Beneficial Microbes for Disease Suppression and Plant Growth Promotion

  • Mukesh MeenaEmail author
  • Prashant Swapnil
  • Andleeb Zehra
  • Mohd Aamir
  • Manish Kumar Dubey
  • Jyoti Goutam
  • R. S. Upadhyay


Plant growth-promoting microorganisms (PGPMs) constitute the microbes that are intricately associated with the plant system and may consist of rhizospheric bacteria, fungi, mycorrhiza, endophytic fungi, actinomycetes, or those having the mutualistic relationship or nonsymbiotic relationship with plants. One of the most remarkable features of these microbes is the adoption of certain ecological niches or may be occupied with multiple niches at a time in the soil ecosystem that makes way for other species to establish the mutual interactions (physical or biochemical) with other microbes (bipartite) or with plants (tripartite). The plant growth promotion by these microbes involves common mechanisms such as nitrogen fixation, siderophore production, phytohormone production, solubilization of mineral phosphates and secretion of novel secondary metabolites having positive effect on plant health. Some beneficial fungi have been found to promote plant growth through increased photosynthetic rate with improved mineral use efficiency and nutrient uptake, as inoculating these microbes with plants lead into increased chlorophyll content and biomass. These indigenous microbes have been also reported to counteract the different abiotic and biotic stress conditions. The mutual interaction observed between beneficial fungi and pathogenic microbes has been investigated at microscopic level which involves certain physical changes such as coiling of beneficial hyphae around the pathogenic hyphae and some cellular changes such as dissolution of host cytoplasm or secretion of antimicrobial compounds or lytic enzymes in the nearby localities that check the growth and reproduction of pathogenic species. The comprehensive knowledge of the functional mechanism of plant growth promotion by these microbes will help to develop strategies against damages covered by various abiotic and biotic stress conditions, and therefore will help in increasing the agricultural production at a global scale.


Plant growth-promoting rhizobacteria (PGPR) Siderophore Nitrogen fixation Phosphate solubilization Phytohormones Antibiotics 



The author Mukesh Meena is thankful to the Head Department of Botany and Programme Coordinator, Centre of Advanced Study in Botany, Banaras Hindu University, and UGC, New Delhi, for providing the necessary facilities for this study.


  1. Abd-Alla MH (1994) Use of organic phosphorus by Rhizobium leguminosarum biovar. Viceae phosphatases. Biol Fertil Soils 18:216–218CrossRefGoogle Scholar
  2. Adam E, Müller H, Erlacher A, Berg G (2016) Complete genome sequences of the Serratia plymuthica strains 3Rp8 and 3Re4-18, two rhizosphere bacteria with antagonistic activity towards fungal phytopathogens and plant growth promoting abilities. Stand Genomic Sci 11(1):61. PubMedCentralCrossRefPubMedGoogle Scholar
  3. Aeron A, Kumar S, Pandey P, Maheshwari DK (2011) Emerging role of plant growth promoting rhizobacteria in agrobiology. In: Maheshwari DK (ed) Bacteria in agrobiology: crop ecosystems. Springer, Berlin/Heidelberg, pp 1–36. Google Scholar
  4. Ahemad M, Kibret M (2014) Mechanisms and applications of plant growth promoting rhizobacteria: current perspectives. J King Saud Univ Sci 26(1):1–20CrossRefGoogle Scholar
  5. Ahmad F, Ahmad I, Khan MS (2005) Indole acetic acid production by the indigenous isolates of Azotobacter and fluorescent Pseudomonas in the presence and absence of tryptophan. Turk J Biol 29:29–34Google Scholar
  6. Aislabie J, Deslippe JR (2013) Soil microbes and their contribution to soil services. In Dymond JR (ed) Ecosystem services in New Zealand–conditions and trends. Manaaki Whenua Press, Lincoln, New Zealand pp 143–161Google Scholar
  7. Akhtar MS, Siddiqui ZA, Wiemken A (2016) Arbuscular mycorrhizal fungi and Rhizobium to control plant fungal diseases. In: Lichtfouse E (ed) Alternative farming systems, biotechnology, drought stress and ecological fertilisation. Springer, Dordrecht, pp 263–292Google Scholar
  8. Alabouvette C, Olivain C, Migheli Q, Steinberg C (2009) Microbiological control of soil borne phytopathogenic fungi with special emphasis on wilt-inducing Fusarium oxysporum. New Phytol 184:529–544CrossRefPubMedGoogle Scholar
  9. Alavi P, Starcher MR, Zachow C, Müller H, Berg G (2013) Root–microbe systems: the effect and mode of interaction of stress protecting agent (SPA) Stenotrophomonas rhizophila DSM14405T. Front Plant Sci 4:141. PubMedCentralCrossRefPubMedGoogle Scholar
  10. Amara U, Khalid R, Hayat R (2015) Soil bacteria and phytohormones for sustainable crop production. In: Maheshwari DK (ed) Bacterial metabolites in sustainable agroecosystem. Springer, Cham, pp 87–103. CrossRefGoogle Scholar
  11. Antoun H, Prévost D (2006) Ecology of plant growth promoting rhizobacteria. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Heidelberg, pp 1–20Google Scholar
  12. Arora NK, Kang SC, Maheshwari DK (2001) Isolation of siderophore producing strains of Rhizobium meliloti and their biocontrol potential against Macrophomina phaseolina that causes charcoal rot of groundnut. Curr Sci 81:673–677Google Scholar
  13. Arshad M, Frankenberger WT Jr (1997) Plant growth regulating substances in the rhizosphere: Microbial production and functions. Adv Agron 62:45–151Google Scholar
  14. Atzorn R, Crozier A, Wheeler CT, Sandberg G (1988) Production of gibberellins and indole-3-acetic acid by Rhizobium phaseoli in relation to nodulation of Phaseolus vulgaris roots. Planta 175:532–538CrossRefPubMedGoogle Scholar
  15. Baby UI, Chandramouli B (1996) Biological antagonism of Trichoderma and Gliocladium sp. against certain primary root pathogens of tea. J Plant Crops 24:249–255Google Scholar
  16. Badenoch-Jones J, Summons RE, Djordjevic MA, Shine J, Letham DS, Rolfe BG (1982) Mass-spectrometric quantification of indole-3-acetic acid in Rhizobium culture supernatants: Relation to root hair curling and nodule initiation. Appl Environ Microbiol 44:275–280PubMedCentralPubMedGoogle Scholar
  17. 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 57:233–266CrossRefPubMedGoogle Scholar
  18. Bakker PA, Berendsen RL, Doornbos RF, Wintermans PC, Pieterse CM (2013) The rhizosphere revisited: root microbiomics. Front Plant Sci 30:165. Google Scholar
  19. Banik S, Dey BK (1982) Available phosphate content of an alluvial soil as influenced by inoculation of some isolated phosphate-solubilizing micro-organisms. Plant Soil 69:353–364CrossRefGoogle Scholar
  20. Bastián F, Cohen A, Piccoli P, Luna V, Baraldi R, Bottini R (1998) Production of indole-3-acetic acid and gibberellins A1 and A3 by Acetobacter diazotrophicus and Herbaspirillum seropedicae in chemically-defined culture media. Plant Growth Regul 24:7–11CrossRefGoogle Scholar
  21. Beneduzi A, Peres D, Da Costa PB, Bodanese Zanettini MH, Passaglia LM (2008) Genetic and phenotypic diversity of plant-growth-promoting bacilli isolated from wheat fields in southern Brazil. Res Microbiol 159:244–250CrossRefPubMedGoogle Scholar
  22. Berendsen RL, Pieterse CM, Bakker PA (2012) The rhizosphere microbiome and plant health. Trends Plant Sci 17:478–486CrossRefPubMedGoogle Scholar
  23. Berg G, Eberl L, Hartmann A (2005) The rhizosphere as a reservoir for opportunistic human pathogenic bacteria. Environ Microbiol 7:1673–1685CrossRefPubMedGoogle Scholar
  24. Berge OMH, Guinebretiér W, Achouak P, Normand T, Heulin P (2002) Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 52:607–616CrossRefPubMedGoogle Scholar
  25. Berraho EL, Lesueur D, Diem HG, Sasson A (1997) Iron requirement and siderophore production in Rhizobium ciceri during growth on an iron-deficient medium. World J Microbiol Biotechnol 13:501–510CrossRefGoogle Scholar
  26. Biswas JC, Ladha JK, Dazzo FB (2000) Rhizobial inoculation influences seedling vigor and yield of rice. Agron J 92:880–886CrossRefGoogle Scholar
  27. Boiero L, Perrig D, Masciarelli O, Penna C, Cassán F, Luna V (2007) Phytohormone production by three strains of Bradyrhizobium japonicum and possible physiological and technological implications. Appl Microbiol Biotechnol 74:874–880CrossRefPubMedGoogle Scholar
  28. Bonfante P, Anca IA (2009) Plants, mycorrhizal fungi, and bacteria: a network of interactions. Annu Rev Microbiol 63:363–383CrossRefPubMedGoogle Scholar
  29. Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis. Nat Commun 1:48.
  30. Borthakur BK, Dutta PK (1992) Prospect of biocontrol of tea diseases in North East India. In: Proceedings of the 31st Toklai Conference, pp 163–168Google Scholar
  31. Bottini R, Cassán F, Piccoli P (2004) Gibberellin production by bacteria and its involvement in plant growth promotion and yield increase. Appl Microbiol Biotechnol 65:497–503CrossRefPubMedGoogle Scholar
  32. Braud A, Jézéquel K, Bazot S, Lebeau T (2009) Enhanced phytoextraction of an agricultural Cr-, Hg- and Pb-contaminated soil by bioaugmentation with siderophore producing bacteria. Chemosphere 74:280–286CrossRefPubMedGoogle Scholar
  33. Brotman Y, Briff E, Viterbo A, Chet I (2008) Role of swollenin, an expansin-like protein from Trichoderma, in plant root colonization. Plant Physiol 147:779–789PubMedCentralCrossRefPubMedGoogle Scholar
  34. Buch A, Archana G, Naresh-Kumar G (2008) Metabolic channeling of glucose towards gluconate in phosphate solubilizing Pseudomonas aeruginosa P4 under phosphorus deficiency. Res Microbiol 159:635–642CrossRefPubMedGoogle Scholar
  35. Bulgarelli D, Schlaeppi K, Spaepen S, Lorenvan V, Themaat E, SchulzeLefert P (2013) Structure and functions of the bacterial micro- biota of plants. Annu Rev Plant Biol 64:807–838CrossRefPubMedGoogle Scholar
  36. Burd GI, Dixon DG, Glick BR (2000) Plant growth-promoting bacteria that decrease heavy metal toxicity in plants. Can J Microbiol 46:237–245CrossRefPubMedGoogle Scholar
  37. Cakmakci R, Erat M, Erdoğan Ü, Dönmez MF (2007) The influence of plant growth-promoting rhizobacteria on growth and enzyme activities in wheat and spinach plants. J Plant Nutr Soil Sci 170:288–295CrossRefGoogle Scholar
  38. Cassán F, Bottini R, Schneider G, Piccoli P (2001) Azospirillum brasilense and Azospirillum lipoferum hydrolyze conjugates of GA20 and metabolize the resultant aglycones to GA1 in seedling of rice dwarf mutants. Plant Physiol 125:2053–2058PubMedCentralCrossRefPubMedGoogle Scholar
  39. Chanclud E, Kisiala A, Emery NRJ, Chalvon V, Ducasse A, Romiti-Michel C, Gravot A, Kroj T, Morel JB (2016) Cytokinin production by the rice blast fungus is a pivotal requirement for full virulence. PLoS Pathog 12(2):e1005457. PubMedCentralCrossRefPubMedGoogle Scholar
  40. Chandra S, Choure K, Dubey RC, Maheshwari DK (2007) Rhizosphere competent Mesorhizobium loti MP6 induce root hair curling, inhibit Sclerotinia sclerotiorum and enhances growth of Indian mustard (Brassica campestris). Braz J Microbiol 38(2):124–130CrossRefGoogle Scholar
  41. Chandramouli MR, Baby UI (2002) Control of thorny stem blight disease of tea with fungicides and biocontrol agents. In: Rethium P, Khan HH, Reddy VM, Mandal KP, Suresh K (eds) Proceedings of plantation crops and development in the New Millennium. Coconut Development Board, Kochi, India, pp 531–534Google Scholar
  42. Chang WT, Chen YC, Jao CL (2007) Antifungal activity and enhancement of plant growth by Bacillus cereus grown on shellfish chitin wastes. Biores Technol 98:1224–1230CrossRefGoogle Scholar
  43. Chen YP, Rekha PD, Arun AB, Shen FT, Lai WA, Young CC (2006) Phosphate solubilizing bacteria from subtropical soil and their tricalcium phosphate solubilizing abilities. Appl Soil Ecol 34:33–41CrossRefGoogle Scholar
  44. Chen L, Liu Y, Wu G, Veronican Njeri K, Shen Q, Zhang N, Zhang R (2016) Induced maize salt tolerance by rhizosphere inoculation of Bacillus amyloliquefaciens SQR9. Physiol Plant 158(1):34–44CrossRefPubMedGoogle Scholar
  45. Chet I (1987) Trichoderma-Application, mode of action, and potential as a biocontrol agent of soilborne pathogenic fungi. Innovative approaches to plant disease control. Wiley, New York, pp 137–160Google Scholar
  46. Comai L, Kosuge T (1980) Involvement of a plasmid deoxyribonucleic acid in indoleacetic acid synthesis in Pseudomonas savastanoi. J Bacteriol 143:950–957PubMedCentralPubMedGoogle Scholar
  47. 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
  48. Cornelis P (2010) Iron uptake and metabolism in Pseudomonads. Appl Microbiol Biotechnol 86:1637–1645CrossRefPubMedGoogle Scholar
  49. Cowan MC (1979) Water use and phosphorus and potassium status of wheat seedlings colonized by Gaeumannomyces graminis on roots of grasses and cereals. Trans Br Mycol Soc 61:471–485Google Scholar
  50. Crowley DE (2006) Microbial siderophores in the plant rhizospheric. In: Barton LL, Abadía J (eds) Iron nutrition in plants and rhizospheric microorganisms. Springer, Dordrecht, pp 169–198CrossRefGoogle Scholar
  51. Crozier A, Kamiya Y, Bishop G, Yokota T (2000) Biosynthesis of hormones and elicitor molecules. In: Buchanan BB, Gruissem W, Jones RL (eds) Biochemistry and molecular biology of plants. American Society of Plant Physiology, Rockville, pp 850–929Google Scholar
  52. Dames JF, Ridsdale CJ (2012) What we know about arbuscular mycorrhizal fungi and associated soil bacteria. Afr J Biotechnol 11:13753–13760Google Scholar
  53. Daniel JF, Filho ER (2007) Peptaibols of Trichoderma. Nat Prod Rep 24:1128–1141CrossRefPubMedGoogle Scholar
  54. Davies PJ (1995) The plant hormones: their nature, occurrence and functions. In: Davies PJ (ed) Plant hormones: physiology, biochemistry and molecular biology. Kluwer, Dordrecht, pp 1–12CrossRefGoogle Scholar
  55. Davies RM, Menge JA (1980) Influence of Glomus fasciculatus and soil phosphorus on Phytophthora root-rot of citrus. Phytopathology 70:447–452CrossRefGoogle Scholar
  56. Dazzo FB, Yanni YG, Rizk R, de Bruijn FJ, Rademaker J, Squartini A, Corich V, Mateos P, Martínez-Molina E, Velázquez E, Biswas JC, Hernandez RJ, Ladha JK, Hill J, Weinman J, Rolfe BG, Vega-Hernández M, Bradford JJ, Hollingsworth RI, Ostrom P, Marshall E, Jain T, Orgambide G, Philip-Hollingsworth S, Triplett E, Malik KA, Maya-Flores J, Hartmann A, UmaliGarcia M, Izaguirre-Mayoral ML (2000) Progress in multinational collaborative studies on the beneficial association between Rhizobium leguminosarum bv. trifolii and rice. In: Ladha JK, Reddy PM (eds) The quest for nitrogen fixation in rice. Los Banos, Philippines, pp 167–189Google Scholar
  57. De la Cruz J, Hidalgo-Gallego A, Lora JM, Benítez T, Pintor-Tora JA, Llobell A (1992) Isolation and characterization of three chitinases from Trichoderma harzianum. Eur J Biochem 206:859–867CrossRefPubMedGoogle Scholar
  58. de Oliveira Mendes G, Moreira de Freitas AL, Liparini Pereira O, Riberio da Silva I, Vassilev NB, Costa MD (2014) Mechanisms of phosphate solubilisation by fungal isolates when exposed to different P sources. Ann Microbiol 64(1):239–249CrossRefGoogle Scholar
  59. Dell’Amico E, Cavalca L, Andreoni V (2008) Improvement of Brassica napus growth under cadmium stress by cadmium resistant rhizobacteria. Soil Biol Biochem 40:74–84CrossRefGoogle Scholar
  60. Deml G, Voges K, Jung G, Winkelmann G (1984) Tetraglycyl ferrichrome – the first heptapeptide ferrichrome. FEBS Lett 173:53–57CrossRefGoogle Scholar
  61. Dey R, Pal KK, Bhatt DM, Chauhan SM (2004) Growth promotion and yield enhancement of peanut (Arachis hypogaea L.) by application of plant growth-promoting rhizobacteria. Microbiol Res 159:371–394CrossRefPubMedGoogle Scholar
  62. Dimkpa C, Svatos A, Merten D, Büchel G, Kothe E (2008) Hydroxamate siderophores produced by Streptomyces acidiscabies E13 bind nickel and promote growth in cowpea (Vigna unguiculata L.) under nickel stress. Can J Microbiol 54(3):163–172Google Scholar
  63. Djamei A, Schipper K, Rabe F, Ghosh A, Vincon V, Kahnt J, Osorio S, Tohge T, Fernie AR, Feussner I, Feussner K, Meinicke P, Stierhof YD, Schwarz H, Mecek B, Mann M, Kahmann R (2011) Metabolic priming by a secreted fungal effector. Nature 478:395–398CrossRefPubMedGoogle Scholar
  64. Djonovic S, Vargas WA, Kolomiets MV, Horndeski M, Wiest A, Kenerley CM (2007) A proteinaceous elicitor Sm1 from the beneficial fungus Trichoderma virens is required for induced systemic resistance in maize. Plant Physiol 145:875–889PubMedCentralCrossRefPubMedGoogle Scholar
  65. Doornbos RF, van Loon LC, Bakker PAHM (2012) Impact of root exudates and plant defense signalling on bacterial communities in the rhizosphere: A review. Agron Sustain Dev 32:227–243CrossRefGoogle Scholar
  66. Drechsel H, Metzger J, Freund S, Jung G, Boelaert JR, Winkelmann G (1991) Rhizoferrin-A novel siderophore from the fungus Rhizopus microsporus var. rhizopodiformis. BioMetals 4:238–243Google Scholar
  67. Duhan JS, Dudeja SS, Khurana AL (1998) Siderophore production in relation to N fixation and iron uptake in pigeon pea-Rhizobium symbiosis. Folia Microbiol 43:421–426CrossRefGoogle Scholar
  68. Dunne C, Moenne-Loccoz Y, de Bruijn FJ, O’Gara F (2000) Overproduction of an inducible extracellular serine protease improves biological control of Pythium ultimum by Stenotrophomonas maltophilia strain W81. Microbiology 146:2069–2078CrossRefPubMedGoogle Scholar
  69. Egamberdiyeva D (2005) Plant-growth-promoting rhizobacteria isolated from a Calcisol in a semi-arid region of Uzbekistan: biochemical characterization and effectiveness. 168(1):94–99Google Scholar
  70. Elad Y, Kirshner B, Yehuda N, Sztjenberg A (1998) Management of powdery mildew and gray mold of cucumber by Trichoderma harzianum T39 and Ampelomyces quisqualis AQ10. Biocontrol 43:241–251CrossRefGoogle Scholar
  71. Elias F, Woyessa D, Muleta D (2016) Phosphate solubilising in potential of rhizosphere fungi isolated from plants in Jimma Zone, Southwest Ethiopia. Int J Microbiol, p 11.
  72. El-Khawas H, Adachi K (1999) Identification and quantification of auxins in culture media of Azospirillum and Klebsiella and their effect on rice roots. Biol Fertil Soils 28:377–381CrossRefGoogle Scholar
  73. Elsharkawy MM, Mousa KM (2015) Induction of systemic resistance against Papaya ring spot virus (PRSV) and its vector Myzus persicae by Penicillium simplicissimum GP17-2 and silica (SiO2) nanopowder. Int J Pest Manag 61(4):353–358CrossRefGoogle Scholar
  74. Emery T (1971) Role of ferrichrome as a ferric ionophore in Ustilago sphaerogena. Biochemis 10:1483–1488CrossRefGoogle Scholar
  75. Emmert E, Klimowicz A, Thomas M, Handelsman J (2004) Genetics of zwittermicin. A production by Bacillus cereus. Appl Environ Microbiol 70:104–113PubMedCentralCrossRefPubMedGoogle Scholar
  76. Etesami H, Alikhani HA, Hosseini HM (2015) Indole-3-acetic acid and 1-aminocyclopropane-1-carboxylate deaminase: Bacterial traits required in rhizosphere, rhizoplane and/or endophytic competence by beneficial bacteria. In: Maheshwari DK (ed) Bacterial metabolites in sustainable agroecosystem. Springer, Cham, pp 183–258. CrossRefGoogle Scholar
  77. Fallik E, Okon Y, Epstein YE, Goldman A, Fischer M (1989) Identification and quantification of IAA and IBA in Azospirillum brasilense inoculated maize roots. Soil Biol Biochem 21:147–153CrossRefGoogle Scholar
  78. Fernández-Martín R, Reyes F, Domenech CE, Cabrera E, Bramley PM, Barrero AF, Avalos J, Cerdá-Olmedo E (1995) Gibberellin biosynthesis in gib mutants of Gibberella fujikuroi. J Biol Chem 270:14970–14974CrossRefPubMedGoogle Scholar
  79. Frankenberger WTJ, Arshad M (1995) Phytohormones in soil: microbial production and function. Dekker, New YorkGoogle Scholar
  80. Frankenberger WT, Poth M (1987) Biosynthesis of indole-3-acetic acid by the pine ectomycorrhizal fungus Pisolithus tinctorius. Appl Environ Microbiol 53(12):2908–2913PubMedCentralPubMedGoogle Scholar
  81. Frankowski J, Lorito M, Scala F, Schmid R, Berg G, Bahl H (2001) Purification and properties of two chitinolytic enzymes of Serratia plymuthica HRO-C48. Arch Microbiol 176(6):421–426CrossRefPubMedGoogle Scholar
  82. Fridlender M, Inbar J, Chet I (1993) Biological control of soilborne plant pathogens by a β-1, 3-glucanase producing Pseudomonas cepacia. Soil Biol Biochem 25:1211–1221CrossRefGoogle Scholar
  83. Fuentes-Ramírez LE, Jiménez Salgado T, Abarca Ocampo IR, Caballero-Mellado J (1993) Acetobacter diazotrophicus, an indoleacetic acid producing bacterium isolated from sugarcane cultivars of México. Plant Soil 154:145–150CrossRefGoogle Scholar
  84. Fulchieri M, Lucangeli C, Bottini R (1993) Inoculation with Azospirillum lipoferum affects growth and gibberellins status of corn seedling roots. Plant Cell Physiol 34:1305–1309Google Scholar
  85. Furukawa T, Koga J, Adachi T, Kishi K, Syono K (1996) Efficient conversion of L-tryptophan to indole-3-acetic acid and/or tryptophol by some species of Rhizoctonia. Plant Cell Physiol 37:899–905CrossRefGoogle Scholar
  86. Gajera HP, Bambharolia RP, Patel SV, Khatrani TJ, Goalkiya BA (2012) Antagonism of Trichoderma spp. against Macrophomina phaseolina: Evaluation of coiling and cell wall degrading enzymatic activities. J Plant Pathol Microb 3:149. Google Scholar
  87. Gallou A, Cranenbrouck S, Declerck S (2009) Trichoderma harzianum elicits defence response genes in roots of potato plantlets challenged by Rhizoctonia solani. Eur J Plant Pathol 124:219–230CrossRefGoogle Scholar
  88. Galuszka P, Vrabka J, Hinsch J, Novak O (2016) Production of phytohormones by phytopathogenic fungus Claviceps purpurea. New Biotechnol 33:S207. doi:10.1016/j.nbt.2016.06.1434Google Scholar
  89. Genrich IB, Dixon DG, Glick BR (1998) A plant growth-promoting bacterium that decreases nickel toxicity in seedlings. Appl Environ Microbiol 64:3663–3668Google Scholar
  90. Gianinazzi-Pearson V, Gollotte A, Dumas-Gaudot E, Franken P, Gianinazzi S (1994) Gene expression and molecular modifications associated with plant responses to infection by arbuscular mycorrhizal fungi. In: Daniels M, Downic JA, Osbourn AE (eds) Advances in molecular genetics of plant-microbe interactions. Kluwer, Dordrecht, pp 179–186CrossRefGoogle Scholar
  91. Glick BR (2014) Bacteria with ACC deaminase can promote plant growth and help to feed the world. Microbiol Res 169(1):30–39CrossRefPubMedGoogle Scholar
  92. Glick BR, Bashan Y (1997) Genetic manipulation of plant growth-promoting bacteria to enhance biocontrol of phytopathogens. Biotechnol Adv 15:353–376CrossRefPubMedGoogle Scholar
  93. Glick BR, Karaturovic DM, Newell PC (1995) A novel procedure for rapid isolation of plant growth promoting Pseudomonas. Can J Microbiol 41:533–536CrossRefGoogle Scholar
  94. Gohlke J, Deeken R (2014) Plant responses to Agrobacterium tumefaciens and crown gall development. Front Plant Sci 5:155. PubMedCentralCrossRefPubMedGoogle Scholar
  95. Goswami D, Vaghela H, Parmar S, Dhandhukia P, Thakker JN (2013) Plant growth promoting potentials of Pseudomonas spp. strain OG isolated from marine water. J Plant Interact 8:281–290CrossRefGoogle Scholar
  96. Goswami D, Dhandhukia P, Patel P, Thakker JN (2014) Screening of PGPR from saline desert of Kutch: Growth promotion in Arachis hypogea by Bacillus licheniformis A2. Microbiol Res 169:66–75CrossRefPubMedGoogle Scholar
  97. Goswami D, Parmar S, Vaghela H, Dhandhukia P, Thakker J (2015) Describing Paenibacillus mucilaginosus strain N3 as an efficient plant growth promoting rhizobacteria (PGPR). Cogent Food Agric 1(1):1000714. Google Scholar
  98. Goswami D, Thakker JN, Dhandhukia PC (2016) Portraying mechanics of plant growth promoting rhizobacteria (PGPR): A review. Cogent Food Agric 2:1127500. Google Scholar
  99. Gottschalk G (1986) Bacterial metabolism. Springer, Berlin/Heidelberg/New YorkCrossRefGoogle Scholar
  100. Goudjal Y, Zamoum M, Sabaou N, Mathieu F, Zitouni A (2016) Potential of endophytic Streptomyces spp. for biocontrol of Fusarium root rot disease and growth promotion of tomato seedlings. Biocontrol Sci Techn 26:1691–1705Google Scholar
  101. Govindasamy V, Senthilkumar M, Magheshwaran V, Kumar U, Bose P, Sharma V, Annapurna K (2011) Bacillus and Paenibacillus spp.: Potential PGPR for sustainable agriculture. In: Maheshwari DK (ed) Plant growth and health promoting bacteria. Springer, Berlin, pp 333–364Google Scholar
  102. Gügi B, Orange N, Hellio F, Burini JF, Guillou C, Leriche F, Guespin-Michel JF (1991) Effect of growth temperature on several exported enzyme activities in the psychrotropic bacterium Pseudomonas fluorescens. J Bacteriol 173:3814–3820PubMedCentralCrossRefPubMedGoogle Scholar
  103. Gutiérrez-Mañero FJ, Ramos-Solano B, Probanza A, Mehouachi JR, Tadeo F, Talon M (2001) The plant-growth-promoting rhizobacteria Bacillus pumilus and Bacillus licheniformis produce high amounts of physiologically active gibberellins. Physiol Plant 111:206–211CrossRefGoogle Scholar
  104. Haas D, Défago G (2005) Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 3:307–319CrossRefPubMedGoogle Scholar
  105. Halder AK, Chakrabartty PK (1993) Solubilization of inorganic phosphate by rhizobium. Folia Microbiol 38:325–330CrossRefGoogle Scholar
  106. Halder AK, Mishra AK, Bhattacharyya P, Chakrabartty PK (1990) Solubilization of rock phosphate by Rhizobium and Bradyrhizobium. J Gen Appl Microbiol 36:81–92CrossRefGoogle Scholar
  107. Harman GE, Howell CR, Viterbo A, Chet I, Lorito M (2004) Trichoderma species-opportunistic, avirulent plant symbionts: A review. Nat Rev Microbiol 2:43–56CrossRefPubMedGoogle Scholar
  108. Harrison MJ (1998) Development of the arbuscular mycorrhizal symbiosis. Curr Opin Plant Biol 1:360–365CrossRefPubMedGoogle Scholar
  109. Hermosa R, Viterbo A, Chet I, Monte E (2012) Plant-beneficial effects of Trichoderma and of its genes. Microbiol 158:17–25CrossRefGoogle Scholar
  110. Heulin T, Achouak W, Berge O, Normand P, Guinebretière MH (2002) Paenibacillus graminis sp. nov. and Paenibacillus odorifer sp. nov., isolated from plant roots, soil and food. Int J Syst Evol Microbiol 52:607–616CrossRefPubMedGoogle Scholar
  111. Hider RC, Kong X (2010) Chemistry and biology of siderophores. Nat Prod Rep 27:637–657CrossRefPubMedGoogle Scholar
  112. Hirsch AM (2004) Plant–microbe symbioses: a continuum from commensalism to parasitism. Symbiosis 37:345–363Google Scholar
  113. Hirsch PR, Mauchline TH (2012) Who’s who in the plant root microbiome? Nat Biotechnol 30:961–962CrossRefPubMedGoogle Scholar
  114. Howell CR (2003) Mechanisms employed by Trichoderma species in the biological control of plant diseases: the history and evolution of current concepts. Plant Dis 87:4–10CrossRefGoogle Scholar
  115. Illmer P, Schinner F (1992) Solubilization of inorganic phosphates by microorganisms isolated from forest soils. Soil Biol Biochem 24:389–395CrossRefGoogle Scholar
  116. Illmer P, Barbato A, Schinner F (1995) Solubilization of hardly-soluble AlPO4 with P-solubilizing microorganisms. Soil Biol Biochem 27(3):265–270CrossRefGoogle Scholar
  117. Iman M (2008) Effect of phosphate solubilising fungi on growth and nutrient uptake of soyabean (Glycine max L.) plants. J Appl Sci Res 4:592–598Google Scholar
  118. Islam S, Akanda AM, Prova A, Islam MT, Hossain MM (2016) Isolation and identification of plant growth promoting rhizobacteria from cucumber rhizosphere and their effect on plant growth promotion and disease suppression. Front Microbiol 6:1360. PubMedCentralCrossRefPubMedGoogle Scholar
  119. Jha CK, Saraf M (2015) Plant growth promoting rhizobacteria (PGPR): a review. E3 J Agric Res Dev 5(2):0108–0119Google Scholar
  120. Jha CK, Aeron A, Patel BV, Maheshwari DK, Saraf M (2011) Enterobacter: role in plant growth promotion. In: Maheshwari DK (ed) Bacteria in agrobiology: plant growth responses. Springer, Heidelberg, pp 159–182CrossRefGoogle Scholar
  121. Jha CK, Patel B, Saraf M (2012) Stimulation of the growth of Jatropha curcas by the plant growth promoting bacterium Enterobacter cancerogenus MSA2. World J Microbiol Biotechnol 28:891–899CrossRefPubMedGoogle Scholar
  122. Kakar KU, Ren XL, Nawaz Z, Cui ZQ (2016) A consortium of rhizobacterial strains and biochemical growth elicitors improve cold and drought stress tolerance in rice (Oryza sativa L.) Plant Biol 18(3):471–183CrossRefPubMedGoogle Scholar
  123. Kamble S, Hadapad AB, Eapan S (2013) Evaluation of transgenic lines of Indian mustard (Brassica juncea L. Czern and Coss) expressing synthetic cryAc gene for resistance to Plutella xylostella. Plant Cell Tissue Organ Cult 115(3):321. CrossRefGoogle Scholar
  124. Kannahi M, Senbagam N (2014) Studies on siderophore production by microbial isolates obtained from rhizosphere soil and its antibacterial activity. J Chem Pharm Res 6(4):1142–1145Google Scholar
  125. Kaymak HC (2011) Potential of PGPR in agricultural innovations. In: Maheshwari DK (ed) Plant growth and health promoting bacteria. Springer, Berlin/Heidelberg, pp 45–79. Google Scholar
  126. Khalid M, Arshad M, Khalid A, Zahir ZA (2001) Biosynthesis of auxins by Azotobacter. Pak J Soil Sci 20:1–10Google Scholar
  127. King RW, Evans LT (2003) Gibberellins and flowering of grasses and cereals: prising open the lid of the “Florigen” black box. Annu Rev Plant Physiol Plant Mol Biol 54:307–328CrossRefGoogle Scholar
  128. Korolev N, Rav David D, Elad Y (2008) The role of phytohormones in basal resistance and Trichoderma-induced systemic resistance to Botrytis cinerea in Arabidopsis thaliana. BioControl 53:667–683CrossRefGoogle Scholar
  129. Kucey RMN, Janzen HH, Leggett ME (1989) Microbially mediated increases in plant-available phosphorus. Adv Agron 42:199–228CrossRefGoogle Scholar
  130. Leclere V, Bechet M, Adam A, Guez JS, Wathelet B, Ongena M, Thonart P, Gancel F, Chollet-Imbert M, Jacques P (2005) Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism’s antagonistic and biocontrol activities. Appl Environ Microbiol 71:4577–4584PubMedCentralCrossRefPubMedGoogle Scholar
  131. Lee J, Postmaster A, Soon HP, Keast D, Carson KC (2012) Siderophore production by actinomycetes isolates from two soil sites in Western Australia. Bio Metals 25:285–296Google Scholar
  132. Leong SA, Neilands JB (1982) Siderophore production by phytopathogenic microbial species. Arch Biochem Biophys 218:351–359CrossRefPubMedGoogle Scholar
  133. Li J, Liu W, Luo L, Dong D, Liu T, Zhang T, Lu C, Liu D, Zhang D, Wu H (2015) Expression of Paenibacillus polymyxa β-1,3-1,4-glucanase in Streptomyces lydicus A01 improves its biocontrol effect against Botrytis cinerea. Biol Control 90:141–147CrossRefGoogle Scholar
  134. Lichter A, Barash I, Valinsky L, Manulis S (1995) The genes involved in cytokinin biosynthesis in Erwinia herbicola pv. gypsophilae, characterization and role in gall formation. J Bacteriol 177:4457–4465PubMedCentralCrossRefPubMedGoogle Scholar
  135. Loper JE, Henkels MD (1999) Utilization of heterologous siderophores enhances levels of iron available to Pseudomonas putida in the rhizosphere. Appl Environ Microbiol 65:5357–5363PubMedCentralPubMedGoogle Scholar
  136. Loper JE, Nowak-Thompson B, Whistler CA, Hagen MJ, Corbell NA, Henkels MD, Stockwell V (1997) Biological control mediated by antifungal metabolite production and resource competition: An overview. In: Ogoshi A, Kobayashi K, Homma Y, Kodama F, Kondo N, Akino S (eds) Plant growth-promoting rhizobacteria: present status and future prospects. OECD, Paris, pp 73–79Google Scholar
  137. Lorito M, Woo SL, D’Ambrosio M, Harman GE, Hayes CK, Kubicek CP, Scala F (1996) Synergistic interaction between cell wall degrading enzymes and membrane affecting compounds. Mol Plant Microbe Interact 9:206–213CrossRefGoogle Scholar
  138. Lu Z, Tombolini R, Woo S, Zeilinger S, Lorito M, Jansson JK (2004) In vivo study of Trichoderma-pathogen-plant interactions, using constitutive and inducible green fluorescent protein reporter systems. Appl Environ Microbiol 70:3073–7081PubMedCentralCrossRefPubMedGoogle Scholar
  139. Lu CG, Liu WC, Qiu JY, Wang HM, Liu T, Liu DW (2008) Identification of an antifungal metabolite produced by a potential biocontrol actinomyces strain A01. Braz J Microbiol 39:701–707PubMedCentralCrossRefPubMedGoogle Scholar
  140. Ludden PW, Okon Y, Burris RH (1978) The nitrogenase system of Spirillum lipoferum. Biochem J 173:1001–1003PubMedCentralCrossRefPubMedGoogle Scholar
  141. Lugtenberg BJ, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 63:541–556CrossRefPubMedGoogle Scholar
  142. Mahamuni SV, Wani PV, Patil AS (2012) Isolation of phosphate solubilising fungi from rhizosphere of sugarcane & sugar beet using Tcp & Rp solubilisation. Asian J Biochem Pharm Res 1(2):237–244Google Scholar
  143. Maheshwari DK, Dheeman S, Agarwal M (2015) Phytohormone-producing PGPR for sustainable agriculture. In: Maheshwari DK (ed) Bacterial metabolites in sustainable agroecosystem. Springer, Cham, pp 159–182. CrossRefGoogle Scholar
  144. Manulis S, Haviv-Chesner A, Brandl MT, Lindow SE, Barash I (1998) Differential involvement of indole-3-acetic acid biosynthetic a pathways in pathogenicity and epiphytic fitness of Erwinia herbicola pv. gypsophilae. Mol Plant-Microbe Interact 11:634–642CrossRefPubMedGoogle Scholar
  145. Marasco R, Rolli E, Vigani G, Borin S, Sorlini C, Ouzari H, Zocchi G, Daffonchio D (2013) Are drought-resistance promoting bacteria cross-compatible with different plant models? Plant Signal Behav 8(10):e26741. PubMedCentralCrossRefPubMedGoogle Scholar
  146. Martinez C, Blanc F, Le Claire E, Besnard O, Nicole M, Baccou JC (2001) Salicylic acid and ethylene pathways are differentially activated in melon cotyledons by active or heat denatured cellulase from Trichoderma longibrachiatum. Plant Physiol 127:334–344PubMedCentralCrossRefPubMedGoogle Scholar
  147. Martino E, Perotto S (2010) Mineral transformations by mycorrhizal fungi. Geomicrobiol J 27:609–623Google Scholar
  148. Marx DH (1969) The influence of ectotrophic mycorrhizal fungi on the resistance of pine roots to pathogenic infections. II. Production, identification, and biological activity of antibiotics produced by Leucopaxillus cerealis var. piceina. Phytopathology 59(4):411–417PubMedGoogle Scholar
  149. Mayak S, Tirosh T, Glick BR (2004) Plant growth-promoting bacteria that confer resistance to water stress in tomatoes and peppers. Plant Sci 166(2):525–530CrossRefGoogle Scholar
  150. Meena M, Swapnil P, Zehra A, Dubey MK, Upadhyay RS (2017) Antagonistic assessment of Trichoderma spp. by producing volatile and non-volatile compounds against different fungal pathogens. Arch Phytopathology Plant Protect 50:629–648Google Scholar
  151. Mendes R, Garbeva P, Raaijmakers JM (2013) The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiol Rev 37:634–663CrossRefPubMedGoogle Scholar
  152. Mishra N, Khan SS, Sundari SK (2016) Native isolate of Trichoderma: a biocontrol agent with unique stress tolerance properties. World J Microbiol Biotechnol 32:130, CrossRefPubMedGoogle Scholar
  153. Moe LA (2013) Amino acids in the rhizosphere: from plants to microbes. Am J Bot 100:1692–1705CrossRefPubMedGoogle Scholar
  154. Morán-Diez E, Hermosa R, Ambrosino P, Cardoza RE, Gutiérrez S, Lorito M, Monte E (2009) The ThPG1 endopolygalacturonase is required for the Trichoderma harzianum–plant beneficial interaction. Mol Plant Microbe Interact 22:1021–1031CrossRefPubMedGoogle Scholar
  155. Morris RO (1986) Genes specifying auxin and cytokinin biosynthesis in pathogens. Ann Rev Plant Physiol 37:509–538CrossRefGoogle Scholar
  156. Nadeem SM, Ahmad M, Zahir ZA, Javaid A, Ashraf M (2014) The role of mycorrhizae and plant growth promoting rhizobacteria (PGPR) in improving crop productivity under stressful environments. Biotechnol Adv 32:429–448CrossRefPubMedGoogle Scholar
  157. Naglot A, Goswami S, Rahman I, Shrimali DD, Yadav KK, Gupta VK, Rabha AJ, Gogoi HK, Veer V (2015) Antagonistic potential of native Trichoderma viride strain against potent tea fungal pathogens in North East India. Plant Pathol J 31(3):278–289PubMedCentralCrossRefPubMedGoogle Scholar
  158. Naveed M, Mister B, Reichenauer TG, Wieczorek K, Sessitsch A (2014) Increased drought stress resilience of maize through endophytic colonization by Burkholderia phytofirmans PsJN and Enterobacter sp. FD17. Environ Exp Bot 97:30–39CrossRefGoogle Scholar
  159. Nenwani V, Doshi P, Saha T, Rajkumar S (2010) Isolation and characterization of a fungal isolate for phosphate solubilisation and plant growth promoting activity. J Yeast Fungal Res 1:9–14Google Scholar
  160. Noel TC, Sheng C, Yost CK, Pharis RP, Hynes MF (1996) Rhizobium leguminosarum as a plant growth promoting rhizobacterium: direct growth promotion of canola and lettuce. Can J Microbiol 42:279–283CrossRefPubMedGoogle Scholar
  161. Noordman WH, Reissbrodt R, Bongers RS, Rademaker JL, Bockelmann W, Smit G (2006) Growth stimulation of Brevibacterium sp. by siderophores. J Appl Microbiol 101(3):637–646CrossRefPubMedGoogle Scholar
  162. Oberson A, Frossard E, Bühlmann C, Mayer J, Mäder P, Lüscher A (2013) Nitrogen fixation and transfer in grass clover leys under organic and conventional cropping systems. Plant Soil 371:237–255CrossRefGoogle Scholar
  163. Ongena M, Jacques P, Tour Y, Destain J, Jabrane A, Thonart P (2005) Involvement of fengycin-type lipopeptides in the multifaceted biocontrol potential of Bacillus subtilis. Appl Microbiol Biotechnol 69:29–38CrossRefPubMedGoogle Scholar
  164. Parniske M (2008) Arbuscular mycorrhiza: the mother of plant root endosymbioses. Nat Rev Microbiol 6:763–775CrossRefPubMedGoogle Scholar
  165. Patel K, Goswami D, Dhandhukia P, Thakker J (2015) Techniques to study microbial phytohormones. In: Maheshwari DK (ed) Bacterial metabolites in sustainable agro-ecosystem. Springer, Cham, pp 1–27. Google Scholar
  166. Patkar RN, Benke PI, Qu Z, Chen YY, Yang F, Swarup S, Naqvi NI (2015) A fungal monooxygenase-derived jasmonate attenuates host innate immunity. Nat Chem Biol 11:733–740CrossRefPubMedGoogle Scholar
  167. Patten CL, Glick BR (1996) Bacterial biosynthesis of indole-3-acetic acid. Can J Microbiol 42:207–220CrossRefPubMedGoogle Scholar
  168. Phi Q-T, Yu-Mi P, Keyung-Jo S, Choong-Min R, Seung-Hwan P, Jong-Guk K, Sa-Youl G (2010) Assessment of root-associated Paenibacillus polymyxa groups on growth promotion and induced systemic resistance in pepper. J Microbiol Biotechnol 20:1605–1613PubMedGoogle Scholar
  169. Ponmurugan P, Baby UI, Rajkumar R (2007) Growth, photosynthetic and biochemical responses of tea cultivers infected with various diseases. Photosynthetica 45:143–146CrossRefGoogle Scholar
  170. Pope PB, Smith W, Denman SE, Tringe SG, Barry K, Hugenholtz P, McSweeney CS, McHardy AC, Morrison M (2011) Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 333:646–648CrossRefPubMedGoogle Scholar
  171. Prasad R, Kumar M, Varma A (2015) Role of PGPR in soil fertility and plant health. In: Egamberdieva D, Shrivastava S, Varma A (eds) Plant-growth-promoting rhizobacteria (PGPR) and medicinal plants, vol 42. Springer, Heidelberg/New York/London, pp 247–262Google Scholar
  172. Puri A, Padda KP, Chanway CP (2016) Seedling growth promotion and nitrogen fixation by a bacterial endophyte Paenibacillus polymyxa P2b-2R and its GFP derivative in corn in a long-term trial. Symbiosis 69:123–129CrossRefGoogle Scholar
  173. Rajkumar M, Nagendran R, Lee KJ, Lee WH, Kim SZ (2006) Influence of plant growth promoting bacteria and Cr6+ on the growth of Indian mustard. Chemosphere 62:741–748CrossRefPubMedGoogle Scholar
  174. Ramos-Solano B, Barriuso J, Gutiérrez-Mañero FJ (2008) Physiological and molecular mechanisms of plant growth promoting rhizobacteria (PGPR). In: Ahmad I, Pichtel J, Hayat S (eds) Plant–bacteria interactions: Strategies and techniques to promote plant growth. Wiley VCH, Weinheim, pp 41–54. CrossRefGoogle Scholar
  175. Rani A, Souche YS, Goel R (2009) Comparative assessment of in situ bioremediation potential of cadmium resistant acidophilic Pseudomonas putida 62BN and alkalophilic Pseudomonas monteilii 97AN strains on soybean. Int Biodeterior Biodegrad 63:62–66CrossRefGoogle Scholar
  176. Rao MS, Reddy PP, Nagesh M (1998) Evaluation of plant based formulations of Trichoderma harzianum for the management of Meloidogyne incognita on eggplant. Nematologia Mediterranea 26:59–62Google Scholar
  177. Rashmi S, Maurya S, Upadhyay RS (2016) The improvement of competitive saprophytic capabilities of Trichoderma species through the use of chemical mutagens. Braz J Microbiol 47:10–17PubMedCentralCrossRefPubMedGoogle Scholar
  178. Ratledge C (1987) Iron metabolism in mycobacteria. In: Winkelmann G, Van der Helm D, Neilands JB (eds) Iron transport in microbes, plants and animals. VCH Publishers, New York, pp 207–222Google Scholar
  179. Reddy PP, Rao MS, Nagesh M (1996) Management of citrus nematode, Tylenchulus semipenetrans, by integration of Trichoderma harzianum with oil cakes. Nematologia Mediterranea 24:265–267Google Scholar
  180. Redman RS, Sheehan KB, Stout RG, Rodriguez RJ, Henson JM (2002) Thermotolerance generated by plant/fungal symbiosis. Science 298:1581–1581CrossRefPubMedGoogle Scholar
  181. Reineke G, Heinze B, Schirawski J, Buettner H, Kahmann R, Basse CW (2008) Indole-3-acetic acid (IAA) biosynthesis in the smut fungus Ustilago maydis and its relevance for increased IAA levels in infected tissue and host tumour formation. Mol Plant Pathol 9:339–355CrossRefPubMedGoogle Scholar
  182. Reinoso H, Dauría C, Luna V, Pharis R, Bottini R (2002) Dormancy in peach (Prunus persica L.) flower buds VI. Effects of gibberellins and an acyl cyclohexanedione (Cimectacarb) on bud morphogenesis in field experiments with orchard trees and on cuttings. Can J Bot 80:656–663CrossRefGoogle Scholar
  183. Renshaw JC, Robson GD, Trinci APJ, Wiebe MG, Livens FR, Collison D, Taylor RJ (2002) Fungal siderophores: structures, functions and applications. Mycol Res 106:1123–1142CrossRefGoogle Scholar
  184. Roberto F, Kosuge T (1987) Phytohormone metabolism in Pseudomonas syringae subsp savastanoi. In: Fox JE, Jacob M (eds) Molecular biology of plant growth control. A.R. Liss Inc, New York, pp 371–380Google Scholar
  185. Roberts SC, Shuler ML (1997) Large scale plant cell culture. Curr Opin Biotechnol 8:154–159CrossRefPubMedGoogle Scholar
  186. Rodrı́guez H, Fraga R (1999) Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv 17:319–339. S0734-9750(99)00014-2 CrossRefPubMedGoogle Scholar
  187. Rodrı́guez H, Fraga R, Gonzalez T, Bashan Y (2006) Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil 287:15–21CrossRefGoogle Scholar
  188. Roesti D, Gaur R, Johri BN, Imfeld G, Sharma S, Kawaljeet K, Aragno M (2006) Plant growth stage, fertiliser management and bio-inoculation of arbuscular mycorrhizal fungi and plant growth promoting rhizobacteria affect the rhizobacterial community structure in rain-fed wheat fields. Soil Biol Biochem 38:1111–1120CrossRefGoogle Scholar
  189. Rojas MC, Hedden P, Gaskin P, Tudzynski B (2001) The P450-1 gene of Gibberella fujikuroi encodes a multifunctional enzyme in gibberellin biosynthesis. Proc Natl Acad Sci USA 98:5838–5843PubMedCentralCrossRefPubMedGoogle Scholar
  190. Rosendahl S (1985) Interactions between the vesicular-arbuscular mycorrhizal fungus Glomus intraradices and Aphanomyces euteiches root rot of peas. J Phytopathol 114:31–40CrossRefGoogle Scholar
  191. Rotblat B, Enshell-Seijffers D, Gershoni JM, Schuster S, Avni A (2002) Identification of an essential component of the elicitation active site of the EIX protein elicitor. Plant J 32:1049–1055CrossRefPubMedGoogle Scholar
  192. Saifullah P, Thomas BJ (1996) Studies on the parasitism of Globodera rostochiensis by Trichoderma harzianum using low temperature scanning electron microscopy. Afro-Asian J Nematol 6:117–122Google Scholar
  193. Saikia R, Varghese S, Singh BP, Arora DK (2009) Influence of mineral amendment on disease suppressive activity of Pseudomonas fluorescens to Fusarium wilt of chickpea. Microbiol Res (4):365–373Google Scholar
  194. Sakthivel U, Karthikeyan B (2012) Isolation and characterization of plant growth promoting rhizobacteria (PGPR) from the rhizosphere of Coleus forskohlii grown soil. Int J Rec Sci Res 3(5):288–296Google Scholar
  195. Salisbury FB (1994) The role of plant hormones. In: Wilkinson RE (ed) Plant–environment interactions. Marcel Dekker, New York, pp 39–81Google Scholar
  196. Salisbury FB, Ross CW (1992) Plant physiology. Wadsworth, BelmontGoogle Scholar
  197. Sarma RK, Saikia R (2014) Alleviation of drought stress in mung bean by strain Pseudomonas aeruginosa GGRJ2. Plant Soil 377:111–126CrossRefGoogle Scholar
  198. Schäfer P, Khatabi B, Kogel KH (2007) Root cell death and systemic effects of Piriformospora indica: a study on mutualism. FEMS Microbiol Lett 275:1–7CrossRefPubMedGoogle Scholar
  199. Schnider-Keel U, Seematter A, Maurhofer M, Blumer C, Duffy B, Gigot-Bonnefoy C, Reimmann C, Notz R, Défago G, Haas D, Keel C (2000) Autoinduction of 2,4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. J Bacteriol 182:1215–1225PubMedCentralCrossRefPubMedGoogle Scholar
  200. Schouteden N, De Waele D, Panis B, Vos CM (2015) Arbuscular mycorrhizal fungi for the biocontrol of plant-parasitic nematodes: a review of the mechanisms involved. Front Microbiol 6:1280. doi:10.3389/fmicb.2015.01280 PubMedCentralCrossRefPubMedGoogle Scholar
  201. Schrey SD, Erkenbrack E, Früh E, Fengler S, Hommel K, Horlacher N, Schulz D, Ecke M, Kulik A, Fiedler H-P, Hampp R, Tarkka MT (2012) Production of fungal and bacterial growth modulating secondary metabolites is widespread among mycorrhiza-associated streptomycetes. BMC Microbiol 12:164. doi:10.1186/1471-2180-12-164 PubMedCentralCrossRefPubMedGoogle Scholar
  202. Segarra G, Casanova E, Bellido D, Odena MA, Oliveira E, Trillas I (2007) Proteome, salicylic acid, and jasmonic acid changes in cucumber plants inoculated with Trichoderma asperellum strain T34. Proteomics 7:3943–3952CrossRefPubMedGoogle Scholar
  203. Segarra G, Van der Ent S, Trillas I, Pieterse CMJ (2009) MYB72, a node of convergence in induced systemic resistance triggered by a fungal and a bacterial beneficial microbe. Plant Biol (Stuttg) 11:90–96CrossRefGoogle Scholar
  204. Sekar S, Kandavel D (2010) Interaction of plant growth promoting rhizobacteria (PGPR) and endophytes with medicinal plants – new avenues for phytochemicals. J Phytol 2(7):91–100Google Scholar
  205. Seldin L, Van Elsas JD, Penido EGC (1984) Bacillus azotofixans sp. nov., a nitrogen-fixing species from Brazilian soils and grass roots. Int J Syst Bacteriol 34:451–456CrossRefGoogle Scholar
  206. Sharon E, Bar-Eyal M, Chet I, Herrera-Estrella A, Kleifeld O, Spiegel Y (2001) Biocontrol of the root-knot nematode Meloidogyne javanica by Trichoderma harzianum. Phytopathology 91:687–693Google Scholar
  207. Sharon E, Chet I, Viterbo A, Bar-Eyal M, Nagan H, Samuels GJ, Spiegel Y (2007) Parasitism of Trichoderma on Meloidogyne javanica and role of the gelatinous matrix. Eur J Plant Pathol 118:247–258CrossRefGoogle Scholar
  208. Shen X, Hu H, Peng H, Wang W, Zhang X (2013) Comparative genomic analysis of four representative plant growth-promoting rhizobacteria in Pseudomonas. BMC Genomics 14:271. PubMedCentralCrossRefPubMedGoogle Scholar
  209. Shi M, Chen L, Wang X-W, Zhang T, Zhao P-B, Song X-Y, Sun C-Y, Chen X-L, Zhou B-C, Zhang Y-Z (2012) Antimicrobial peptaibols from Trichoderma pseudokoningii induce programmed cell death in plant fungal pathogens. Microbiol 158:166–175CrossRefGoogle Scholar
  210. Shivanna MB, Meera MS, Hyakumachi M (1994) Sterile fungi from Zoysiagrass rhizosphere as plant growth promoters in spring wheat. Can J Microbiol 40:637–644CrossRefGoogle Scholar
  211. Shoresh M, Yedidia I, Chet I (2005) Involvement of jasmonic acid/ethylene signaling pathway in the systemic resistance induced in cucumber by Trichoderma asperellum T203. Phytopathology 95:76–84CrossRefPubMedGoogle Scholar
  212. Shoresh M, Harman GE, Mastouri F (2010) Induced systemic resistance and plant responses to fungal biocontrol agents. Ann Rev Phytopathol 48:21–43CrossRefGoogle Scholar
  213. Siddikee MA, Chauhan PS, Anandham R, Han GH, Sa T (2010) Isolation, characterization, and use for plant growth promotion under salt stress, of ACC deaminase producing halotolerant bacteria derived from coastal soil. J Microbiol Biotecnol 20:1577–1584CrossRefGoogle Scholar
  214. Singh RP, Jha PN (2016) The multifarious PGPR Serratia marcescens CDP-13 augments induced systemic resistance and enhanced salinity tolerance of Wheat (Triticum aestivum L.). PLoS One 11(6), e0155026,
  215. Singh PP, Shin YC, Park CS, Chung YR (1999) Biological control of Fusarium wilt of cucumber by chitinolytic bacteria. Phytopathology 89:92–99CrossRefPubMedGoogle Scholar
  216. Sivan A, Chet I (1989) The possible role of competition between Trichoderma harzianum and Fusarium oxysporum on rhizosphere colonisation. Phytopathology 79:198–203CrossRefGoogle Scholar
  217. Skrary FA, Cameron DC (1998) Purification and characterization of a Bacillus licheniformis phosphatase specific for D-alpha-glycerphosphate. Arch Biochem Biophys 349:27–35CrossRefGoogle Scholar
  218. Smith SE, Facelli E, Pope S, Smith FA (2010) Plant performance in stressful environments: interpreting new and established knowledge of the roles of arbuscular mycorrhizas. Plant Soil 326:3–20CrossRefGoogle Scholar
  219. Spiegel Y, Sharon E, Bar-Eyal M, Van Assche A, Van Kerckhove S, Vanachter A, Viterbo A, Chet I (2006) Evaluation and mode of action of Trichoderma isolates as a biocontrol agent against plant-parasitic nematodes. In: Proceedings of IOBC Meeting, Spa, Belgium, IOBC, BulletinGoogle Scholar
  220. Sponsel VM (2003) Gibberellins. In: Henry HL, Norman AW (eds) Encyclopedia of hormones, vol 2. Academic, London, pp 29–40CrossRefGoogle Scholar
  221. Sujatha M, Devi PSV, Reddy TP (2011) Insect pest of castor (Ricinus communis L) and their management strategies. In: Reddy VD, Rao PN, Rao KV (eds) Pests and pathogens: management strategies. CRC Press, Boca Raton, pp 177–198Google Scholar
  222. Tank N, Saraf M (2010) Salinity-resistant plant growth promoting rhizobacteria ameliorates sodium chloride stress on tomato plants. J Plant Interact 5:51–58CrossRefGoogle Scholar
  223. Thakuria D, Talukdar NC, Goswami C, Hazarika S, Boro RC, Khan MR (2004) Characterization and screening of bacteria from rhizosphere of rice grown in acidic soils of Assam. Curr Sci 86:978–985Google Scholar
  224. Thaller MC, Berlutti F, Schippa S, Iori P, Passariello C, Rossolini GM (1995) Heterogeneous patterns of acid phosphatases containing low-molecular-mass polypeptides in members of the family Enterobacteriaceae. Int J Syst Bacteriol 4:255–261CrossRefGoogle Scholar
  225. Theis KR, Heckla AL, Verge JR, Holekamp KE (2008) The ontogeny of pasting behavior in free-living spotted hyenas, Crocuta crocuta. In: Hurst JL, Beynon RJ, Roberts SC, Wyatt TD (ed) Chemical signals in vertebrates, vol 11. Springer, New York, pp 179–187Google Scholar
  226. Thieken A, Winkelmann G (1992) Rhizoferrin: a complexone type siderophore of the Mocorales and entomophthorales (Zygomycetes). FEMS Microbiol Lett 94:37–41CrossRefGoogle Scholar
  227. Tien T, Gaskin M, Hubbel D (1979) Plant growth substances produced by Azospirillum brasilense and their effect on the growth of pearl millet (Pennisetum americanum L.) Appl Environ Microbiol 37:1016–1024PubMedCentralPubMedGoogle Scholar
  228. Timmusk S, Wagner EGH (1999) The plant growth-promoting rhizobacteria Paenibacillus polymyxa induces changes in Arabidopsis thaliana gene expression: a possible connection between biotic and abiotic stress responses. Mol Plant-Microbe Interact 12:951–959CrossRefPubMedGoogle Scholar
  229. Tiwari S, Charu L, Chauhan PS, Nautiyal CS (2016) Pseudomonas putida attunes morpho-physiological, biochemical and molecular responses in Cicer arietinum L. during drought stress and recovery. Plant Physiol Biochem 99:108–117CrossRefPubMedGoogle Scholar
  230. Toumatia O, Compant S, Yekkour A, Goudjal Y, Sabaou N, Mathieu F, Sessitsch A, Zitouni A (2016) Biocontrol and plant growth promoting properties of Streptomyces mutabilis strain IA1 isolated from a Saharan soil on wheat seedlings and visualization of its niches of colonization. S Afr J Bot 105:234–239CrossRefGoogle Scholar
  231. Tripathi M, Munot HP, Shouch Y, Meyer JM, Goel R (2005) Isolation and functional characterization of siderophore-producing lead- and cadmium-resistant Pseudomonas putida KNP9. Curr Microbiol 5:233–237CrossRefGoogle Scholar
  232. Tsavkelova E, Oeser B, Oren-Young L, Israeli M, Sasson Y, Tudzynski B, Sharon A (2012) Identification and functional characterization of indole-3-acetamide-mediated IAA biosynthesis in plant-associated Fusarium species. Fungal Genet Biol 49:48–57CrossRefPubMedGoogle Scholar
  233. Valencia GB, Vargas VH, Soto JNU, Jimenez NN, Corral JH (2011) Trichoderma sp native from chili region of Poanas, Durango, Mexico antagonist against phytopathogenic fungi. Am J Agric Biol Sci 2011:185–188Google Scholar
  234. Van Loon LC, Bakker PAHM (2006) Induced systemic resistance as a mechanism of disease suppression by rhizobacteria. In: Siddiqui ZA (ed) PGPR: biocontrol and biofertilization. Springer, Dordrecht, pp 39–66Google Scholar
  235. Verma M, Brar KS, Tyagi RD, R Surampalli YB, Valero JR (2007) Starch industry waste water as a substrate for antagonist, Trichoderma viride production. Bioresource Technol 98:2154–2162CrossRefGoogle Scholar
  236. Vessey JK (2003) Plant growth-promoting rhizobacteria as biofertilizers. Plant Soil 255:571–586CrossRefGoogle Scholar
  237. Vigo C, Norman JR, Hooker JE (2000) Biocontrol of pathogen Phytophthora parasitica by arbuscular mycorrhizal fungi is a consequence of effects on infection loci. Plant Pathol 49:509–514CrossRefGoogle Scholar
  238. Vinale F, Sivasithamparam K, Ghisalberti EL, Woo SL, Nigro M, Marra R, Lombardi N, Pascale A, Ruocco M, Lanzuise S, Manganiello G, Lorito M (2014) Trichoderma secondary metabolites active on plants and fungal pathogens. Open Mycol J 8:127–139CrossRefGoogle Scholar
  239. Viterbo A, Horwitz BA (2010) Mycoparasitism. In: Borkovich KA, Ebbole DJ (eds) Cellular and molecular biology of filamentous fungi. Washington: Am Soc Microbiol 42:676–693Google Scholar
  240. von der Weid I, Duarte GF, van Elsas JD, Seldin L (2002) Paenibacillus brasilensis sp. nov., a novel nitrogen fixing species isolated from the maize rhizosphere in Brazil. Int J Syst Evol Microbiol 52:2147–2153PubMedGoogle Scholar
  241. Wakelin S, Young S, Gerard E, Mander C, O’Callaghan M (2016) Isolation of root-associated Pseudomonas and Burkholderia spp. with biocontrol and plant growth-promoting traits. Biocontrol Sci Tech 27(1):139–143, CrossRefGoogle Scholar
  242. Waller F, Achatz B, Baltruschat H, Fodor J, Becker K, Fischer M, Heier T, Huckelhoven R, Neumann C, Wettstein D, Franken P, Kogel KH (2005) The endophytic fungus Piriformospora indica reprograms barley to salt-stress tolerance, disease resistance, and higher yield. Proc Natl Acad Sci USA 102:13386–13391PubMedCentralCrossRefPubMedGoogle Scholar
  243. Wallner A, Blatzer M, Schrettl M, Sarg B, Lindner H, Haas H (2009) Ferricrocin, a siderophore involved in intra- and transcellular iron distribution in Aspergillus fumigatus. Appl Environ Microbiol 75:4194–4196PubMedCentralCrossRefPubMedGoogle Scholar
  244. Wang X, Wang L, Wang J, Jin P, Liu H, Zhang Y (2014) Bacillus cereus AR156-induced resistance to Colletotrichum acutatum is associated with priming of defense responses in loquat fruit. PLoS One 9, e112494, PubMedCentralCrossRefPubMedGoogle Scholar
  245. Wani PA, Khan MS (2010) Bacillus species enhance growth parameters of chickpea (Cicer arietinum L.) in chromium stressed soils. Food Chem Toxicol 48:3262–3267CrossRefPubMedGoogle Scholar
  246. Wani PA, Khan MS, Zaidi A (2007) Synergistic effects of the inoculation with nitrogen fixing and phosphate solubilizing rhizobacteria on the performance of field grown chickpea. J Plant Nutr Soil Sci 170:283–287CrossRefGoogle Scholar
  247. Werner A, Zadworny M (2002) In vitro evidence of mycoparasitism of the ectomycorrhizal fungus Laccaria laccata against Mucor hiemalis in the rhizosphere of Pinus sylvestris. Mycorrhiza 13:41–47CrossRefPubMedGoogle Scholar
  248. Weston LA, Mathesius U (2013) Flavonoids: their structure, biosynthesis and role in the rhizosphere, including allelopathy. J Chem Ecol 39:283–297CrossRefPubMedGoogle Scholar
  249. Whipps JM (2001) Microbial interactions and biocontrol in the rhizosphere. J Exp Bot 52:487–511CrossRefPubMedGoogle Scholar
  250. Windham GL, Windham MT, Williams WP (1989) Effects of Trichoderma spp. on maize growth and Meloidogyne arenaria reproduction. Plant Dis 73:493–449CrossRefGoogle Scholar
  251. Winkelmann G (2007) Ecology of siderophores with special reference to the fungi. BioMetals 20(3-4):379–392CrossRefPubMedGoogle Scholar
  252. Wittenberg JB, Wittenberg BA, Day DA, Udvardi MK, Appleby CA (1996) Siderophore bound iron in the peribacteroid space of soybean root nodules. Plant Soil 178:161–169CrossRefGoogle Scholar
  253. Wong WS, Tan SN, Ge L, Chen X, Yong JWH (2015) The importance of phytohormones and microbes in biofertilizers. In: Maheshwari DK (ed) Bacterial metabolites in sustainable agroecosystem. Springer, Cham, pp 105–158. CrossRefGoogle Scholar
  254. Wu Q, Bai LQ, Liu WC, Li YY, CG L, Li YQ, KH F, CJ Y, Chen J (2013a) Construction of a Streptomyces lydicus A01 transformant with a chit42 gene from Trichoderma harzianum P1 and evaluation of its biocontrol activity against botrytis cinerea. J Microbiol 51:166–173CrossRefPubMedGoogle Scholar
  255. Wu Q, Bai LQ, Liu WC, Li YY, CG L, Li YQ, Lin ZY, Wang M, Xue CS, Chen J (2013b) Construction of Streptomyces lydicus A01 transformant with the chit33 gene from Trichoderma harzianum CECT2413 and its biocontrol effect on Fusaria. Chin Sci Bull (26):3266–3273Google Scholar
  256. Yasser MM, Mousa ASM, Massoud ON, Nasr SH (2014) Solubilization of inorganic phosphate by phosphate solubilising fungi isolated from Egyptian soils. J Biol Earth Sci 4(1):B83–B90Google Scholar
  257. Zahir ZA, Abbas AS, Khalid M, Arshad M (2000) Substrate dependent microbially derived plant hormones for improving growth of maize seedling yield by inoculation with plant growth promoting rhizobacteria. Pak J Biol Sci 3:289–291CrossRefGoogle Scholar
  258. Zeilinger S, Galhaup C, Payer K, Woo SL, Mach RL, Fekete C, Lorito M, Kubicek CP (1999) Chitinase gene expression during mycoparasitic interaction of Trichoderma harzianum with its host. Fungal Genet Biol 26:131–140CrossRefPubMedGoogle Scholar
  259. Zhang H, Kim MS, Sun Y, Dowd SE, Shi H, Paré PW (2008) Soil bacteria confer plant salt tolerance by tissue-specific regulation of the sodium transporter HKT1. Mol Plant Microbe Interact 21(6):737–744CrossRefPubMedGoogle Scholar
  260. Zhang S, Yantai G, Xu B (2016) Application of plant-growth-promoting fungi Trichoderma longibrachiatum T6 enhances tolerance of wheat to salt stress through improvement of antioxidative defense system and gene expression. Front Plant Sci 7:1405. doi:10.3389/fpls.2016.01405 PubMedCentralPubMedGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2017

Authors and Affiliations

  • Mukesh Meena
    • 1
    Email author
  • Prashant Swapnil
    • 1
  • Andleeb Zehra
    • 1
  • Mohd Aamir
    • 1
  • Manish Kumar Dubey
    • 1
  • Jyoti Goutam
    • 1
  • R. S. Upadhyay
    • 1
  1. 1.Department of Botany, Institute of ScienceBanaras Hindu UniversityVaranasiIndia

Personalised recommendations