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Applications of Microorganisms in Agriculture

  • Khirood DoleyEmail author
  • Ajinkya Terkar
  • Mahesh Borde
Chapter
  • 20 Downloads
Part of the Microorganisms for Sustainability book series (MICRO, volume 22)

Abstract

At present, the major global challenge is to accomplish future food security without interfering with the present environment or ecosystem. The global crop production suffers largely due to several pests, insects, or diseases which are being controlled widely by the use of detrimental agrochemicals which are now being considered to damage our health and ecosystem. Therefore, various other alternatives of biological origin are being looked upon for their application as bio-fertilizer or biological control agents such as arbuscular mycorrhizal fungi (AMF), Trichoderma spp., plant growth-promoting rhizobacteria (PGPR), and endophytes. Moreover, many other probable microorganisms are still being discovered, and their ecological roles are being studied as well. Therefore, appropriate selection and investigation for applying them effectively with the use of novel technologies have huge potential to safeguard our future food and environment. In addition, many underlying mechanisms which are previously unknown during interaction for crop health improvement can be unveiled by the use of modern technologies such as clustered regularly interspaced short palindromic repeats (CRISPR/Cas), transcriptomics, proteomics, genomics, etc. Even plant growth-promoting traits are being tailored by the use of modern gene engineering techniques which will definitely improve overall plant health, thereby leading to food security. Thus, this chapter presents a brief overview of recent trends in application of various microbial interactions with the twenty-first century technology for crop productivity and overall sustainability of our agricultural ecosystem for our future generation.

Keywords

Agrochemicals Biological Ecosystem Environment Novel technology 

Notes

Acknowledgments

We wish to thank the University Grants Commission (UGC), New Delhi, for financial support.

References

  1. Alizadeh H, Behboudi K, Ahmadzadeh M, Javan-Nikkhah M, Zamioudis C, Pieterse CMJ, Bakker PAHM (2013) Induced systemic resistance in cucumber and Arabidopsis thaliana by the combination of Trichoderma harzianum Tr6 and Pseudomonas sp. Ps14. Biol Control 65:14–23CrossRefGoogle Scholar
  2. Alvarez B, Biosca EG (2017) Bacteriophage-based bacterial wilt biocontrol for an environmentally sustainable agriculture. Front Plant Sci 8:1218.  https://doi.org/10.3389/fpls.2017.01218CrossRefPubMedPubMedCentralGoogle Scholar
  3. Babalola O (2010) Beneficial bacteria of agricultural importance. Biotechnol Lett 32:1559–1570.  https://doi.org/10.1007/s10529-010-0347-0CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bailly A, Weisskopf L (2017) Mining the volatilomes of plant-associated microbiota for new biocontrol solutions. Front Microbiol 8:1638.  https://doi.org/10.3389/fmicb.2017.01638CrossRefPubMedPubMedCentralGoogle Scholar
  5. Balog A, Hartel T, Loxdale HD, Wilson K (2017) Differences in the progress of the biopesticide revolution between the EU and other major crop-growing regions. Pest Manag Sci 73:2203–2208.  https://doi.org/10.1002/ps.4596CrossRefPubMedPubMedCentralGoogle Scholar
  6. Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF (2015) Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nat Plants 1:15145CrossRefGoogle Scholar
  7. Barriuso J, Solano BR, Mañero FJG (2008) Protection against pathogen and salt stress by four plant growth-promoting rhizobacteria isolated from Pinus sp. on Arabidopsis thaliana. Phytopathology 98:666–672CrossRefPubMedPubMedCentralGoogle Scholar
  8. Belhaj K, Chaparro-Garcia A, Kamoun S, Patron NJ, Nekrasov V (2015) Editing plant genomes with CRISPR/Cas9. Curr Opin Biotechnol 32:76–84CrossRefPubMedPubMedCentralGoogle Scholar
  9. Benitez T, Rincon AM, Limon MC, Codon AC (2004) Biocontrol mechanisms of Trichoderma strains. Int Microbiol 7:249–260PubMedPubMedCentralGoogle Scholar
  10. Besset-Manzoni Y, Rieusset L, Joly P, Comte G, Prigent-Combaret C (2018) Exploiting rhizosphere microbial cooperation for developing sustainable agriculture strategies. Environ Sci Pollut Res 25:29953–29970.  https://doi.org/10.1007/s11356-017-1152-2CrossRefGoogle Scholar
  11. Bhunchoth A, Phironrit N, Leksomboon C, Chatchawankanphanich O, Kotera S, Narulita E, Kawasaki T, FujieM YT (2015) Isolation of Ralstonia solanacearum infecting bacteriophages from tomato fields in Chiang Mai, Thailand, and their experimental use as biocontrol agents. J Appl Microbiol 118:1023–1033.  https://doi.org/10.1111/jam.12763CrossRefPubMedPubMedCentralGoogle Scholar
  12. Bonfante P, Genre A (2010) Mechanisms underlying beneficial plant—fungus interactions in mycorrhizal symbiosis. Nat Commun 1:48.  https://doi.org/10.1038/ncomms1046CrossRefPubMedPubMedCentralGoogle Scholar
  13. Buysens S, Heungens K, Poppe J, Hofte M (1996) Involvement of Pyochelin and pioverdin in suppression of Pseudomonas aeruginosa 7NSK2. Appl Environ Microbiol 62:865–871CrossRefPubMedPubMedCentralGoogle Scholar
  14. Cangelosi B, Curir P, Beruto M, Monroy F, Borriello R (2017) Protective effects of arbuscular mycorrhizae against Fusarium oxysporum F. Sp. Ranunculi in Ranunculus Asiaticus cultivations for flower crop. J Hortic Sci Res 1:36–41Google Scholar
  15. Carvalho SD, Castillo JA (2018) Influence of light on plant–phyllosphere interaction. Front Plant Sci 9:1482.  https://doi.org/10.3389/fpls.2018.01482CrossRefPubMedPubMedCentralGoogle Scholar
  16. Chandrasekaran J, Brumin M, Wolf D, Leibman D, Klap C, Pearlsman M, Sherman A, Arazi T, Gal-On A (2016) Development of broad virus resistance in non-transgenic cucumber using CRISPR/Cas9 technology. Mol Plant Pathol 17:1140–1153.  https://doi.org/10.1111/mpp.12375CrossRefPubMedPubMedCentralGoogle Scholar
  17. Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124:803–814.  https://doi.org/10.1016/j.cell.2006.02.008CrossRefPubMedPubMedCentralGoogle Scholar
  18. Contreras-Cornejo HA, Macias-Rodriguez L, Alfaro-Cuevas R, Lopez-Bucio J (2014) Trichoderma spp. improve growth of arabidopsis seedlings under salt stress through enhanced root development, osmolite production, and Na+ elimination through root exudates. Mol Plant-Microbe Interact 27:503–514.  https://doi.org/10.1094/MPMI-09-13-0265-RCrossRefPubMedPubMedCentralGoogle Scholar
  19. Crutcher FK, Moran-Diez ME, Ding SL, Liu J, Horwitz B, Mukherjee PK, Kenerley CM (2015) A paralog of the proteinaceous elicitor SM1 is involved in colonization of maize roots by Trichoderma virens. Fungal Biol 119:476–486.  https://doi.org/10.1016/j.funbio.2015.01.004CrossRefPubMedPubMedCentralGoogle Scholar
  20. Dalpe Y (2005) Mycorrhizae: a potential tool for plant protection but not a panacea. Phytoprotection 86:53–59CrossRefGoogle Scholar
  21. Devi S, Sreenivasulu Y, Rao K (2017) Protective role of Trichoderma logibrachiatum (WT2) on Lead induced oxidative stress in Helianthus annus L. Indian J Exp Biol 55:235–241Google Scholar
  22. El-Borollosy AM, Oraby MM (2012) Induced systemic resistance against Cucumber mosaic cucumovirus and promotion of cucumber growth by some plant growth-promoting rhizobacteria. Ann Agric Sci 57:91–97CrossRefGoogle Scholar
  23. Emmett BD, Youngblut ND, Buckley DH, Drinkwater LE (2017) Plant phylogeny and life history shape rhizosphere bacterial microbiome of summer annuals in an agricultural field. Front Microbiol 8:2414.  https://doi.org/10.3389/fmicb.2017.02414CrossRefPubMedPubMedCentralGoogle Scholar
  24. European Union (2009) Directive 2009/128/EC of the European Parliament and of the Council establishing a framework for Community action to achieve the sustainable use of pesticides. Official J EU http://eur-lex.europa.eu/search.html?qid=1456841738609&text=2009/128&scope=EURLEX&type=quick&lang=en. Accessed August 2018
  25. FAO (2019) The state of food and agriculture 2019. Moving forward on food loss and waste reduction. Rome. Licence: CC BY-NC-SA 3.0 IGOGoogle Scholar
  26. Fiorilli V, Catoni M, Miozzi L, Novero M, Accotto GP, Lanfranco L (2009) Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus. New Phytol 184:975–987CrossRefPubMedPubMedCentralGoogle Scholar
  27. Fu SF, Sun PF, Lu HY, Wei JY, Xiao HS, Fang WT, Cheng BY, Chou JY (2016) Plant growth-promoting traits of yeasts isolated from the phyllosphere and rhizosphere of Drosera spatulata Lab. Fungal Biol 120:433–448.  https://doi.org/10.1016/j.funbio.2015.12.006CrossRefPubMedPubMedCentralGoogle Scholar
  28. Gahukar RT (2014) Potential and utilization of plant products in pest control. In: Abrol DP (ed) Insect pest management: current concepts and ecological perspectives. Elsevier Inc., New York, NY, pp 125–139Google Scholar
  29. Garcia-Ruiz MT, Knapp AN, Garcia-Ruiz H (2018) Profile of genetically modified plants authorized in Mexico. GM Crops and Food 9:152–168.  https://doi.org/10.1080/21645698.2018.1507601CrossRefPubMedPubMedCentralGoogle Scholar
  30. Gill SS, Gill R, Trivedi DK, Anjum NA, Sharma KK (2016) Piriformospora indica: potential and significance in plant stress tolerance. Front Microbiol 7:332.  https://doi.org/10.3389/fmicb.2016.00332CrossRefPubMedPubMedCentralGoogle Scholar
  31. Giovannetti M, Sbrana C (1998) Meeting a non-host: the behavior of AM fungi. Mycorrhiza 8:123–130CrossRefGoogle Scholar
  32. Godde JS, Bickerton A (2006) The repetitive DNA elements called CRIPRs and their associated genes: evidence of horizontal transfer among prokaryotes. J Mol Evol 62:718–729CrossRefPubMedPubMedCentralGoogle Scholar
  33. Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced repeats. Nucleic Acids Res 35:W52–W57CrossRefPubMedPubMedCentralGoogle Scholar
  34. Gupta M, DeKelver RC, Palta A, Clifford C, Gopalan S, Miller JC, Novak S, Desloover D, Gachotte D, Connell J, Flook J, Patterson T, Robbins K, Rebar EJ, Gregory PD, Urnov FD, Petolino JF (2012) Transcriptional activation of Brassica napus beta-ketoacyl-ACP synthase II with an engineered zinc finger protein transcription factor. Plant Biotechnol J 10:783–791CrossRefPubMedPubMedCentralGoogle Scholar
  35. Gupta S, Gupta R, Sharma S (2014) Impact of pesticides on plant growth promotion of Vigna radiata and non-target microbes: comparison between chemical- and bio-pesticides. Ecotoxicology 23:1015–1021.  https://doi.org/10.1007/s10646-014-1245-3CrossRefPubMedPubMedCentralGoogle Scholar
  36. Guzmán-Guzmán P, Alemán-Duarte MI, Delaye L, Herrera-Estrella A, Olmedo-Monfil V (2017) Identification of effector-like proteins in Trichoderma spp. and role of hydrophobin in the plant-fungus interaction and mycoparasitism. BMC Genet 18:16.  https://doi.org/10.1186/s12863-017-0481-yCrossRefPubMedPubMedCentralGoogle Scholar
  37. Gveroska B, Ziberoski J (2012) Trichoderma harzianum as a biocontrol agent against Alternaria alternata on tobacco. Appl Technol Innovat 7:67–76.  https://doi.org/10.15208/ati.2012.9CrossRefGoogle Scholar
  38. Hao Z, Xie W, Chen B (2019) Arbuscular mycorrhizal symbiosis affects plant immunity to viral infection and accumulation. Viruses 11:1–12.  https://doi.org/10.3390/v11060534
  39. Harman GE (2000) Myths and dogmas of biocontrol-changes in perceptions derived from research on Trichoderma harzianum T-22. Plant Dis 84:377–393CrossRefPubMedPubMedCentralGoogle Scholar
  40. 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 293:1129–1133CrossRefPubMedPubMedCentralGoogle Scholar
  41. Hogenhout SA, Van der Hoorn RAL, Terauchi R, Kamoun S (2009) Emerging concepts in effector biology of plant-associated organisms. Mol Plant-Microbe Interact 22:115–122CrossRefPubMedPubMedCentralGoogle Scholar
  42. Huang Y, Mijiti G, Wang Z, Yu W, Fan H, Zhang R, Liu Z (2015) Functional analysis of the class II hydrophobins gene HFB2-6 from the biocontrol agent Trichoderma asperellum ACCC30536. Microbiol Res 171:8–20.  https://doi.org/10.1016/j.micres.2014.12.004CrossRefPubMedPubMedCentralGoogle Scholar
  43. Jaganathan D, Ramasamy K, Sellamuthu G, Jayabalan S, Venkataraman G (2018) CRISPR for crop improvement: an update review. Front Plant Sci 9:985.  https://doi.org/10.3389/fpls.2018.00985CrossRefPubMedPubMedCentralGoogle Scholar
  44. Jansson JK, Hofmockel KS (2018) The soil microbiome—from metagenomics to metaphenomics. Curr Opin Microbiol 43:162–168CrossRefPubMedPubMedCentralGoogle Scholar
  45. Jia H, Zhang Y, Orbovic V, Xu J, White FF, Jones JB, Wang N (2017) Genome editing of the disease susceptibility gene CsLOB1 in citrus confers resistance to citrus canker. Plant Biotechnol J 15:817–823CrossRefPubMedPubMedCentralGoogle Scholar
  46. Jiang W, Zhou H, Bi H, Fromm M, Yang B, Weeks DP (2013) Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res 41:e188CrossRefPubMedPubMedCentralGoogle Scholar
  47. Jin Y, Liu H, Luo D, Yu N, Dong W, Wang C, Zhang X, Dai H, Yang J, Wang E (2016) DELLA proteins are common components of symbiotic rhizobial and mycorrhizal signalling pathways. Nat Commun 7:12433CrossRefPubMedPubMedCentralGoogle Scholar
  48. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821.  https://doi.org/10.1126/science.1225829CrossRefPubMedPubMedCentralGoogle Scholar
  49. Jung SC, Martinez-Medina A, Lopez-Raez JA, Pozo MJ (2012) Mycorrhiza-induced resistance and priming of plant defenses. J Chem Ecol 38:651–664CrossRefPubMedPubMedCentralGoogle Scholar
  50. Kamthan A, Chaudhuri A, Kamthan M, Datta A (2016) Genetically modified (GM) crops: milestones and new advances in crop improvement. Theor Appl Genet 129:1639.  https://doi.org/10.1007/s00122-016-2747-6CrossRefPubMedPubMedCentralGoogle Scholar
  51. Keinan A, Clark AG (2012) Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336:740–743CrossRefPubMedPubMedCentralGoogle Scholar
  52. Khalili E, Sadravi M, Naeimi S, Khosravi V (2012) Biological control of rice brown spot with native isolates of three trichoderma species. Braz J Microbiol 43:297–305.  https://doi.org/10.1590/S1517-83822012000100035CrossRefPubMedPubMedCentralGoogle Scholar
  53. Kiely P, Haynes J, Higgins C, Franks A, Mark G, Morrissey J, O’gara F (2006) Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere. Microb Ecol 51:257–266CrossRefPubMedPubMedCentralGoogle Scholar
  54. Kim H, Kim ST, Ryu J, Kang BC, Kim JS, Kim SG (2017) CRISPR/Cpf1-mediated DNA-free plant genome editing. Nat Commun 8:14406CrossRefPubMedPubMedCentralGoogle Scholar
  55. Kloepper JW (2003) A review of mechanisms for plant promotion by PGPR. In: Reddy MS, Anandaraj M (eds) Abstracts and short papers. 6th International PGPR workshop, 5-10 October 2003. Indian Institute of Spices Research, Calicut, India, pp 81–92Google Scholar
  56. Kong G, Wan L, Deng YZ, Yang W, Li W, Jiang L, Situ J, Xi P, Li M, Jiang Z (2019) Pectin acetylesterase PAE5 is associated with the virulence of plant pathogenic oomycete Peronophythora litchii. Physiol Mol Plant Pathol 106:16–22CrossRefGoogle Scholar
  57. Kumar S (2012) Biopesticides: a need for food and environmental safety. J Biofertil Biopestic 3:4Google Scholar
  58. Kumar A, Verma JP (2018) Does plant—microbe interaction confer stress tolerance in plants: a review? Microbiol Res 207:41–52CrossRefPubMedPubMedCentralGoogle Scholar
  59. Lanver D, Tollot M, Schweizer G, Lo Presti L, Reissmann S, Ma LS, Schuster M, Tanaka S, Liang L, Ludwig N, Kahmann R (2017) Ustilago maydis effectors and their impact on virulence. Nat Rev Microbiol 15:409–421CrossRefPubMedPubMedCentralGoogle Scholar
  60. Lee BD, Dutta S, Ryu H, Yoo SJ, Suh DS, Park K (2015) Induction of systemic resistance in Panax ginseng against Phytophthora cactorum by native Bacillus amyloliquefaciens HK34. J Ginseng Res 39:213–220.  https://doi.org/10.1016/j.jgr.2014.12.002CrossRefPubMedPubMedCentralGoogle Scholar
  61. Leff JW, Fierer N (2013) Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 8(3):e59310.  https://doi.org/10.1371/journal.pone.0059310CrossRefPubMedPubMedCentralGoogle Scholar
  62. Li X, Zhou W, Ren Y, Tian X, Lv T, Wang Z, Fang J, Chu C, Yang J, Bu Q (2017) High-efficiency breeding of early-maturing rice cultivars via CRISPR/Cas9-mediated genome editing. J Genet Genomics 44:175–178CrossRefPubMedPubMedCentralGoogle Scholar
  63. Li J, Zhang Y, Zhang Y, Yu PL, Pan H, Rollins JA (2018) Introduction of large sequence inserts by CRISPR-Cas9 to create pathogenicity mutants in the multinucleate filamentous pathogen Sclerotinia sclerotiorum. MBio 9:1–19CrossRefGoogle Scholar
  64. Lopez-Arredondo D, Gonzalez-Morales SI, Bello-Bello E, Alejo-Jacuinde G, Herrera L (2015) Engineering food crops to grow in harsh environment [v1; ref status: indexed, http://f1000r.es/5f1]. F1000Res 4:651.  https://doi.org/10.12688/f1000research.6538.1CrossRefPubMedPubMedCentralGoogle Scholar
  65. Loya LJ, Hower AA Jr (2002) Population dynamics, persistence, and efficacy of the entomopathogenic nematode Heterorhabditis bacteriophora (Oswego strain) in association with the clover root curculio (Coleoptera: Curculionidae) in Pennsylvania. Environ Entomol 31:1240–1250CrossRefGoogle Scholar
  66. Lu K, Wu B, Wang J, Zhu W, Nie H, Qian J, Huang W, Fang Z (2018) Blocking amino acid transporter OsAAP3 improves grain yield by promoting outgrowth buds and increasing tiller number in rice. Plant Biotechnol J 16:1710–1722CrossRefPubMedPubMedCentralGoogle Scholar
  67. Luginbuehl LH, Oldroyd GED (2017) Understanding the arbuscule at the heart of endomycorrhizal symbioses in plants. Curr Biol 27:R952–R963CrossRefPubMedPubMedCentralGoogle Scholar
  68. Ma Z, Michailides TJ (2005) Advances in understanding molecular mechanisms of fungicide resistance and molecular detection of resistant genotypes in phytopathogenic fungi. Crop Prot 24:853–863CrossRefGoogle Scholar
  69. Macovei A, Sevilla NR, Cantos C, Jonson GB, Slamet-Loedin I, Cermák T, Voytas DF, Choi IR, Chadha-Mohanty P (2018) Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. Plant Biotechnol J 16:1918–1927CrossRefPubMedPubMedCentralGoogle Scholar
  70. Maghari BM, Ardekani AM (2011) Genetically modified foods and social concerns. Avicenna J Med Biotech 3:109–117Google Scholar
  71. Mendes LW, Kuramae EE, Navarrete AA, van Veen JA, Tsai SM (2014) Taxonomical and functional microbial community selection in soybean rhizosphere. ISME J 8:1577–1587.  https://doi.org/10.1038/ismej.2014.17CrossRefPubMedPubMedCentralGoogle Scholar
  72. Mendoza-Mendoza A, Zaid R, Lawry R, Hermosa R, Monte E, Horwitz BA, Mukherjee PK (2018) Molecular dialogues between Trichoderma and roots: role of the fungal secretome. Fungal Biol Rev 32:62–85.  https://doi.org/10.1016/j.fbr.2017.12.001CrossRefGoogle Scholar
  73. Michavila G, Adler C, De Gregorio PR, Lami MJ, Di Santo MCC, Zenoff AM, de Cristobal RE, Vincent PA (2017) Pseudomonas protegens CS1 from the lemon phyllosphere as a candidate for citrus canker biocontrol agent. Plant Biol 19:608–617CrossRefPubMedPubMedCentralGoogle Scholar
  74. Mnyone LL, Koenraadt CJM, Lyimo IN, Mpingwa MW, Takken W, Russell TL (2010) Anopheline and culicine mosquitoes are not repelled by surfaces treated with the entomopathogenic fungi Metarhizium anisopliae and Beauveria bassiana. Parasit Vectors 3:80CrossRefPubMedPubMedCentralGoogle Scholar
  75. Mona SA, Hashem A, Abdulaziz EF, Alqarawi C, Wafi D, Soliman K, Wirth S, Egamberdieva D (2017) Increased resistance of drought by Trichoderma harzianum fungal treatment correlates with increased secondary metabolites and proline content. J Integr Agric 16:1751–1757CrossRefGoogle Scholar
  76. Moran-Diez E, Hermosa R, Ambrosino P, Cardoza RE, Gutierrez S, Lorito M, Monte E (2009) The ThPG1 endopolygalacturonase is required for the Trichoderma harzianum-plant beneficial interaction. Mol Plant Microbe In 22:1021–1031CrossRefGoogle Scholar
  77. Moscatiello R, Sello S, Ruocco M, Barbulova A, Cortese E, Nigris S, Baldan B, Chiurazzi M, Mariani P, Lorito M, Navazio L (2018) The hydrophobin HYTLO1 secreted by the biocontrol fungus Trichoderma longibrachiatum triggers a NAADP-mediated calcium signalling pathway in Lotus japonicus. Int J Mol Sci 19:E2596.  https://doi.org/10.3390/ijms19092596CrossRefPubMedPubMedCentralGoogle Scholar
  78. Mueller UG, Sachs JL (2015) Engineering microbiomes to improve plant and animal health. Trends Microbiol 23:606–617.  https://doi.org/10.1016/j.tim.2015.07.009CrossRefPubMedPubMedCentralGoogle Scholar
  79. Mukherjee PK, Latha J, Hadar R, Horwitz BA (2003) TmkA, a mitogen-activated protein kinase of Trichoderma virens, is involved in biocontrol properties and repression of conidiation in the dark. Eukaryot Cell 2:446–455CrossRefPubMedPubMedCentralGoogle Scholar
  80. Mwajita M, Murage H, Tani A, Kahangi EM (2013) Evaluation of rhizosphere, rhizoplane and phyllosphere bacteria and fungi isolated from rice in Kenya for plant growth promoters. Springerplus 2:606.  https://doi.org/10.1186/2193-1801-2-606CrossRefPubMedPubMedCentralGoogle Scholar
  81. Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S (2017) Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci Rep 7:482CrossRefPubMedPubMedCentralGoogle Scholar
  82. Oku S, Komatsu A, Nakashimada Y, Tajima T, Kato J (2014) Identification of Pseudomonas fluorescens chemotaxis sensory proteins for malate, succinate, and fumarate and their involvement in root colonization. Microbes Environ 29:413–419CrossRefPubMedPubMedCentralGoogle Scholar
  83. Olanrewaju OS, Glick BR, Babalola OO (2017) Mechanisms of action of plant growth promoting bacteria. World J Microbiol Biotechnol 33:197.  https://doi.org/10.1007/s11274-017-2364-9CrossRefPubMedPubMedCentralGoogle Scholar
  84. Omann M, Zeilinger S (2010) How a mycoparasite employs g-protein signaling: using the example of Trichoderma. J Signal Transduct 2010:123126.  https://doi.org/10.1155/2010/123126CrossRefPubMedPubMedCentralGoogle Scholar
  85. Pelczar MJ, Chan ECS, Creig NR (1988) Microbiology. Tata Mcgraw-Hill, Publishing Company Limited, New Delhi, pp 560–580Google Scholar
  86. Peng A, Chen S, Lei T, Xu L, He Y, Wu L, Yao L, Zou X (2017) Engineering canker-resistant plants through CRISPR/Cas9-targeted editing of the susceptibility gene CsLOB1 promoter in citrus. Plant Biotechnol J 15:1509–1519.  https://doi.org/10.1111/pbi.12733CrossRefPubMedPubMedCentralGoogle Scholar
  87. Pereira JAP, Vieira IJC, Freitas MSM, Prins CL, Martins MA, Rodrigues R (2015) Effects of arbuscular mycorrhizal fungi on Capsicum spp. J Agric Sci 154:828–849CrossRefGoogle Scholar
  88. Pozo MJ, Azcón-Aguilar C (2007) Unraveling mycorrhiza-induced resistance. Curr Opin Plant Biol 10:393–398.  https://doi.org/10.1016/j.pbi.2007.05.004CrossRefPubMedPubMedCentralGoogle Scholar
  89. Prater CA, Redmond C, Barney W, Bonning BC, Potter DA (2006) Microbial control of black cutworm (Lepidoptera: Noctuidae) in turfgrass using Agrotis ipsilon multiple nucleopolyhedrovirus. J Econ Entomol 99:1129–1137CrossRefPubMedPubMedCentralGoogle Scholar
  90. Qaim M, Zilberman D (2003) Yield effects of genetically modified crops in developing countries. Science 299:900–902.  https://doi.org/10.1126/science.1080609CrossRefPubMedPubMedCentralGoogle Scholar
  91. Rocha-Ramirez V, Omero C, Chet I, Horwitz BA, Herrera-Estrella A (2002) Trichoderma atroviride G-protein α-subunit gene tga 1 is involved in mycoparasitic coiling and conidiation. Eukaryot Cell 1:594–605.  https://doi.org/10.1128/EC.1.4.594-605.2002CrossRefPubMedPubMedCentralGoogle Scholar
  92. Sabbagh SK, Roudini M, Panjehkeh N (2017) Systemic resistance induced by Trichoderma harzianum and Glomus mosseae on cucumber damping-off disease caused by Phytophthora melonis. Arch Phytopathol Plant Protect 50:375–388CrossRefGoogle Scholar
  93. Salas-Marina MA, Isordia-Jasso MI, Islas-Osuna MA, Delgado-Sánchez P, Jiménez-Bremont JF, Rodríguez-Kessler M, Rosales-Saavedra MT, Herrera-Estrella A, Casas-Flores S (2015) The Epl1 and Sm1 proteins from Trichoderma atroviride and Trichoderma virens differentially modulate systemic disease resistance against different life style pathogens in Solanum lycopersicum. Front Plant Sci 23:77.  https://doi.org/10.3389/fpls.2015.00077CrossRefGoogle Scholar
  94. Salvioli A, Bonfante P (2013) Systems biology and “omics” tools: a cooperation for next-generation mycorrhizal studies. Plant Sci 203–204:107–114.  https://doi.org/10.1016/j.plantsci.2013.01.001CrossRefPubMedPubMedCentralGoogle Scholar
  95. Santoyo G, Moreno-Hagelsieb G, del Carmen Orozco-Mosqueda M, Glick BR (2016) Plant growth-promoting bacterial endophytes. Microbiol Res 183:92–99CrossRefPubMedPubMedCentralGoogle Scholar
  96. Saravanakumar K, Fan L, Fu K, Yu C, Wang M, Xia H, Sun J, Li Y, Chen J (2016) Cellulase from Trichoderma harzianum interacts with roots and triggers induced systemic resistance to foliar disease in maize. Sci Rep 10:35543.  https://doi.org/10.1038/srep35543CrossRefGoogle Scholar
  97. Saravanakumar K, Li Y, Yu C, Wang QQ, Wang M, Sun J, Chen J (2017) Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot. Sci Rep 7:1771.  https://doi.org/10.1038/s41598-017-01680-wCrossRefPubMedPubMedCentralGoogle Scholar
  98. 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.  https://doi.org/10.3389/fmicb.2015.01280CrossRefPubMedPubMedCentralGoogle Scholar
  99. Schuster M, Kahmann R (2019) CRISPR-Cas9 genome editing approaches in filamentous fungi and Oomycetes. Fungal Genet Biol 130:43–53CrossRefPubMedPubMedCentralGoogle Scholar
  100. Sengupta A, Gunri SK (2015) Microbial intervention in agriculture: an overview. Afr J Microbiol Res 9:1215–1226CrossRefGoogle Scholar
  101. Shafique HA, Sultana V, Ehteshamul-Haque S, Athar M (2016) Management of soilborne diseases of organic vegetables. J Plant Prot Res 56:221–230CrossRefGoogle Scholar
  102. Sharif M, Claassen N (2011) Action mechanisms of arbuscular mycorrhizal fungi in phosphorus uptake by Capsicum annuum L. Pedosphere 21:502–511.  https://doi.org/10.1016/S1002-0160(11)60152-5CrossRefGoogle Scholar
  103. Shoresh M, Harman GE, Mastouri F (2010) Induced systemic resistance and plant responses to fungal Biocontrol agents. Annu Rev Phytopathol 48:21–43CrossRefPubMedPubMedCentralGoogle Scholar
  104. Singh A, Taylor LE 2nd, Vander Wall TA, Linger J, Himmel ME, Podkaminer K, Adney WS, Decker SR (2015) Heterologous protein expression in Hypocrea jecorina: a historical perspective and new developments. Biotechnol Adv 33:142–154.  https://doi.org/10.1016/j.biotechadv.2014.11.009CrossRefPubMedPubMedCentralGoogle Scholar
  105. Singh R, Parihar P, Singh M, Bajguz A, Kumar J, Singh S, Singh VP, Prasad SM (2017) Uncovering potential applications of Cyanobacteria and algal metabolites in biology, agriculture and medicine: current status and future prospects. Front Microbiol 8:515CrossRefPubMedPubMedCentralGoogle Scholar
  106. Smith SE, Smith FA (2011) Roles of arbuscular mycorrhizas in plant nutrition and growth: new paradigms from cellular to ecosystem scales. Annu Rev Plant Biol 62:227–250CrossRefPubMedPubMedCentralGoogle Scholar
  107. Soda N, Verma L, Giri J (2018) CRISPR-Cas9 based plant genome editing: significance, opportunities and recent advances. Plant Physiol Biochem 131:2–11.  https://doi.org/10.1016/j.plaphy.2017.10.024CrossRefPubMedPubMedCentralGoogle Scholar
  108. Sorek R, Lawrence CM, Wiedenheft B (2011) CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu Rev Biochen 82:237–266CrossRefGoogle Scholar
  109. Spaepen S, Vanderleyden J (2011) Auxin and plant-microbe interactions. Cold Spring Harb Perspect Biol 3:a001438CrossRefPubMedPubMedCentralGoogle Scholar
  110. Sperschneider J, Gardiner DM, Dodds PN, Tini F, Covarelli L, Singh KB, Manners JM, Taylor JM (2016) EffectorP: predicting fungal effector proteins from secretomes using machine learning. New Phytol 210:743–761CrossRefPubMedPubMedCentralGoogle Scholar
  111. Srilatha B (2011) Nanotechnology in agriculture. J Nanomedic Nanotechnol 2:1–5Google Scholar
  112. Téllez-Vargas J, Rodríguez-Monroy M, López-Meyer M, Montes-Belmont R, Sepúlveda-Jiménez G (2017) Trichoderma asperellum ameliorates phytotoxic effects of copper in onion (Allium cepa L.). Environ Exp Bot 136:85–93.  https://doi.org/10.1016/j.envexpbot.2017.01.009CrossRefGoogle Scholar
  113. Thomazella DPDT, Brail Q, Dahlbeck D, Staskawicz BJ (2016) CRISPR-Cas9 mediated mutagenesis of a DMR6 ortholog in tomato confers broad-spectrum disease resistance. bioRxiv.Google Scholar
  114. Tripathi JN, Ntui VO, Ron M, Muiruri SK, Britt A, Tripathi L (2019) CRISPR/Cas9 editing of endogenous banana streak virus in the B genome of Musa spp. overcomes a major challenge in banana breeding. Commun Boil 2:46CrossRefGoogle Scholar
  115. Tyc O, Zweers H, De Boer W, Garbeva P (2015) Volatiles in inter-specific bacterial interactions. Front Microbiol 6:1412.  https://doi.org/10.3389/fmicb.2015.01412CrossRefPubMedPubMedCentralGoogle Scholar
  116. Vacheron J, Renoud S, Muller D, Babalola OO, Prigent-Combaret C (2015) Alleviation of abiotic and biotic stresses in plants by Azospirillum. In: Cassan FD, Okon Y, Creus C (eds) Handbook for Azospirillum: technical issues and protocols. Springer, Berlin, Heidelberg, pp 333–365Google Scholar
  117. Van Der Heijden MGA, Bardgett RD, Van Straalen NM (2008) The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol Lett 11:296–310.  https://doi.org/10.1111/j.1461-0248.2007.01139.xCrossRefPubMedPubMedCentralGoogle Scholar
  118. Viterbo A, Chet I (2010) TasHyd1, a new hydrophobin gene from the biocontrol agent Trichoderma asperellum, is involved in plant root colonization. Mol Plant Pathol 7:4.  https://doi.org/10.1111/j.1364-3703.2006.00335.xCrossRefGoogle Scholar
  119. Vitorino LC, Bessa LA (2017) Technological microbiology: development and applications. Front Microbiol 8:827.  https://doi.org/10.3389/fmicb.2017.00827CrossRefPubMedPubMedCentralGoogle Scholar
  120. Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840CrossRefPubMedPubMedCentralGoogle Scholar
  121. Wang Q, Coleman JJ (2019) CRISPR/Cas9-mediated endogenous gene tagging in Fusarium oxysporum. Fungal Genet Boil 126:17–24CrossRefGoogle Scholar
  122. Wang L, Chen L, Li R, Zhao R, Yang M, Sheng J, Shen L (2017a) Reduced drought tolerance by CRISPR/Cas9-mediated SlMAPK3 mutagenesis in tomato plants. J Agric Food Chem 65:8674–8682.  https://doi.org/10.1021/acs.jafc.7b02745CrossRefPubMedPubMedCentralGoogle Scholar
  123. Wang W, Shi J, Xie Q, Jiang Y, Yu N, Wang E (2017b) Nutrient exchange and regulation in arbuscular mycorrhizal symbiosis. Mol Plant 10:1147–1158CrossRefPubMedPubMedCentralGoogle Scholar
  124. Wang X, Tu M, Wang D, Liu J, Li Y, Li Z, Wang Y, Wang X (2019) CRISPR/Cas9-mediated efficient targeted mutagenesis in grape in the first generation. Plant Biotechnol J 16:844–855CrossRefGoogle Scholar
  125. Wensing A, Braun SD, Buttner P, Expert D, Volksch B, Ullrich MS, Weingart H (2010) Impact of siderophore production by Pseudomonas syringae pv. Syringae 22d/93 on epiphytic fitness and biocontrol activity against Pseudomonas syringae pv. glycinea 1a/96. Appl Environ Microbiol 76:2704–2711.  https://doi.org/10.1128/AEM.02979-09CrossRefPubMedPubMedCentralGoogle Scholar
  126. Werner S, Polle A, Brinkmann N (2016) Belowground communication: impacts of volatile organic compounds (VOCs) from soil fungi on other soil-inhabiting organisms. Appl Microbiol Biotechnol 100:8651–8665.  https://doi.org/10.1007/s00253-016-7792-1CrossRefPubMedPubMedCentralGoogle Scholar
  127. West SA, Griffin AS, Gardner A (2007) Evolutionary explanations for cooperation. Curr Biol 17:R661–R672CrossRefPubMedPubMedCentralGoogle Scholar
  128. Williams TR, Moyne AL, Harris LJ, Marco ML (2013) Season, irrigation, leaf age, and Escherichia coli inoculation influence the bacterial diversity in the lettuce phyllosphere. PLoS One 8(7):e68642.  https://doi.org/10.1371/journal.pone.0068642CrossRefPubMedPubMedCentralGoogle Scholar
  129. Woo SL, Pepe O (2018) Microbial consortia: promising probiotics as plant biostimulants for sustainable agriculture. Front Plant Sci 9:1801.  https://doi.org/10.3389/fpls.2018.01801CrossRefPubMedPubMedCentralGoogle Scholar
  130. Xie K, Zhang J, Yang Y (2014) Genome-wide prediction of highly specific guide RNA spacers for CRISPR–Cas9-Mediated genome editing in model plants and major crops. Mol Plant 7:923–926CrossRefPubMedPubMedCentralGoogle Scholar
  131. Yang D, Pomraning K, Kopchinskiy A, Karimi Aghcheh R, Atanasova L, Chenthamara K, Baker SE, Zhang R, Shen Q, Freitag M, Kubicek CP, Druzhinina IS (2015) Genome sequence and annotation of Trichoderma parareesei, the ancestor of the cellulase producer Trichoderma reesei. Genome Announc 3:e00885–e00815.  https://doi.org/10.1128/genomeA.00885-15CrossRefPubMedPubMedCentralGoogle Scholar
  132. Youssef MMA, Eissa MFM (2014) Biofertilizers and their role in management of plant parasitic nematodes. A review. E3 J Biotechnol Pharm Res 5:1–6Google Scholar
  133. Yu X, Ai C, Xin L, Zhou G (2011) The siderophore producing bacterium, Bacillus subtilis CAS15, as a biocontrol effect on Fusarium wilt and promotes the growth of pepper. Eur J Soil Biol 47:138–145CrossRefGoogle Scholar
  134. Zhang C, Wohlhueter R, Zhang H (2016) Genetically modified foods: a critical review of their promise and problems. Food Sci Human Wellness 5:116–123CrossRefGoogle Scholar
  135. Zhang S, Liu Q, Han Y, Han J, Yan Z, Wang Y, Zhang X (2019) Nematophin, an antimicrobial dipeptide compound from Xenorhabdus nematophila YL001 as a potent biopesticide for Rhizoctonia solani control. Front Microbiol 10:1765.  https://doi.org/10.3389/fmicb.2019.01765. eCollection 2019CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  1. 1.Department of BotanySavitribai Phule Pune UniversityPuneIndia

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