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Seed Endophytes in Crop Plants: Metagenomic Approaches to Study the Functional Roles and Interactions

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Seed Endophytes

Abstract

Seed endophytes play a key role in increasing plant health and growth in both managed and natural ecosystems. These can be applied in agricultural production or for the phytoremediation of pollutants. However, because of their capacity to confer plant beneficial effects, efficient colonization of the plant environment is of utmost importance. The majority of endophytes derives from the soil environment. They may migrate to the rhizosphere and subsequently the rhizoplane of their hosts before they are able to show beneficial effects. These endophytes can also penetrate plant roots, and may move to aerial plant parts. A better understanding on colonization processes has been obtained mostly by microscopic visualization as well as by analyzing the characteristics of mutants carrying disfunctional genes potentially involved in colonization. In this chapter we describe the different metagenomic approaches of seed colonization and survey the known mechanisms responsible for endophytic competence. The understanding of seed colonization processes is important to better predict how endophytes interact with seeds.

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References

  • Akinsanya MA, Goh JK, Lim SP, Ting ASY (2015) Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology. Genomics Data 6:159–163

    Article  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arachevaleta M, Bacon C, Hoveland C, Radcliffe D (1989) Effect of the tall fescue endophyte on plant response to environmental stress. Agron J 81:83–90

    Article  Google Scholar 

  • Araújo WL, Marcon J, Maccheroni W, van Elsas JD, van Vuurde JW, Azevedo JL (2002) Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 68:4906–4914

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bacon C, Hinton D (1997) Isolation and culture of endophytic bacteria and fungi. ASM Press, Washington, DC

    Google Scholar 

  • Barac T et al (2004) Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants. Nat Biotechnol 22:583

    Article  CAS  PubMed  Google Scholar 

  • Barnett MJ, Toman CJ, Fisher RF, Long SR (2004) A dual-genome symbiosis chip for coordinate study of signal exchange and development in a prokaryote–host interaction. Proc Natl Acad Sci 101:16636–16641

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bartholdy B, Berreck M, Haselwandter K (2001) Hydroxamate siderophore synthesis by Phialocephala fortinii, a typical dark septate fungal root endophyte. Biometals 14:33–42

    Article  CAS  PubMed  Google Scholar 

  • Bashan Y, Harrison SK, Whitmoyer RE (1990) Enhanced growth of wheat and soybean plants inoculated with Azospirillum brasilense is not necessarily due to general enhancement of mineral uptake. Appl Environ Microbiol 56:769–775

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bezerra J, Santos M, Svedese V, Lima D, Fernandes M, Paiva L, Souza-Motta C (2012) Richness of endophytic fungi isolated from Opuntia ficus-indica mill. (Cactaceae) and preliminary screening for enzyme production. World J Microbiol Biotechnol 28:1989–1995

    Article  CAS  PubMed  Google Scholar 

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

  • Bischoff KM, Wicklow DT, Jordan DB, de Rezende ST, Liu S, Hughes SR, Rich JO (2009) Extracellular hemicellulolytic enzymes from the maize endophyte Acremonium zeae. Curr Microbiol 58:499–503

    Article  CAS  PubMed  Google Scholar 

  • Brinkerhoff L, Hunter R (1963) Internally infected seed as a source of inoculum for the primary cycle of bacterial blight of cotton. Phytopathology 53:1397–1401

    Google Scholar 

  • Brundrett MC (2006) Understanding the roles of multifunctional mycorrhizal and endophytic fungi. In: Microbial root endophytes. Springer, Heidelberg, pp 281–298

    Chapter  Google Scholar 

  • Camilios-Neto D et al (2014) Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes. BMC Genomics 15:378

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cankar K, Kraigher H, Ravnikar M, Rupnik M (2005) Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiol Lett 244:341–345

    Article  CAS  PubMed  Google Scholar 

  • Carroll G (1988) Fungal endophytes in stems and leaves: from latent pathogen to mutualistic symbiont. Ecology 69:2–9

    Article  Google Scholar 

  • Carroll GC (1991) Fungal associates of woody plants as insect antagonists in leaves and stems. In: Barbosa P, Krischik VA, Jones CG (eds) Microbial mediation of plant-herbivore interactions. John Wiley and Son, New York, pp 253–271

    Google Scholar 

  • Casas C, Omacini M, Montecchia MS, Correa OS (2011) Soil microbial community responses to the fungal endophyte Neotyphodium in Italian ryegrass. Plant Soil 340:347–355

    Article  CAS  Google Scholar 

  • Chareprasert S, Piapukiew J, Thienhirun S, Whalley AJ, Sihanonth P (2006) Endophytic fungi of teak leaves Tectona grandis L. and rain tree leaves Samanea saman Merr. World J Microbiol Biotechnol 22:481–486

    Article  Google Scholar 

  • Chen C, Bauske E, Musson G, Rodriguez-Kabana R, Kloepper J (1995) Biological control of Fusarium wilt on cotton by use of endophytic bacteria. Biol Control 5:83–91

    Article  Google Scholar 

  • Chen Y, Mei R, Lu S, Liu L, Kloepper J (1996) The use of yield increasing bacteria (YIB) as plant growth-promoting rhizobacteria in Chinese agriculture. In: Utkhede RS, Gupta VK (eds) Management of soil born diseases. Kalyani Publishers, Ludhiana, pp 165–184

    Google Scholar 

  • Clay K, Holah J (1999) Fungal endophyte symbiosis and plant diversity in successional fields. Science 285:1742–1744

    Article  CAS  PubMed  Google Scholar 

  • Das A (2009) Symbiosis: the art of living. In: Varma A, Kharkwal AC (eds) Symbiotic fungi principles and practice. Springer, Berlin

    Google Scholar 

  • De Bary A (1879) Die erscheinung der symbiose. Verlag von Karl J Trübner, Strasbourg

    Google Scholar 

  • Delmotte N et al (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc Natl Acad Sci 106:16428–16433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Devaraju R, Satish S (2011) Endophytic mycoflora of Mirabilis jalapa L. and studies on antimicrobial activity of its endophytic Fusarium sp. Soc Appl Sci 2:75–79

    Google Scholar 

  • Dinkins RD, Barnes A, Waters W (2010) Microarray analysis of endophyte-infected and endophyte-free tall fescue. J Plant Physiol 167:1197–1203

    Article  CAS  PubMed  Google Scholar 

  • Dinsdale EA et al (2008) Functional metagenomic profiling of nine biomes. Nature 452:629

    Article  CAS  PubMed  Google Scholar 

  • Döbereiner J (1992) Recent changes in concepts of plant bacteria interactions: endophytic N2 fixing bacteria. Ciência Cult 44:310–313

    Google Scholar 

  • Dong Y, Glasner JD, Blattner FR, Triplett EW (2001) Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames. Appl Environ Microbiol 67:1911–1921

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Downie JA (2010) The roles of extracellular proteins, polysaccharides and signals in the interactions of rhizobia with legume roots. FEMS Microbiol Rev 34:150–170

    Article  CAS  PubMed  Google Scholar 

  • Dudeja S, Giri R, Saini R, Suneja-Madan P, Kothe E (2012) Interaction of endophytic microbes with legumes. J Basic Microbiol 52:248–260

    Article  CAS  PubMed  Google Scholar 

  • Elango F, Lozano J (1980) Transmission of Xanthomonas manihotis in seed of cassava (Manihot esculenta). Plant Dis 64:784–786

    Article  Google Scholar 

  • Espinosa-Urgel M, Salido A, Ramos J-L (2000) Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J Bacteriol 182:2363–2369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Felitti S et al (2006) Transcriptome analysis of Neotyphodium and Epichloë grass endophytes. Fungal Genet Biol 43:465–475

    Article  CAS  PubMed  Google Scholar 

  • Firrincieli A et al (2015) Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1. Front Microbiol 6:978

    Article  PubMed  PubMed Central  Google Scholar 

  • Fisher P, Petrini O, Scott HL (1992) The distribution of some fungal and bacterial endophytes in maize (Zea mays L.). New Phytol 122:299–305

    Article  PubMed  Google Scholar 

  • Fouts DE et al (2008) Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice. PLoS Genet 4:e1000141

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fox R, Manners J, Myers A (1972) Ultrastructure of tissue disintegration and host reactions in potato tubers infected by Erwinia carotovora var. atroseptica. Potato Res 15:130–145

    Article  Google Scholar 

  • Fryar S, Yuen T, Hyde K, Hodgkiss I (2001) The influence of competition between tropical fungi on wood colonization in streams. Microb Ecol 41:245–251

    Article  PubMed  Google Scholar 

  • Fukasawa Y, Osono T, Takeda H (2009) Effects of attack of saprobic fungi on twig litter decomposition by endophytic fungi. Ecol Res 24:1067

    Article  Google Scholar 

  • Gagné S, Richard C, Rousseau H, Antoun H (1987) Xylem-residing bacteria in alfalfa roots. Can J Microbiol 33:996–1000

    Article  Google Scholar 

  • Gangadevi V, Muthumary J (2008) Isolation of Colletotrichum gloeosporioides, a novel endophytic taxol-producing fungus from the leaves of a medicinal plant, Justicia gendarussa. Mycol Balc 5:1–4

    Google Scholar 

  • Gardner JM, Feldman AW, Zablotowicz RM (1982) Identity and behavior of xylem-residing bacteria in rough lemon roots of Florida citrus trees. Appl Environ Microbiol 43:1335–1342

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gehring CA, Cobb NS, Whitham TG (1997) Three-way interactions among ectomycorrhizal mutualists, scale insects, and resistant and susceptible pinyon pines. Am Nat 149:824–841

    Article  CAS  PubMed  Google Scholar 

  • Germaine K (2007) Construction of endophytic xenobiotic degrader bacteria for improving the phytoremediation of organic pollutants. PhD thesis, Institute of Technology Carlow, Carlow

    Google Scholar 

  • Glienke-Blanco C, Aguilar-Vildoso CI, Vieira MLC, Barroso PAV, Azevedo JL (2002) Genetic variability in the endophytic fungus Guignardia citricarpa isolated from citrus plants. Genet Mol Biol 25:251–255

    Article  CAS  Google Scholar 

  • Goodman R (1982) The infection process. Phytopathogenic prokaryotes 1:31–62

    Article  Google Scholar 

  • Granér G, Persson P, Meijer J, Alström S (2003) A study on microbial diversity in different cultivars of Brassica napus in relation to its wilt pathogen, Verticillium longisporum. FEMS Microbiol Lett 224:269–276

    Article  PubMed  CAS  Google Scholar 

  • Grum M, Camloh M, Rudolph K, Ravnikar M (1998) Elimination of bean seed-borne bacteria by thermotherapy and meristem culture. Plant Cell Tissue Organ Cult 52:79–82

    Article  Google Scholar 

  • Guo L et al (2015) A host plant genome (Zizania latifolia) after a century-long endophyte infection. Plant J 83:600–609

    Article  CAS  PubMed  Google Scholar 

  • Hallmann J, Kloepper J, Rodriguez-Kabana R, Sikora R (1995) Endophytic rhizobacteria as antagonists of Meloidogyne incognita on cucumber. Phytopathology 85:136

    Google Scholar 

  • Hamayun M et al (2009) Cladosporium sphaerospermum as a new plant growth-promoting endophyte from the roots of Glycine max (L.) Merr. World J Microbiol Biotechnol 25:627–632

    Article  CAS  Google Scholar 

  • He X et al (2012) Diversity and decomposition potential of endophytes in leaves of a Cinnamomum camphora plantation in China. Ecol Res 27:273–284

    Article  Google Scholar 

  • Hert DG, Fredlake CP, Barron AE (2008) Advantages and limitations of next-generation sequencing technologies: a comparison of electrophoresis and non-electrophoresis methods. Electrophoresis 29:4618–4626

    Article  CAS  PubMed  Google Scholar 

  • Hettich RL, Pan C, Chourey K, Giannone RJ (2013) Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities. ACS Publications, Washington, DC

    Google Scholar 

  • Hollis JP (1951) Bacteria in healthy potato tissue. Phytopathology 41:350–366

    Google Scholar 

  • Huang J-S (1986) Ultrastructure of bacterial penetration in plants. Annu Rev Phytopathol 24:141–157

    Article  Google Scholar 

  • Jacobs MJ, Bugbee WM, Gabrielson DA (1985) Enumeration, location, and characterization of endophytic bacteria within sugar beet roots. Can J Bot 63:1262–1265

    Article  Google Scholar 

  • Johnson NC, Graham JH, Smith F (1997) Functioning of mycorrhizal associations along the mutualism–parasitism continuum. New Phytol 135:575–585

    Article  Google Scholar 

  • Johnson LJ, Johnson RD, Schardl CL, Panaccione DG (2003) Identification of differentially expressed genes in the mutualistic association of tall fescue with Neotyphodium coenophialum. Physiol Mol Plant Pathol 63:305–317

    Article  CAS  Google Scholar 

  • Jones WJ (2010) High-throughput sequencing and metagenomics. Estuar Coasts 33:944–952

    Article  Google Scholar 

  • Joseph B, Priya RM (2011) Bioactive compounds from Endophytes and their potential in American. J Biochem Mol Biol 1:291–309

    Google Scholar 

  • Jumpponen A, Jones KL, Mattox JD, Yaege C (2010) Massively parallel 454-sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites. Mol Ecol 19:41–53

    Article  PubMed  Google Scholar 

  • Kaul S, Gupta S, Ahmed M, Dhar MK (2012) Endophytic fungi from medicinal plants: a treasure hunt for bioactive metabolites. Phytochem Rev 11:487–505

    Article  CAS  Google Scholar 

  • Knief C et al (2012) Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J 6:1378

    Article  CAS  PubMed  Google Scholar 

  • Korkama-Rajala T, Müller MM, Pennanen T (2008) Decomposition and fungi of needle litter from slow-and fast-growing Norway spruce (Picea abies) clones. Microb Ecol 56:76

    Article  PubMed  Google Scholar 

  • Krings M, Taylor TN, Hass H, Kerp H, Dotzler N, Hermsen EJ (2007) Fungal endophytes in a 400-million-yr-old land plant: infection pathways, spatial distribution, and host responses. New Phytol 174:648–657

    Article  PubMed  Google Scholar 

  • Kuan T-L, Minsavage G, Gabrielson R (1985) Detection of Xanthomonas campestris pv. Carotae in carrot seed. Plant Dis 69:758–760

    Article  Google Scholar 

  • Kumar S, Kaushik N, Edrada-Ebel R, Ebel R, Proksch P (2011) Isolation, characterization, and bioactivity of endophytic fungi of Tylophora indica. World J Microbiol Biotechnol 27:571–577

    Article  Google Scholar 

  • Kumaresan V (2002) Endophytes assemblages in young mature and senescent leaves of Rhizophora apiculata: evidence for the role of endophytes in mangrove litter degradation. Fungal Divers 9:81–91

    Google Scholar 

  • Kusari S, Singh S, Jayabaskaran C (2014) Biotechnological potential of plant-associated endophytic fungi: hope versus hype. Trends Biotechnol 32:297–303

    Article  CAS  PubMed  Google Scholar 

  • Lalande R, Bissonnette N, Coutlée D, Antoun H (1989) Identification of rhizobacteria from maize and determination of their plant-growth promoting potential. Plant Soil 115:7–11

    Article  Google Scholar 

  • Lee S, Flores-Encarnacion M, Contreras-Zentella M, Garcia-Flores L, Escamilla J, Kennedy C (2004) Indole-3-acetic acid biosynthesis is deficient in Gluconacetobacter diazotrophicus strains with mutations in cytochrome c biogenesis genes. J Bacteriol 186:5384–5391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lery LM, Hemerly AS, Nogueira EM, von Krüger WM, Bisch PM (2011) Quantitative proteomic analysis of the interaction between the endophytic plant-growth-promoting bacterium Gluconacetobacter diazotrophicus and sugarcane. Mol Plant-Microbe Interact 24:562–576

    Article  CAS  PubMed  Google Scholar 

  • Lewis D (1985) Symbiosis and mutualism: crisp concepts and soggy semantics. In: Boucher DH (ed) The biology of mutualism. Oxford University Press, Oxford

    Google Scholar 

  • Liu K, Ding X, Deng B, Chen W (2009) Isolation and characterization of endophytic taxol-producing fungi from Taxus chinensis. J Ind Microbiol Biotechnol 36:1171

    Article  CAS  PubMed  Google Scholar 

  • López-López A, Rogel MA, Ormeno-Orrillo E, Martínez-Romero J, Martínez-Romero E (2010) Phaseolus vulgaris seed-borne endophytic community with novel bacterial species such as Rhizobium endophyticum sp. nov. Syst Appl Microbiol 33:322–327

    Article  PubMed  Google Scholar 

  • Lu C, Shen Y (2007) A novel ansamycin, naphthomycin K from Streptomyces sp. J Antibiot 60:649

    Article  CAS  Google Scholar 

  • Mahaffee W et al (1997) Spatial and temporal colonization of Phaseolus vulgaris by the bacterial endophytes Pseudomonas fluorescens strain 89B-27 and Enterobacter asburiae strain JM22. Appl Environ Microbiol. https://doi.org/10.1128/AEM.02846-17

  • Malinowski DP, Alloush GA, Belesky DP (2000) Leaf endophyte Neotyphodium coenophialum modifies mineral uptake in tall fescue. Plant Soil 227:115–126

    Article  CAS  Google Scholar 

  • Mano H, Tanaka F, Watanabe A, Kaga H, Okunishi S, Morisaki H (2006) Culturable surface and endophytic bacterial flora of the maturing seeds of rice plants (Oryza sativa) cultivated in a paddy field. Microbes Environ 21:86–100

    Article  Google Scholar 

  • Manter DK, Delgado JA, Holm DG, Stong RA (2010) Pyrosequencing reveals a highly diverse and cultivar-specific bacterial endophyte community in potato roots. Microb Ecol 60:157–166

    Article  PubMed  Google Scholar 

  • Maron P-A, Ranjard L, Mougel C, Lemanceau P (2007) Metaproteomics: a new approach for studying functional microbial ecology. Microb Ecol 53:486–493

    Article  CAS  PubMed  Google Scholar 

  • Martínez-García PM, Ruano-Rosa D, Schilirò E, Prieto P, Ramos C, Rodríguez-Palenzuela P, Mercado-Blanco J (2015) Complete genome sequence of Pseudomonas fluorescens strain PICF7, an indigenous root endophyte from olive (Olea europaea L.) and effective biocontrol agent against Verticillium dahliae. Stand Genomic Sci 10:10

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mastretta C et al (2009) Endophytic bacteria from seeds of Nicotiana tabacum can reduce cadmium phytotoxicity. Int J Phytoremediation 11:251–267

    Article  CAS  Google Scholar 

  • McInroy JA, Kloepper JW (1995) Survey of indigenous bacterial endophytes from cotton and sweet corn. Plant Soil 173:337–342

    Article  CAS  Google Scholar 

  • Molina LG, Cordenonsi da Fonseca G, GLd M, de Oliveira LFV, JBd C, Kulcheski FR, Margis R (2012) Metatranscriptomic analysis of small RNAs present in soybean deep sequencing libraries. Genet Mol Biol 35:292–303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mousa WK, Raizada MN (2013) The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective. Front Microbiol 4:65

    Article  PubMed  PubMed Central  Google Scholar 

  • Mukhopadhyay K, Garrison NK, Hinton DM, Bacon CW, Khush GS, Peck HD, Datta N (1996) Identification and characterization of bacterial endophytes of rice. Mycopathologia 134:151–159

    Article  CAS  PubMed  Google Scholar 

  • Müller MM, Valjakka R, Suokko A, Hantula J (2001) Diversity of endophytic fungi of single Norway spruce needles and their role as pioneer decomposers. Mol Ecol 10:1801–1810

    Article  PubMed  Google Scholar 

  • Mundt JO, Hinkle NF (1976) Bacteria within ovules and seeds. Appl Environ Microbiol 32:694–698

    CAS  PubMed  PubMed Central  Google Scholar 

  • Musson G, McInroy J, Kloepper J (1995) Development of delivery systems for introducing endophytic bacteria into cotton. Biocontrol Sci Tech 5:407–416

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Neilands J (1995) Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 270:26723–26726

    Article  CAS  PubMed  Google Scholar 

  • Nikolic B, Schwab H, Sessitsch A (2011) Metagenomic analysis of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) operon of an uncultured bacterial endophyte colonizing Solanum tuberosum L. Arch Microbiol 193:665–676

    Article  CAS  PubMed  Google Scholar 

  • Old KM, Nicolson TH (1978) The root cortex as part of a microbial continuum. In: Loutit MW, Miles JAR (eds) Microbial ecology. SpringerVerlag, Berlin, pp 291–294

    Chapter  Google Scholar 

  • Omacini M, Chaneton EJ, Ghersa CM, Müller CB (2001) Symbiotic fungal endophytes control insect host–parasite interaction webs. Nature 409:78

    Article  CAS  PubMed  Google Scholar 

  • Osono T (2003) Effects of prior decomposition of beech leaf litter by phyllosphere fungi on substrate utilization by fungal decomposers. Mycoscience 44:0041–0045

    Article  Google Scholar 

  • Osono T (2006) Role of phyllosphere fungi of forest trees in the development of decomposer fungal communities and decomposition processes of leaf litter. Can J Microbiol 52:701–716

    Article  CAS  PubMed  Google Scholar 

  • Osono T, Hirose D (2009) Effects of prior decomposition of Camellia japonica leaf litter by an endophytic fungus on the subsequent decomposition by fungal colonizers. Mycoscience 50:52–55

    Article  Google Scholar 

  • Parker MP (1995) Plant fitness variation caused by different mutualist genotypes. Ecology 76:1525–1535

    Article  Google Scholar 

  • Parker MA (1999) Mutualism in metapopulations of legumes and rhizobia. Am Nat 153:S48–S60

    Article  PubMed  Google Scholar 

  • Patriquin D, Döbereiner J (1978) Light microscopy observations of tetrazolium-reducing bacteria in the endorhizosphere of maize and other grasses in Brazil. Can J Microbiol 24:734–742

    Article  CAS  PubMed  Google Scholar 

  • Patriquin D, Döbereiner J, Jain D (1983) Sites and processes of association between diazotrophs and grasses. Can J Microbiol 29:900–915

    Article  Google Scholar 

  • Petrini O (1986) Taxonomy of endophytic fungi of aerial plant tissues. In: Fokkema NJ, Van Den Huevel J (eds) Microbiology of the phyllosphere. Cambridge University Press, Cambridge, pp 175–187

    Google Scholar 

  • Pirttilä AM, Laukkanen H, Pospiech H, Myllylä R, Hohtola A (2000) Detection of intracellular bacteria in the buds of scotch pine (Pinus sylvestris L.) by in situ hybridization. Appl Environ Microbiol 66:3073–3077

    Article  PubMed  PubMed Central  Google Scholar 

  • Pleban S, Ingel F, Chet I (1995) Control of Rhizoctonia solani and Sclerotium rolfsii in the greenhouse using endophytic Bacillus spp. Eur J Plant Pathol 101:665–672

    Article  Google Scholar 

  • Posada F, Vega FE (2006) Inoculation and colonization of coffee seedlings (Coffea arabica L.) with the fungal entomopathogen Beauveria bassiana (Ascomycota: Hypocreales). Mycoscience 47:284–289

    Article  Google Scholar 

  • Premjanu N, Jayanthy C (2012) Endophytic fungi a repository of bioactive compounds-a review. Intl J Inst Phar Life Sci 2:135–162

    Google Scholar 

  • Promputtha I, Hyde KD, McKenzie EH, Peberdy JF, Lumyong S (2010) Can leaf degrading enzymes provide evidence that endophytic fungi becoming saprobes? Fungal Divers 41:89–99

    Article  Google Scholar 

  • Pullen CB et al (2003) Occurrence and non-detectability of maytansinoids in individual plants of the genera Maytenus and Putterlickia. Phytochemistry 62:377–387

    Article  CAS  PubMed  Google Scholar 

  • Qiu X, Pei Y, Wang Y, Zhang F (1990) Isolation of pseudomonads from cotton plants and their effect on seedling diseases. Acta Phytophylacica Sinica 17:303–306

    Google Scholar 

  • Qiu M, Xie R, Shi Y, Chen H, Wen Y, Gao Y, Hu X (2010) Isolation and identification of endophytic fungus SX01, a red pigment producer from Ginkgo biloba L. World J Microbiol Biotechnol 26:993–998

    Article  CAS  Google Scholar 

  • Quadt-Hallmann A, Kloepper J (1996) Immunological detection and localization of the cotton endophyte Enterobacter asburiae JM22 in different plant species. Can J Microbiol 42:1144–1154

    Article  CAS  Google Scholar 

  • Quadt-Hallmann A, Hallmann J, Kloepper J (1997) Bacterial endophytes in cotton: location and interaction with other plant-associated bacteria. Can J Microbiol 43:254–259

    Article  CAS  Google Scholar 

  • Rand FV, Cash LC (1921) Stewart’s disease of corn. J Agric Res 21:263–264

    Google Scholar 

  • Redecker D, Kodner R, Graham LE (2000) Glomalean fungi from the Ordovician. Science 289:1920–1921

    Article  CAS  PubMed  Google Scholar 

  • Rodriguez RJ et al (2008) Stress tolerance in plants via habitat-adapted symbiosis. ISME J 2:404

    Article  PubMed  Google Scholar 

  • Roos IM, Hattingh M (1983) Scanning electron microscopy of Pseudomonas syringae pv, morsprunorum on sweet cherry leaves. J Phytopathol 108:18–25

    Article  Google Scholar 

  • Russell JR et al (2011) Biodegradation of polyester polyurethane by endophytic fungi. Appl Environ Microbiol 77:6076–6084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ryan RP, Germaine K, Franks A, Ryan DJ, Dowling DN (2008) Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 278:1–9

    Article  CAS  PubMed  Google Scholar 

  • Schaad NW, Cheong S, Tamaki S, Hatziloukas E, Panopoulos NJ (1995) A combined biological and enzymatic amplification (BIO-PCR) technique to detect Pseudomonas syringae pv. Phaseolicola in bean seed extracts. Phytopathology 85:243–246

    Article  CAS  Google Scholar 

  • Schaad NW, Jones JB, Chun W (2001) Laboratory guide for the identification of plant pathogenic bacteria, vol 3. APS Press, Urbana

    Google Scholar 

  • Selim K, El-Beih A, AbdEl-Rahman T, El-Diwany A (2011) Biodiversity and antimicrobial activity of endophytes associated with Egyptian medicinal plants. Mycosphere 2:669–678

    Article  Google Scholar 

  • Sessitsch A et al (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36

    Article  CAS  PubMed  Google Scholar 

  • Sette L, Passarini M, Delarmelina C, Salati F, Duarte M (2006) Molecular characterization and antimicrobial activity of endophytic fungi from coffee plants. World J Microbiol Biotechnol 22:1185–1195

    Article  CAS  Google Scholar 

  • Sharrock K, Parkes S, Jack H, Rees-George J, Hawthorne B (1991) Involvement of bacterial endophytes in storage rots of buttercup squash (Cucurbita maxima D. hybrid ‘Delica’). N Z J Crop Hortic Sci 19:157–165

    Article  Google Scholar 

  • 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:e00621–e00615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh SK, Strobel GA, Knighton B, Geary B, Sears J, Ezra D (2011) An endophytic Phomopsis sp. possessing bioactivity and fuel potential with its volatile organic compounds. Microb Ecol 61:729–739

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strobel G, Daisy B, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67:257–268

    Article  CAS  PubMed  Google Scholar 

  • Suryanarayanan TS (2013) Endophyte research: going beyond isolation and metabolite documentation. Fungal Ecol 6:561–568

    Article  Google Scholar 

  • Taghavi S et al (2010) Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638. PLoS Genet 6:e1000943

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Tefera T, Vidal S (2009) Effect of inoculation method and plant growth medium on endophytic colonization of sorghum by the entomopathogenic fungus Beauveria bassiana. BioControl 54:663–669

    Article  Google Scholar 

  • Terekhova V, Semenova T (2005) The structure of micromycete communities and their synecologic interactions with basidiomycetes during plant debris decomposition. Microbiology 74:91–96

    Article  CAS  Google Scholar 

  • Thormann MN, Currah RS, Bayley SE (2003) Succession of microfungal assemblages in decomposing peatland plants. Plant Soil 250:323–333

    Article  CAS  Google Scholar 

  • Toju H, Yamamoto S, Sato H, Tanabe AS, Gilbert GS, Kadowaki K (2013) Community composition of root-associated fungi in a Q uercus-dominated temperate forest:“codominance” of mycorrhizal and root-endophytic fungi. Ecol Evol 3:1281–1293

    Article  PubMed  PubMed Central  Google Scholar 

  • Tombolini R, Jansson JK (1998) Monitoring of GFP-tagged bacterial cells. In: Bioluminescence methods and protocols. Springer, New York, pp 285–298

    Chapter  Google Scholar 

  • Tombolini R, Unge A, Davey ME, de Bruijn FJ, Jansson JK (1997) Flow cytometric and microscopic analysis of GFP-tagged Pseudomonas fluorescens bacteria. FEMS Microbiol Ecol 22:17–28

    Article  CAS  Google Scholar 

  • Tomsheck AR et al (2010) Hypoxylon sp., an endophyte of Persea indica, producing 1, 8-cineole and other bioactive volatiles with fuel potential. Microb Ecol 60:903–914

    Article  CAS  PubMed  Google Scholar 

  • Tripathi AK, Verma SC, Chowdhury SP, Lebuhn M, Gattinger A, Schloter M (2006) Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int J Syst Evol Microbiol 56:1677–1680

    Article  CAS  PubMed  Google Scholar 

  • Uszkoreit J, Plohnke N, Rexroth S, Marcus K, Eisenacher M (2014) The bacterial proteogenomic pipeline. BMC Genomics 15:S19

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Hecke MM, Treonis AM, Kaufman JR (2005) How does the fungal endophyte Neotyphodium coenophialum affect tall fescue (Festuca arundinacea) rhizodeposition and soil microorganisms? Plant Soil 275:101–109

    Article  CAS  Google Scholar 

  • Villacieros M et al (2003) Colonization behaviour of Pseudomonas fluorescens and Sinorhizobium meliloti in the alfalfa (Medicago sativa) rhizosphere. Plant Soil 251:47–54

    Article  CAS  Google Scholar 

  • Visalakchi S, Muthumary J (2009) Antimicrobial activity of the new endophytic Monodictys castaneae SVJM139 pigment and its optimization. Afr J Microbiol Res 3:550–556

    CAS  Google Scholar 

  • Wang Y, Ohara Y, Nakayashiki H, Tosa Y, Mayama S (2005) Microarray analysis of the gene expression profile induced by the endophytic plant growth-promoting rhizobacteria, Pseudomonas fluorescens FPT9601-T5 in Arabidopsis. Mol Plant-Microbe Interact 18:385–396

    Article  CAS  PubMed  Google Scholar 

  • Wei G, Kloepper JW, Tuzun S (1991) Induction of systemic resistance of cucumber to Colletotrichum orbiculare by select strains of plant growth-promoting rhizobacteria. Phytopathology 81:1508–1512

    Article  Google Scholar 

  • Wei G, Kloepper J, Tuzun S (1996) Induced systemic resistance to cucumber diseases and increased plant growth by plant growth-promoting rhizobacteria under field conditions. Phytopathology 86:121

    Google Scholar 

  • Wilson D (1995) Endophyte: the evolution of a term, and clarification of its use and definition. Oikos 73:274–276

    Article  Google Scholar 

  • Xi C, Lambrecht M, Vanderleyden J, Michiels J (1999) Bi-functional gfp-and gusA-containing mini-Tn5 transposon derivatives for combined gene expression and bacterial localization studies. J Microbiol Methods 35:85–92

    Article  CAS  PubMed  Google Scholar 

  • Xin G, Zhang G, Kang JW, Staley JT, Doty SL (2009) A diazotrophic, indole-3-acetic acid-producing endophyte from wild. Biol Fertil Soils 45:669–674

    Article  CAS  Google Scholar 

  • Young C, Bryant M, Christensen M, Tapper B, Bryan G, Scott B (2005) Molecular cloning and genetic analysis of a symbiosis-expressed gene cluster for lolitrem biosynthesis from a mutualistic endophyte of perennial. Mol Gen Genomics 274:13–29

    Article  CAS  Google Scholar 

  • Zgadzaj R et al (2015) A legume genetic framework controls infection of nodules by symbiotic and endophytic bacteria. PLoS Genet 11:e1005280

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang X, Ren A, Ci H, Gao Y (2010) Genetic diversity and structure of Neotyphodium species and their host Achnatherum sibiricum in a natural grass–endophyte system. Microb Ecol 59:744–756

    Article  PubMed  Google Scholar 

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Acknowledgment

The authors are grateful to the Department of Microbiology, Akal College of Basic Science, Eternal University, Himachal Pradesh, for providing the facilities and financial support.

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  1. Department of Microbiology, Eternal University, Sirmaur, Himachal Pradesh, India

    Priyanka Verma

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  1. Priyanka Verma
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  1. Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India

    Satish Kumar Verma

  2. Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA

    James Francis White, Jr

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Verma, P. (2019). Seed Endophytes in Crop Plants: Metagenomic Approaches to Study the Functional Roles and Interactions. In: Verma, S., White, Jr, J. (eds) Seed Endophytes. Springer, Cham. https://doi.org/10.1007/978-3-030-10504-4_23

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