Root-Associated Bacteria: Rhizoplane and Endosphere

  • Reeta Goel
  • Vinay Kumar
  • Deep Kumar Suyal
  • Biplab Dash
  • Prahalad Kumar
  • Ravindra SoniEmail author


Root-associated microbiota, primarily from the region of rhizoplane and endosphere, have an influential role for promoting plant growth and development. These microbial communities either directly or indirectly affect the root and subsequently the whole plant. However, several studies have been conducted to explore the hidden bacterial world found in rhizoplane and endosphere through several novel techniques for determining their role in enhancing plant growth. In the following sections of this chapter, we are going to discuss the present status of root-associated microbial research.


Rhizosphere Rhizoplane Endosphere Bacteria 


  1. Alain K, Querellou J (2009) Cultivating the uncultured: limits, advances and future challenges. Extremophiles 13:583–594PubMedCrossRefGoogle Scholar
  2. Al-Awadhi H, El-Nemr I, Mahmoud H, Sorkhoh NA, Radwan SS (2009) Plant-associated bacteria as tools for the phytoremediation of oily nitrogen-poor soils. Int J Phytoremediation 11:11–27CrossRefGoogle Scholar
  3. Aleklett K, Leff J, Fierer N, Hart M (2015) Wild plant species growing closely connected in a subalpine meadow host distinct root-associated bacterial communities. Peer J 3:e804PubMedPubMedCentralCrossRefGoogle Scholar
  4. 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:e53214PubMedPubMedCentralCrossRefGoogle Scholar
  5. Andria V, Reichenauer TG, Sessitsch A (2009) Expression of alkane monooxygenase (alkB) genes by plant-associated bacteria in the rhizosphere and endosphere of Italian ryegrass (Lolium multiflorum L.) grown in diesel contaminated soil. Environ Pollut 157:3347–3350PubMedCrossRefGoogle Scholar
  6. Anjum N, Chandra R (2015) Endophytic bacteria: optimization of isolation procedure from various medicinal plants and their preliminary characterization. Asian J Pharm Clin Res 8(4):233–238Google Scholar
  7. Araujo WL, Maccheroni W Jr, Aguilar-Vildoso CI, Barroso PAV, Saridakis HO, Azevedo JL (2001) Variability and interactions between endophytic bacteria and fungi isolated from leaf tissues of citrus rootstocks. Can J Microbiol 47:229–236PubMedCrossRefGoogle Scholar
  8. Araujo WL, Marcon J, Maccheroni W Jr, Elsas JDV, Vuurde JLV, Azevedo JL (2002) Diversity of endophytic bacterial populations and their interaction with Xylella fastidiosa in citrus plants. Appl Environ Microbiol 68:4906–4914PubMedPubMedCentralCrossRefGoogle Scholar
  9. Bai Y, D’Aoust F, Smith DL, Driscoll BT (2002) Isolation of plant-growth-promoting Bacillus strains from soybean root nodules. Can J Microbiol 48:230–238PubMedCrossRefGoogle Scholar
  10. Bai Y, Zhou X, Smith D (2003) Enhanced soybean plant growth due to coinoculation of Bacillus strains with Bradyrhizobium japonicum. Crop Sci 43:1774–1781CrossRefGoogle Scholar
  11. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266PubMedCrossRefGoogle Scholar
  12. Barahona E, Navazo A, Yousef-Coronado F, de Cárcer DA, Martinez-Granero F, Espinosa-Urgel M, Martín M, Rivilla R (2010) Efficient rhizosphere colonization by Pseudomonas fluorescens f113 mutants unable to form biofilms on abiotic surfaces. Environ Microbiol 12(12):3185–3195PubMedCrossRefGoogle Scholar
  13. Barea JM (2015) Future challenges and perspectives for applying microbial biotechnology in sustainable agriculture based on a better understanding of plant-microbiome interactions. J Soil Sci Plant Nutr 15:261–282Google Scholar
  14. Berg G, Zachow C, Lottmann J, Gotz M, Costa R, Smalla K (2005) Impact of plant species and site on rhizosphere-associated fungi antagonistic to Verticillium dahliae Kleb. Appl Environ Microbiol 71(8):4203–4213PubMedPubMedCentralCrossRefGoogle Scholar
  15. Berg G, Hallmann J. Schulz B, Boyle C, Sieber T (2006) Control of plant pathogenic fungi with bacterial endophytes. Springer, Berlin, pp 53–69Google Scholar
  16. Brader G, Compant S, Mitter B, Trognitz F, Sessitsch A (2014) Metabolic potential of endophytic bacteria. Curr Opin Biotechnol 27:30–37PubMedPubMedCentralCrossRefGoogle Scholar
  17. Bulgarelli D, Rott M, Schlaeppi K, Ver Loren van Themaat E, Ahmadinejad N, Assenza F, Rauf P, Huettel B, Reinhardt R, Schmelzer E (2012) Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota. Nature 488:91–95PubMedCrossRefGoogle Scholar
  18. Cavaglieri L, Orlando J, Etcheverry M (2009) Rhizosphere microbial community structure at different maize plant growth stages and root locations. Microbiol Res., 31 164(4):391–399PubMedCrossRefGoogle Scholar
  19. Chelius MK, Triplett EW (2000a) Immunolocalization of dinitrogenase reductase produced by Klebsiella pneumoniae in association with Zea mays L. Appl Environ Microbiol 66:783–787PubMedPubMedCentralCrossRefGoogle Scholar
  20. Chelius MK, Triplett EW (2000b) Diazotrophic endophytes associated with maize. In: Triplett EW (ed) Prokaryotic nitrogen fixation: a model system for the analysis of a biological process. Horizon Scientific Press, Wymondham, pp 779–791Google Scholar
  21. Chi F, Shen SH, Cheng HP, Jing YX, Yanni YG, Dazzo FB (2005) Ascending migration of endophytic rhizobia, from roots to leaves, inside rice plants and assessment of benefits to rice growth physiology. Appl Environ Microbiol 71(11):7271–7278PubMedPubMedCentralCrossRefGoogle Scholar
  22. Compant S, Kaplan H, Sessitsch A, Nowak J, Ait Barka E, Clement C (2008) Endophytic colonization of Burkholderia phytofirmans strain PsJN in Vitis vinifera L.: from the rhizosphere to inflorescence tissues. FEMS Microbiol Ecol 63:84–93PubMedCrossRefGoogle Scholar
  23. 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 42:669–678CrossRefGoogle Scholar
  24. Compant S, Mitter B, Colli-Mull JG, Gangl H, Sessitsch A (2011) Endophytes of grapevine flowers, berries and seeds: identification of cultivable bacteria, comparison with other plant parts, and visualization of niches of colonization. Microb Ecol 62:188–197PubMedCrossRefGoogle Scholar
  25. Compant S, Saima M, Lebrihi A, Florence M (2013) Visualization of grapevine root colonization by the Saharan soil isolate Saccharothrix algeriensis NRRL B-24137 using DOPE-FISH microscopy. Plant Soil 370(1–2):583–591CrossRefGoogle Scholar
  26. Conn VM, Franco CMM (2004) Analysis of endophytic actinobacterial population in the roots of wheat (Triticum aestivum L.) by terminal restriction fragment length polymorphism and sequencing of 16S rRNA clones. Appl Environ Microbiol 70:787–1794Google Scholar
  27. De Souza AO, Pamphile A, De Mello-Sartori CL, Da Rocha C, Azevedo JL (2004) Plant-microbe interactions between maize (Zea mays L.) and endophytic microorganisms observed by scanning electron microscopy. Acta Scientiarum Biol Sci 26:357–359Google Scholar
  28. Dennis Paul G, Miller AJ, Clark IM, Taylor RG, Valsami-Jones E, Hirsch PR (2008) A novel method for sampling bacteria on plant root and soil surfaces at the microhabitat scale. J Microbiol Methods 75:12–18PubMedCrossRefGoogle Scholar
  29. Deora A, Hashidoko Y, Islam MT, Tahara S (2005) Antagonistic rhizoplane bacteria induce diverse morphological alterations in Peronosporomycete hyphae during in vitro interaction. Eur J Plant Pathol 112:311–322CrossRefGoogle Scholar
  30. Dibbern D, Schmalwasser A, Lueders T, Totsche KU (2014) Selective transport of plant root-associated bacterial populations in agricultural soils upon snowmelt. Soil Biol Biochem 69:187–196CrossRefGoogle Scholar
  31. Dinkins RD, Barnes A, Waters W (2010) Microarray analysis of endophyte-infected and endophyte-free tall fescue. J Plant Physiol 167:1197–1203PubMedCrossRefGoogle Scholar
  32. 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):911–920CrossRefGoogle Scholar
  33. Eevers N, Gielen M, Sánchez-López A, Jaspers S, White JC, Vangronsveld J, Weyens N (2015) Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media. Microb Biotechnol 8(4):707–715PubMedPubMedCentralCrossRefGoogle Scholar
  34. Eller G, Frenzel P (2001) Changes in activity and community structure of methane-oxidizing bacteria over the growth period of rice. Appl Environ Microbiol 67:2395–2403PubMedPubMedCentralCrossRefGoogle Scholar
  35. Elvira-Recuenco M, van Vuurde JWL (2000) Natural incidence of endophytic bacteria in pea cultivars under field conditions. Can J Microbiol 46:1036–1041PubMedCrossRefGoogle Scholar
  36. Firáková S, Šturdíková M, Múčková M (2007) Bioactive secondary metabolites produced by microorganisms associated with plants, Section Botany, Institute of Botany, , Institute of Botany, Slovak Academy of Sciences. Biologia 62(3):251–257CrossRefGoogle Scholar
  37. Galbraith EA, Antonopoulos DA, White BA (2004) Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model. Environ Microbiol 6:928–937PubMedCrossRefGoogle Scholar
  38. Giongo A, Anelise B, Adriana A, Kayser LV, Roberto SM, Luiz EF, Zanettini B, Helena M, Pereira PLM (2010) Isolation and characterization of two plant growth-promoting bacteria from the rhizoplane of a legume (Lupinus albescens) in sandy soil. Rev Bras Ciênc Solo 34(2):361–369CrossRefGoogle Scholar
  39. Gottel NR, Castro HF, Kerley M, Yang Z, Pelletier DA, Podar M, Karpinets T, Uberbacher E, Tuskan GA, Vilgalys R, Doktycz MJ, Schadt CW (2011) Distinct microbial communities within the endosphere and rhizosphere of Populus deltoides roots across contrasting soil types. Appl Environ Microbiol 77:5934–5944PubMedPubMedCentralCrossRefGoogle Scholar
  40. Govindasamy V, Franco CMM, Gupta VVSR (2014) Endophytic actinobacteria: diversity and ecology. In: Advances in endophytic research. Springer, New Delhi, India. pp 27–59Google Scholar
  41. Hacquard S, Garrido-Oter R, Gonzalez A, Spaepen S, Ackermann G, Lebeis S, McHardy AC, Dangl JL, Knight R, Ley R, Schulze-Lefert P (2015) Microbiota and host nutrition across plant and animal kingdoms. Cell Host Microbe 17:603–616PubMedCrossRefGoogle Scholar
  42. Han J, Xia D, Li L, Lang L, Zhang L (2009) Diversity of culturable bacteria isolated from root domains of Moso Bamboo (Phyllostachys edulis). Microb Ecol 58:363PubMedCrossRefGoogle Scholar
  43. Han J, Song Y, Liu Z, Hu Y (2011) Culturable bacterial community analysis in the root domains of two varieties of tree peony (Paeonia ostii). FEMS Microbiol Lett 322(1):15–24PubMedCrossRefGoogle Scholar
  44. Han SI, Lee HJ, Whang KS (2014) Chitinophaga polysaccharea sp. nov., an exopolysaccharide-producing bacterium isolated from the rhizoplane of Dioscorea japonica. Int J Syst Evol Microbiol 64(1):55–59PubMedCrossRefGoogle Scholar
  45. Hang F, Yanchang L, Qiongguang L (2013) Endophytic bacterial communities in tomato plants with differential resistance to Ralstonia solanacearum. Afr J Microbiol Res 7:1311–1318CrossRefGoogle Scholar
  46. Hardoim PR, van Overbeek LS, van Elsas JD (2008) Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol 16:463–471PubMedCrossRefGoogle Scholar
  47. Hinsinger P, Bengough AG, Vetterlein D, Young I (2009) Rhizosphere: biophysics, biogeochemistry and ecological relevance. Plant Soil 321:117–152CrossRefGoogle Scholar
  48. Hong Y, Liao D, Hu A, Wang H, Chen J, Khan S, Su J, Li (2015) Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing. Can J Microbiol, 61 (10): 723–733Google Scholar
  49. Hoque MS, Broadhurst LM, Thrall PH (2011) Genetic characterization of root nodule bacteria associated with Acacia salicina and Acacia stenophylla (Mimosaceae) across south eastern Australia. Int J Syst Evol Microbiol 61(2):299–309PubMedCrossRefGoogle Scholar
  50. Huang WY, Cai Y, Hyde KD, Corke H, Sun M (2008) Biodiversity of endophytic fungi associated with 29 traditional Chinese medicinal plants. Fungal Divers 33:61–75Google Scholar
  51. Ibanez F, Angelini J, Taurian T, Tonelli ML, Fabra A (2009) Endophytic occupation of peanut nodules by opportunistic Gammaproteobacteria. Syst Appl Microb 32(1):49–55CrossRefGoogle Scholar
  52. Ikeda S, Kaneko T, Ohkubo T, Rallos LE (2009) Development of a bacterial cell enrichment method and its application to the community analysis in soybean stems. Microb Ecol 58:703–714PubMedCrossRefGoogle Scholar
  53. Ikeda S, Okubo T, Anda M, Nakashita H (2010) Community and genome-based views of plant-associated bacteria: plant–bacterial interactions in soybean and rice. Plant Cell Physiol 51:1398–1410PubMedCrossRefGoogle Scholar
  54. Ikenaga M, Muraoka Y, Toyota K, Kimura M (2002) Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis. Biol Fertil Soils 36:397–340CrossRefGoogle Scholar
  55. Islam MT, Hashidoko Y, Deora A, Ito T, Tahara S (2005) Suppression of damping-off disease in host plants by the rhizoplane bacterium Lysobacter sp. strain SB-K88 is linked to plant colonization and antibiosis against soilborne peronosporomycetes. Appl Environ Microbiol 71(7):3786–3796PubMedPubMedCentralCrossRefGoogle Scholar
  56. Johri JK, Surange S, Nautiyal CS (1999) Occurrence of salt, pH and temperature tolerant phosphate solubilizing bacteria in alkaline soils. Curr Microbiol 39:89–93PubMedCrossRefGoogle Scholar
  57. Johri BN, Sharma A, Virdi JS (2003) Rhizobacterial diversity in India and its influence on soil and plant health. Adv Biochem Eng Biotechnol 84:49–89PubMedGoogle Scholar
  58. Joseph B, Mini Priya R (2011) Bioactive compounds from endophytes and their potential in pharmaceutical effect: a review. Am J Biochem Mol Biol 1(3):291–309CrossRefGoogle Scholar
  59. Kaewkla O, Franco CMM (2013) Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees. Microb Ecol 65:384–393PubMedCrossRefGoogle Scholar
  60. Kämpfer P, McInroy JA, Glaeser SP (2015) Chryseobacterium rhizoplanae sp. nov., isolated from the rhizoplane environment. Antonie Van Leeuwenhoek 107(2):533–538PubMedCrossRefGoogle Scholar
  61. Kgomotso M, Maropola A, Ramond JB, Trindade M (2015) Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). J Microbiol Methods 112:104–117CrossRefGoogle Scholar
  62. Khan MU, Sessitsch A, Harris M, Fatima K, Imran A, Arslan M, Shabir G, Khan QM, Afzal M (2015) Cr-resistant rhizo and endophytic bacteria associated with Prosopis juliflora and their potential as phytoremediation enhancing agents in metal-degraded soils. Front Plant Sci 6(5):755Google Scholar
  63. Kishore GK, Pande S, Podile AR (2005) Phylloplane bacteria increase seedling emergence, growth and yield of field-grown groundnut (Arachis hypogaea L.) Lett Appl Microbiol 40(4):260–268PubMedCrossRefGoogle Scholar
  64. Knief C (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front Plant Sci 5:216PubMedPubMedCentralCrossRefGoogle Scholar
  65. Kowalchuk GA, Buma DS, de Boer W, Klinkhamer PGL, van Veen JA (2002) Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms. Antonie Van Leeuwenhoek 81:509–520PubMedCrossRefGoogle Scholar
  66. Kuklinsky-Sobral J, Araujo 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 6:1244–1251PubMedCrossRefGoogle Scholar
  67. Kuklinsky-Sobral J, Araujo WL, Mendes R, Pizzirani-Kleiner AA, Azevedo JL (2005) Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide. Plant Soil 273:91–99CrossRefGoogle Scholar
  68. Lau JA, Lennon JT (2011) Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits. New Phytol 192:215–224PubMedCrossRefGoogle Scholar
  69. Lau JA, Lennon JT (2012) Rapid responses of soil microorganisms improve plant fitness in novel environments. Proc Natl Acad Sci U S A 109:14058–14062PubMedPubMedCentralCrossRefGoogle Scholar
  70. Lee HJ, Cho GY, Chung SH, Whang KS (2014) Streptomyces panaciradicis sp. nov., a β-glucosidase-producing bacterium isolated from ginseng rhizoplane. Int J Syst Evol Microbiol 64:3816–3820PubMedCrossRefGoogle Scholar
  71. Li JH, Wang ET, Chen WF, Chen WX (2008) Genetic diversity and potential for promotion of plant growth detected in nodule endophytic bacteria of soybean grown in Heilongjiang province of China. Soil Biol Biochem 40:238–246CrossRefGoogle Scholar
  72. Ma Y, Zhang C, Oliveira RS, Freitas H, Luo Y (2016) Bio augmentation with endophytic bacterium E6S homologous to Achromobacter piechaudii enhances Metal Rhizo accumulation in Host Sedum plumbizincicola. Front Plant Sci 7:75PubMedPubMedCentralGoogle Scholar
  73. Madhaiyan M, Poonguzhali S, Saravanan VS, Kwon SW (2014) Rhodanobacter glycinis sp. nov., a yellow pigmented gammaproteobacterium isolated from the rhizoplane of field-grown soybean. Int J Syst Evol Microbiol 64:2023–2028PubMedCrossRefGoogle Scholar
  74. Mano H, Morisaki H (2008) Endophytic bacteria in the rice plant. Microbes Environ 23:109–117PubMedCrossRefGoogle Scholar
  75. Manter DK, Kolodny EH, Hansen EM, Parke JL (2010) Virulence, sporulation, and elicitin production in three clonal lineages of Phytophthora ramorum. Physiol Mol Plant Pathol 74:317–322CrossRefGoogle Scholar
  76. Matsuzawa H, Tanaka Y, Tamaki H, Kamagata Y, Mori K (2010) Culture-dependent and independent analyses of the microbial communities inhabiting the giant duckweed (Spirodela polyrrhiza) rhizoplane and isolation of a variety of rarely cultivated organisms within the phylum Verrucomicrobia. Microbes Environ/JSME 25(4):302–308CrossRefGoogle Scholar
  77. Maurya MK, Singh R, Tomer A (2014) In vitro evaluation of antagonistic activity of Pseudomonas fluorescens against fungal pathogen. J Biopest 7(1):43–46Google Scholar
  78. Mengoni A, Pini F, Shu WS, Huang LN, Bazzicalupo M (2009) Plant-by-plant variations of leaf-associated bacterial communities in the nickel-hyper accumulator Alyssum bertolonii Desv. Microb Ecol 58:660–667PubMedCrossRefGoogle Scholar
  79. Mercado-Blanco J (2015) Life of microbes inside the plant. In: Lugtenberg B (ed) Principles of plant- microbe interactions. Springer, Heidelberg, pp 25–32Google Scholar
  80. Miliute I, Buzaite O, Stanys V (2015) Bacterial endophytes in agricultural crops and their role in stress tolerance: a review. Zemdirbyste-Agriculture 102(4):465–478CrossRefGoogle Scholar
  81. Monteiro RA, Balsanelli E, Tuleski T, Faoro H, Cruz LM, Wassem R, de Baura VA, Tadra-Sfeir MZ, Weiss V, DaRocha WD, Muller-Santos M, Chubatsu LS, Huergo LF, Pedrosa FO, de Souza EM (2012) Genomic comparison of the endophyte Herbaspirillum seropedicae SmR1 and the phytopathogen Herbaspirillum rubrisubalbicans M1 by suppressive subtractive hybridization and partial genome sequencing. FEMS Microbiol Ecol 80:441–451PubMedCrossRefGoogle Scholar
  82. Muraoka Y, Hamakawa E, Toyota K, Kimura M (2000) Observation of microbial colonization on the surface of rice roots along with their development and degradation. Soil Sci Plant Nutr 46:491–502Google Scholar
  83. Muratova A, Hubner T, Narula N, Wand H, Turkovskaya O, Kuschk P, Jahn R, Merbach W (2003) Rhizosphere microflora of plants used for the phytoremediation of bitumen-contaminated soil. Microbiol Res 158:151–161PubMedCrossRefGoogle Scholar
  84. Nair DN, Padmavathy S (2014) Impact of endophytic microorganisms on plants, environment and humans. Sci World J 2014: 11Google Scholar
  85. Nguyen C (2003) Rhizodeposition of organic C by plants: mechanisms and controls. Agronomie 23:375–396CrossRefGoogle Scholar
  86. Normander B, Prosser JI (2000) Bacterial origin and community composition in the barley phytosphere as a function of habitat and presowing conditions. Appl Environ Microbiol 66:4372–4377PubMedPubMedCentralCrossRefGoogle Scholar
  87. Nunan N, Daniell TJ, Singh BK, Papert A, McNicol JW, Prosser JI (2005) Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques. Appl Environ Microbiol 71(11):6784–6792PubMedPubMedCentralCrossRefGoogle Scholar
  88. Ofek-Lalzar M, Sela N, Goldman-Voronov M, Green SJ, Hadar Y, Minz D (2014) Niche and host associated functional signatures of the root surface microbiome. Nat Commun 5:49–50CrossRefGoogle Scholar
  89. Owen NL, Hundley N (2004) Endophytes–the chemical synthesizers inside plants. Sci Prog 87(2):79–99PubMedCrossRefGoogle Scholar
  90. Prieto P, Schiliro E, Maldonado-González MM, Valderrama R, Barroso-Albarracín JB, Mercado-Blanco J (2011) Root hairs play a key role in the endophytic colonization of olive roots by Pseudomonas spp. with biocontrol activity. Microb Ecol 62:435–445PubMedPubMedCentralCrossRefGoogle Scholar
  91. Raaijmakers JM, Vlami M, de Souza JT (2002) Antibiotic production by bacterial biocontrol agents. Antonie Van Leeuwenhoek 81:537–547PubMedCrossRefGoogle Scholar
  92. Raja S, Subhashini P, Thangaradjou T (2016) Differential methods of localisation of fungal endophytes in the seagrasses. Mycology 7(3):112–123CrossRefGoogle Scholar
  93. Ravikumar M, Malani Devi S (2014) Occurrence of fungal flora in water, air, soil ecosystem and screening of fungal enzymes. Int J Adv Multidiscip Res 1(1):52–62Google Scholar
  94. Reinhold-Hurek B, Bunger W, Burbano CS, Sabale M, Hurek T (2015) Roots shaping their microbiome: global hot spots for microbial activity. Annu Rev Phytopathol 53:403–424PubMedCrossRefGoogle Scholar
  95. Richter-Heitmann T, Eickhorst T, Knauth S, Friedrich MW, Schmidt H (2016) Evaluation of strategies to separate root-associated microbial communities: a crucial choice in rhizobiome research. Front Microbiol 7:773PubMedPubMedCentralCrossRefGoogle Scholar
  96. Robinson RJ, Fraaije BA, Clark IM, Jackson RW, Hirsch PR, Mauchline TH (2016) Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability. Plant Soil 405:381–396CrossRefGoogle Scholar
  97. Rosenblueth M, Martínez-Romero E (2006) Bacterial endophytes and their interactions with hosts. Mol Plant Microbe Interact 19(8):827–837Google Scholar
  98. Ryan PR, Delhaize E (2001) Function and mechanism of organic anion exudation from plant roots. Annu Rev Plant Physiol Mol Biol 52:527–560CrossRefGoogle Scholar
  99. Schlaeppi K, Bulgarelli D (2015) The plant microbiome at work. Mol. Plant Microbe Interact 28:212–217CrossRefGoogle Scholar
  100. Schmidt H, Eickhorst T (2014) Detection and quantification of native microbial populations on soil-grown rice roots by catalyzed reporter deposition fluorescence in situ hybridization. FEMS Microbiol Ecol 87:390–402PubMedCrossRefGoogle Scholar
  101. Sessitsch A, Hardoim P, Doring J, Weilharter A, Krause A, Woyke T, Mitter B, Hauberg-Lotte L, Friedrich F, Rahalkar M, Hurek T, Sarkar A, Bodrossy L, van Overbeek L, Brar D, van Elsas JD, Reinhold-Hurek B (2012) Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol Plant-Microbe Interact 25:28–36PubMedCrossRefGoogle Scholar
  102. Singer MJ, Donald NM (2006) Soils: an introduction. Pearson Education, New JerseyGoogle Scholar
  103. Strobel G, Daisy B, Castillo U, Harper J (2004) Natural products from endophytic microorganisms. J Nat Prod 67:257–268PubMedCrossRefGoogle Scholar
  104. Surette M, Sturz A, Lada R, Nowak J (2003) Bacterial endophytes in processing carrots (Daucus carota L. Var. sativus): their localization, population density, biodiversity and their effects on plant growth. Plant Soil 253:381–390CrossRefGoogle Scholar
  105. Sylvia D, Fuhrmann J, Hartel P, Zuberer D (2005) Principles and applications of soil microbiology. Pearson Education, New JerseyGoogle Scholar
  106. Thomas P (2011) Intense association of non-culturable endophytic bacteria with antibiotic-cleansed in vitro watermelon and their activation in degenerating cultures. Plant Cell Rep 30:2313–2325PubMedCrossRefGoogle Scholar
  107. Tokala RK, Strap JL, Jung CM, Crawford DL (2002) Novel plant-microbe rhizosphere interaction involving Streptomyces lydicus WYEC108 and the pea plant (Pisum sativum). Appl Environ Microbiol 68:2161–2171PubMedPubMedCentralCrossRefGoogle Scholar
  108. Trujillo ME, Riesco R, Benito Pand Carro L (2015) Endophytic Actinobacteria and the interaction of Micromonospora and nitrogen nixing plants. Front Microbiol 6:1341PubMedPubMedCentralCrossRefGoogle Scholar
  109. Turner TR, Ramakrishnan K, Walshaw J, Heavens D, Alston M, Swar-beck D, Osbourn A, Grant A, Poole PS (2013) Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME 7:2248–2258CrossRefGoogle Scholar
  110. Van Overbeek LS, Saikkonen K (2016) Impact of bacterial–fungal interactions on the colonization of the endosphere. Trends Plant Sci 21:3Google Scholar
  111. Vendramin E, Gastaldo A, Tondello A, Baldan B, Villani M, Squartini A (2010) Identification of two fungal endophytes associated with the endangered orchid Orchis militaris L. J Microbiol Biotechnol 2:630–636Google Scholar
  112. Villacieros M, Power B, Sanchez-Contreras M, Lloret J, Oruezábal RI, Martín M, Bonilla I, Whelan C, Dowling DN, Rivilla R (2003) Colonization behaviour of Pseudomonas fluorescens and Sinorhizobium meliloti in the alfalfa (Medicago sativa) rhizosphere. Plant Soil 251:47–54CrossRefGoogle Scholar
  113. Visioli G, Vamerali T, Mattarozzi M, Dramis L, Sanangelantoni AM (2015) Combined endophytic inoculants enhance nickel phytoextraction from serpentine soil in the hyperaccumulator Noccaea caerulescens. Front Plant Sci 6:638Google Scholar
  114. Wagner MR et al (2014) Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 17:717–726PubMedPubMedCentralCrossRefGoogle Scholar
  115. Zamioudis C, Pieterse CMJ (2012) Modulation of host immunity by beneficial microbes. Mol Plant-Microbe Interact 25:139–150PubMedCrossRefGoogle Scholar
  116. Zhang HW, Song YC, Tan RX (2006) Biology and chemistry of endophytes. Nat Prod Rep 23:753–771PubMedCrossRefGoogle Scholar
  117. Zhang X, Gao J, Cao Y, Sheirdi RA, Wang X, Xhang L (2015) Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots. Int J Syst Evol Microbiol 65:2931–2936PubMedCrossRefGoogle Scholar
  118. Zinniel DK, Lambercht P, Beth Harris N, Feng Z, Kuczmarski D, Highley P, Ishimaru CA, Arunakumari A, Barletta RG, Vidaver AK (2002) Isolation and characterization of endophytic colonizing bacteria from agronomic crops and prairie plants. Appl Environ Microbiol 68:2198–2208PubMedPubMedCentralCrossRefGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Reeta Goel
    • 1
  • Vinay Kumar
    • 2
  • Deep Kumar Suyal
    • 1
  • Biplab Dash
    • 3
  • Prahalad Kumar
    • 3
  • Ravindra Soni
    • 3
    Email author
  1. 1.Department of Microbiology, College of Basic Sciences and HumanitiesG. B. Pant University of Agriculture & TechnologyPantnagarIndia
  2. 2.ICAR-National Institute of Biotic Stress ManagementRaipurIndia
  3. 3.Department of Agricultural Microbiology, College of AgricultureIndira Gandhi Krishi VishvaVidyalayaRaipurIndia

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