Abstract
Endophytes live in the internal tissues of plants without causing any visible damage to their hosts. They provide many beneficial effects to their hosts which range from promoting the plant growth to providing protection against various biotic and abiotic stresses to the host. They have also been considered to play direct or indirect roles in the synthesis of various biomolecules obtained from their host. However, most of the endophytes isolated and characterized so far have been culture dependent, and their number has been very low. Culture-independent studies of endophytes include high-throughput assays like transcriptomics, proteomics, etc. These high-throughput assays have predicted much higher numbers of endophytes as compared to the culture-dependent studies. The high-throughput assays have helped in deciphering the phylogenetic analysis of the whole microbiome of the plant and indicated very strong and deeper role of the endophytes in the host than anticipated before. However, in the absence of any gold standard approach for isolation and proper characterization of these endophytes, the high-throughput omics-based assays remain isolated to the particular hosts only. Their true potential in agriculture or crop protection will not be utilized. Therefore, the complex interaction of endophytes with their hosts needs to be studied by combining the omics-based assays with the culture-dependent methods, which can actually provide the true study material and their appropriate analysis.
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References
Shaw D (1989) Book review (A Dictionary of Plant Pathology. by Paul Holliday. Cambridge University Press, Cambridge (UK), New York, New Rochelle, Melbourne, Sydney, 1989. 369pp). Australas Plant Pathol 18:106
Schulz B, Boyle C (2006) Microbial root endophytes. In: Microbial root endophytes. Springer, Berlin/Heidelberg, pp 1–14
Bernardi-Wenzel J, GarcÃa A, Filho CJR, Prioli AJ, Pamphile JA (2010) Evaluation of foliar fungal endophyte diversity and colonization of medicinal plant Luehea divaricata (Martius et Zuccarini). Biol Res 43:375–384
GarcÃa A, Rhoden SA, Filho CJR, Nakamura CV, Pamphile JA (2012) Diversity of foliar endophytic fungi from the medicinal plant Sapindus saponaria L. and their localization by scanning electron microscopy. Biol Res 45:139–148
Orlandelli RC, Alberto RN, Rubin Filho CJ, Pamphile JA (2012) Diversity of endophytic fungal community associated with Piper hispidum (Piperaceae) leaves. Genet Mol Res 11:1575–1585
Rhoden SA, Garcia A, Rubin Filho CJ, Azevedo JL, Pamphile JA (2012) Phylogenetic diversity of endophytic leaf fungus isolates from the medicinal tree Trichilia elegans (Meliaceae). Genet Mol Res 11:2513–2522
Leme AC, Bevilaqua MRR, Rhoden SA, Mangolin CA, Machado MFPS, Pamphile JA (2013) Molecular characterization of endophytes isolated from Saccharum spp based on esterase and ribosomal DNA (ITS1-5.8S-ITS2) analyses. Genet Mol Res 12:4095–4105
Saikkonen K (2004) Evolution of endophyte? Plant symbioses. Trends Plant Sci 9:275–280
Partida-MartÃnez LP, Heil M (2011) The microbe-free plant: fact or artifact? Front. Plant Sci 2:100
Timmusk S, Paalme V, Pavlicek T, Bergquist J, Vangala A, Danilas T et al (2011) Bacterial distribution in the rhizosphere of wild barley under contrasting microclimates. PLoS One 6:e17968
Ali S, Charles TC, Glick BR (2012) Delay of flower senescence by bacterial endophytes expressing 1-aminocyclopropane-1-carboxylate deaminase. J Appl Microbiol 113:1139–1144
Coutinho BG, Licastro D, Mendonça-Previato L, Cámara M, Venturi V (2015) Plant-influenced gene expression in the rice endophyte Burkholderia kururiensis M130. Mol Plant-Microbe Interact 28:10–21
Strobel G, Daisy B, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67:257–268
Smith SA, Tank DC, Boulanger LA, Bascom-Slack CA, Eisenman K, Kingery D et al (2008) Bioactive endophytes warrant intensified exploration and conservation. PLoS One 3:e3052
Azevedo JL, Maccheroni WJR, Araújo W, Pereira J (2002) Microrganismos endofÃticos e seu papel em plantas tropicais. In: Biotecnol avanços na Agric e na agroindústria. EDUCS, Caxias do Sul, pp 235–268
Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471
Marasco R, Rolli E, Ettoumi B, Vigani G, Mapelli F, Borin S et al (2012) A drought resistance-promoting microbiome is selected by root system under desert farming. PLoS One 7:e48479
Rashid S, Charles TC, Glick BR (2012) Isolation and characterization of new plant growth-promoting bacterial endophytes. Appl Soil Ecol 61:217–224
Santoyo G, Moreno-Hagelsieb G, del Carmen Orozco-Mosqueda M, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183:92–99
Compant S, Clément C, Sessitsch A (2010) Plant growth-promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol Biochem 42:669–678
Gourion B, Berrabah F, Ratet P, Stacey G (2015) Rhizobium-legume symbioses: the crucial role of plant immunity. Trends Plant Sci 20:186–194
Sessitsch A, Hardoim P, Döring J, Weilharter A, Krause A, Woyke T et al (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36
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 19:181–188
Beltran-Garcia MJ, White JF, Prado FM, Prieto KR, Yamaguchi LF, Torres MS et al (2014) Nitrogen acquisition in Agave tequilana from degradation of endophytic bacteria. Sci Rep 4(6938):1–7
RodrÃguez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17:319–339
Kuklinsky-Sobral J, Araújo WL, Mendes R, Geraldi IO, Pizzirani-Kleiner AA, Azevedo JL (2004) Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environ Microbiol 6:1244–1251
Sessitsch A, Reiter B, Berg G (2004) Endophytic bacterial communities of field-grown potato plants and their plant-growth-promoting and antagonistic abilities. Can J Microbiol 50:239–249
Pieterse CMJ, Leon-Reyes A, Van Der Ent S, Van Wees SCM (2009) Networking by small-molecule hormones in plant immunity. Nat Chem Biol 5:308–316
Zúñiga A, Poupin MJ, Donoso R, Ledger T, Guiliani N, R a G et al (2013) Quorum sensing and indole-3-acetic acid degradation play a role in colonization and plant growth promotion of Arabidopsis thaliana by Burkholderia phytofirmans PsJN. Mol Plant-Microbe Interact 26:546–553
Bhore SJ, Ravichantar N, Loh CY (2010) Screening of endophytic bacteria isolated from leaves of Sambung Nyawa [Gynura procumbens (Lour.) Merr.] for cytokinin-like compounds. Bioinformation 5:191–197
Shahzad R, Waqas M, Khan AL, Asaf S, Khan MA, Kang SM et al (2016) Seed-borne endophytic Bacillus amyloliquefaciens RWL-1 produces gibberellins and regulates endogenous phytohormones of Oryza sativa. Plant Physiol Biochem 106:236–243
Tian BY, Cao Y, Zhang KQ (2015) Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots. Sci Rep 5(17087):1–15
Toumatia O, Compant S, Yekkour A, Goudjal Y, Sabaou N, Mathieu F et al (2016) Biocontrol and plant growth promoting properties of Streptomyces mutabilis strain IA1 isolated from a Saharan soil on wheat seedlings and visualization of its niches of colonization. South African J Bot 105:234–239
Miraglia M, Marvin HJP, Kleter GA, Battilani P, Brera C, Coni E et al (2009) Climate change and food safety: an emerging issue with special focus on Europe. Food Chem Toxicol 47:1009–1021
Tudela D, Primo-Millo E (1992) 1-Aminocyclopropane-1-carboxylic acid transported from roots to shoots promotes leaf abscission in Cleopatra mandarin (Citrus reshni Hort. ex Tan.) seedlings rehydrated after water stress. Plant Physiol 100:131–137
Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169:30–39
Karthikeyan B, Joe MM, Islam MR, Sa T (2012) ACC deaminase containing diazotrophic endophytic bacteria ameliorate salt stress in Catharanthus roseus through reduced ethylene levels and induction of antioxidative defense systems. Symbiosis 56:77–86
Ali S, Charles TC, Glick BR (2014) Amelioration of high salinity stress damage by plant growth-promoting bacterial endophytes that contain ACC deaminase. Plant Physiol Biochem 80:160–167
Zhang Y-F, He L-Y, Chen Z-J, Wang Q-Y, Qian M, Sheng X-F (2011) Characterization of ACC deaminase-producing endophytic bacteria isolated from copper-tolerant plants and their potential in promoting the growth and copper accumulation of Brassica napus. Chemosphere 83:57–62
Subramanian P, Mageswari A, Kim K, Lee Y, Sa T (2015) Psychrotolerant endophytic Pseudomonas sp. strains OB155 and OS261 induced chilling resistance in tomato plants (Solanum lycopersicum mill.) by activation of their antioxidant capacity. Mol Plant-Microbe Interact 28:1073–1081
Su F, Jacquard C, Villaume S, Michel J, Rabenoelina F, Clément C et al (2015) Burkholderia phytofirmans PsJN reduces impact of freezing temperatures on photosynthesis in Arabidopsis thaliana. Front Plant Sci 6:810
Sheibani-Tezerji R, Rattei T, Sessitsch A, Trognitz F, Mitter B (2015) Transcriptome profiling of the endophyte burkholderia phytofirmans psjn indicates sensing of the plant environment and drought stress. MBio 6:1–11
Rungin S, Indananda C, Suttiviriya P, Kruasuwan W, Jaemsaeng R, Thamchaipenet A (2012) Plant growth enhancing effects by a siderophore-producing endophytic streptomycete isolated from a Thai jasmine rice plant (Oryza sativa L. cv. KDML105). Antonie van Leeuwenhoek. Int J Gen Mol Microbiol 102:463–472
Ahmed E, Holmström SJM (2014) Siderophores in environmental research: roles and applications. Microb Biotechnol 7:196–208
Verma VC, Singh SK, Prakash S (2011) Bio-control and plant growth promotion potential of siderophore producing endophytic Streptomyces from Azadirachta indica A. Juss. J Basic Microbiol 51:550–556
Aznar A, Chen NWG, Thomine S, Dellagi A (2015) Immunity to plant pathogens and iron homeostasis. Plant Sci 240:90–97
Le Cocq K, Gurr SJ, Hirsch PR, Mauchline TH (2017) Exploitation of endophytes for sustainable agricultural intensification. Mol Plant Pathol 18:469–473
Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37
Han Q, Wu F, Wang X, Qi H, Shi L, Ren A et al (2015) The bacterial lipopeptide iturins induce Verticillium dahliae cell death by affecting fungal signalling pathways and mediate plant defence responses involved in pathogen-associated molecular pattern-triggered immunity. Environ Microbiol 17:1166–1188
hui CJ, Song GC, Ryu CM (2016) Sweet scents from good bacteria: case studies on bacterial volatile compounds for plant growth and immunity. Plant Mol Biol 90:677–687
D’Alessandro M, Erb M, Ton J, Brandenburg A, Karlen D, Zopfi J et al (2014) Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions. Plant Cell Environ 37:813–826
Marquez-Santacruz HA, Hernandez-Leon R, Orozco-Mosqueda MC, Velazquez-Sepulveda I, Santoyo G (2010) Diversity of bacterial endophytes in roots of Mexican husk tomato plants (Physalis ixocarpa) and their detection in the rhizosphere. Genet Mol Res 9:2372–2380
Germida JJ, Siciliano SD, De Freitas JR, Seib AM (1998) Diversity of root-associated bacteria associated with field-grown canola (Brassica napus L.) and wheat (Triticum aestivum L.). FEMS Microbiol Ecol 26:43–50
Romero FM, Marina M, Pieckenstain FL (2014) The communities of tomato (Solanum lycopersicum L.) leaf endophytic bacteria, analyzed by 16S-ribosomal RNA gene pyrosequencing. FEMS Microbiol Lett 351:187–194
Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW (1997) Bacterial endophytes in agricultural crops. Can J Microbiol 43:895–914
Sturz AV, Nowak J (2000) Endophytic communities of rhizobacteria and the strategies required to create yield enhancing associations with crops. Appl Soil Ecol 15:183–190
Rosenblueth M, MartÃnez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant-Microbe Interact 19:827–837
Shi Y, Yang H, Zhang T, Sun J, Lou K (2014) Illumina-based analysis of endophytic bacterial diversity and space-time dynamics in sugar beet on the north slope of Tianshan mountain. Appl Microbiol Biotechnol 98:6375–6385
Truyens S, Weyens N, Cuypers A, Vangronsveld J (2015) Bacterial seed endophytes: genera, vertical transmission and interaction with plants. Environ Microbiol Rep 7:40–50
Sørensen J, Sessitsch A 2015 Plant-associated bacteria lifestyle and molecular interactions; Jan Dirk van Elsas, Jack T. Trevors, Janet K. Jansson Modern soil microbiology, Boca Raton : CRC Press 2nd 211–236
Roos IMM, Hattingh MJ (1983) Scanning electron microscopy of Pseudomonas syringae pv, morsprunorum on sweet cherry leaves. J Phytopathol 108:18–25
Gagné S, Rıchard C, Rousseau H, Antoun H (1987) Xylem-residing bacteria in alfalfa roots. Can J Microbiol 33:996–1000
Scott RI, Chard JM, Hocart MJ, Lennard JH, Graham DC (1996) Penetration of potato tuber lenticels by bacteria in relation to biological control of blackleg disease. Potato Res 39:333–344
Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, Colauto NB et al (2011) Genome of herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 7(5):1–10
Wisniewski-Dyé F, Borziak K, Khalsa-Moyers G, Alexandre G, Sukharnikov LO, Wuichet K et al (2011) Azospirillum genomes reveal transition of bacteria from aquatic to terrestrial environments. PLoS Genet 7:e1002430
Li L, Sinkko H, Montonen L, Wei G, Lindström K, Räsänen LA (2012) Biogeography of symbiotic and other endophytic bacteria isolated from medicinal Glycyrrhiza species in China. FEMS Microbiol Ecol 79:46–68
Li C-H, Zhao M-W, Tang C-M, Li S-P (2010) Population dynamics and identification of endophytic bacteria antagonistic toward plant-pathogenic fungi in cotton root. Microb Ecol 59:344–356
Chen T, Chen Z, Ma GH, Du BH, Shen B, Ding YQ et al (2014) Diversity and potential application of endophytic bacteria in ginger. Genet Mol Res 13:4918–4931
Jasim B, Joseph AA, John CJ, Mathew J, Radhakrishnan EK (2014) Isolation and characterization of plant growth promoting endophytic bacteria from the rhizome of Zingiber officinale. 3 Biotech 4:197–204
Rohini S, Aswani R, Kannan M, Sylas VP, Radhakrishnan EK (2018) Culturable endophytic bacteria of ginger rhizome and their remarkable multi-trait plant growth-promoting features. Curr Microbiol 75:505–511
Arunachalam CGP (2010) Studies on bioprospecting of endophytic bacteria from the medicinal plant of Andrographis Paniculata for their antimicrobial activity and antibiotic susceptibility pattern. Int J Curr Pharm Res 2:68–68
Singh AK, Sharma RK, Sharma V, Singh T, Kumar R, Kumari D (2017) Isolation, morphological identification and in vitro antibacterial activity of endophytic bacteria isolated from Azadirachta indica (neem) leaves. Vet World 10:510–516
Kumar A, Arokiaswamy RA, Rajesh Kannan V (2015) Exploration of endophytic microorganisms from selected medicinal plants and their control potential to multi drug resistant pathogens. J Med Plants Stud 49:49–57
Sinha A, Priya R, Nimisha M, Jabez Osborne W (2015) Impact of endophytic Ralstonia sp. from Aloe vera gel and its antimicrobial activity. Asian J Pharm Clin Res 8:259–262
Akinsanya MA, Goh JK, Lim SP, ASY T (2015) Diversity, antimicrobial and antioxidant activities of culturable bacterial endophyte communities in Aloe vera. FEMS Microbiol Lett 362(23):1–8
Bredow C, Azevedo JL, Pamphile JA, Mangolin CA, Rhoden SA (2015) In silico analysis of the 16S rRNA gene of endophytic bacteria, isolated from the aerial parts and seeds of important agricultural crops. Genet Mol Res 14:9703–9721
Shidore T, Dinse T, Öhrlein J, Becker A, Reinhold-Hurek B (2012) Transcriptomic analysis of responses to exudates reveal genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72. Environ Microbiol 14:2775–2787
Dos-Santos CM, de Souza DG, Balsanelli E, Cruz LM, de Souza EM, Baldani JI et al (2017) A culture-independent approach to enrich endophytic bacterial cells from sugarcane stems for community characterization. Microb Ecol 74:453–465
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Chaubey, B. (2018). Isolation of Endophytes: The Gold Standard?. In: Jha, S. (eds) Endophytes and Secondary Metabolites. Reference Series in Phytochemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-76900-4_25-1
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