Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Agrios GN. 1.  2005. Plant Pathology San Diego, CA: Academic, 5th ed.. [Google Scholar]
  2. Aimé S, Alabouvette C, Steinberg C, Olivain C. 2.  2013. The endophytic strain Fusarium oxysporum Fo47: a good candidate for priming the defense responses in tomato roots. Mol. Plant-Microbe Interact. 26:918–26 [Google Scholar]
  3. Akagi Y, Akamatsu H, Otani H, Kodama M. 3.  2009. Horizontal chromosome transfer, a mechanism for the evolution and differentiation of a plant-pathogenic fungus. Eukaryot. Cell 8:1732–38 [Google Scholar]
  4. Álvarez B, Biosca EG, López MM. 4.  2010. On the life of Ralstonia solanacearum, a destructive bacterial plant pathogen. Current Research, Technology and Education Topics in Applied Microbiology and Microbial Biotechnology A Mendez Vilas 267–69 Badajoz, Spain: Formatex [Google Scholar]
  5. Amtmann A, Troufflard S, Armengaud P. 5.  2008. The effect of potassium nutrition on pest and disease resistance in plants. Physiol. Plant. 133:682–91 [Google Scholar]
  6. Antunes LC, Ferreira RB, Buckner MM, Finlay BB. 6.  2010. Quorum sensing in bacterial virulence. Microbiology 156:2271–82 [Google Scholar]
  7. Araki H, Tian D, Goss EM, Jakob K, Halldorsdottir SS. 7.  et al. 2006. Presence/absence polymorphism for alternative pathogenicity islands in Pseudomonas viridiflava, a pathogen of Arabidopsis. . PNAS 103:5887–92 [Google Scholar]
  8. Arnold DL, Jackson RW, Waterfield NR, Mansfield JW. 8.  2007. Evolution of microbial virulence: the benefits of stress. Trends Genet 23:293–300 [Google Scholar]
  9. Bartoli C, Roux F, Lamichhane JR. 9.  2016. Molecular mechanisms underlying the emergence of bacterial pathogens: an ecological perspective. Mol. Plant Pathol. 17:303–10 [Google Scholar]
  10. Berendsen RL, Pieterse CMJ, Bakker PAHM. 10.  2012. The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–86 [Google Scholar]
  11. Berendsen RL, van Verk MC, Stringlis IA, Zamioudis C, Tommassen J. 11.  et al. 2015. Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417. BMC Genom 16:1–23 [Google Scholar]
  12. Bertsch C, Ramírez-Suero M, Magnin-Robert M, Larignon P, Chong J. 12.  et al. 2013. Grapevine trunk diseases: complex and still poorly understood. Plant Pathol 62:243–65 [Google Scholar]
  13. Block A, Schmelz E, Jones JB, Klee HJ. 13.  2005. Coronatine and salicylic acid: the battle between Arabidopsis and Pseudomonas for phytohormone control. Mol. Plant Pathol 6:79–83 [Google Scholar]
  14. Bonfante P, Anca I-A. 14.  2009. Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu. Rev. Microbiol. 63:863–83 [Google Scholar]
  15. Bonneau L, Huguet S, Wipf D, Pauly N, Truong H-N. 15.  2013. Combined phosphate and nitrogen limitation generates a nutrient stress transcriptome favorable for arbuscular mycorrhizal symbiosis in Medicago truncatula. New Phytol 199:188–202 [Google Scholar]
  16. Bowler C, Fluhr R. 16.  2000. The role of calcium and activated oxygens as signals for controlling cross-tolerance. Trends Plant Sci 5:241–46 [Google Scholar]
  17. Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A. 17.  2014. Metabolic potential of endophytic bacteria. Curr. Opin. Biotechnol. 27:30–37 [Google Scholar]
  18. Brown SH, Scott J, Bhaheetharan J, Sharpee WC, Milde L. 18.  et al. 2009. Oxygenase coordination is required for morphological transition and the host/fungal interaction of Aspergillus flavus. . Mol. Plant-Microbe Interact. 7:882–94 [Google Scholar]
  19. Bruez E, Vallance J, Gerbore J, Lecomte P, Da Costa J-P. 19.  et al. 2014. Analyses of the temporal dynamics of fungal communities colonizing the healthy wood tissues of esca leaf-symptomatic and asymptomatic vines. PLOS ONE 9:e95928 [Google Scholar]
  20. Bruez E, Haidar R, Alou MT, Vallance J, Bertsch C. 20.  et al. 2015. Bacteria in a wood fungal disease: characterization of bacterial communities in wood tissues of esca-foliar symptomatic and asymptomatic grapevines. Front. Microbiol. 6:1137 [Google Scholar]
  21. Chatterjee S, Almeida RPP, Lindow S. 21.  2008. Living in two worlds: the plant and insect lifestyles of Xylella fastidiosa. . Annu. Rev. Phytopathol. 46:243–71 [Google Scholar]
  22. Christensen MJ, Voisey CR. 22.  2009. Tall fescue-endophyte symbiosis. Tall Fescue for the Twenty-First Century HA Fribourg, DB Hannaway, CP West 251–72 Madison, WI: Am. Soc. Agron. [Google Scholar]
  23. Christensen SA, Kolomiets MV. 23.  2011. The lipid language of plant-fungal interactions. Fungal Genet. Biol. 48:4–14 [Google Scholar]
  24. Combès A, Ndoye I, Bance C, Bruzaud J, Djediat C. 24.  et al. 2012. Chemical communication between the endophytic fungus Paraconiothyrium variabile and the phytopathogen Fusarium oxysporum. . PLOS ONE 7:e47313 [Google Scholar]
  25. Compant S, Clément C, Sessitsch A. 25.  2010. Plant growth–promoting bacteria in the rhizo- and endosphere of plants: their role, colonization, mechanisms involved and prospects for utilization. Soil Biol. Biochem. 42:669–78 [Google Scholar]
  26. Compant S, Duffy B, Nowak J, Clément C, Ait Barka E. 26.  2005. Use of plant growth–promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl. Environ. Microbiol. 71:4951–59 [Google Scholar]
  27. Compant S, Kaplan H, Ait Barka E, Sessitsch A, Nowak J. 27.  et al. 2008. Endophytic colonization of Burkholderia phytofirmans strain PsJN in Vitis vinifera L: from rhizosphere to inflorescence tissues. FEMS Microbiol. Ecol 63:84–93 [Google Scholar]
  28. Compant S, Saikkonen K, Mitter B, Campisano A, Mercado-Blanco J. 28.  2016. Editorial special issue: soil, plants and endophytes. Plant Soil 405:11–11 [Google Scholar]
  29. Compant S, van der Heijden MG, Sessitsch A. 29.  2010. Climate change effects on beneficial plant-microorganism interactions. FEMS Microbiol. Ecol. 73:197–214 [Google Scholar]
  30. Cook DE, Mesarich CH, Thomma BPHJ. 30.  2015. Understanding plant immunity as a surveillance system to detect invasion. Annu. Rev. Phytopathol. 53:541–63 [Google Scholar]
  31. Darsonval A, Darrasse A, Meyer D, Demarty M, Durand K. 31.  et al. 2008. The type III secretion system of Xanthomonas fuscans subsp. fuscans is involved in the phyllosphere colonization process and in transmission to seeds of susceptible beans. Appl. Environ. Microbiol 74:2669–78 [Google Scholar]
  32. Effmert U, Kalderas J, Warnke R, Piechulla B. 32.  2012. Volatile mediated interactions between bacteria and fungi in the soil. J. Chem. Ecol. 38:665–703 [Google Scholar]
  33. Foyer CH, Rasool B, Davey JW, Hancock RD. 33.  2016. Cross-tolerance to biotic and abiotic stresses in plants: a focus on resistance to aphid infestation. J. Exp. Bot. 67:2025–37 [Google Scholar]
  34. Francl LJ. 34.  2001. The disease triangle: a plant pathological paradigm revisited. Plant Health Instr https://doi.org/10.1094/PHI-T-2001-0517-01 [Crossref] [Google Scholar]
  35. Fravel D, Olivain C, Alabouvette C. 35.  2003. Fusarium oxysporum and its biocontrol. New Phytol 157:493–502 [Google Scholar]
  36. Fuqua C, Parsek MR, Greenberg EP. 36.  2001. Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu. Rev. Genet. 35:439–68 [Google Scholar]
  37. Galán JE. 37.  2009. Common themes in the design and function of bacterial effectors. Cell Host Microbe 5:571–79 [Google Scholar]
  38. Gao X, Huang Q, Zhao Z, Han Q, Ke X. 38.  et al. 2016. Studies on the infection, colonization, and movement of Pseudomonas syringae pv. actinidiae in kiwifruit tissues using a GFPuv-labeled strain. PLOS ONE 11:e0151169 [Google Scholar]
  39. Garbeva P, Hordijk C, Gerards S, De Boer W. 39.  2014. Volatile-mediated interactions between phylogenetically different soil bacteria. Front. Microbiol. 5:285–90 [Google Scholar]
  40. Gassmann W, Appel HM, Oliver MJ. 40.  2016. The interface between abiotic and biotic stress responses. J. Exp. Bot. 67:2023–24 [Google Scholar]
  41. Gent DH, Mahaffee WF, McRoberts N, Pfender WF. 41.  2013. The use and role of predictive systems in disease management. Annu. Rev. Phytopathol. 51:267–89 [Google Scholar]
  42. Giauque H, Hawkes CV. 42.  2013. Climate affects symbiotic fungal endophyte diversity and performance. Am. J. Bot. 100:1435–44 [Google Scholar]
  43. Gourion B, Berrabah F, Ratet P, Stacey G. 43.  2015. Rhizobium-legume symbioses: the crucial role of plant immunity. Trends Plant Sci 20:186–94 [Google Scholar]
  44. Grube M, Berg G. 44.  2009. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fungal Biol. Rev. 23:72–85 [Google Scholar]
  45. Haidar R, Deschamps A, Roudet J, Calvo-Garrido C, Bruez E. 45.  et al. 2016. Multi-organ screening of efficient bacterial control agents against two major pathogens of grapevine. Biol. Control 92:55–65 [Google Scholar]
  46. Hajishengallis G, Lamont RJ. 46.  2016. Dancing with the stars: how choreographed bacterial interactions dictate nososymbiocity and give rise to keystone pathogens, accessory pathogens, and pathobionts. Trends Microbiol 24:477–89 [Google Scholar]
  47. Hallmann J. 47.  2001. Plant interactions with endophytic bacteria. Biotic Interactions in Plant-Pathogen Associations MJ Jeger, NJ Spence 87–120 Wallingford, UK: CABI Publ. [Google Scholar]
  48. Hallmann J, Quadt-Hallmann A, Mahaffee WF, Kloepper JW. 48.  1997. Bacterial endophytes in agricultural crops. Can. J. Microbiol. 43:895–914 [Google Scholar]
  49. Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S. 49.  et al. 2015. The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes. Microbiol. Mol. Biol. Rev. 79:293–320 [Google Scholar]
  50. Hirano SS, Upper CD. 50.  2000. Bacteria in the leaf ecosystem with emphasis on Pseudomonas syringae: a pathogen, ice nucleus, and epiphyte. Microbiol. Mol. Biol. Rev. 64:624–53 [Google Scholar]
  51. Hofstetter V, Buyck B, Croll D, Viret O, Couloux A. 51.  et al. 2012. What if esca disease of grapevine were not a fungal disease?. Fungal Divers 54:51–67 [Google Scholar]
  52. Hua J. 52.  2013. Modulation of plant immunity by light, circadian rhythm, and temperature. Curr. Opin. Plant Biol. 16:406–13 [Google Scholar]
  53. Hunziker L, Boenisch D, Groenhagen U, Bailly A, Schulz S. 53.  et al. 2015. Pseudomonas strains naturally associated with potato plants produce volatiles with high potential for inhibition of Phytophthora infestans. . Appl. Environ. Microbiol. 81:821–30 [Google Scholar]
  54. Hurley B, Lee D, Mott A, Wilton M, Liu J. 54.  et al. 2014. The Pseudomonas syringae type III effector HopF2 suppresses Arabidopsis stomatal immunity. PLOS ONE 9:e114921 [Google Scholar]
  55. Iniguez AL, Dong Y, Carter HD, Ahmer BM, Stone JM. 55.  et al. 2005. Regulation of enteric endophytic bacterial colonization by plant defenses. Mol. Plant Microbe Interact. 18:169–78 [Google Scholar]
  56. Imam J, Singh PK, Shukla P. 56.  2016. Plant-microbe interactions in post genomic era: perspectives and applications. Front. Microbiol. 7:1488 [Google Scholar]
  57. James EK, Gyaneshwar P, Mathan N, Barraquio QL, Reddy PM. 57.  et al. 2002. Infection and colonization of rice seedlings by the plant growth–promoting bacterium Herbaspirillum seropedicae Z67. Mol. Plant-Microbe Interact. 15:894–906 [Google Scholar]
  58. Jimenez-Fernandez D, Landa BB, Kang S, Jimenez-Diaz RM, Navas-Cortes JA. 58.  2013. Quantitative and microscopic assessment of compatible and incompatible interactions between chickpea cultivars and Fusarium oxysporum f. sp. ciceris races. PLOS ONE 8:e61360 [Google Scholar]
  59. Jones JD, Dangl JL. 59.  2006. The plant immune system. Nature 444:323–29 [Google Scholar]
  60. Keane P, Kerr A. 60.  1997. Factors affecting disease development. Plant Pathogens and Plant Diseases JF Brown, HJ Ogle 287–98 Armidale, Aust.: Rockvale Publ. [Google Scholar]
  61. Kloepper JW, McInroy JA, Liu K, Hu C-H. 61.  2013. Symptoms of fern distortion syndrome resulting from inoculation with opportunistic endophytic fluorescent Pseudomonas spp. PLOS ONE 8:e58531 [Google Scholar]
  62. Kloppholz S, Kuhn H, Requena N. 62.  2011. A secreted fungal effector of Glomus intraradices promotes symbiotic biotrophy. Curr. Biol. 21:1204–9 [Google Scholar]
  63. Kumar AS, Lakshmanan V, Caplan JL, Powell D, Czymmek KJ. 63.  et al. 2012. Rhizobacteria Bacillus subtilis restricts foliar pathogen entry through stomata. Plant J 72:694–706 [Google Scholar]
  64. Lamichhane JR, Venturi V. 64.  2015. Synergisms between microbial pathogens in plant disease complexes: a growing trend. Front. Plant Sci. 6:385 [Google Scholar]
  65. Lara-Chavez A, Lowman S, Kim S, Tang Y, Zhang J. 65.  et al. 2015. Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN. J. Exp. Bot. 66:4337–50 [Google Scholar]
  66. LaSarre B, Federle MJ. 66.  2013. Exploiting quorum sensing to confuse bacterial pathogens. Microbiol. Mol. Bio. Rev. 77:73–111 [Google Scholar]
  67. Lemaire B, Janssens S, Smets E, Dessein S. 67.  2012. Endosymbiont transmission mode in bacterial leaf nodulation as revealed by a population genetic study of Psychotria leptophylla. . Appl. Environ. Microbiol. 78:284–87 [Google Scholar]
  68. Li E, Ling J, Wang G, Xiao J, Yang Y. 68.  et al. 2015. Comparative proteomics analyses of two races of Fusarium oxysporum f. sp. conglutinans that differ in pathogenicity. Sci. Rep 5:13663 [Google Scholar]
  69. Lima WC, Paquola ACM, Varani AM, Van Sluys M-A, Menck CFM. 69.  2008. Laterally transferred genomic islands in Xanthomonadales related to pathogenicity and primary metabolism. FEMS Microbiol. Lett. 281:87–97 [Google Scholar]
  70. López-Fernández S, Sonega P, Moretto M, Pancher M, Engelen K. 70.  et al. 2015. Whole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria. Front. Microbiol. 6:419 [Google Scholar]
  71. Ma L-J. 71.  2014. Horizontal chromosome transfer and rational strategies to manage Fusarium vascular wilt diseases. Mol. Plant Pathol. 15:763–66 [Google Scholar]
  72. Ma L-J, Geiser DM, Proctor RH, Rooney AP, O'Donnell K. 72.  et al. 2013. Fusarium pathogenomics. Annu. Rev. Microbiol. 67:399–416 [Google Scholar]
  73. Ma L-J, Kistler HC, Rep M. 73.  2012. Evolution of plant pathogenicity in Fusarium species. Evolution of Virulence in Eukaryotic Microbes LD Sibley, BJ Howlett, J Heitman 486–98 Hoboken, NJ: Wiley & Sons [Google Scholar]
  74. Ma L-J, van der Does HC, Borkovich KA, Coleman JJ, Daboussi MJ. 74.  et al. 2010. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464:367–73 [Google Scholar]
  75. Malmierca MG, Izquierda-Bueno I, McCormick SP, Cardoza RE, Alexander NJ. 75.  et al. 2016. Trichothecenes and aspinolides produced by Trichoderma arundinaceum regulate expression of Botrytis cinerea involved in virulence and growth. Environ. Microbiol 18:3991–4004 [Google Scholar]
  76. Mansvelt EL, Hattingh MJ. 76.  1987. Scanning electron microscopy of colonization of pear leaves by Pseudomonas syringae pv. syringae. . Can. J. Bot. 65:2517–22 [Google Scholar]
  77. Marchetti M, Capela D, Glew M, Cruveiller S, Chane-Woon-Ming B. 77.  et al. 2010. Experimental evolution of a plant pathogen into a legume symbiont. PLOS Biol 8:e1000280 [Google Scholar]
  78. Marquez LM, Redman RS, Rodriguez RJ, Roossinck MJ. 78.  2007. A virus in a fungus in a plant: three-way symbiosis required for thermal tolerance. Science 315:513515 [Google Scholar]
  79. Mattinen L, Somervuo P, Nykyri J, Nissinen R, Kouvonen P. 79.  et al. 2008. Microarray profiling of host-extract-induced genes and characterization of the type VI secretion cluster in the potato pathogen Pectobacterium atrospeticum. . Microbiology 154:2387–96 [Google Scholar]
  80. McCormick SP. 80.  2013. Microbial detoxification of mycotoxins. J. Chem. Ecol. 39:907–18 [Google Scholar]
  81. Millet YA, Danna CH, Clay NK, Songnuan W, Simon MD. 81.  et al. 2010. Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 22:973–90 [Google Scholar]
  82. Minerdi D, Moretti M, Gilardi G, Barberio C, Gullino ML. 82.  et al. 2008. Bacterial ectosymbionts and virulence silencing in a Fusarium oxysporum strain. Environ. Microbiol. 10:1725–41 [Google Scholar]
  83. Misas-Villamil JC, Kolodziejek I, Crabill E, Kaschani F, Niessen S. 83.  et al. 2013. Pseudomonas syringae pv. syringae uses proteasome inhibitor syringolin A to colonize from wound infection sites. PLOS Pathog 9:e1003281 [Google Scholar]
  84. Mitter B, Petric A, Chain PG, Trognitz F, Nowak J, Sessitsch A. 84.  2013. Genome analysis, ecology, and plant growth promotion of the endophyte Burkholderiaphytofirmans strain PsJN. Molecular Microbial Ecology of the Rhizosphere FJ de Bruijn 865–74 Hoboken, NJ: Wiley & Sons [Google Scholar]
  85. Mitter B, Pfaffenbichler N, Flavell R, Compant S, Antonielli L. 85.  et al. 2017. A new approach to modify plant microbiomes and traits by introducing beneficial bacteria at flowering into progeny seeds. Front. Microbiol. 8:11 [Google Scholar]
  86. Mortier V, Holsters M, Goormachtig S. 86.  2012. Never too many? How legumes control nodule numbers. Plant Cell Environ 35:245–58 [Google Scholar]
  87. Moulin L, James EK, Klonowska A, Miana de Faria S, Simon MF. 87.  2015. Phylogeny, diversity, geographical distribution, and host range of legume-nodulating Betaproteobacteria: What is the role of plant taxonomy?. Biological Nitrogen Fixation FJ de Bruijn 177–90 Hoboken, NJ: Wiley & Sons [Google Scholar]
  88. Newman M-A, Sundelin T, Nielsen J, Erbs G. 88.  2013. MAMP (microbe-associated molecular pattern) triggered immunity in plants. Front. Plant Sci. 4:139 [Google Scholar]
  89. Niu D-D, Liu H-X, Jiang C-H, Wang Y-P, Wang Q-Y. 89.  et al. 2011. The plant growth–promoting rhizobacterium Bacillus cereus AR156 induces systemic resistance in Arabidopsis thaliana by simultaneously activating salicylate- and jasmonate/ethylene-dependent signaling pathways. Mol. Plant-Microbe Interact 24:533–42 [Google Scholar]
  90. O'Donnell K, Gueidan C, Sink S, Johnston PR, Crous PW. 90.  et al. 2009. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex. Fungal Genet. Biol. 46:936–48 [Google Scholar]
  91. Olivain C, Alabouvette C. 91.  1999. Process of tomato root colonization by a pathogenic strain of Fusarium oxysporum f. sp. lycopersici in comparison with a non-pathogenic strain. New Phytol 141:497–510 [Google Scholar]
  92. Olivain C, Humbert C, Nahalkova J, Fatehi J, L'Haridon F, Alabouvette C. 92.  2006. Colonization of tomato root by pathogenic and nonpathogenic Fusarium oxysporum strains inoculated together and separately into the soil. Appl. Environ. Microbiol. 72:1523–31 [Google Scholar]
  93. Partida-Martinez LP, Hertweck C. 93.  2005. Pathogenic fungus harbours endosymbiotic bacteria for toxin production. Nature 437:884–88 [Google Scholar]
  94. Pedron T, Sansonetti P. 94.  2008. Commensals, bacterial pathogens and intestinal inflammation: an intriguing menage a trois. Cell Host Microbe 3:344–47 [Google Scholar]
  95. Pel MJC, Pieterse CMJ. 95.  2012. Microbial recognition and evasion of host immunity. J. Exp. Bot. 64:1237–48 [Google Scholar]
  96. Pel MJC, Van Dijken AJH, Bardoel BW, Seidl MF, Van der Ent S. 96.  et al. 2014. Pseudomonas syringae evades host immunity by degrading flagellin monomers with alkaline protease AprA. Mol. Plant-Microbe Interact. 27:603–10 [Google Scholar]
  97. Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. 97.  2013. Going back to the roots: the microbial ecology of the rhizosphere. Nat. Rev. Microbiol. 11:789–99 [Google Scholar]
  98. Piromyou P, Songwattana P, Greetatorn T, Okubo T, Kakizaki KC. 98.  et al. 2015. The type III secretion system (T3SS) is a determinant for rice-endophyte colonization by non-photosynthetic Bradyrhizobium. Microbes Environ 30:291–300 [Google Scholar]
  99. Perez-Nadales E, Di Pietro A. 99.  2011. The membrane mucin Msb2 regulates invasive growth and plant infection in Fusarium oxysporum. . Plant Cell 23:1171–85 [Google Scholar]
  100. Pitman AR, Jackson RW, Mansfield JW, Kaitell V, Thwaites R. 100.  et al. 2005. Exposure to host resistance mechanisms drives evolution of bacterial virulence in plants. Curr. Biol 15:2230–35 [Google Scholar]
  101. Plett JM, Khachane A, Ouassou M, Sundberg B, Kohler A. 101.  et al. 2014. Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots. New Phytol 202:270–86 [Google Scholar]
  102. Presti L, Lanver D, Schweizer G, Tanaka S, Liang L. 102.  et al. 2015. Fungal effectors and plant susceptibility. Annu. Rev. Plant Biol. 66:513–45 [Google Scholar]
  103. Preston GM, Bertrand N, Rainey PB. 103.  2001. Type III secretion in plant growth–promoting Pseudomonas fluorescens SBW25. Mol. Microbiol. 41:999–1014 [Google Scholar]
  104. Prieto P, Schilirò E, Maldonado-González MM, Valderrama R, Barroso-Albarracín JB. 104.  et al. 2011. Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microb. Ecol. 62:435–45 [Google Scholar]
  105. Qiu H, Cai G, Luo J, Bhattacharya D, Zhang N. 105.  2016. Extensive horizontal gene transfers between plant pathogenic fungi. BMC Biol 14:41 [Google Scholar]
  106. Rangel de Souza ALS, De Souza SA, De Oliveira MVV, Ferraz TM, Figueiredo FAMMA. 106.  et al. 2016. Endophytic colonization of Arabidopsis thaliana by Gluconacetobacter diazotrophicus and its effect on plant growth promotion, plant physiology, and activation of plant defense. Plant Soil 399:257–70 [Google Scholar]
  107. Reinhold-Hurek B, Hurek T. 107.  2011. Living inside plants: bacterial endophytes. Curr. Opin. Plant Biol. 14:435–43 [Google Scholar]
  108. Rezzonico F, Binder C, Défago G, Moënne-Loccoz Y. 108.  2005. The type III secretion system of biocontrol Pseudomonas fluorescens KD targets the phytopathogenic Chromista Pythium ultimum and promotes cucumber protection. Mol. Plant-Microbe Interact 18:991–1001 [Google Scholar]
  109. Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA. 109.  et al. 2011. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat. Rev. Microbiol. 9:344–55 [Google Scholar]
  110. Scharf DH, Heinekamp T, Brakhage AA. 110.  2014. Human and plant fungal pathogens: the role of secondary metabolites. PLOS Pathog 10:e1003859 [Google Scholar]
  111. Schell MA, Ulrich RL, Ribot WJ, Brueggemann EF, Hines HB. 111.  et al. 2007. Type VI secretion is a major virulence determinant in Burkholderia mallei. . Mol. Microbiol. 64:1466–85 [Google Scholar]
  112. Schmidt R, Cordovez V, De Boer W, Raaijmakers J. 112.  2015. Volatile affairs in microbial interactions. ISME J 9:2329–35 [Google Scholar]
  113. Schroeckh V, Scherlach K, Nützmann H-W, Shelest E, Schmidt-Heck W. 113.  et al. 2009. Intimate bacterial-fungal interaction triggers biosynthesis of archetypal polyketides in Aspergillus nidulans. . PNAS 106:14558–63 [Google Scholar]
  114. Seth EC, Taga ME. 114.  2014. Nutrient cross-feeding in the microbial world. Front. Microbiol. 5:350 [Google Scholar]
  115. Shapiro LR, Scully ED, Straub TJ, Park J, Stephenson AG. 115.  et al. 2016. Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host-restricted plant pathogen Erwinia tracheiphila. Genome Biol. Evol. 8:649–64 [Google Scholar]
  116. Shcherbakova LA, Odintsova TI, Stakheev AA, Fravel DR, Zavriev SK. 116.  2015. Identification of a novel small cysteine-rich protein in the fraction from the biocontrol Fusarium oxysporum strain CS-20 that mitigates Fusarium wilt symptoms and triggers defense responses in tomato. Front. Plant Sci 6:1207 [Google Scholar]
  117. Sheibani-Tezerji R, Naveed M, Jehl M-A, Sessitsch A, Rattei T, Mitter B. 117.  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 [Google Scholar]
  118. Sheibani-Tezerji R, Rattei T, Sessitsch A, Trognitz F, Mitter B. 118.  2015. Transcriptome profiling of the endophyte Burkholderia phytofirmans PsJN indicates sensing of the plant environment and drought stress. mBio 6:e00621–15 [Google Scholar]
  119. Shidore T, Dinse T, Öhrlein J, Becker A, Reinhold-Hurek B. 119.  2012. Transcriptomic analysis of response to exudates reveals genes required for rhizosphere competence of the endophyte Azoarcus sp. strain BH72. Environ. Microbiol. 14:2775–87 [Google Scholar]
  120. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ. 120.  2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241–44 [Google Scholar]
  121. Sukno SA, García VM, Shaw BD, Thon MR. 121.  2008. Root infection and systemic colonization of maize by Colletotrichum graminicola. . Appl. Environ. Microbiol. 74:823–32 [Google Scholar]
  122. Surico G, Mugnai L, Marchi G. 122.  2006. Older and more recent observations on esca: a critical overview. Phytopathol. Mediterr. 45:68–86 [Google Scholar]
  123. Suzuki N, Rivero RM, Shulaev V, Blumwald E, Mittler R. 123.  2013. Abiotic and biotic stress combinations. New Phytol 203:32–43 [Google Scholar]
  124. Tampakaki AP. 124.  2014. Commonalities and differences of T3SSs in rhizobia and plant pathogenic bacteria. Front. Plant Sci. 5:114 [Google Scholar]
  125. Tellström V, Usadel B, Thimm O, Stitt M, Küster H, Niehaus K. 125.  2007. The lipopolysaccharide of Sinorhizobiummeliloti suppresses defense-associated gene expression in cell cultures of the host plant Medicago truncatula. . Plant Physiol. 143:825–37 [Google Scholar]
  126. Toben H, Rudolph K. 126.  1997. Control of umbel blight and seed decay of coriander (Pseudomonas syringae pv. coriandricola). Developments in Plant Pathology, Vol. 9 K Rudolph, TJ Burr, JW Mansfield, D Stead, A Vivian, J von Kietzell 611–16 Boston, MA: Kluwer Acad. [Google Scholar]
  127. Torres-Cortes G, Ghignone S, Bonfante P, Schuessler A. 127.  2015. Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: transkingdom gene transfer in an ancient mycoplasma-fungus association. PNAS 112:7785–90 [Google Scholar]
  128. Trdá L, Fernandez O, Boutrot F, Héloir M-C, Kelloniemi J. 128.  et al. 2014. The grapevine flagellin receptor VvFLS2 differentially recognizes flagellin-derived epitopes from the endophytic growth-promoting bacterium Burkholderia phytofirmans and plant pathogenic bacteria. New Phytol 201:1371–84 [Google Scholar]
  129. Uroz S, Dessaux Y, Uroz P. 129.  2009. Quorum sensing and quorum quenching: the Yin and Yang of bacterial communication. ChemBioChem 20:205–16 [Google Scholar]
  130. Uroz S, Heininsalo J. 130.  2008. Degradation of N-acyl homoserine lactone quorum sensing signal molecules by forest root-associated fungi. FEMS Microbiol. Ecol. 65:271–78 [Google Scholar]
  131. van der Does HC, Duyvesteijn RG, Goltstein PM, van Schie CC, Manders EM. 131.  et al. 2008. Expression of effector gene SIX1 of Fusarium oxysporum requires living plant cells. Fungal Genet. Biol 45:1257–64 [Google Scholar]
  132. van der Wolf JM, van der Zouwen PS. 132.  2010. Colonization of cauliflower blossom (Brassica oleracea) by Xanthomonas campestris pv. campestris, via flies (Calliphora vomitoria) can result in seed infestation. J. Phytopathol 158:726–32 [Google Scholar]
  133. van der Wolf JM, van der Zouwen PS, van der Heijden L. 133.  2013. Flower infection of Brassica oleracea with Xanthomonas campestris pv. campestris results in high levels of seed infection. Eur. J. Plant Pathol 136:103–11 [Google Scholar]
  134. Vanga BR, Ramakrishnan P, Butler RC, Toth IK, Ronson CW. 134.  et al. 2015. Mobilization of horizontally acquired island 2 is induced in planta in the phytopathogen Pectobacterium atrosepticum SCRI1043 and involves the putative relaxase ECA0613 and quorum sensing. Environ. Microbiol. 17:7430–44 [Google Scholar]
  135. Vayssier-Taussat M, Albina E, Citti C, Cosson J-F, Jacques M-A. 135.  et al. 2014. Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Front. Cell. Infect. Microbiol. 4:29 [Google Scholar]
  136. Veloso J, Díaz J. 136.  2012. Fusarium oxysporum Fo47 confers protection to pepper plants against Verticillium dahliae and Phytophthora capsici, and induces the expression of defence genes. Plant Pathol 61:281–88 [Google Scholar]
  137. Veresoglou S, Barto E, Menexes G, Rillig M. 137.  2013. Fertilization affects severity of disease caused by fungal plant pathogens. Plant Pathol 62:961–69 [Google Scholar]
  138. Viollet A, Pivato B, Mougel C, Cleyet-Marel J-C, Gubry-Rangin C. 138.  et al. 2016. Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities. Mycorrhiza 27:23 [Google Scholar]
  139. Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL. 139.  et al. 2016. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat. Commun. 7:12151 [Google Scholar]
  140. Weintraub PG, Beanland L. 140.  2006. Insect vectors of phytoplasmas. Annu. Rev. Entomol. 51:91–111 [Google Scholar]
  141. Williams P. 141.  2007. Quorum sensing, communication and cross-kingdom signalling in the bacterial world. Microbiology 153:3923–38 [Google Scholar]
  142. Yadeta KA, Thomma BPHJ. 142.  2013. The xylem as battleground for plant hosts and vascular wilt pathogens. Front. Plant Sci. 4:97 [Google Scholar]
  143. Zamioudis C, Pieterse CM. 143.  2012. Modulation of host immunity by beneficial microbes. Mol. Plant-Microbe Interact. 25:139–50 [Google Scholar]
  144. Zavaleta-Mancera HA, Valencia-Botín AJ, Mendoza-Onofre LE, Silva-Rojas HV, Valadez-Moctezuma E. 144.  2007. Use of green fluorescent protein to monitor the colonization of Pseudomonas syringae subsp. syringae on wheat seeds. Microsc. Microanal. J 13:298–99 [Google Scholar]
  145. Zeidler D, Zahringer U, Gerber I, Dubery I, Hartung T. 145.  et al. 2004. Immunity in Arabidopsis thaliana: Lipopolysaccharides activate nitric oxide synthase (NOS) and induce defense genes. PNAS 101:15811–16 [Google Scholar]
  146. Zimmerman NB, Vitousek PM. 146.  2011. Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape. PNAS 109:13022–27 [Google Scholar]
  147. Zgadzaj R, Garrido OR, Jensen DB, Koprivova A, Schulze LP, Radutoiu S. 147.  2016. Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. PNAS 113:E7996–8005 [Google Scholar]

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error