Microbiome: Effect on Plant System, Current Application and Future Aspect

  • Pragati Sahai
  • Vivek Kumar


The Holobiont is the overall plant biochemistry that involves plant kingdom along with microbial world of bacteria and viruses interactive with plant world. The microbiome is the large Holobiont that gives plant health and stability as the microbes in its Holobiont provide resistance to abiotic and biotic stress and also to antibiotics and drugs apart from being part of plant nutrition and nutrient uptake. By understanding the plant and its microbiome, the application and modifications in the application can be studied.


Holobiont Microbiome Plant nutrition Antibiotic Abiotic stress 


  1. Agler MT, Ruhe J, Kroll S, Morhenn C, Kim ST, Weigel D, Kemen EM (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol 14(1):e1002352CrossRefPubMedPubMedCentralGoogle Scholar
  2. Atamna-Ismaeel N, Finkel OM, Glaser F, Sharon I, Schneider R, Post AF, Spudich JL, von Mering C, Vorholt JA, Iluz D, Béjà O (2011) Microbial rhodopsins on leaf surfaces of terrestrial plantsemi_2554. Environ Microbiol 14:140–146PubMedPubMedCentralCrossRefGoogle Scholar
  3. Atamna-Ismaeel N, Finkel OM, Glaser F, Sharon I, Schneider R, Post AF, Spudich JL, von Mering C, Vorholt JA, Iluz D, Béjà O (2012) Microbial rhodopsins on leaf surfaces of terrestrial plants. Environ Microbiol 14(1):140–146PubMedCrossRefPubMedCentralGoogle Scholar
  4. Beckers B, De Beeck MO, Weyens N, Boerjan W, Vangronsveld J (2017) Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees. Microbiome 5(1):25PubMedPubMedCentralCrossRefGoogle Scholar
  5. Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17(8):478–486PubMedPubMedCentralCrossRefGoogle Scholar
  6. Berg G, Smalla K (2009) Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiol Ecol 68(1):1–13PubMedCrossRefPubMedCentralGoogle Scholar
  7. Berg G, Zachow C, Müller H, Philipps J, Tilcher R (2013) Next-generation bio-products sowing the seeds of success for sustainable agriculture. Agronomy 3:648CrossRefGoogle Scholar
  8. Berg G, Köberl M, Rybakova D, Müller H, Grosch R, Smalla K (2017) Plant microbial diversity is suggested as the key to future biocontrol and health trends. FEMS Microbiol Ecol 93(5)Google Scholar
  9. Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193:96–102PubMedCrossRefGoogle Scholar
  10. Bitas V, Kim HS, Bennett JW, Kang S (2013) Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health. Mol Plant-Microbe Interact 26(8):835–843PubMedCrossRefGoogle Scholar
  11. Boller T, Felix G (2009) A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors. Annu Rev Plant Biol 60:379–406PubMedCrossRefGoogle Scholar
  12. Bouffaud ML, Poirier MA, Muller D, Moënne-Loccoz Y (2014) Root microbiome relates to plant host evolution in maize and other Poaceae. Environ Microbiol 16(9):2804–2814PubMedCrossRefGoogle Scholar
  13. Bulgarelli D, Rott M, Schlaeppi K, van Themaat EVL, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E, Peplies J (2013a) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 501(7468):S25Google Scholar
  14. Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P (2013b) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838PubMedCrossRefGoogle Scholar
  15. Cankar K, Kraigher H, Ravnikar M, Rupnik M (2005) Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst). FEMS Microbiol Lett 244(2):341–345PubMedCrossRefGoogle Scholar
  16. Cole BJ, Fletcher M, Waters J, Wetmore K, Blow MJ, Deutschbauer AM, Dangl JL, Visel A (2015) Genetic control of plant root colonization by the biocontrol agent, Pseudomonas fluorescens (No. LBNL-178476). Lawrence Berkeley National Laboratory (LBNL), BerkeleyGoogle Scholar
  17. Cook RJ, Thomashow LS, Weller DM, Fujimoto D, Mazzola M, Bangera G, Kim DS (1995) Molecular mechanisms of defense by rhizobacteria against root disease. Proc Natl Acad Sci 92(10):4197–4201PubMedCrossRefGoogle Scholar
  18. Dangl JL, Horvath DM, Staskawicz BJ (2013) Pivoting the plant immune system from dissection to deployment. Science 341(6147):746–751PubMedCrossRefGoogle Scholar
  19. Duhamel M, Vandenkoornhuyse P (2013) Sustainable agriculture: possible trajectories from mutualistic symbiosis and plant neodomestication. Trends Plant Sci 18(11):597–600PubMedCrossRefGoogle Scholar
  20. Edwards J, Johnson C, Santos-Medellín C, Lurie E, Podishetty NK, Bhatnagar S, Eisen JA, Sundaresan V (2015) Structure, variation, and assembly of the root-associated microbiomes of rice. Proc Natl Acad Sci 112(8):E911–E920PubMedCrossRefGoogle Scholar
  21. Finkel OM, Castrillo G, Paredes SH, González IS, Dangl JL (2017) Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 38:155–163PubMedPubMedCentralCrossRefGoogle Scholar
  22. Frederickson ME (2013) Rethinking mutualism stability: cheaters and the evolution of sanctions. Q Rev Biol 88(4):269–295PubMedCrossRefGoogle Scholar
  23. Friesen ML (2012) Widespread fitness alignment in the legume–rhizobium symbiosis. New Phytol 194(4):1096–1111PubMedCrossRefGoogle Scholar
  24. Fu SF, Wei JY, Chen HW, Liu YY, Lu HY, Chou JY (2015) Indole-3-acetic acid: A widespread physiological code in interactions of fungi with other organisms. Plant Signal Behav 10(8):e1048052PubMedPubMedCentralCrossRefGoogle Scholar
  25. Gilbert JA, Meyer F, Jansson J, Gordon J, Pace N, Tiedje J, Ley R, Fierer N, Field D, Kyrpides N, Glöckner FO (2010) The earth microbiome project: meeting report of the “1 st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6 th 2010. Stand Genomic Sci 3(3):249PubMedPubMedCentralCrossRefGoogle Scholar
  26. Glick BR (2012) Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:1CrossRefGoogle Scholar
  27. Guerrero R, Margulis L, Berlanga M (2013) Symbiogenesis: the holobiont as a unit of evolution. Int Microbiol 16(3):133–143PubMedGoogle Scholar
  28. Hacquard S, Spaepen S, Garrido-Oter R, Schulze-Lefert P (2017) Interplay between innate immunity and the plant microbiota. Annu Rev Phytopathol 55(1):565PubMedCrossRefPubMedCentralGoogle Scholar
  29. Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16(10):463–471PubMedCrossRefPubMedCentralGoogle Scholar
  30. Hardoim PR, Van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring 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):293–320PubMedPubMedCentralCrossRefGoogle Scholar
  31. Hartmann A, Schikora A (2012) Quorum sensing of bacteria and trans-kingdom interactions of N-acyl homoserine lactones with eukaryotes. J Chem Ecol 38(6):704–713PubMedCrossRefPubMedCentralGoogle Scholar
  32. Hartmann A, Rothballer M, Schmid M (2008) Lorenz Hiltner, a pioneer in rhizosphere microbial ecology and soil bacteriology research. Plant Soil 312(1–2):7–14CrossRefGoogle Scholar
  33. Hartmann M, Frey B, Mayer J, Mäder P, Widmer F (2015) Distinct soil microbial diversity under long-term organic and conventional farming. ISME J 9(5):1177PubMedCrossRefGoogle Scholar
  34. Heckman DS, Geiser DM, Eidell BR, Stauffer RL, Kardos NL, Hedges SB (2001) Molecular evidence for the early colonization of land by fungi and plants. Science 293(5532):1129–1133PubMedCrossRefGoogle Scholar
  35. Johnson BJ (1993) Response of tall fescue to plant growth regulators and mowing frequencies. J Environ Hortic 11(4):163–167Google Scholar
  36. Jones JD, Dangl JL (2006) The plant immune system. Nature 444(7117):323PubMedCrossRefGoogle Scholar
  37. Kemen E (2014) Microbe–microbe interactions determine oomycete and fungal host colonization. Curr Opin Plant Biol 20:75–81PubMedCrossRefGoogle Scholar
  38. Kiers ET, Van Der Heijden MG (2006) Mutualistic stability in the arbuscular mycorrhizal symbiosis: exploring hypotheses of evolutionary cooperation. Ecology 87(7):1627–1636PubMedCrossRefPubMedCentralGoogle Scholar
  39. Kiers ET, Rousseau RA, West SA, Denison RF (2003) Host sanctions and the legume-rhizobium mutualism. Nature 425(6953):78PubMedCrossRefPubMedCentralGoogle Scholar
  40. Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A, Palmer TM (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333(6044):880–882PubMedCrossRefPubMedCentralGoogle Scholar
  41. Lee B, Farag MA, Park HB, Kloepper JW, Lee SH, Ryu CM (2012) Induced resistance by a long-chain bacterial volatile: elicitation of plant systemic defense by a C13 volatile produced by Paenibacillus polymyxa. PloS One 7(11):e48744PubMedPubMedCentralCrossRefGoogle Scholar
  42. Lemanceau P, Blouin M, Muller D, Moënne-Loccoz Y (2017) Let the core microbiota be functional. Trends Plant Sci 22:583PubMedCrossRefPubMedCentralGoogle Scholar
  43. Lopez-Velasco G, Carder PA, Welbaum GE, Ponder MA (2013) Diversity of the spinach (Spinacia oleracea) spermosphere and phyllosphere bacterial communities. FEMS Microbiol Lett 346(2):146–154PubMedCrossRefPubMedCentralGoogle Scholar
  44. Lugtenberg B, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556PubMedPubMedCentralCrossRefGoogle Scholar
  45. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488(7409):86PubMedPubMedCentralCrossRefGoogle Scholar
  46. Margulis L, Fester R (eds) (1991) Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. MIT Press, Cambridge, MA/LondonGoogle Scholar
  47. McIntire EJ, Fajardo A (2014) Facilitation as a ubiquitous driver of biodiversity. New Phytol 201(2):403–416PubMedCrossRefPubMedCentralGoogle Scholar
  48. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37(5):634–663PubMedCrossRefGoogle Scholar
  49. Morris JJ, Lenski RE, Zinser ER (2012) The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss. MBio 3(2):e00036–e00012PubMedPubMedCentralCrossRefGoogle Scholar
  50. Mueller UG, Sachs JL (2015) Engineering microbiomes to improve plant and animal health. Trends Microbiol 23(10):606–617CrossRefGoogle Scholar
  51. Müller H, Berg C, Landa BB, Auerbach A, Moissl-Eichinger C, Berg G (2015) Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees. Front Microbiol 6Google Scholar
  52. Pendergast TH, Burke DJ, Carson WP (2013) Belowground biotic complexity drives aboveground dynamics: a test of the soil community feedback model. New Phytol 197(4):1300–1310PubMedCrossRefGoogle Scholar
  53. Peñuelas J, Terradas J (2014) The foliar microbiome. Trends Plant Sci 19(5):278–280PubMedCrossRefGoogle Scholar
  54. Peñuelas J, Asensio D, Tholl D, Wenke K, Rosenkranz M, Piechulla B, Schnitzler JP (2014) Biogenic volatile emissions from the soil. Plant Cell Environ 37(8):1866–1891PubMedCrossRefGoogle Scholar
  55. Philippot L, Raaijmakers JM, Lemanceau P, Van Der Putten WH (2013) Going back to the roots: the microbial ecology of the rhizosphere. Nat Rev Microbiol 11(11):789–799PubMedCrossRefGoogle Scholar
  56. Porter SS, Simms EL (2014) Selection for cheating across disparate environments in the legume-rhizobium mutualism. Ecol Lett 17(9):1121–1129PubMedCrossRefGoogle Scholar
  57. Prestat E, David MM, Hultman J, Taş N, Lamendella R, Dvornik J, Mackelprang R, Myrold DD, Jumpponen A, Tringe SG, Holman E (2014) FOAM (functional ontology assignments for metagenomes): a hidden Markov model (HMM) database with environmental focus. Nucleic Acids Res 42(19):e145–e145PubMedPubMedCentralCrossRefGoogle Scholar
  58. Ratcliff WC, Denison RF (2009) Rhizobitoxine producers gain more poly-3-hydroxybutyrate in symbiosis than do competing rhizobia, but reduce plant growth. ISME J 3(7):870PubMedCrossRefGoogle Scholar
  59. Reinhold-Hurek B, Bünger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hotspots for microbial activity. Annu Rev Phytopathol 53:403–424PubMedCrossRefGoogle Scholar
  60. 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(2):187–194PubMedCrossRefGoogle Scholar
  61. Rybakova D, Cernava T, Köberl M, Liebminger S, Etemadi M, Berg G (2016a) Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus. Plant Soil 405(1–2):125–140CrossRefGoogle Scholar
  62. Rybakova D, Schmuck M, Wetzlinger U, Varo-Suarez A, Murgu O, Müller H, Berg G (2016b) Kill or cure? The interaction between endophytic Paenibacillus and Serratia strains and the host plant is shaped by plant growth conditions. Plant Soil 405(1–2):65–79CrossRefGoogle Scholar
  63. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Paré PW, Kloepper JW (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci 100(8):4927–4932PubMedCrossRefGoogle Scholar
  64. Sachs JL, Simms EL (2006) Pathways to mutualism breakdown. Trends Ecol Evol 21(10):585–592PubMedCrossRefGoogle Scholar
  65. Sachs JL, Mueller UG, Wilcox TP, Bull JJ (2004) The evolution of cooperation. Q Rev Biol 79(2):135–160PubMedCrossRefGoogle Scholar
  66. Sachs JL, Skophammer RG, Regus JU (2011) Evolutionary transitions in bacterial symbiosis. Proc Nat Acad Sci 108(supplement 2):10800–10807PubMedCrossRefGoogle Scholar
  67. Sánchez-Cañizares C, Jorrín B, Poole PS, Tkacz A (2017) Understanding the holobiont: the interdependence of plants and their microbiome. Curr Opin Microbiol 38:188–196PubMedCrossRefGoogle Scholar
  68. Santhanam R, Weinhold A, Goldberg J, Oh Y, Baldwin IT (2015) Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proc Natl Acad Sci 112(36):E5013–E5020PubMedCrossRefPubMedCentralGoogle Scholar
  69. Schenk ST, Schikora A (2015) AHL-priming functions via oxylipin and salicylic acid. Front Plant Sci 5:784PubMedPubMedCentralCrossRefGoogle Scholar
  70. Schlaeppi K, Dombrowski N, Oter RG, van Themaat EVL, Schulze-Lefert P (2014) Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives. Proc Natl Acad Sci 111(2):585–592PubMedCrossRefPubMedCentralGoogle Scholar
  71. Schmidt H, Eickhorst T (2013) Spatio-temporal variability of microbial abundance and community structure in the puddled layer of a paddy soil cultivated with wetland rice (Oryza sativa L.). Appl Soil Ecol 72:93–102CrossRefGoogle Scholar
  72. Souza RC, Mendes IC, Reis-Junior FB, Carvalho FM, Nogueira MA, Vasconcelos ATR, Vicente VA, Hungria M (2016) Shifts in taxonomic and functional microbial diversity with agriculture: how fragile is the Brazilian Cerrado? BMC Microbiol 16(1):42PubMedPubMedCentralCrossRefGoogle Scholar
  73. Swenson W, Wilson DS, Elias R (2000) Artificial ecosystem selection. Proc Natl Acad Sci 97(16):9110–9114PubMedCrossRefPubMedCentralGoogle Scholar
  74. Van Overbeek L, Van Elsas JD (2008) Effects of plant genotype and growth stage on the structure of bacterial communities associated with potato (Solanum tuberosum L.). FEMS Microbiol Ecol 64(2):283–296PubMedCrossRefPubMedCentralGoogle Scholar
  75. Vázquez-de-Aldana BR, García-Criado B, Vicente-Tavera S, Zabalgogeazcoa I (2013) Fungal endophyte (Epichloë festucae) alters the nutrient content of Festuca rubra regardless of water availability. PloS One 8(12):e84539PubMedPubMedCentralCrossRefGoogle Scholar
  76. Venturi V, Keel C (2016) Signaling in the rhizosphere. Trends Plant Sci 21(3):187–198PubMedCrossRefGoogle Scholar
  77. Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10(12):828–840PubMedCrossRefGoogle Scholar
  78. Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T (2014) Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 17(6):717–726PubMedPubMedCentralCrossRefGoogle Scholar
  79. Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T (2015) Corrigendum to Wagner et al.: natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 18(2):218–220CrossRefGoogle Scholar
  80. Werner GD, Strassmann JE, Ivens AB, Engelmoer DJ, Verbruggen E, Queller DC, Noë R, Johnson NC, Hammerstein P, Kiers ET (2014) Evolution of microbial markets. Proc Natl Acad Sci 111(4):1237–1244PubMedCrossRefGoogle Scholar
  81. Xiong W, Li Z, Liu H, Xue C, Zhang R, Wu H, Li R, Shen Q (2015) The effect of long-term continuous cropping of black pepper on soil bacterial communities as determined by 454 pyrosequencing. PloS One 10(8):e0136946PubMedPubMedCentralCrossRefGoogle Scholar
  82. Zachow C, Berg C, Müller H, Monk J, Berg G (2016) Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens. J Biotechnol 235:162–170PubMedCrossRefGoogle Scholar
  83. Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32(5):723–735PubMedCrossRefPubMedCentralGoogle Scholar
  84. Zolla G, Badri DV, Bakker MG, Manter DK, Vivanco JM (2013) Soil microbiomes vary in their ability to confer drought tolerance to Arabidopsis. Appl Soil Ecol 68:1–9CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • Pragati Sahai
    • 1
  • Vivek Kumar
    • 2
  1. 1.Amity Institute of BiotechnologyAmity UniversityNoidaIndia
  2. 2.Himalayan School of BiosciencesSwami Rama Himalayan UniversityJolly Grant, DehradunIndia

Personalised recommendations