal cell-wall integrity MAPK cascade is crucial for hyphal network formation and maintenance of restrictive growth of Epichloe festucae in symbiosis with Lolium perenne. Mol Plant Microbe Interact 28:69–85. https://doi.org/10.1094/MPMI-06-14-0183-R
Berendsen RL, Vismans G, Yu K, Song Y, De Jonge R, Burgman WP, Burmolle M, Herschend J, Bkker PA, Pieterse CM (2018) Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME J 12(6):1496–1507. https://doi.org/10.1038/s41396-018-0093-1
Berrocal A, Oviedo C, Nickerson KW, Navarrete J (2014) Quorum sensing activity and control of yeast-mycelium dimorphism in Ophiostoma floccosum. Biotechnol Lett 36(7):1503–1513. https://doi.org/10.1007/s10529-014-1515-5
Bharadwaj R, Jagadeesan H, Kumar SR et al (2020) Molecular mechanisms in grass-Epichloë interactions: towards endophyte driven farming to improve plant fitness and immunity. World J Microbiol Biotechnol 36:92. https://doi.org/10.1007/s11274-020-02868-5
Bhargava N, Singh SP, Sharma A, Sharma P, Capalash N (2015) Attenuation of quorum sensing-mediated virulence of Acinetobacter baumannii by Glycyrrhiza glabra flavonoids. Future Microbiol 10(12):1953–1968. https://doi.org/10.2217/fmb.15.107
Blee KA, Anderson AJ (2000) Defence responses in plants to arbuscular mycorrhizal fungi. In: Podila GK, Douds DD (eds) Current advances in mycorrhizae research. APS Press, Minnesota, pp 27–44
Blilou I, Bueno P, Ocampo JA, Garcia-Garrido JM (2000a) Induction of catalase and ascorbate peroxidase activities in tobacco roots inoculated with the arbuscular mycorrhizal fungus Glomus mosseae. Mycol Res 104(6):722–725. https://doi.org/10.1017/S095375629900204X
Blilou I, Ocampo JA, Garcia-Garrido JM (2000b) Induction of Ltp (Lipid transfer protein) and Pal (Phenylalanine Ammonia-Lyase) gene expression in rice roots colonized by arbuscular mycorrhizal fungus Glomus mosseae. J Environ Bot 51(353):1969–1977. https://doi.org/10.1093/jexbot/51.353.1969
Bohm M, Hurek T, Reinhold-Hurek B (2007) Twitching motility is essential for endophytic rice colonization by the N2-fixing endophyte Azoarcus sp. strain BH72. Mol Plant Microbe Interact 20(5):526–533. https://doi.org/10.1094/MPMI-20-5-0526
Boller T, Felix G (2009) A renaissance of elicitors: Perception of microbe-associated molecular patterns and danger signals by pattern- recognition receptors. Ann Rev Plant Biol 60:379–406. https://doi.org/10.1146/annurev.arplant.57.032905.105346
Bonfante P, Anca I-A (2009) Plants, mycorrhizal fungi and bacteria: a network of interactions. Annu Rev Microbiol 63(1):363–383. https://doi.org/10.1146/annurev.micro.091208.073504
Bonfante P, Genre A, Faccio A, Martini I, Schauser L, Stougaard J, Webb J, Parniske M (2000) The Lotus japonicas LjSym4 gene is required for the successful symbiotic infection of root epidermal cells. Mol Plant Microbe Interact 13(10):1109–1120. https://doi.org/10.1094/MPMI.2000.13.10.1109
Botella L, Diez JJ (2011) Phylogenic diversity of fungal endophytes in Spanish stands of Pinus halepensis. Fungal Divers 47(1):9–18. https://doi.org/10.1007/s13225-010-0061-1
Bouyahya A, Dakka N, Et-Touys A, Abrini J, Bakri Y (2017) Medicinal plant products targeting quorum sensing for combating bacterial infections. Asian Pac J Trop Med 10(8):729–743. https://doi.org/10.1016/j.apjtm.2017.07.021
Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27(100):30–37. https://doi.org/10.1016/j.copbio.2013.09.012
Brader G, Compant S, Vescio K, Mitter B, Trognitz F, Ma L-J, Sessitsch A (2017) Ecology and genomic insights into plant-pathogenic and plant-nonpathogenic endophytes. Annu Rev Phytopathol 55(1):61–83. https://doi.org/10.1146/annurev-phytol-080516-035641
Chagas MBO, Prazeres Dos Santos I, Nascimento da Silva LC, Correia MTDS, Magali de Araujo J, Lucia de Menezes V (2017) Antimicrobial activity of cultivable endophytic fungi associated with Hancornia speciosa gomes bark. Open Microbiol J 11:179–188. https://doi.org/10.2174/187428580171101010179
Chandra S (2012) Endophytic fungi: novel sources of anticancer lead molecules. Appl Microbiol Biotechnol 95(1):47–59. https://doi.org/10.1007/s00253-012-4128-7
Chapela I, Petrini O, Petrini IE (1990) Unusual ascospore germination in Hypoxylon fragiforme: first steps in the establishment of an endophytic symbiosis. Canadian J Bot 68(12):2571–2575. https://doi.org/10.1139/b90-324
Chen H, Fink GR (2006) Feedback control of morphogenesis in fungi by aromatic alcohols. Genes Dev 20(9):1150–1161. https://doi.org/10.1101/gad.1411806
Chen H, Fujita M, Feng Q, Clardy J, Fink GR (2004) Tyrosol is a quorum-sensing molecule in Candida albicans. Proc Natl Acad Sci USA 101(14):5048–5052. https://doi.org/10.1073/pnas.0401416101
Chernin L, Toklikishvili N, Ovadis M, Kim S, Ben-Ari J, Khmel I, Vainstein A (2011) Quorum-sensing quenching by rhizobacterial volatiles. Environ Microbiol Rep 3(6):698–704. https://doi.org/10.1111/j.1758-2229.2011.00284.x
Chetia H, Kabiraj D, Bharali B, Ojha S, Barkataki MP, Saikia D, Singh T, Mosahari PV, Sharma P, Bora U (2019) Exploring the benefits of endophytic fungi via omics. In: Singh BP (ed) Advances in endophytic fungal research. Springer, New York, pp 51–81. https://doi.org/10.1007/978-3-030-03589-1_4
Choi HK, Kim SI, Song JY, Son JS, Hong SS, Durzan DJ, Lee HJ (2001) Localization of paclitaxel in suspension culture of Taxus chinensis. J Microbiol Biotechnol 11(3):458–462
Christensen MJ, Bennett RJ, Schmid J (2002) Growth of Epichloe/Neotyphodium and endophytes in leaves of Lolium and Festuca grasses. Mycol Res 106(1):93–106. https://doi.org/10.1017/S095375620100510X
Cornforth DM, Popat R, McNally L, Gurney J, Scott-Phillips TC, Ivens A, Diggle SP, Brown SP (2014) Combinatorial quorum sensing allows bacteria to resolve their social and physical environment. Proc Natl Acad Sci USA 111(11):4280–4284. https://doi.org/10.1073/pnas.1319175111
Cruz-Miranda O, Folch-Mallol J, Martínez-Morales F et al (2020) Identification of a Huperzine A-producing endophytic fungus from Phlegmariurus taxifolius. Mol Biol Rep 47:489–495. https://doi.org/10.1007/s11033-019-05155-1
Cugini C, Calfee MW, Farrow JM, Morales DK, Pesci EC, Hogan D (2007) Farnesol, a common sesquiterpene, inhibits PQS production in Pseudomonas aeruginosa. Mol Microbiol 65(4):896–906. https://doi.org/10.1111/j.1365-2958.2007.05840.x
Dai CC, Chen Y, Tian LS, Shi Y (2010) Correlation between invasion by endophytic fungus Phomopsis sp. and enzyme production. Afr J Agr Res 5(11):1324–1340. https://doi.org/10.5897/AJAR09.541
Das A, Varma A (2009) Symbiosis: the art of living. In: Varma A, Kharkwal AC (eds) Symbiotic fungi: principles and practice. Springer, Berlin, pp 1–28. https://doi.org/10.1007/978-3-540-95894-9_1
Datnoff LE, Elmer WH, Huber DM (eds) (2007) Mineral nutrition and plant disease. APS Press, St. Paul, pp 155–175
Dawande AK, Gajbhiye ND, Charde VN, Banginwar YS (2019) Assessment of endophytic fungal isolates for its Antibiofilm activity on Pseudomonas aeruginosa. Inter J Scient Res Biol Sci 6(3):8186. https://doi.org/10.26438/ijsrbs/v6i3.8186
De Bary A (1866) Morphologie and Physiologie der Pilze, Flechten und Myxomyceten Vol. 2. Leipzig: Hofmeister’s Handbook of Physiological Botany. https://doi.org/10.5962/bhl.title.120970
De Jonge R, Van Esse HP, Kombrink A, Shinya T, Desaki Y, Bours R, Thomma BPHJ (2010) Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants. Science 329(5994):953–955. https://doi.org/10.1126/science.1190859
de Weert S, Vermeiren H, Mulders IH, Kuiper I, Hendrickx N, Bloemberg GV, Vanderleyden J, De Mot R, Lugtenberg BJ (2002) Flagella-driven chemotaxis towards exudate components is an important trait for tomato root colonization by Pseudomonas fluorescens. Mol Plant Microbe Interact 15(11):1173–1180. https://doi.org/10.1094/MPMI.2002.15.11.1173
Deepika VB, Vohra M, Mishra S, Dorai K, Rai P, Satyamoorthy K, Murali TS (2020) DNA demethylation overcomes attenuation of colchicine biosynthesis in an endophytic fungus Diaporthe. J Biotechnol 323:33–41. https://doi.org/10.1016/j.jbiotec.2020.07.019
Deising HB, Werner S, Wernitz M (2000) The role of fungal appressoria in plant infection. Microb Infect 2(13):1631–1641. https://doi.org/10.1016/s1286-4579(00)01319-8
Deshmukh S, Hückelhoven R, Schafer P, Imani J, Sharma M, Weiss M, Waller F, Kogel KH (2006) The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley. Proc Natl Acad Sci 103(49):18450–18457. https://doi.org/10.1073/pnas.0605697103
Dong YH, Wang LH, Zhang LH (2007) Quorum-quenching microbial infections: mechanisms and implications. Philos Trans R Soc Lond B Biol Sci 362(1483):1201–1211. https://doi.org/10.1098/rstb.2007.2045
Eaton CJ, Cox MP, Ambrose B, Becker M, Hesse U, Schardl CL, Scott B (2010) Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis. Plant Physiol 159(2):871. https://doi.org/10.1104/pp.110.158451
Eaton CJ, Cox MP, Scott B (2011) What triggers grass endophytes to switch from mutualism to pathogenism? Plant Sci. Elsevier 180(2):190–195. https://doi.org/10.1016/j.plantsci.2010.10.002
Elbeltagy A, Nishioka K, Suzuki H, Sato T, Sato YI, Morisaki H, Mitsui H, Minamisawa K (2000) Isolation and characterization of endophytic bacteria from wild and traditionally cultivated rice varieties. Soil Sci Plant Nutr 46(3):617–629. https://doi.org/10.1080/00380768.2000.10409127
Epstein L, Laccetti LB, Staples RC, Hoch HC (1987) Cell-substratum adhesive protein involved in surface contact responses of the bean rust fungus. Physiol Mol Plant Pathol 30(3):373–388. https://doi.org/10.1016/0885-5765(87)90018-X
Eyberger AL, Dondapati R, Porter JRJ (2006) Endophyte fungal isolates from Podophyllum peltatum produce podophyllotoxin. Nat Prod 69(8):1121–1124. https://doi.org/10.1021/np060174f
Eydoux L, Farrer EC (2020) Does salinity affect lifestyle switching in the plant pathogen Fusarium solani? Access Microbiol 2:6. https://doi.org/10.1099/acmi.0.000114
Fabiano CC, Tezotto T, Favarin JL, Polacco JC, Mazzafera P (2015) Essentiality of nickel in plants: a role in plant stresses. Front Plant Sci 6:754. https://doi.org/10.3389/fpls.2015.00754
Farouk HM, Eman, Attia EZ, El-Katany MH (2019) Hydrolytic enzyme production of endophytic fungi isolated from soybean (Glycine max). J Mod Res 2(1):1–7. https://doi.org/10.21608/jmr.2019.15748.1008
Felix G, Duran JD, Volko S, Boller T (1999) Plants have a sensitive perception system for the most conserved domain of bacterial flagellin. Plant J 18(3):265–276. https://doi.org/10.1046/J.1365-313x.1999.00265.x
Fernandez I, Cosme M, Stringlis IA, Yu K, De Jonge R, Van Wees SCM, Van der Heiijden MGA (2019) Molecular dialogue between arbuscular mycorrhizal fungi and the non-host plant Arabidopsis thaliana switsches from initial detection to antagonism. New Phytol 223(2):867–881. https://doi.org/10.1111/nph.15798
Fernandez-Gonzalez A, Villadas PJ, Gomez-Lama Cabanas C, Valverde-Corredor A, Belaj A, Mercado-Blanco J, Fernández-López M (2019) Defning the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection. Sci Rep 9:20423. https://doi.org/10.1038/s41598-019-56977-9
Fernando DR, Baker AJM, Woodrow IE (2009) Physiological responses in Macadamia integrifolia on exposure to Manganese treatment. Austral J Bot 57(5):406–413. https://doi.org/10.1071/BT09077
Ferreira LVM, Carvalho F, Andrade JFC et al (2020) Co-inoculation of selected nodule endophytic rhizobacterial strains with Rhizobium tropici promotes plant growth and controls damping off in common bean. Pedosphere Volume 30:98–108. https://doi.org/10.1016/S1002-0160(19)60825-8
Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 103(3):626–631. https://doi.org/10.1073/pnas.0507535103
Figueroa M, Jarmusch AK, Raja HA, El-Elimat T, Kavanaugh JS, Horswill AR, Cooks RG, Cech NB, Oberlies NH (2014) Polyhydroxyanthraquinones as quorum sensing inhibitors from the guttates of Penicillium restrictum and their analysis by desorption electrospray ionization mass spectrometry. J Nat Prod 77(6):1351–1358. https://doi.org/10.1021/np5000704
Fones HN, Preston GM (2012) Reactive oxygen and oxidative stress tolerance in plant pathogenic Pseudomonas. FEMS Microbiol Lett 327(1):1–8. https://doi.org/10.1111/j.1574-6968.2011.02449.x
Fourie R, Ells R, Swart CW, Sebolai OM, Albertyn J, Pohl CH (2016) Candida albicans and Pseudomonas aeruginosa interaction, with focus on the role of eicosanoids. Front Physiol 7:64. https://doi.org/10.3389/fphys.2016.00064
Franken P (2012) The plant strengthening root endophyte Piroformospora indica: potential application and the biology behind. Appl Microbiol Biotechnol 96(6):1455–1464. https://doi.org/10.1007/s00253-012-4506-1
Freeman S, Horowitz S, Sharon A (2001) Pathogenic and non-pathogenic lifestyles in Colletotrichum acutatum from strawberry and other plants. Phytopathology 91(10):986–992. https://doi.org/10.1094/PHYTO.2001.91.10.986
Fuqua C, Parsek MR, Greenberg EP (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet 35:439–468. https://doi.org/10.1146/annurev.genet.35.102401.090913
Galon Y, Finkler A, Fromm H (2010) Calcium-regulated transcription in plants. Mol Plant 3(4):653–669. https://doi.org/10.1093/mp/ssq019
Glaeser SP, Imani J, Alabid I, Guo H, Kumar N, Kämpfer P, Hardt M, Blom J, Goesmann A, Rothballer M et al (2016) Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME J 10:871–884. https://doi.org/10.1038/ismej.2015.163
Gomez-Gomez L, Boller T (2000) FLS2: An LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. Mol Cell 5(6):1003–1011. https://doi.org/10.1016/S1097-2765(00)80265-8
Gori K, Knudsen PB, Nielsen KF, Arneborg N, Jespersen L (2011) Alcohol based quorum sensing plays a role in adhesion and sliding motility of the yeast Debaryomyces hansenii. FEMS Yeast Research 11(8):643–652. https://doi.org/10.1111/j.1567-1364.2011.00755.x
Grant M, Lamb C (2006) Systemic immunity. Curr Opin Plant Biol 9(4):414–420. https://doi.org/10.1016/j.pbi.2006.05.013
Grennan AK (2006) Plant response to bacterial pathogens. Overlap between innate and gene-for-gene defense response. Plant Physiol 142(3):809–811. https://doi.org/10.1104/pp.106.900207
Grobe N, Lamshoft M, Orth RG, Drager B, Kutchan TM, Zenk MH, Spiteller M (2010) Urinary excretion of morphine and biosynthetic precursors in mice. Proc Natl Acad Sci USA 107(18):8147–8152. https://doi.org/10.1073/pnas.1003423107
Gunatilaka AAL (2006) Natural products from plant-associated microorganisms: Distribution, structural diversity, bioactivity, and implication of their occurrence. J Nat Prod 69(3):509–526. https://doi.org/10.1021/np058128n
Gunawardena AHLAN, Greenwood JS, Dengler NG (2004) Programmed cell death remodels lace plant leaf shape during development. Plant Cell 16(1):60–73. https://doi.org/10.1105/tpc.016188
Guo B, Wang Y, Sun X, Tang K (2008) Bioactive natural products from endophytes: A review. Appl Biochem Microbiol 44(2):136–142. https://doi.org/10.1134/S0003683808020026
Guo H, Ma A, Zhao G, Yun J, Liu X, Zhang H, Zhuang G (2010) Effect of farnesol on Penicillium decumbens’s morphology and cellulase production. Bioresources 6(3):3252–3259. https://doi.org/10.15376/BIORES.6.3252-3259
Guo Y, Matsuoka Y, Miura T, Nishizawa T, Ohta H, Narisawa K (2018) Complete genome sequence of Agrobacterium pusense VsBac-Y9, a bacterial symbiont of the dark septate endophytic fungus Veronaeopsis simplex Y34 with potential for improving fungal colonization in roots. J Biotechnol 284:31–36. https://doi.org/10.1016/j.jbiotec.2018.07.045
Gupta SK, Rai AK, Kanwar SS, Sharma TR (2012) Comparative analysis of zinc finger proteins involved in plant disease resistance. PLoS One 7(8):e42578. https://doi.org/10.1371/journal.pone.0042578
Hallmann J (2001) Plant interactions with endophytic bacteria. In: Jeger MJ, Spence NJ (eds) Biotic interactions in plant-pathogen associations. CABI Publishing, Wallingford, pp 87–119. https://doi.org/10.1079/9780851995120.0000
Hardoim PR, Van Overbeek LS, Van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16(10):463–471. https://doi.org/10.1016/j.tim.2008.07.008
Hardoim PR, Van Overbeek LS, Berg G, Pirttila AM, Compant S, Campisano A, Doring M, Sessitsch A (2015) The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol Mol Biol Rev. 79(3):293–320. https://doi.org/10.1128/MMBR.00050-14
Hartmann A, Rothballer M, Hense BA, Schröder P (2014) Bacterial quorum sensing compounds are important modulators of microbe-plant interactions. Front Plant Sci 5:131. https://doi.org/10.3389/fpls.2014.00131
Haryani Y, Hilma R, Dilfira N, Martalinda T, Puspita F, Friska A, Juwita D, Faringa A, Ardi F (2020). Antibacterial activity of Achromobacter sp. and Bacillus sp. bacterial endophytes derived from Mangrove Ceriops tagal (Perr.) C.B.Robb. IOP Conference Series: Materials Science and Engineering. 833:012013. https://doi.org/10.1088/1757-899X/833/1/012013
Hashimoto K, Eckert C, Anschütz U, Scholz M, Held K, Waadt R, Reyer A, Hippler M, Becker D, Kudla J (2012) Phosphorylation of calcineurin B-like (CBL) calcium sensor proteins by their CBL-interacting protein kinases (CIPKs) is required for full activity of CBL–CIPK complexes toward their target proteins. J Biol Chem 287(11):7956–7968. https://doi.org/10.1074/jbc.M111.279331
Hassani MA, Duran P, Hacquard S (2018) Microbial interactions within the plant holobiont. Microbiome 6(1):58. https://doi.org/10.1186/s40168-018-0445-0
Hata K, Futai K (1993) Effect of needle aging on the total colonization rate of endophytic fungi on Pinus thunbergii and Pinus densiflora needles. J Jpn Forest Soc 75(4):338–341. https://doi.org/10.11519/jjfs1953.75.4_338
Heinig U, Scholz S, Jennewein S (2013) Getting to the bottom of Taxol biosynthesis by fungi. Fungal Divers 60(1):161–170. https://doi.org/10.1007/s13225-013-0228-7
Herbers K, Meuwly P, Frommer WB, Metraux JP, Sonnewald U (1996) Systemic acquired resistance mediated by the ectopic expression of invertase: Possible hexose sensing in the secretory pathway. The Plant Cell 8(5):793–803. https://doi.org/10.1105/tpc.8.5.793
Higgins KL, Arnold AE, Coley P, Kursar T (2014) Communities of fungal endophyte in tropical forest grasses: highly diverse hostand habitat generalists characterized by strong spatial structure. Fungal Ecol 8:1–11. https://doi.org/10.1016/j.funeco.2013.12.005
Hilbert M, Novero M, Rovenich H, Mari S, Carolin G, Bonfante P, Zuccaro A (2019) MLO differentially regulates barley root colonization by beneficial endophytic and mycorrhizal fungi. Front Plant Sci 10:1687. https://doi.org/10.3389/fpls.2019.01678
Hoffman MT, Gunatilaka MK, Wijeratne K, Gunatilaka L, Arnold AE (2013) Endohyphal bacterium enhances production of indole-3-acetic acid by a foliar fungal endophyte. PLoS One 8(9):e73132. https://doi.org/10.1371/journal.pone.0073132
Hogan DA (2006) Quorum sensing: alcohols in a social situation. Curr Biol 16(12):R457–R458. https://doi.org/10.1016/j.cub.2006.05.035
Hong K-W, Koh C-L, Sam C-K, Yin Y-F, Chan K-G (2012) Quorum quenching revisited—from signal decays to signaling confusion. Sensors 12(4):4661–4696. https://doi.org/10.3390/s1204044661
Hornby JM, Jensen EC, Lisec AD, Tasto JJ, Jahnke B, Shoemaker R, Dussault P, Nickerson KW (2001) Quorum sensing in the dimorphic fungus Candida albicans is mediated by farnesol. Appl Environ Microbiol 67(7):2982–2992. https://doi.org/10.1128/AEM.67.7.2982-2992.2001
Howitz KT, Sinclair DA (2008) Xenohormesis: sensing the chemical cues of other species. Cell 133(3):387–391. https://doi.org/10.1016/j.cell.2008.04.019
Huang AC, Jiang T, Liu YX, Bai Y-C, Reed J, Qu B, Goossens A, Nutzmann H-W, Bai Y, Osbourn A (2019) A specialized metabolic network selectively modulates Arabidopsis root microbiota. Science 364(6440):eaau6389. https://doi.org/10.1126/science.aau6389
Huber DM (1980) The role of mineral nutrition in defense. In: Horsfall JG, Cowling EB (eds) Plant disease, An advanced treatise, volume 5. How plants defend themselves. Academic Press, New York, pp 381–406
Hughes DT, Sperandio V (2008) Inter-kingdom signalling: communication between bacteria and their hosts. Nat Rev Microbiol 6(2):111–120. https://doi.org/10.1038/nrmicro1836
Imaizumi-Anraku H, Takeda N, Charpentier M, Perry J, Miwa H, Umehara Y, Kouchi H, Murakami Y, Mulder L, Vickers K, Pike J, Downie JA, Wang T, Sato S, Asamizu EE, Tabata S, Yoshikawa M, Murooka Y, Wu G, Kawaguchi M, Kawasaki S, Parniske M, Hayashi M (2005) Plastid proteins crucial for symbiotic fungal and bacterial entry into plant roots. Nature 433(7025):527–531. https://doi.org/10.1038/nature03237
Ismail AS, Valastyan JS, Bassler BL (2016) A host-produced autoinducer-2 mimic activates bacterial quorum sensing. Cell Host Microbe 19(4):470–480. https://doi.org/10.1016/j.chom.2016.02.020
Jacobs S, Zechmann B, Molitor A, Trujillo M, Petutschnig E, Lipka V, Schafer P (2011) Broad-spectrum suppression of innate immunity is required for colonization of Arabidopsis roots by the fungus Piriformospora indica. Plant Physiol 156(2):726–740. https://doi.org/10.1104/pp.111.176446
Jacoby RP, Koprivova A, Kopriva S (2020) Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. J Exp Bot eraa424. https://doi.org/10.1093/jxb/eraa424
Jayaprakasha GK, Rao LJM, Sakariah KK (2003) Volatile constituents from Cinnamomum zeylanicum fruit stalks and their antioxidant activities. J Agric Food Chem 5(15):4344–4348. https://doi.org/10.1021/jf034169i
Jinzhong Cai, Shaogui HE, Jia HU (2015) Research of Ephedra endophytic fungi in production of ephedra alkaloids. Chinese J Biochem Pharmaceut 35(10):18–21
Jogawat A, Meena MK, Kundu A, Verma M, Vadassery J (2020) Calcium channel CNGC19 mediates basal defense signalling to regulate colonization by Pirifomrospora indica in Arabidopsis thaliana roots. J Exper Bot 71(9):2752–2768. https://doi.org/10.1093/jxb/eraa028
Jones JDG, Dangl JL (2006) The plant immune system. Nature 444(7117):323–329. https://doi.org/10.1038/nature05286
Joshi JR, Burdman S, Lipsky A, Yariv S, Yedidia I (2016) Plant phenolic acids affect the virulence of Pectobacterium aroidearum and P. carotovorum ssp. brasiliense via quorum sensing regulation. Mol Plant Pathol 17(4):487–500. https://doi.org/10.1111/mpp.12295
Kaddes A, Fauconnier ML, Sassi K, Nasraoui B, Jijakli MH (2019) Endophytic fungal volatile compounds as solution for sustainable agriculture. Molecules 24(6):1065. https://doi.org/10.3390/molecules24061065
Kaul S, Ahmed M, Zargar K, Sharma P, Dhar MK (2012) Prospecting endophytic fungal assemblage of Digitalis lanata Ehrh. (Foxglove) as a novel source of digoxin: a cardiac glycoside. 3 Biotech 3(4): 335–340. https://doi.org/10.1007/s13205-012-0106-0
Kazan K, Lyons R (2014) Intervention of phytohormone pathways by pathogen effectors. Plant Cell 26(6):2285–2309. https://doi.org/10.1105/tpc.114.125419
Khare E, Mishra J, Arora NK (2018) Multifaceted interactions between endophytes and plant: Developments and Prospects. Front Microbiol 9:2732. https://doi.org/10.3389/fmicb.2018.02732
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):1208–1228. https://doi.org/10.1039/c1np00008j
Kim S-H, Park H-D (2013) Ginger extract inhibits biofilm formation by Pseudomonas aeruginosa PA14. PLoS ONE 8(9):e76106. https://doi.org/10.1371/journal.pone.0076106
Kloppholz S, Kuhn H, Requena N (2011) A secreted fungal effector of Glomus intraradices promotes symbiotic biotrophy. Curr Biol 21(14):1204–1209. https://doi.org/10.1016/j.cub.2011.06.044
Kobayashi DY, Crouch JA (2009) Bacterial–fungal interactions: from pathogens to mutualistic endosymbionts. Annu Rev Phytopathol 47:63–82. https://doi.org/10.1146/annurev-phyto-080508-081729
Kogel K-H, Franken P, Huckelhoven R (2006) Endophyte or parasite-what decides? Curr Opin Plant Biol 9(4):358–363. https://doi.org/10.1016/j.pbi.2006.05.001
Koh KH, Tham FY (2011) Screening of traditional Chinese medicinal plants for quorum-sensing inhibitors activity. J Microbiol Immunol Infect 44(2):144–148. https://doi.org/10.1016/j.jmii.2009.10.001
Kokubo Y, Nishizaka M, Ube N, Yabuta Y, Tebayashi S, Ueno K, Taketa S, Ishihara A (2017) Distribution of the tryptophan pathway-derived defensive secondary metabolites gramine and benzoxazinones in Poaceae. Biosci Biotechnol Biochem 81:431–440. https://doi.org/10.1080/09168451.2016.1256758
Koprivova A, Schuck S, Jacoby RP, Klinkhammer I, Welter B, Leson L, Martyn A, Nauen J, Grabenhorst N, Mandelkow JF, Zuccaro A, Zeier J, Kopriva S (2019) Root-specific camalexin biosynthesis controls the plant growth promoting effects of multiple bacterial strains. Proc Natl Acad Sci USA 116(31):15735–15744. https://doi.org/10.1073/pnas.1818604116
Kudjordjie EN, Sapkota R, Steffensen SK et al (2019) Maize synthesized benzoxazinoids affect the host associated microbiome. Microbiome 7:59. https://doi.org/10.1186/s40168-019-0677-7
Kumar A, Patil D, Rajamohanan PR, Ahmad A (2013) Isolation, purification and characterization of vinblastine and vincristine from endophytic fungus Fusarium oxysporum isolated from Catharanthus roseus. PLoS ONE 8(9):e71805. https://doi.org/10.1371/journal.pone.0071805
Kumar RV, Pratap S, Mishra P (2019) Endophytes as emphatic communication barriers of quorum sensing in Gram-positive and Gram-negative bacteria-a review. Environ Sustain 2:455–468. https://doi.org/10.1007/s42398-019-00079-9
Kumara PM, Zuehlke S, Priti V, Ramesha BT, Ravikanth G, Vasudeva R, Santoshkumar TR, Spiteller M, Shaanker RU (2012) Fusarium proliferatum, an endophytic fungus from Dysoxylum binectariferum produces rohitukine, a chromane alkaloid possessing anti-cancer activity. Antonie Van Leeuwenhoek 101(2):323–329. https://doi.org/10.1007/s10482-011-9638-2
Kunkel BN, Brooks DM (2002) Cross talk between signalling pathways in pathogen defense. Curr Opin Plant Biol 5(4):325–331. https://doi.org/10.1016/S1369-5266(02)00275-3
Kusari S, Spiteller M (2012) Camptothecin: recent advances in plant endophyte research. In: Patro LR (ed) Natural Resources Conservation and Management. Manglam Publications, New Delhi, pp 1–32
Kusari S, Lamshöft M, Zuhlke S, Spiteller M (2008) An endophytic fungus from Hypericum perforatum that produces hypericin. J Nat Prod 71(2):159–162. https://doi.org/10.1021/np070669k
Kusari S, Lamshoft M, Spiteller M (2009a) Aspergillus fumgigatus 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. https://doi.org/10.1111/j.1365-2672.2009.04285.x
Kusari S, Zuhlke S, Spiteller M (2009b) An endophytic fungus from Camptotheca acuminata that produces camptothecin and analogues. J Nat Prod 72(1):2–7. https://doi.org/10.1021/np800455b
Kusari S, Zuhlke S, Kosuth J, Cellarova E, Spiteller M (2009c) Light independent metabolomics of endophytic Thielavia subthermophila provides insight into microbial hypericin biosynthesis. J Nat Prod 72(10):1825–1835. https://doi.org/10.1021/np9002977
Kusari S, Zühlke S, Spiteller M (2011a) 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. https://doi.org/10.1021/np1008398
Kusari S, Ko-suth J, Cellarova E, Spiteller M (2011b) Survival-strategies of endophytic Fusarium solani against indigenous camptothecin biosynthesis. Fungal Ecol 4(3):219–223. https://doi.org/10.1016/j.funeco.2010.11.002
Kusari S, Hertweck C, SpitellerM (2012a) Chemical ecology of endophytic fungi: origins of secondary metabolites. Chem Biol 19(7):792–798. https://doi.org/10.1016/j.chembiol.2012.06.004
Kusari S, Verma VC, Lamshoft M, Spiteller M (2012b) An endophytic fungus from Azadirachta indica A Juss. that produces azadirachtin. World J Microbiol Biotechnol 28(3):1287–1294. https://doi.org/10.1007/s11274-011-0876-2
Kusari P, Kusari S, Lamshoft M, Sezgin S, Spiteller M, Kayser O (2014) Quorum quenching is an antivirulence strategy employed by endophytic bacteria. Appl Microbiol Biotechnol 98(16):7173–7183. https://doi.org/10.1007/s00235-0145807-3
Kusari P, Kusari S, Spiteller M, Kayser O (2015) Implications of endophyte-plant crosstalk in light of quorum responses for plant biotechnology. Appl Microbiol Biotechnol 99:5383–5390
Lahrmann U, Zuccaro A (2012) Opprimo ergo sum–evasion and suppression in the root endophytic fungus Piriformospora indica. Mol Plant Microbe Interact 25(6):727–737. https://doi.org/10.1094/MPMI-11-11-0291
Lahrmann U, Dinga Y, Banhara A, Rath M, Hajirezaeid MR, Dohlemanna S, Wirend NV, Parniskeb M, Zuccaroa A (2013) Host-related metabolic cues affect colonization strategies of a root endophyte. Proc Natl Acad Sci 110(34):13965–13970. https://doi.org/10.1073/pnas.1301653110
Lambais MR (2000) Regulation of plant defence-related genes in arbuscular mycorrhizae. In: Podila GK, Douds DD (eds) Current Advances in mycorrhizal research. APS Press, Minnesota USA, pp 45–59
Lambais MR, Mehdy MC (1998) Spatial distribution of chitinases and β-1, 3-glucanse transcripts in bean arbuscular mycorrhizal roots under low and high soil phosphate conditions. New Phytol 140(1):33–42. https://doi.org/10.1046/j.1469-8137.1998.00259
LaSarre B, Federle MJ (2013) Exploiting quorum sensing to confuse bacterial pathogens. Microbiol Mol Biol Rev 77(1):73–111. https://doi.org/10.1128/MMBR.00046-12
Lee JC, Strobel GA, Lobkovsky E, Clardy J (1996) Torreyanic acid: a selectively cytotoxic quinone dimer from the endophytic fungus Pestalotiopsis microspora. J Org Chem 61(10):3232–3233. https://doi.org/10.1021/jo960471x
Lee H, Chang YC, Nardone G, Kwon-Chung KJ (2007) TUP1 disruption in Cryptococcus neoformans uncovers a peptide-mediated density-dependent growth phenomenon that mimics quorum sensing. Mol Microbiol 64(3):591–601. https://doi.org/10.1111/j.1365-2958.2007.05666.x
Leuchtmann A, Clay K (1990) Isozyme variation in the Acremonium/Epichloe fungal endophyte complex. Phytopathology 80:1133–1139. https://doi.org/10.1094/Phyto-80-1133
Levy A, Chang BJ, Abbott LK, Kuo J, Harnett G, Inglis TJJ (2003) Invasion of spores of the arbuscular mycorrhizal fungus Gigaspora decipiens by Burkholderia spp. Appl Environ Microbiol 69(10):6250–6256. https://doi.org/10.1128/aem.69.10.6250-6256.2003
Li S, Zhang Z, Cain A, Wang B, Long M, Taylor J (2005) Antifungal activity of camptothecin, trifolin, and hyperoside isolated from Camptotheca acuminata. J Agric Food Chem 53(1):32–37. https://doi.org/10.1021/jf0484780
Li G, Kusari S, Golz C, Laatsch H, Strohmann C, Spiteller M (2017) Epigenetic modulation of endophytic Eupenicillium sp. LG41 by a histone deacetylase inhibitor for production of decalin-containing compounds. J Nat Prod 80(4):983–988. https://doi.org/10.1021/acs.jnatprod.6b00997
Lim FY, Sanchez JF, Wang CC, Keller NP (2012) Toward awakening cryptic secondary metabolite gene clusters in filamentous fungi. Methods Enzymol 517:303–324. https://doi.org/10.1016/B978-0-12-404634-4.00015-2
Lindstrom JT, Belanger FC (1994) Purification and characterization of an endophytic fungal proteinase that is abundantly expressed in the host grass. Plant Physiol 106(1):7–16. https://doi.org/10.1104/pp.106.1.7
Liu J, Blaylock LA, Endre G, Cho J, Town CD, VandenBosch KA, Harrison MJ (2003) Transcript profiling coupled with spatial expression analyses reveals genes involved in distinct developmental stages of an arbuscular mycorrhizal symbiosis. Plant Cell 15(9):2106–2123. https://doi.org/10.1105/tpc.014183
Liu H, Senthilkumar R, Ma G, Zou Q, Zhu K, Tian D, Hua MS, Oelmuller R, Yeh KW (2019) Piriformospora indica-induced phytohormone changes and root colonization strategies are highly host-specific. Plant Signal Behav 14:9. https://doi.org/10.1080/15592324.2019.1632688
Lopez-Fernandez S, Sonega P, Moretto M, Pancher M, Engelen K, Pertot I, Campisano A (2015) Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria. Front Microbiol 6:419. https://doi.org/10.3389/fmicb.2015.00419
Lopez-Gomez M, Sandal N, Stougaard J, Boller T (2012) Interplay of flg22-induced defence responses and nodulation in Lotus japonicus. J Exp Bot 63(1):393–401. https://doi.org/10.1093/jxb/err291
Lopez-Raez JA, Pozo MJ, García-garrido JM (2011) Strigolactones: a cry for help in the rhizosphere. Botany 89:513–522. https://doi.org/10.1139/b11-046
Lopez-Raez JA, Shirasu K, Foo E (2017) Strigolactones in plant interactions with beneficial and detrimental organisms: the yin and yang. Trends Plant Sci 22(6):527–537. https://doi.org/10.1016/j.tplants.2017.03.011
Lu Y, Shao DY, Shi JL, Huang QS, Yang H, Jin ML (2016) Strategies for enhancing resveratrol production and the expression of pathway enzymes. Appl Microbiol Biotechnol 100(17):7404–7421. https://doi.org/10.1007/s00253-016-7723-1
Lu Y, Ye C, Che JX, Xu XG, Shao DY, Jiang CM, Liu YL, Shi JL (2019) Genomic sequencing, genome-scale metabolic network reconstruction and in silico flux analysis of the grape endophytic fungus Alternaria sp.MG1. Microb Cell Factories 18(1):13. https://doi.org/10.1186/s12934-019-1063-7
Ludwig-Muller J (2015) Plants and endophytes: equal partners in secondary metabolite production? Biotechnol Lett 37(7):1325–1334. https://doi.org/10.1007/s10529-015-1814-4
Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ, Pietro AD, Dufresne M, Freitag M, Grabherr M, Henrissat B, Houterman PM, Kang S (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464(7287):367–373. https://doi.org/10.1038/nature08850
MacDonald RM, Chandler MR (1981) Bacterium-like organelles in the vesicular-arbuscular mycorrhizal fungus Glomus caledonius. New Phytol 89(2):241–246. https://doi.org/10.1111/j.1469-8137.1981.tb07486.x
Machida K, Tanaka T, Yano Y, Otani S, Taniguchi M (1999) Farnesol-induced growth inhibition in Saccharomyces cerevisiae by a cell cycle mechanism. Microbiology 145(2):293–299. https://doi.org/10.1099/13500872-145-2-293
Macho AP, Zipfel C (2014) Plant PRRs and the activation of innate immune signalling. Mol Cell 54(2):263–272. https://doi.org/10.1016/j.molcel.2014.03.028
Mandyam KG, Jumpponen A (2014) Mutualism-parasitism paradigm synthesized from results of root-endophyte models. Front Microbiol 5:776. https://doi.org/10.3389/fmicb.2014.00776
Márquez 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. https://doi.org/10.1126/science.1136237
Martín-Rodríguez AJ, Reyes F, Martín J, Pérez-Yépez J, León-Barrios M, Couttolenc A, Espinoza C, Trigos A, Martín VS, Norte M, Fernández JJ (2014) Inhibition of bacterial quorum sensing by extracts from aquatic fungi: first report from marine endophytes. Mar Drugs 12(11):5503–5526. https://doi.org/10.3390/md12115503
Meena H, Mishra R, Ranganathan S, Sarma VV, Ampasala DR, Kalia VC, Lee JK, Siddhardha B (2020) Phomopsis tersa as Inhibitor of Quorum Sensing System and Biofilm Forming Ability of Pseudomonas aeruginosa. Indian J Microbiol 60:70–77. https://doi.org/10.1007/s12088-019-00840-y
Mendes R, Kruijt M, De Bruijn I, Dekkers E, Van Der Voort M, Schneider JH, Piceno YM, DeSantis TZ, Andersen GL, Bakker PA, Raaijimakers JM (2011) Deciphering the rhizosphere microbiome for disease suppressive bacteria. Science 332(6033):1097–1100. https://doi.org/10.1126/science.1203980
Mendoza-Mendoza A, Zaid R, Lawry R, Hermosa R, Monte E, Horwitz BA, Mukherjee PK (2018) Molecular dialogues between Trichoderma and roots: Role of the fungal secretome. Fungal Biol Rev 32(2):62–85. https://doi.org/10.1016/j.fbr.2017.12.001
Mengistu AA (2020) Endophytes: Colonization, behaviour, and their role in defense mechanism. Int J Microbiol. https://doi.org/10.1155/2020/6927219
Metz A, Haddad A, Worapong J, Long D, Ford E, HessWM SGA (2000) Induction of the sexual stage of Pestalotiopsis microspora, a taxol producing fungus. Microbiology 146(8):2079–2089. https://doi.org/10.1099/00221287-146-8-2079
Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55(1):165–199. https://doi.org/10.1146/annurev.micro.55.1.165
Millet YA, Danna CH, Clay NK, Songnuan W, Simon MD, Werck-Reichhart D, Ausubel FM (2010) Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 22(3):973–990. https://doi.org/10.1105/tpc.109.069658
Minerdi D, Moretti M, Gilardi G, Barberio C, Gullino ML, Garibaldi A (2008) Bacterial ectosymbionts and virulence silencing in a Fusarium oxysporum strain. Environ Microbiol 10(7):1725–1741. https://doi.org/10.1111/j.1462-2920.2008.01594.x
Mishra R, Kushveer JS, Majumder D, Sarma VV (2020) Stimulation of secondary metabolite production in Hypoxylon anthochroum by naturally occurring epigenetic modifiers. J Food Meas Charact 14:946–962. https://doi.org/10.1007/s11694-019-00345-8
Moricca S, Ragazzi A (2008) Fungal endophytes in Mediterranean oak forests: a lesson from Discula quercina. Phytopathol 98(4):380–386. https://doi.org/10.1094/PHYTO-98-4-0380
Mousa WK, Shearer C, Limay-rios V, Ettinger CL, Eisen JA, Raizada MN (2016) Root-hair endophyte stacking in finger millet creates a physicochemical barrier to trap the fungal pathogen Fusarium graminearum. Nat Microbiol 1:16167. https://doi.org/10.1038/nmicrobiol.2016.167
Mur LAJ, Kenton P, Atzorn R, Miersch O, Wasternack C (2006) The outcomes of concentration-specific Interactions between salicylate and jasmonate signaling include synergy, antagonism and oxidative stress leading to cell death. Plant Physiol 140(1):249–262. https://doi.org/10.1104/pp.105.072348
Nair DN, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J:1–11. https://doi.org/10.1155/2014/250693
Nanda AK, Andrio E, Marino D, Pauly N, Dunand C (2010) Reactive oxygen species during plant-microorganism early interactions. J Integ Plant Biol 52(2):195–204. https://doi.org/10.1111/j.1744-7909.2010.00933.x
Natrah FM, Defoirdt T, Sorgeloos P, Bossier P (2011) Disruption of bacterial cell-to-cell communication by marine organisms and its relevance to aquaculture. Mar Biotechnol 13(2):109–126. https://doi.org/10.1007/s10126-010-9346-3
Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PloS One 7(4):e35498. https://doi.org/10.1371/journal.pone.0035498
Nealson KH, Hastings JW (1979) Bacterial bioluminescence: its control and ecological significance. Microbiol Rev 43(4):496–518
Nicholson RL, Epstein L (1991) Adhesion of fungi to the plant surface: prerequisite for pathogenesis. In: Cole GT, Hoch HC (eds) The Fungal spore and disease initiation in plants and animals. Plenum Press, New York, pp 3–23. https://doi.org/10.1007/978-1-4899-2635-7_1
Nizam S, Qiang X, Wawra S, Nostadt R, Getzke F, Schwanke F, Zuccaro A (2019) Serendipita indica E5’NT modulates extracellular nucleotide levels in the plant apoplast and affects fungal colonization. EMBO Rep 20:e47430. https://doi.org/10.15252/embr.201847430
Noman A, Aqeel M, Khalid N, Islam W, Sanaullah T, Anwar M, Khan S, Ye W, Lou Y (2019) Zinc finger protein transcription factors: integrated line of action for plant antimicrobial activity. Microb Pathog 132:141–149. https://doi.org/10.1016/j.micpath.2019.04.042
Nurnberger T, Kemmerling B (2009) PAMP-triggered basal immunity in plants. Adv Bot Res 51:1–38. https://doi.org/10.1016/S0065-2296(09)51001-4
Oh S-Y, Kim M, Eimes JA, Lim YW (2018) Effect of fruiting body bacteria on the growth of Tricholoma matsutake and its related molds. PLoS One 13:e0190948. https://doi.org/10.1371/journal.pone.0190948
Orozco-Cardenas ML, Narvaez-Vasquez J, Ryan CA (2001) Hydrogen peroxide acts as a second messenger for the induction of defense genes in tomato plants in response to wounding, systemin, and methyl jasmonate. Plant Cell 13(1):179–191. https://doi.org/10.1105/tpc.13.1.179
Padje AV, Whiteside MD, Kiers ET (2016) Signals and cues in the evolution of plant-microbe communication. Curr Opin Plant Biol 32:47–52. https://doi.org/10.1016/j.pbi.2016.06.006
Palem PP, Kuriakose GC, Jayabaskaran C (2015) An endophytic fungus, Talaromyces radicus, isolated from Catharanthus roseus, produces vincristine and vinblastine, which induce apoptotic cell death. PLoS ONE 10(12):e0144476. https://doi.org/10.1371/journal.pone.0144476
Pascale A, Proietti S, Pantelides IS, Stringlis IA (2020) Modulation of the root microbiome by plant molecules: the basis for targeted disease suppression and plant growth promotion. Front Plant Sci 10:1741. https://doi.org/10.3389/fpls.2019.01741
Patil MG, Pagare J, Patil SN, Sidhu AK (2015) Extracellular Enzymatic Activities of Endophytic Fungi Isolated from Various Medicinal Plants. Int J Curr Microbiol App Sci 4(3):1035–1042
Pel MJC, Pieterse CMJ (2013) Microbial recognition and evasion of host immunity. J Exp Bot 64(5):1237–1248. https://doi.org/10.1093/jxb/ers262
Pel MJC, Van Dijken AJH, Bardoel BW, Seidl MF, Van der Ent S, Van Strijp JAG, Pieterse CMJ (2014) Pseudomonas syringae evades host immunity by degrading flagellin monomers with alkaline protease AprA. Mol Plant Microbe Interact 27(7):603–610. https://doi.org/10.1094/MPMI-02-14-0032-R
Perez-Montano F, Jimenez-Guerrero I, Sanchez-Matamoros C, Lopez- Baena FJ, Ollero FJ, Rodriguez-Carvajal MA, Bellogin RA, Espuny MR (2013) Rice and bean AHL-mimic quorum-sensing signals specifically interfere with the capacity to form biofilms by plant-associated bacteria. Res Microbiol 164(7):749–760. https://doi.org/10.1016/j.resmic.2013.04.001
Peter AE, Sudhakar P, Sandeep BV, Rao BG (2019) Antimicrobial and anti-quorum sensing activities of medicinal plants. In: Bramhachari P (ed) Implication of quorum sensing and biofilm formation in medicine, agriculture and food industry. Springer, Singapore, pp 189–217. https://doi.org/10.1007/978-981-32-9409-714
Pieterse CM, Leon-Reyes A, Van der Ent S, Van Wees SC (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5(5):308–316. https://doi.org/10.1038/nchembio.164
Pieterse CMJ, Van der Does D, Zamioudis C, Leon-Reyes A, Van Wees SCM (2012) Hormonal modulation of plant immunity. Annu Rev Cell Dev Biol 28(1):489–521. https://doi.org/10.1146/annurev-cellbio-092910-154055
Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Van Wees SCM, Bakker PAHM (2014) Induced systemic resistance by beneficial microbes. Annu Rev Phytopathol 52:347–375. https://doi.org/10.1146/annurev-phytol-082712-102340
Plett JM, Martin FM (2018) Know your enemy, embrace your friend: using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms. Plant J 93(4):729–746. https://doi.org/10.1111/tpj.13802
Plett JM, Daguerre Y, Wittulsky S, Vayssieres A, Deveau A, Melton SJ, Martin F (2014) Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes. Proc Natl Acad Sci USA 111(22):8299–8304. https://doi.org/10.1073/pnas.1322671111
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. https://doi.org/10.1021/np0502802
Qian X, Li H, Wang Y (2019) Leaf and root endospheres harbor lower fungal diversity and less complex fungal co-occurrence patterns than rhizosphere. Front Microbiol 10:1015. https://doi.org/10.3389/fmicb.2019.01015
Qiao C, Penton CR, Xiong W, Liu C, Wang R, Liu Z, Xu X, Li R, Shen Q (2019) Reshaping the rhizosphere microbiome by bio-organic amendment to enhance crop yield in a maize-cabbage rotation system. Appl Soil Ecol 142:136–146. https://doi.org/10.1016/j.apsoil.2019.04.014
Rai M, Agarkar G (2014) Plant-fungal interactions: what triggers the fungi to switch among lifestyles? Crit Rev Microbiol 42(3):428–438. https://doi.org/10.3109/1040841X.2014.958052
Raina S, Odell M, Keshavarz T (2010) Quorum sensing as a method for improving sclerotiorin production in Penicillium sclerotiorum. J Biotechnol 148(2–3):91–98. https://doi.org/10.1016/j.jbiotec.2010.04.009
Raina S, De Vizio D, Palonen EK, Odell M, Brandt AM, Soini J, Keshavarz T (2012) Is quorum sensing involved in lovastatin production in the filamentous fungus Aspergillus terreus? Process Biochem 47(5):843–852. https://doi.org/10.1016/j.procbio.2012.02.021
Rajesh PS, Rai VR (2013) Hydrolytic enzymes and quorum sensing inhibitors from endophytic fungi of Ventilago madraspatana Gaertn. Biocatal Agric Biotechnol 2(2):120–124. https://doi.org/10.1016/j.bcab.2013.01.002
Rajesh PS, Rai VR (2014) Molecular identification of aiiA homologous gene from endophytic Enterobacter species and in silico analysis of putative tertiary structure of AHL-lactonase. Biochem Biophys Res Commun 443(1):290–295. https://doi.org/10.1016/j.bbrc.2013.11.101
Rashmi M, Meena H, Meena C, Kushveer JS, Busi S, Murali A, Sarma VV (2018) Anti-quorum sensing and antibiofilm potential of Alternaria alternata, a foliar endophyte of Carica papaya, evidenced by QS assays and in-silico analysis. Fungal Biol 122(10):998–1012. https://doi.org/10.1016/j.funbio.2018.07.003
Redecker D, Kodner R, Graham LE (2000) Glomalean Fungi from the Ordovician. Science 289(5486):1920–1921. https://doi.org/10.1126/science.289.5486.1920
Redman RS, Dunigan DD, Rodriguez RJ (2001) Fungal symbiosis: from mutualism to parasitism, who controls the outcome, host or invader? New Phytol 151(3):705–716. https://doi.org/10.1046/j.0028-646x.2001.00210.x
Reinhold-Hurek B, Maes T, Gemmer S, Van Montagu M, Hurek T (2006) An endoglucanase is involved in infection of rice roots by the not-cellulose-metabolizing endophyte Azoarcus sp. strain BH72. Mol Plant-Microbe Interact 19(2):181–188. https://doi.org/10.1094/MPMI-19-0181
Roca MG, Arlt J, Jeffree CE, Read ND (2005) Cell biology of conidial anastomosis tubes in Neurospora crassa. Eukaryot Cell 4(5):911–919. https://doi.org/10.1128/EC.4.5.911-919.2005
Rodriguez RJ, Roossinck M (2012) Viruses, fungi and plants: crosskingdom communication and mutualism. In: Witzany G (ed) Biocommunication of fungi. Springer, pp 219–227. https://doi.org/10.1007/978-94-007-4264-2-14
Rodriguez RJ, Redman RS, Henson JM (2004) The role of fungal symbiosis in the adaptation of plants to high stress environments. Mitig Adapt Strat Gl 9(3):261–272. https://doi.org/10.1023/B:MITI.0000029922.31111
Rosenblueth M, Martínez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant Microbe Interact 19(8):827–837. https://doi.org/10.1094/MPMI-19-0827
Rozpadek P, Domka AM, Nosek M, Wazny R, Jedrzejczyk RJ, Wiciarz M, Turnau K (2018) The Role of Strigolactone in the Cross-Talk between Arabidopsis thaliana and the Endophytic Fungus Mucor sp. Front Microbiol 9:441. https://doi.org/10.3389/fmicb.2018.00441
Rutledge PJ, Challis GL (2015) Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13(8):509–523. https://doi.org/10.1038/nrmicro3496
Sachin N, Manjunatha BL, Mohana Kumara P, Ravikanth G, Shweta S, Suryanarayanan TS, Ganeshaiah KN, Uma Shaanker R (2013) Do endophytic fungi possess pathway genes for plant secondary metabolites? Curr Sci 104(2):178–182
Safari M, Amache R, Esmaeilishirazifard E, Keshavarz T (2014) Microbial metabolism of quorum-sensing molecules acylhomoserine lactones, γ-heptalactone and other lactones. Appl Microbiol Biotechnol 98(8):3401–3412. https://doi.org/10.10007/s00253-014-5518-9
Saikkonen K, Faeth SH, Helander M, Sullivan TJ (1998) Fungal endophytes: a continuum of interactions with host plants. Annu Rev Ecol Syst 29(1):319–343. https://doi.org/10.1146/annurev.ecolsys.29.1.319
Sauer K, Camper AK (2001) Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J Bacteriol 183(22):6579–6589. https://doi.org/10.1128/JB.183.22.6579-6589.2001
Saunders M, Kohn LM (2008) Host-synthesized secondary compounds influence the in vitro interactions between fungal endophytes of maize. Appl Environ Microbiol 74(1):136–114. https://doi.org/10.1128/AEM.01538-07
Schardl CL (2001) Epichloe festucae and related mutualistic symbionts of grasses. Fungal Genet Biol 33(2):69–82. https://doi.org/10.1006/fgbi.2001.1275
Schardl CL, Liu J, White JK, Finkel RA, An Z, Siegel M (1991) Molecular phylogenetic relationship of non-pathogenic grass mycosymbionts and clavicipitaceous plant pathogens. Plant Syst Evol 178(1–2):27–41. https://doi.org/10.1007/BF00937980
Schardl CL, Leuchtmann A, Spiering MJ (2004) Symbioses of grasses with seed borne fungal endophytes. Annu Rev Plant Biol 55:315–340. https://doi.org/10.1146/annurev.arplant.55.031903.141735
Schelkle M, Peterson RL (1997) Suppression of common root pathogens by helper bacteria and ectomycorrhizal fungi in vitro. Mycorrhiza 6:481–485. https://doi.org/10.1007/s005720050151
Schenk ST, Stein E, Kogel K-H, Schikora A (2012) Arabidopsis growth and defense are modulated by bacterial quorum sensing molecules. Plant Signal Behav 7(2):178–181. https://doi.org/10.4161/psb.18789
Scherlach K, Hertweck C (2009) Triggering cryptic natural product biosynthesis in microorganisms. Org Biomol Chem 7(9):1753–1760. https://doi.org/10.1039/b821578b
Schroeckh V, Scherlach K, Nützmann HW, Shelest E, Schmidt-Heck W, Schuemann J, Martin K, Hertweck C, Brakhage AA (2009) Intimate bacterial–fungal interaction triggers biosynthesis of archetypal polyketidesin Aspergillus nidulans. Proc Natl Acad Sci USA 106(34):14558–14563. https://doi.org/10.1073/pnas.0901870106
Schulz B, Boyle C (2005) The endophytic continuum. Mycol Res 109(6):661–686. https://doi.org/10.1017/S095375620500273X
Schulz B, Boyle C (2006) What are endophytes? In: Schulz BJE, Boyle CJC, Sieber TN (eds) Microbial Root Endophytes. Springer-Verlag, Berlin, pp 1–13. https://doi.org/10.1007/3-540-33526-9_1
Schulz B, Rommert AK, Dammann U, Aust HJ, Strack D (1999) The endophyte-host interaction: a balanced antagonism. Mycol Res 103(10):1275–1283. https://doi.org/10.1017/S0953756299008540
Schulz B, Boyle C, Draeger S, Rommert A-K, Krohn K (2002) Endophytic fungi: a source of novel biologically active secondary metabolites. Mycol Res 106(9):996–1004. https://doi.org/10.1017/S0953756202006342
Schulz B, Haas S, Junker C, Andree N, Schobert M (2015) Fungal endophytes are involved in multiple balanced antagonisms. Curr Sci 109(1):39–45
Sharma VK, Kumar J, Singh DK, Mishra A, Verma SK, Gond SK, Kumar A, Singh N, Kharwar RN (2017) Induction of cryptic and bioactive metabolites through natural dietary components in an endophytic fungus Colletotrichum gleosporioides. Front Microbiol 8:1126. https://doi.org/10.3389/fmicb.2017.01126
Shastry RP, Dolan SK, Abdelhamid Y, Vittal RR, Welch M (2018) Purification and characterisation of a quorum quenching AHL lactonase from the endophytic bacterium Enterobacter sp. CS66. FEMS Microbiol Lett 365(9):fny054. https://doi.org/10.1093/femsle/fny054
Sheibani-Tezerji R, Naveed M, Jehl M-A, Sessitsch A, Rattei T, Mitter B (2015) The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements. Front Microbiol 6:440. https://doi.org/10.3389/fmicb.2015.00440
Shweta S, Zuehlke S, Ramesha BT, Priti V, Mohana Kumar P, Ravikanth G, Spiteller M, Vasudeva R, Uma Shaanker R (2010) Endophytic fungal strains of Fusarium solani, from Apodytes dimidiata E.Mey. ex Arn (Icacinaceae) produce camptothecin, 10-hydroxy camptothecin and 9-methoxycamptothecin. Phytochemistry 71(1):117–122. https://doi.org/10.1016/j.phytochem.2009.09.030
Shweta S, Shivanna MB, Gurumurthy BR et al (2014) Inhibition of fungal endophytes by camptothecine produced by their host plan Nothapodytes nimmoniana (Grahm) Mabb. (Icacinaceae). Curr Sci 107(6):994–1000. https://doi.org/10.18520/CS/V107/16/994-1000
Singh BP (ed) (2019) Advances in endophytic fungal research: Present status and future challenges. Fungal Biol, Springer
Singh VK, Singh AK, Kumar A (2017) Disease management of tomato through PGPB: current trends and future perspective. 3. Biotech 7(4):255. https://doi.org/10.1007/s13205-017-0896-1
Singh VK, Singh AK, Singh PP, Kumar A (2018) Interaction of plant growth promoting bacteria with tomato under abiotic stress: A review. Agr Ecosyst Environ 267:129–140. https://doi.org/10.1016/j.agee.2018.08.020
Sirikantaramas S, Sudo H, Asano T (2007) Transport of camptothecin in hairy roots of Ophiorrhiza pumila. J Phytochem 68(22–24):2881–2886. https://doi.org/10.1016/j.phytochem.2007.08.028
Sirikantaramas S, Yamazaki M, Saito K (2008) Mutations in topoisomerase I as a self-resistancemechanismcoevolved with the production of the anticancer alkaloid camptothecin in plants. ProcNatl Acad Sci 105(18):6782–6786. https://doi.org/10.1073/pnas.0801038105
Sirikantaramas S, Yamazaki M, Saito K (2009) A survival strategy: the coevolution of the camptothecin biosynthetic pathway and self-resistance mechanism. Phytochemistry 70(15–16):1894–1898. https://doi.org/10.1016/j.phytochem.2009.07.034
Sirikantaramas S, Yamazaki M, Saito K (2014) How plants avoid the toxicity of self produced defense bioactive compounds. In: Osbourn A, Goss RJ, Carter GT (eds) Natural products: discourse, diversity, and design. Wiley, Hoboken, pp 67–82. https://doi.org/10.1002/9781118794623.ch4
Soliman SSM, Raizada MN (2013) Interactions between co-habitating fungi elicit synthesis of Taxol from an endophytic fungus in host Taxus plants. Front Microbiol 4:3. https://doi.org/10.3389/fmicb.2013.00003
Soliman SSM, Greenwood JS, Bombarely A, Mueller LA, Tsao R, Mosser DD, Raizada MN (2015) An endophyte constructs fungicide-containing extracellular barriers for its host plant. Curr Biol 25(19):2570–2576. https://doi.org/10.1016/j.cub.2015.08.027
Soltani J, Pakvaz S (2016) Endohyphal bacteria from fungal endophytes of the Mediterranean cypress (Cupressus sempervirens) exhibit in vitro bioactivity. Forest Pathology 46:569–581. https://doi.org/10.1111/efp.12274
Somssich IE, Hahlbrock K (1998) Pathogen defence in plants – a paradigm of biological complexity. Trends Plant Sci 3(3):86–90. https://doi.org/10.1016/S1360-1385(98)01199-6
Spoel SH, Johnson JS, Dong X (2007) Regulation of trade-offs between plant defenses against pathogens with different lifestyles. Proc Natl Acad Sci USA 104(47):18842–18847. https://doi.org/10.1073/pnas.0708139104
Staples RC, Macko V (1980) Formation of infection structures as a recognition response in fungi. Experimental Mycol 4(1):2–16. https://doi.org/10.1016/0147-5975(80)90045-6
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. https://doi.org/10.1126/science.8097061
Stringlis IA, Yu K, Feussner K, De Jonge R, Van Bentum S, Van Verk MC, Berendsen RL, Bakker PA, Feussner I, Pieterse CM (2018) MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health. Proc Natl Acad Sci USA 115(22):E5213–E5222. https://doi.org/10.1073/pnas.1722335115
Strobel GA (2002) Microbial gifts from rain forests. Can J Plant Pathol 24(1):14–20. https://doi.org/10.1080/07060660109506965
Strobel GA (2011) Muscodor species-endophytes with biological promise. Photochem Rev 10(2):163–172. https://doi.org/10.1007/s11101-010-9163-3
Strobel GA, Hess WM (1997) Glucosylation of the peptide leucinostatin A produced by an endophytic fungus of European yew, may protect the host from leucinostatin toxicity. Chem Biol 4(7):529–536. https://doi.org/10.1016/s1074-5521(97)90325-2
Strobel G, Daisy B, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67(2):257–268. https://doi.org/10.1021/np030397v
Suarez-Moreno ZR, Devescovi G, Myers M, Hallack L, Mendonça-Previato L, Caballero-Mellado J, Venturi V (2010) Commonalities and differences in regulation of N-acyl homoserine lactone quorum sensing in the beneficial plant-associated Burkholderia species cluster. Appl Environ Microbiol 76(13):4302–4317. https://doi.org/10.1128/AEM.03086-09
Sun Y, Luo H, Li Y, Sun C, SongJ NY, Dong L, Lv A, Tramontano E, Chen S (2011) Pyrosequencing of the Camptotheca acuminate transcriptome reveals putative genes involved in camptothecin biosynthesis and transport. BMC Genomics C7–533(12):1–11. https://doi.org/10.1186/1471-2164-12-533
Sun Y, Li L, Macho AP, Han Z, Hu Z, Zipfel C, Chai J (2013) Structural basis for flg22-induced activation of the Arabidopsis FLS2- BAK1 immune complex. Science 342(6158):624–628. https://doi.org/10.1126/science.1243825
Talaat NB (2019) Role of reactive oxygen species signaling in plant growth and development. In: Hasanuzzaman M, Fotopoulos V, Nahar K, Fujita M (eds) Reactive oxygen, nitrogen and sulfur species in plants. John Wiley & Sons, USA, pp 225–266. https://doi.org/10.1002/9781119468677.ch10
Tan RX, Zou WX (2001) Endophytes: a rich source of functional metabolites. Nat Prod Rep 18(4):448–459. https://doi.org/10.1039/b100918o
Tanaka A, Christensen MJ, Takemoto D, Park P, Scotta B (2006) Reactive oxygen species play a role in regulating a fungus–perennial ryegrass mutualistic interaction. Plant Cell 18(4):1052–1066. https://doi.org/10.1105/tpc.105.039263
Tanaka A, Takemoto D, Hyon GS, Park P, Scott B (2008) NoxA activation by the small GTPase RacA is required to maintain a mutualistic symbiotic association between Epichloë festucae and perennial ryegrass. Mol Microbiol 68:1165–1178. https://doi.org/10.1111/j.1365-2958.2008.06217.x
Teplitski M, Mathesius U, Rumbaugh KP (2011) Perception and degradation of N-acyl homoserine lactone quorum sensing signals by mammalian and plant cells. Chem Rev 111(1):100–116. https://doi.org/10.1021/cr100045m
Thatcher LF, Manners JM, Kazan K (2009) Fusarium oxysporum hijacks COI1-mediated jasmonate signaling to promote disease development in Arabidopsis. Plant J 58(6):927–939. https://doi.org/10.1111/j.1365-313X.2009.03831.x
Thi Minh Le T, Thi Hong Hoang A, Thi Bich Le T et al (2019) Isolation of endophytic fungi and screening of Huperzine A–producing fungus from Huperzia serrata in Vietnam. Sci Rep 9:16152. https://doi.org/10.1038/s41598-019-52481-2
Tian Y, Amand S, Buisson D, Kunz C, Hachette F, Dupont J, Nay B, Prado S (2014) The fungal leaf endophyte Paraconiothyrium variabile specifically metabolizes the host plant metabolome for its own benefit. Phytochemistry 108:95–101. https://doi.org/10.1016/j.phytochem.2014.09.021
Torres MA (2010) ROS in biotic interactions. Physiol Plantarum 138(4):414–429. https://doi.org/10.1111/j.1399-3054.2009.01326.x
Toti I, Chapela IH, Petrini (1992) Morphometric evidence for host-specific strain formation in Discula umbrinella. Mycol Res 96(6):420–424. https://doi.org/10.1016/S0953-7562(09)81085-X
Tourneroche A, Lami R, Hubas C, Blanchet E, Vallet M, Escoubeyrou K, Paris A, Prado S (2019) Bacterial-fungal interactions in the kelp endomicrobiota Drive Autoinducer-2 Quorum Sensing. Front Microbiol 10:1693. https://doi.org/10.3389/fmicb.2019.01693
Tsuda K, Katagiri F (2010) Comparing signaling mechanisms engaged in pattern triggered and effector-triggered immunity. Curr Opin Plant Biol 13(4):459–465. https://doi.org/10.1016/j.pbi.2010.04.006
Unterseher M, Schnittler M (2010) Species richness analysis and ITS rDNA phylogeny revealed the majority of cultivable foliar endophytes from beech (Fagus sylvatica). Fungal Ecol 3(4):366–738. https://doi.org/10.1016/j.funeco.2010.03.001
Van den Burg HA, Harrison SJ, Joosten MHAJ, Vervoort J, De Wit PJGM (2006) Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection. Mol Plant Microbe Interat 19(12):1420–1430. https://doi.org/10.1094/MPMI-19-1420
Vasanthakumari MM, Jadhav SS, Sachin N, Vinod G, Shweta S, Manjunatha BL, Kumara PM, Ravikanth G, Nataraja KN, Uma Shaanker R (2015) Restoration of camptothecin production in attenuated endophytic fungus on re-inoculation into host plant and treatment with DNA methyltransferase inhibitor. World J Microbiol Biotechnol 31(10):1629–1639. https://doi.org/10.1007/s11274-015-1916-0
Verma VC, Gond SK, Mishra A, Kumar A, Kharwar RN, Gange AC (2009) Endophytic actinomycetes from Azadirachta indica A. Juss.: isolation, diversity and anti-microbial activity. Microb Ecol 57(4):749–756. https://doi.org/10.1007/s00248-008-9450-3
Verma VC, Lobkovsky E, Gange AC, Singh SK, Prakash S (2011) Piperine production by endophytic fungus Periconia sp. isolated from Piper longum L. J Antibiot 64(6):427–431. https://doi.org/10.1038/ja.2011.27
Viret O, Toti L, Chapela 1H, Petrini O (1994) The role of the extracellular sheath in recognition and attachment of conidia of Discula umbrinella (Bok & Br.) Moroleet to the host surface. New Phytol 127(1):123–131.https://doi.org/10.1111/j.1469-8173.1994.tb04266.x
Von Rad U, Klein I, Dobrev PI, Kottova J, Zazimalova E, Fekete A, Hartmann A, Schmitt-Kopplin P, Durner J (2008) Response of Arabidopsis thaliana to Nhexanoyl- DL-homoserine-lactone, a bacterial quorum sensing molecule produced in the rhizosphere. Planta 229(1):73–85. https://doi.org/10.1007/s00425-008-0811-4
Wang W-X (2016) Crosstalk and antibacterial molecules from endophytes harboured in Narcissus tazeta and Buxus sinica. https://doi.org/10.17877/DE290R-17001
Wang WX, Kusari S, Sezgin S, Lamshöft M, Kusari P, Kayser O, Spiteller M (2015) Hexacyclopeptides secreted by an endophytic fungus Fusarium solani N06 act as crosstalk molecules in Narcissus tazetta. Appl Microbiol Biotechnol 99(18):7651–7662. https://doi.org/10.1007/s00253-015-6653-7
Wang Q, Ge C, Xu S et al (2020) The endophytic bacterium Sphingomonas SaMR12 alleviates Cd stress in oilseed rape through regulation of the GSH-AsA cycle and antioxidative enzymes. BMC Plant Biol 20:63. https://doi.org/10.1186/s12870-020-2273-1
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
Wawra S, Fesel P, Widmer H, Timm M, Seibel J, Leson L, Zuccaro A (2016) The fungal-specific beta-glucan-binding lectin FGB1 alters cell-wall composition and suppresses glucan-triggered immunity in plants. Nat Commun 7:13188. https://doi.org/10.1038/ncomms13188
Williams P, Winzer K, Chan WC, Camara M (2007) Look who’s talking: communication and quorum sensing in the bacterial world. Philos Trans R Soc Lond B Biol Sci 362(1483):1119–1134. https://doi.org/10.1098/rstb.2007.2039
Williams HE, Steele JC, Clements MO, Keshavarz T (2012) γ-Heptalactone is an endogenously produced quorum-sensing molecule regulating growth and secondary metabolite production by Aspergillus nidulans. Appl Microbiol Biotechnol 96(3):773–781. https://doi.org/10.1007/s00253-012-4065-5
Xin DW, Liao S, Xie ZP, Hann DR, Steinle L, Boller T, Staehelin C (2012) Functional analysis of NopM, a novel E3 ubiquitin ligase (NEL) domain effector of Rhizobium sp. strain NGR234. PLoS Pathog 8(5):e1002707. https://doi.org/10.1371/journal.ppat.1002707
Xu F, Kapos P, Cheng YT, Li M, Zhang Y, Li X (2014) NLR-associating transcription factor bHLH84 and its paralogs function redundantly in plant immunity. PLoS Pathogens 10(8):e1004312. https://doi.org/10.1371/journal.ppat.1004312
Yang Y, Zhao H, Barrero RA, Zhang B, Sun G, Wilson IW, Xie F, Walker KD, Parks JW, Bruce R, Guo G, Chen L, Zhang Y, Huang X, Tang Q, Liu H, Bellgard MI, Qiu D, Lai J, Hoffman A (2014) Genome sequencing and analysis of the paclitaxel-producing endophytic fungus Penicillium aurantiogriseum NRRL 62431. BMC Genomics 15(1):69. https://doi.org/10.1186/1471-2164-15-69
Yazaki K (2005) Transporters of secondary metabolites. Curr Opin Plant Biol 8(3):301–307. https://doi.org/10.1016/j.pbi.2005.03.011
Yin H, Sun YH (2011) Vincamine-producing endophytic fungus isolated from Vinca minor. Phytomedicine 18(8–9):802–805. https://doi.org/10.1016/j.phymed.2011.01.005
You F, Han T, Wu JZ, Huang BK, Qin LP (2009) Antifungal secondary metabolites from endophytic Verticillium sp. Biochem Syst Ecol 37(3):162–165. https://doi.org/10.1016/j.bse.2009.03.008
Young DH, Michelotti EL, Swindell CS, Krauss NE (1992) Antifungal properties of taxol and various analogues research articles. Experientia 48(9):882–885. https://doi.org/10.1007/BF02118425
Yu K, Tichelaar R, Liu Y, Savant N, Lagendijk E, Van Kuijk SJL, Berendsen RL (2019) Plant-beneficial Pseudomonas spp. suppress local root immune responses by gluconic acid-mediated lowering of environmental pH. Curr Biol D-19-00852. https://doi.org/10.2139/ssrn.3396501
Yuan ZL, Chen YC, Tang Y (2009) Diverse non-mycorrhizal fungal endophytes inhabiting an epiphyte, medicinal orchid (Dendrobium nobile): estimation and characterization. World J of Microbiol Biotechnol 25(2):295. https://doi.org/10.1007/s11274-008-9893-1
Zachow C, Fatehi J, Cardinale M, Tilcher R, Berg G (2010) Strain-specific colonization pattern of Rhizoctonia antagonists in the root system of sugar beet. FEMS Microbiol Eco 74(1):124–135. https://doi.org/10.1111/j.1574-6941.2010.00930.x
Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant Microbe Interact 25(2):139–150. https://doi.org/10.1094/MPMI-06-11-0179
Zeidler D, Zahringer U, Gerber I, Dubery I, Hartung T, Bors W, Hutzler P, Durner J (2004) Innate immunity in Arabidopsis thaliana: lipopolysaccharides activate nitric oxide synthase (NOS) and induce defense genes. Proc Natl Acad Sci USA 101(44):15811–15816. https://doi.org/10.1073/pnas.0404536101
Zhang L, Guo B, Li H, Zeng S, Shao H, Gu S, Wei R (2000) Preliminary study on the isolation of endophytic fungus of Catharanthus roseus and its fermentation to produce products of therapeutic value. Chin Tradit Herbal Drug 31(11):805–807
Zhang K, Halitschke R, Yin C, Liu C-J, Gan S-S (2013) Salicylic acid 3 hydroxylase regulates Arabidopsis leaf longevity by mediating salicylic acid catabolism. Proc Natl Acad Sci USA 110(36):14807–14812. https://doi.org/10.1073/pnas.1302702110
Zhang L, Feng G, Declerck S (2018) Signal beyond nutrient, fructose, exuded by an arbuscular mycorrhizal fungus triggers phytate mineralization by a phosphate solubilizing bacterium. ISME J 12:2339–2351. https://doi.org/10.1038/s41396-018-0171-4
Zhao J, Zhou L, Wang J, Shan T, Zhong L, Liu X, Gao X (2010) Endophytic fungi for producing bioactive compounds originally from their host plants. In: Mendez-Vilas A (ed) Current research, technology and education in tropics in applied microbiology and microbial biotechnology, 1st edn. Formatex Research Center, Badajoz, pp 567–576
Zhou J, Yang T, Mei YZ, Kang L, Dai CC (2014) Laccase production by Phomopsis liquidambari B3 cultured with food waste and wheat straw as the main nitrogen and carbon sources. J Air Waste Manage 64(10):1154–1163. https://doi.org/10.1080/10962247.2014.930077
Zhou J, Li X, Chen Y, Dai CC (2017) De novo transcriptome assembly of Phomopsis liquidambari provides Insights into genes associated with different lifestyles in rice (Oryza sativa L.). Front Plant Sci 8:121. https://doi.org/10.3389/fpls.2017.00121
Zikmundova M, Drandarov K, Bigler L, Hesse M, Werner C (2002) Biotransformation of 2-benzoxazolinone and 2-hydroxy-1, 4-benzoxazin-3-one by endophytic fungi isolated from Aphelandra tetragona. Appl Env Microbiol 68(10):4863–4870. https://doi.org/10.1128/AEM.68.10.4863-4870.2002
Zipfel C, Oldroyd GE (2017) Plant signalling in symbiosis and immunity. Nature 543(7645):328–336. https://doi.org/10.1038/nature22009
Acknowledgments
The authors are highly thankful to the Head, Department of Botany, University of Jammu (India) for providing laboratory facilities and Council of Scientific and Industrial Research (CSIR) for granting fellowship to the first author.
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This work was supported by Council of Scientific and Industrial Research (CSIR), Grant No. 09/100(0241)/2019-EMR-I.
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Both the authors contributed to the study conception and design, and performed the literature search. Aroosa Jan Mattoo drafted the paper and Dr. Skarma Nonzom critically revised the work.
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Mattoo, A.J., Nonzom, S. Endophytic fungi: understanding complex cross-talks. Symbiosis 83, 237–264 (2021). https://doi.org/10.1007/s13199-020-00744-2
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DOI: https://doi.org/10.1007/s13199-020-00744-2