Application of Microbial Biotechnology in Improving Salt Stress and Crop Productivity

  • Maneesh KumarEmail author
  • Mohd Sayeed Akhtar


Soil salinity is the principal detrimental abiotic stress that globally impedes crop yield. It affects a wide range of biochemical, morphological, physiological, and molecular changes and is responsible for inducing ion toxicity, hormonal disturbance, water uptake, homeostasis disturbance, and oxidative stress. To evade this abiotic stress, many genes are identified, and their mechanisms have been elucidated in Arabidopsis thaliana through the transgenic approaches and also in other plants like Prunus cerasifera, Brassica juncea, Ipomoea batatas, tobacco, etc. Modern tools revolutionized microbial biotechnology by providing a better choice for plant scientists to select or incorporate genes of interest into preferred species or cultivars. Transgenics may regulate the various metabolic pathways including biosynthesis of chlorophyll and osmolyte, ion exchange homeostasis, antioxidant defense mechanism, and additional frontier defense corridors against salinity stress. Exclusively using such gene manipulations, many genetically modified crop varieties like canola, cotton, maize, rice, and soybean are being developed. Many techniques have been introduced for establishing possible sustainability against soil salinity. Apart from this, it also incorporates some receptor genes in crop plants that may sense or escape any changes in soil salinity under environmental condition. Thus, the aim of this chapter is to enlighten the basic importance and modern application of microbial biotechnology to understand the behavior of transgenic crop plants in saline soil. The study also elaborates understanding of molecular machinery for healthy crop production.


Abiotic stress Halophytes Receptors Salinity Transgenics 


  1. Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D (2016) Global agricultural intensification during climate change: a role for genomics. Plant Biotechnol J 14:1095–1098PubMedCrossRefGoogle Scholar
  2. Abrol IP, Yadav JS, Massoud FI (1988) Salt-affected soils and their management. FAO, RomeGoogle Scholar
  3. Agarwal PK, Shukla PS, Gupta K, Jha B (2013) Bioengineering for salinity tolerance in plants: state of the art. Mol Biotechnol 54:102–123PubMedCrossRefGoogle Scholar
  4. Ahanger MA, Akram NA, Ashraf M, Alyemeni MN, Wijaya L, Ahmad P (2017) Plant responses to environmental stresses-from gene to biotechnology. AoB Plants 9:plx025. Scholar
  5. Ahmad P, Azooz MM, Prasad MN (2012) Ecophysiology and responses of plants under salt stress. Springer, BerlinGoogle Scholar
  6. Akpınar BA, Lucas SJ, Budak H (2013) Genomics approaches for crop improvement against abiotic stress. Sci World J 2013:361921. Scholar
  7. Al-Harrasi I, Al-Yahyai R, Yaish MW (2018) Differential DNA methylation and transcription profiles in date palm roots exposed to salinity. PLoS One 13:e0191492PubMedPubMedCentralCrossRefGoogle Scholar
  8. Allen RS, Millgate AG, Chitty JA, Thisleton J, Miller JA, Fist AJ, Gerlach WL, Larkin PJ (2004) RNAi-mediated replacement of morphine with the non-narcotic alkaloid reticuline in opium poppy. Nat Biotechnol 22:1559PubMedCrossRefGoogle Scholar
  9. Alptekin B, Langridge P, Budak H (2017) Abiotic stress miRNomes in the Triticeae. Funct Integr Genom 17:145–170CrossRefGoogle Scholar
  10. Andreu P, Arbeloa A, Lorente P, Marín JA (2011) Early detection of salt stress tolerance of Prunus rootstocks by excised root culture. HortScience 46(1):80–85CrossRefGoogle Scholar
  11. Ashraf M (2002) Salt tolerance of cotton: some new advances. Crit Rev Plant Sci 21:1–30CrossRefGoogle Scholar
  12. Ashraf M, Bashir A (2003) Salt stress induced changes in some organic metabolites and ionic relations in nodules and other plant parts of two crop legumes differing in salt tolerance. Flora-Morphol Distribut Funct Ecol Plants 198:486–498CrossRefGoogle Scholar
  13. Baloglu MC, Kavas M, Gürel S, Gürel E (2018) The use of microorganisms for gene transfer and crop improvement. In: Prasad R, Gill SS, Tuteja N (eds) Crop improvement through microbial biotechnology. Elsevier, Amsterdam, pp 1–25Google Scholar
  14. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefGoogle Scholar
  15. Bartels D, Sunkar R (2005) Drought and salt tolerance in plants. Crit Rev Plant Sci 24:23–58CrossRefGoogle Scholar
  16. Baulcombe D (2004) RNA silencing in plants. Nature 431:356PubMedCrossRefGoogle Scholar
  17. Bednarek PT, Orłowska R, Niedziela A (2017) A relative quantitative methylation-sensitive amplified polymorphism (MSAP) method for the analysis of abiotic stress. BMC Plant Biol 17:79PubMedPubMedCentralCrossRefGoogle Scholar
  18. Bender J (2004) DNA methylation and epigenetics. Annu Rev Plant Biol 55:41–68PubMedCrossRefGoogle Scholar
  19. Bhatnagar-Mathur P, Vadez V, Sharma KK (2008) Transgenic approaches for abiotic stress tolerance in plants: retrospect and prospects. Plant Cell Rep 27:411–424PubMedCrossRefGoogle Scholar
  20. Bian H, Xie Y, Guo F, Han N, Ma S, Zeng Z, Wang J, Yang Y, Zhu M (2012) Distinctive expression patterns and roles of the miRNA393/TIR1 homolog module in regulating flag leaf inclination and primary and crown root growth in rice (Oryza sativa). New Phytol 196:149–161PubMedCrossRefGoogle Scholar
  21. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21PubMedCrossRefGoogle Scholar
  22. Bohnert HJ, Gong Q, Li P, Ma S (2006) Unraveling abiotic stress tolerance mechanisms–getting genomics going. Curr Opin Plant Biol 9:180–188PubMedCrossRefGoogle Scholar
  23. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123:1279–1291PubMedPubMedCentralCrossRefGoogle Scholar
  24. Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. Environ Mol Mutagen 49:61–72PubMedCrossRefGoogle Scholar
  25. Boyko A, Blevins T, Yao Y, Golubov A, Bilichak A, Ilnytskyy Y, Hollunder J, Meins F Jr, Kovalchuk I (2010) Transgenerational adaptation of Arabidopsis to stress requires DNA methylation and the function of Dicer-like proteins. PLoS One 5:e9514PubMedPubMedCentralCrossRefGoogle Scholar
  26. Brozynska M, Omar ES, Furtado A, Crayn D, Simon B, Ishikawa R, Henry RJ (2014) Chloroplast genome of novel rice germplasm identified in northern Australia. Trop Plant Biol 7:111–120PubMedPubMedCentralCrossRefGoogle Scholar
  27. Budak H, Kantar M, Yucebilgili Kurtoglu K (2013) Drought tolerance in modern and wild wheat. Sci World J 2013:548246. Scholar
  28. Budak H, Hussain B, Khan Z, Ozturk NZ, Ullah N (2015) From genetics to functional genomics: improvement in drought signaling and tolerance in wheat. Front Plant Sci 6:1012PubMedPubMedCentralCrossRefGoogle Scholar
  29. Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EV, Schulze-Lefert P (2013) Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838PubMedCrossRefGoogle Scholar
  30. Cabello JV, Chan RL (2012) The homologous homeodomain-leucine zipper transcription factors HaHB1 and AtHB13 confer tolerance to drought and salinity stresses via the induction of proteins that stabilize membranes. Plant Biotechnol J 10:815–825PubMedCrossRefGoogle Scholar
  31. Cabello JV, Arce AL, Chan RL (2012) The homologous HD-Zip I transcription factors HaHB1 and AtHB13 confer cold tolerance via the induction of pathogenesis-related and glucanase proteins. Plant J 69:141–153PubMedCrossRefGoogle Scholar
  32. Cabello JV, Lodeyro AF, Zurbriggen MD (2014) Novel perspectives for the engineering of abiotic stress tolerance in plants. Curr Opin Biotechnol 26:62–70PubMedCrossRefGoogle Scholar
  33. Cao X, Jacobsen SE (2002) Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A 99:S16491–S16498CrossRefGoogle Scholar
  34. Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE (2003) Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation. Curr Biol 13:2212–2217PubMedCrossRefGoogle Scholar
  35. Cao DH, Gao X, Liu J, Kimatu JN, Geng SJ, Wang XP, Zhao J, Shi DC (2011) Methylation sensitive amplified polymorphism (MSAP) reveals that alkali stress triggers more DNA hypomethylation levels in cotton (Gossypium hirsutum L.) roots than salt stress. Afr J Biotechnol 10:18971–18980Google Scholar
  36. Cao HX, Schmutzer T, Scholz U, Pecinka A, Schubert I, Vu GT (2015) Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Front Microbiol 6:526PubMedPubMedCentralGoogle Scholar
  37. Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8:884PubMedCrossRefGoogle Scholar
  38. Chen X (2005) MicroRNA biogenesis and function in plants. FEBS Lett 579:5923–5931PubMedPubMedCentralCrossRefGoogle Scholar
  39. Chen PC, Gu ZM (2015) Regulation of ion homeostasis under salt stress. J Anhui Agric Sci 20:006Google Scholar
  40. Chinnusamy V, Zhu JK (2009a) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12:133–139PubMedPubMedCentralCrossRefGoogle Scholar
  41. Chinnusamy V, Zhu JK (2009b) RNA-directed DNA methylation and demethylation in plants. Sci China Ser C 52:331–343CrossRefGoogle Scholar
  42. Choi CS, Sano H (2007) Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 277:589–600PubMedCrossRefGoogle Scholar
  43. Ciobanu I, Sumalan R (2009) The effects of the salinity stress on the growing rates and physiological characteristics to the Lycopersicum esculentum specie. Bull UASVM Hortic 66:616–620Google Scholar
  44. Coleman-Derr D, Tringe SG (2014) Building the crops of tomorrow: advantages of symbiont-based approaches to improving abiotic stress tolerance. Front Microbiol 5:283PubMedPubMedCentralCrossRefGoogle Scholar
  45. Cramer GR, Urano K, Delrot S, Pezzotti M, Shinozaki K (2011) Effects of abiotic stress on plants: a systems biology perspective. BMC Plant Biol 11:163PubMedPubMedCentralCrossRefGoogle Scholar
  46. Daffonchio D, Hirt H, Berg G (2015) Plant-microbe interactions and water management in arid and saline soils. In: Lugtenberg B (ed) Principles of plant-microbe interactions. Springer, Cham, pp 265–276Google Scholar
  47. Datta A (2013) Genetic engineering for improving quality and productivity of crops. Agric Food Security 2:15CrossRefGoogle Scholar
  48. De Fátima Rosas-Cárdenas F, de Folter S (2017) Conservation, divergence, and abundance of miRNAs and their effect in plants. In: Rajewsky N, Jurga S, Barciszewski J (eds) Plant epigenetics. Springer, Cham, pp 1–22Google Scholar
  49. Dehghan G, Amjad L, Nosrati H (2013) Enzymatic and non-enzymatic antioxidant responses of alfalfa leaves and roots under different salinity levels. Acta Biol Hungar 64:207–217CrossRefGoogle Scholar
  50. Deinlein U, Stephan AB, Horie T, Luo W, Xu G, Schroeder JI (2014) Plant salt-tolerance mechanisms. Trends Plant Sci 19:371–379PubMedPubMedCentralCrossRefGoogle Scholar
  51. Dikilitas M, Karakas S (2014) Crop plants under saline-adapted fungal pathogens: an overview. In: Ahmad P, Rasool S (eds) Emerging technologies and management of crop stress tolerance. Elsevier, London, pp 173–192CrossRefGoogle Scholar
  52. Ditta A (2013) Salt tolerance in cereals: molecular mechanisms and applications. In: Rout GR, Das AB (eds) Molecular stress physiology of plants. Springer, New Delhi, pp 133–154CrossRefGoogle Scholar
  53. Eamens A, Wang MB, Smith NA, Waterhouse PM (2008) RNA silencing in plants: yesterday, today, and tomorrow. Plant Physiol 147:456–468PubMedPubMedCentralCrossRefGoogle Scholar
  54. Eamens A, Curtin SJ, Waterhouse PM (2010) RNA silencing in plants. In: Chong PE, Davey MR (eds) Plant developmental biology-biotechnological perspectives. Springer, Berlin/Heidelberg, pp 277–294CrossRefGoogle Scholar
  55. Elhindi KM, El-Din AS, Elgorban AM (2017) The impact of arbuscular mycorrhizal fungi in mitigating salt-induced adverse effects in sweet basil (Ocimum basilicum L.). Saudi J Biol Sci 24:170–179PubMedCrossRefGoogle Scholar
  56. Fasciglione G, Casanovas EM, Quillehauquy V, Yommi AK, Goñi MG, Roura SI, Barassi CA (2015) Azospirillum inoculation effects on growth, product quality and storage life of lettuce plants grown under salt stress. Sci Hortic 195:154–162CrossRefGoogle Scholar
  57. Finkel OM, Castrillo G, Paredes SH, González IS, Dangl JL (2017) Understanding and exploiting plant beneficial microbes. Curr Opin Plant Biol 38:155–163PubMedPubMedCentralCrossRefGoogle Scholar
  58. Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Acad Sci U S A 93:8449–8454PubMedPubMedCentralCrossRefGoogle Scholar
  59. Flowers TJ (2004) Improving crop salt tolerance. J Exp Bot 55:307–319PubMedCrossRefGoogle Scholar
  60. Fulneček J, Kovařík A (2014) How to interpret methylation sensitive amplified polymorphism (MSAP) profiles. BMC Genet 15:2PubMedPubMedCentralCrossRefGoogle Scholar
  61. Furini A, Koncz C, Salamini F, Bartels D (1997) High level transcription of a member of a repeated gene family confers dehydration tolerance to callus tissue of Craterostigma plantagineum. EMBO J 16:3599–3608PubMedPubMedCentralCrossRefGoogle Scholar
  62. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10:94PubMedPubMedCentralCrossRefGoogle Scholar
  63. Gilbert N, Gewin V, Tollefson J, Sachs J, Potrykus I (2010) How to feed a hungry world. Nature 466:531–532CrossRefGoogle Scholar
  64. Gill SS, Tuteja N (2010) Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem 48:909–930CrossRefGoogle Scholar
  65. Gonzalez AJ, Larraburu EE, Llorente BE (2015) Azospirillum brasilense increased salt tolerance of jojoba during in vitro rooting. Indust Crops Prod 76:41–48CrossRefGoogle Scholar
  66. Gupta B, Huang B (2014) Mechanism of salinity tolerance in plants: physiological, biochemical, and molecular characterization. Int J Genom 18:701596. Scholar
  67. Gursanscky NR, Carroll BJ (2012) Mechanism of small RNA movement. In: Kragler F, Hülskamp M (eds) Short and long distance signaling. Springer, New York, pp 99–130CrossRefGoogle Scholar
  68. Hakeem KR, Akhtar J, Sabir M (2016) Soil science: agricultural and environmental prospectives. Springer, Berlin/HeidelbergCrossRefGoogle Scholar
  69. Haney CH, Samuel BS, Bush J, Ausubel FM (2015) Associations with rhizosphere bacteria can confer an adaptive advantage to plants. Nat Plants 1:15051PubMedPubMedCentralCrossRefGoogle Scholar
  70. Hannon GJ (2002) RNA interference. Nature 418:244CrossRefGoogle Scholar
  71. Hasanuzzaman M, Nahar K, Fujita M, Ahmad P, Chandna R, Prasad MN, Ozturk M (2013) Enhancing plant productivity under salt stress: relevance of poly-omics. In: Ahmad P, Azooz MM, Prasad MNV (eds) Salt stress in plants. Springer, New York, pp 113–156CrossRefGoogle Scholar
  72. Hasanuzzaman M, Nahar K, Rahman A, Al Mahmud J, Hossain S, Alam K, Oku H, Fujita M (2017) Actions of biological trace elements in plant abiotic stress tolerance. In: Naeem M, Ansari AA, Gill SS (eds) Essential plant nutrients: uptake, use efficiency, and management. Springer, Cham, pp 213–274CrossRefGoogle Scholar
  73. Hasegawa PM, Bressan RA, Zhu JK, Bohnert HJ (2000) Plant cellular and molecular responses to high salinity. Annu Rev Plant Biol 51:463–499CrossRefGoogle Scholar
  74. He G, Elling AA, Deng XW (2011) The epigenome and plant development. Annu Rev Plant Biol 62:411–435PubMedCrossRefGoogle Scholar
  75. Hirayama T, Shinozaki K (2010) Research on plant abiotic stress responses in the post-genome era: past, present and future. The Plant J 61:1041–1052PubMedCrossRefGoogle Scholar
  76. Hsieh PH (2016) Maintenance and inheritance of DNA methylation in Arabidopsis. Ph.D. Thesis, UC BerkeleyGoogle Scholar
  77. Huang SS, Ecker JR (2018) Piecing together cis-regulatory networks: insights from epigenomics studies in plants. Syst Biol Med 10:e1411Google Scholar
  78. Huang Z, Zhao L, Chen D, Liang M, Liu Z, Shao H, Long X (2013) Salt stress encourages proline accumulation by regulating proline biosynthesis and degradation in Jerusalem artichoke plantlets. PLoS One 8:e62085PubMedPubMedCentralCrossRefGoogle Scholar
  79. Hussain SS, Kayani MA, Amjad M (2011) Transcription factors as tools to engineer enhanced drought stress tolerance in plants. Biotechnol Prog 27:297–306PubMedCrossRefGoogle Scholar
  80. Imadi SR, Shah SW, Kazi AG, Azooz MM, Ahmad P (2016) Phytoremediation of saline soils for sustainable agricultural productivity. In: Ahmad P (ed) Plant metal interaction. Elsevier, Amsterdam/Boston, pp 455–468CrossRefGoogle Scholar
  81. Jha A, Shankar R (2011) Employing machine learning for reliable miRNA target identification in plants. BMC Genomics 12:636. Scholar
  82. Jin H, Martin C (1999) Multi-functionality and diversity within the plant MYB-gene family. Plant Mol Biol 41:577–585PubMedCrossRefGoogle Scholar
  83. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799PubMedCrossRefGoogle Scholar
  84. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53CrossRefGoogle Scholar
  85. Kawashima T, Berger F (2014) Epigenetic reprogramming in plant sexual reproduction. Nat Rev Genet 15:613PubMedCrossRefGoogle Scholar
  86. Kayikcioglu HH (2012) Short-term effects of irrigation with treated domestic wastewater on microbiological activity of a Vertic xerofluvent soil under Mediterranean conditions. J Environ Manag 102:108–114CrossRefGoogle Scholar
  87. Kolodyazhnaya YS, Kutsokon NK, Levenko BA, Syutikova OS, Rakhmetov DB, Kochetov AV (2009) Transgenic plants tolerant to abiotic stresses. Cytol Genet 43:132–149CrossRefGoogle Scholar
  88. Kumar A, Verma JP (2017) Does plant—Microbe interaction confer stress tolerance in plants: a review. Microbiol Res 207:41–52PubMedCrossRefGoogle Scholar
  89. Kumar G, Purty RS, Sharma MP, Singla-Pareek SL, Pareek A (2009) Physiological responses among Brassica species under salinity stress show strong correlation with transcript abundance for SOS pathway-related genes. J Plant Physiol 166:507–520PubMedCrossRefGoogle Scholar
  90. Kumar V, Kumar M, Sharma S, Prasad R (2017) Probiotics and plant health. Springer, Berlin/HeidelbergCrossRefGoogle Scholar
  91. Kumar H, Kumar M, Kumar J, Topno RK, Kumar P, Rana S, Sahoo GS (2018a) Biological impact of the host plants metabolites of Aspergillus flavus on its growth and its biosynthesis. Int J Curr Res Life Sci 7:1351–1357Google Scholar
  92. Kumar K, Aggarwal C, Singh I, Yadava P (2018b) Microbial genes in crop improvement. In: Prasad R, Gill SS, Tuteja N (eds) Crop improvement through microbial biotechnology. Elsevier, Amsterdam, pp 39–56CrossRefGoogle Scholar
  93. Lamaoui M, Jemo M, Datla R, Bekkaoui F (2018) Heat and drought stresses in crops and approaches for their mitigation. Front Chem 6:26PubMedPubMedCentralCrossRefGoogle Scholar
  94. Läuchli A, Grattan SR (2007) Plant growth and development under salinity stress. In: Jenks MA, Hasegawa PM, Jain SM (eds) Advances in molecular breeding toward drought and salt tolerant crops. Springer, Dordrecht, pp 1–32Google Scholar
  95. Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204PubMedPubMedCentralCrossRefGoogle Scholar
  96. Le Martret B, Poage M, Shiel K, Nugent GD, Dix PJ (2011) Tobacco chloroplast transformants expressing genes encoding dehydroascorbate reductase, glutathione reductase, and glutathione-S-transferase, exhibit altered anti-oxidant metabolism and improved abiotic stress tolerance. Plant Biotechnol J 9:661–673PubMedCrossRefGoogle Scholar
  97. Li E, Bestor TH, Jaenisch R (1992) Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69:915–926CrossRefGoogle Scholar
  98. Liang W, Ma X, Wan P, Liu L (2018) Plant salt-tolerance mechanism: a review. Biochem Biophys Res Commun 495:286–291PubMedCrossRefGoogle Scholar
  99. Lim U, Song MA (2012) Dietary and lifestyle factors of DNA methylation. In: Cancer epigenetics. Humana Press, Totowa, pp 359–376CrossRefGoogle Scholar
  100. Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen SE (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292:2077–2080CrossRefGoogle Scholar
  101. Liu HH, Tian X, Li YJ, Wu CA, Zheng CC (2008) Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana. RNA 14:836–843PubMedPubMedCentralCrossRefGoogle Scholar
  102. Liu C, Lu F, Cui X, Cao X (2010) Histone methylation in higher plants. Annu Rev Plant Biol 61:395–420PubMedCrossRefGoogle Scholar
  103. Liu D, Wang L, Liu C, Song X, He S, Zhai H, Liu Q (2014) An Ipomoea batatas iron-sulfur cluster scaffold protein gene, IbNFU1, is involved in salt tolerance. PLoS One 9:e93935PubMedPubMedCentralCrossRefGoogle Scholar
  104. Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC (2012) Defining the core Arabidopsis thaliana root microbiome. Nature 488:86PubMedPubMedCentralCrossRefGoogle Scholar
  105. Luo X, Wu J, Li Y, Nan Z, Guo X, Wang Y, Zhang A, Wang Z, Xia G, Tian Y (2013) Synergistic effects of GhSOD1 and GhCAT1 overexpression in cotton chloroplasts on enhancing tolerance to methyl viologen and salt stresses. PLoS One 8:e54002PubMedPubMedCentralCrossRefGoogle Scholar
  106. Mahfouz MM (2010) RNA-directed DNA methylation: mechanisms and functions. Plant Signal Behav 5:806–816PubMedPubMedCentralCrossRefGoogle Scholar
  107. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38:S31PubMedCrossRefGoogle Scholar
  108. Malone CD, Hannon GJ (2009) Small RNAs as guardians of the genome. Cell 136:656–668PubMedPubMedCentralCrossRefGoogle Scholar
  109. Mariani L, Ferrante A (2017) Agronomic management for enhancing plant tolerance to abiotic stresses—drought, salinity, hypoxia, and lodging. Horticulture 3:52CrossRefGoogle Scholar
  110. Marks RA, Smith JJ, Cronk Q, McLetchie DN (2018) Variation in the bacteriome of the tropical liverwort, Marchantia inflexa, between the sexes and across habitats. Symbiosis 75:93–101CrossRefGoogle Scholar
  111. Mateos JL, Bologna NG, Palatnik JF (2011) Biogenesis of plant microRNAs. In: Erdmann, Volker A, Barciszewski J (eds) Non coding RNAs in plants, Springer, Berlin/Heidelberg, pp 251–268Google Scholar
  112. Mathieu O, Bender J (2004) RNA-directed DNA methylation. J Cell Sci 117:4881–4888PubMedCrossRefGoogle Scholar
  113. Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15:394PubMedCrossRefGoogle Scholar
  114. Meister G, Tuschl T (2004) Mechanisms of gene silencing by double-stranded RNA. Nature 431:343PubMedCrossRefGoogle Scholar
  115. Miller GA, Suzuki N, Ciftci-Yilmaz SU, Mittler RO (2010) Reactive oxygen species homeostasis and signalling during drought and salinity stresses. Plant Cell Environ 33:453–467PubMedCrossRefGoogle Scholar
  116. Miransari M (2014) Use of microbes for the alleviation of soil stresses. Springer, BerlinCrossRefGoogle Scholar
  117. Mittler R, Blumwald E (2010) Genetic engineering for modern agriculture: challenges and perspectives. Annu Rev Plant Biol 61:443–462PubMedCrossRefGoogle Scholar
  118. Miura A, Nakamura M, Inagaki S, Kobayashi A, Saze H, Kakutani T (2009) An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. The EMBO J 28:1078–1086PubMedCrossRefGoogle Scholar
  119. Moeller L, Wang K (2008) Engineering with precision: tools for the new generation of transgenic crops. AIBS Bull 58:391–401Google Scholar
  120. Morinaga T (1934) Interspecific hybridization in Brassica. Cytologia 6:62–67CrossRefGoogle Scholar
  121. Munns R (2002) Comparative physiology of salt and water stress. Plant Cell Environ 25:239–250CrossRefGoogle Scholar
  122. Munns R (2005) Genes and salt tolerance: bringing them together. New Phytol 167:645–663PubMedCrossRefGoogle Scholar
  123. Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681PubMedCrossRefGoogle Scholar
  124. Munns R, James RA, Läuchli A (2006) Approaches to increasing the salt tolerance of wheat and other cereals. J Exp Bot 57:1025–1043PubMedCrossRefGoogle Scholar
  125. 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 32:429–448PubMedCrossRefGoogle Scholar
  126. Niu X, Bressan RA, Hasegawa PM, Pardo JM (1995) Ion homeostasis in NaCl stress environments. Plant Physiol 109:735–742PubMedPubMedCentralCrossRefGoogle Scholar
  127. Numan M, Bashir S, Khan Y, Mumtaz R, Shinwari ZK, Khan AL, Khan A, Ahmed AH (2018) Plant growth promoting bacteria as an alternative strategy for salt tolerance in plants: a review. Microbiol Res 209:21–32PubMedCrossRefGoogle Scholar
  128. Ofek-Lalzar M, Sela N, Goldman-Voronov M, Green SJ, Hadar Y, Minz D (2014) Niche and host-associated functional signatures of the root surface microbiome. Nat Commun 5:4950PubMedCrossRefGoogle Scholar
  129. Parnell JJ, Berka R, Young HA, Sturino JM, Kang Y, Barnhart DM, DiLeo MV (2016) From the lab to the farm: an industrial perspective of plant beneficial microorganisms. Front Plant Sci 7Google Scholar
  130. Pasquinelli AE, Ruvkun G (2002) Control of developmental timing by microRNAs and their targets. Annu Rev Cell Devel Biol 18:495–513CrossRefGoogle Scholar
  131. Peschansky VJ, Wahlestedt C (2014) Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics 9:3–12PubMedCrossRefGoogle Scholar
  132. Pitman MG, Läuchli A (2002) Global impact of salinity and agricultural ecosystems. In: Läuchli A, Lüttge U (eds) Salinity: environment-plants-molecules. Springer, Dordrecht, pp 3–20Google Scholar
  133. Popova OV, Dinh HQ, Aufsatz W, Jonak C (2013) The RdDM pathway is required for basal heat tolerance in Arabidopsis. Mol Plant 6:396–410PubMedPubMedCentralCrossRefGoogle Scholar
  134. Rajewsky N, Jurga S, Barciszewski J (2017) Plant epigenetics. Springer, ChamCrossRefGoogle Scholar
  135. Rajwanshi R, Chakraborty S, Jayanandi K, Deb B, Lightfoot DA (2014) Orthologous plant microRNAs: microregulators with great potential for improving stress tolerance in plants. Theor Appl Genet 127:2525–2543PubMedCrossRefGoogle Scholar
  136. Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z (2017) Crop breeding chips and genotyping platforms: progress, challenges, and perspectives. Mol Plant 10:1047–1064PubMedCrossRefGoogle Scholar
  137. Reddy MP, Sanish S, Iyengar ER (1992) Photosynthetic studies and compartmentation of ions in different tissues of Salicornia brachiata under saline conditions. Photosynthetica Praha 26:173–179Google Scholar
  138. Rengasamy P (2006) World salinization with emphasis on Australia. J Exp Bot 57:1017–1023PubMedCrossRefGoogle Scholar
  139. Rengasamy P (2010) Soil processes affecting crop production in salt-affected soils. Funct Plant Biol 37:613–620CrossRefGoogle Scholar
  140. Rodriguez-Uribe L, Higbie SM, Stewart JM, Wilkins T, Lindemann W, Sengupta-Gopalan C, Zhang J (2011) Identification of salt responsive genes using comparative microarray analysis in Upland cotton (Gossypium hirsutum L.). Plant Sci 180:461–469PubMedCrossRefGoogle Scholar
  141. Rolli E, Marasco R, Vigani G, Ettoumi B, Mapelli F, Deangelis ML, Gandolfi C, Casati E, Previtali F, Gerbino R, Pierotti Cei F (2015) Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait. Environ Microbiol 17:316–331PubMedCrossRefGoogle Scholar
  142. Ronemus MJ, Galbiati M, Ticknor C, Chen J, Dellaporta SL (1996) Demethylation-induced developmental pleiotropy in Arabidopsis. Science 273:654–657PubMedPubMedCentralCrossRefGoogle Scholar
  143. Roy B, Noren SK, Mandal AB, Basu AK (2011) Genetic engineering for abiotic stress tolerance in agricultural crops. Biotechnol 10:1–22CrossRefGoogle Scholar
  144. Roy SJ, Negrão S, Tester M (2014) Salt resistant crop plants. Curr Opin Biotechnol 26:115–124PubMedCrossRefGoogle Scholar
  145. Sabir P, Ashraf MU, Hussain M, Jamil AM (2009) Relationship of photosynthetic pigments and water relations with salt tolerance of proso millet (Panicum miliaceum L.) accessions. Pak J Bot 41:2957–2964Google Scholar
  146. Sadhana B (2014) Arbuscular Mycorrhizal Fungi (AMF) as a biofertilizer-a review. Int J Curr Microbiol Appl Sci 3:384–400Google Scholar
  147. Saeed Akram M, Ashraf M, Shahbaz M, Aisha Akram N (2009) Growth and photosynthesis of salt-stressed sunflower (Helianthus annuus) plants as affected by foliar-applied different potassium salts. J Plant Nutri Soil Sci 172:884–893CrossRefGoogle Scholar
  148. Scarpeci TE, Zanor MI, Mueller-Roeber B, Valle EM (2013) Overexpression of AtWRKY30 enhances abiotic stress tolerance during early growth stages in Arabidopsis thaliana. Plant Mol Biol 83:265–277PubMedCrossRefGoogle Scholar
  149. Sevillano L, Sanchez-Ballesta MT, Romojaro F, Flores FB (2009) Physiological, hormonal and molecular mechanisms regulating chilling injury in horticultural species. Postharvest technologies applied to reduce its impact. J Sci Food Agric 89:555–573CrossRefGoogle Scholar
  150. Shahbaz M, Ashraf M, Al-Qurainy F, Harris PJ (2012) Salt tolerance in selected vegetable crops. Crit Rev Plant Sci 31:303–320CrossRefGoogle Scholar
  151. Sharma R, Singh RM, Malik G, Deveshwar P, Tyagi AK, Kapoor S, Kapoor M (2009) Rice cytosine DNA methyltransferases–gene expression profiling during reproductive development and abiotic stress. FEBS J 276:6301–6311PubMedCrossRefGoogle Scholar
  152. Shokri-Gharelo R, Noparvar PM (2018) Molecular response of canola to salt stress: insights on tolerance mechanisms. Peer J 6:e4822. Scholar
  153. Shrivastava P, Kumar R (2015) Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation. Saudi J Biol Sci 22:123–131PubMedCrossRefGoogle Scholar
  154. Shukla PS, Shotton K, Norman E, Neily W, Critchley AT, Prithiviraj B (2017) Seaweed extract improve drought tolerance of soybean by regulating stress-response genes. AoB Plants 10(1):051Google Scholar
  155. Singh KB, Foley RC, Oñate-Sánchez L (2002) Transcription factors in plant defense and stress responses. Curr Opin Plant Biol 5:430–436PubMedCrossRefGoogle Scholar
  156. Singh CP, Chaudhary NS, Kannan B, Karan R (2018) Targeted genome editing for crop improvement in post genome-sequencing era. In: Prasad R, Gill SS, Tuteja N (eds) Crop improvement through microbial biotechnology. Elsevier, Amsterdam, pp 373–390CrossRefGoogle Scholar
  157. Solís MT, Rodríguez-Serrano M, Meijón M, Cañal MJ, Cifuentes A, Risueño MC, Testillano PS (2012) DNA methylation dynamics and MET1a-like gene expression changes during stress-induced pollen reprogramming to embryogenesis. J Exp Bot 63:6431–6444PubMedPubMedCentralCrossRefGoogle Scholar
  158. Stein H, Honig A, Miller G, Erster O, Eilenberg H, Csonka LN, Szabados L, Koncz C, Zilberstein A (2011) Elevation of free proline and proline-rich protein levels by simultaneous manipulations of proline biosynthesis and degradation in plants. Plant Sci 181:140–150PubMedCrossRefGoogle Scholar
  159. Tao H, Yang JJ, Shi KH (2015) Non-coding RNAs as direct and indirect modulators of epigenetic mechanism regulation of cardiac fibrosis. Exp Opin Therap Targe 19:707–716CrossRefGoogle Scholar
  160. Tavakkoli E, Rengasamy P, McDonald GK (2010) High concentrations of Na+ and Cl ions in soil solution have simultaneous detrimental effects on growth of faba bean under salinity stress. J Exp Bot 61:4449–4459PubMedPubMedCentralCrossRefGoogle Scholar
  161. Tester M, Davenport R (2003) Na+ tolerance and Na+ transport in higher plants. Ann Bot 91:503–527PubMedPubMedCentralCrossRefGoogle Scholar
  162. Thao NP, Tran VL (2016) Enhancement of plant productivity in the post-genomics era. Curr Genomics 17:295–296PubMedPubMedCentralCrossRefGoogle Scholar
  163. Tran LS, Burritt DJ, Bhattacharjee S, Wani SH, Hossain MA (2016) Drought stress tolerance in plants. Springer, ChamGoogle Scholar
  164. Tuna AL, Kaya C, Ashraf M, Altunlu H, Yokas I, Yagmur B (2007) The effects of calcium sulphate on growth, membrane stability and nutrient uptake of tomato plants grown under salt stress. Environ Exp Bot 59:173–178CrossRefGoogle Scholar
  165. Van Der Heijden MG, De Bruin S, Luckerhoff L, Van Logtestijn RS, Schlaeppi K (2016) A widespread plant-fungal-bacterial symbiosis promotes plant biodiversity, plant nutrition and seedling recruitment. ISME J 10:389PubMedCrossRefGoogle Scholar
  166. Varshney RK, Pandey MK, Puppala N (2017) Future prospects for Peanut improvement. In: The Peanut genome. Springer, Cham, pp 165–169CrossRefGoogle Scholar
  167. Vessey JK (2003) Plant Soil 255(2):571–586CrossRefGoogle Scholar
  168. Vinocur B, Altman A (2005) Recent advances in engineering plant tolerance to abiotic stress: achievements and limitations. Curr Opin Biotechnol 16:123–132CrossRefGoogle Scholar
  169. Volkov V (2015) Salinity tolerance in plants. Quantitative approach to ion transport starting from halophytes and stepping to genetic and protein engineering for manipulating ion fluxes. FrontPlant Sci 6:873Google Scholar
  170. Wang LJ, He SZ, Zhai H, Liu DG, Wang YN, Liu QC (2013a) Molecular cloning and functional characterization of a salt tolerance-associated gene IbNFU1 from sweet potato. J Integr Agric 12:27–35CrossRefGoogle Scholar
  171. Wang L, Liang W, Xing J, Tan F, Chen Y, Huang L, Cheng CL, Chen W (2013b) Dynamics of chloroplast proteome in salt-stressed mangrove Kandelia candel (L.) Druce. J Proteome Res 12:5124–5136PubMedCrossRefGoogle Scholar
  172. Wang B, Sun YF, Song N, Wei JP, Wang XJ, Feng H, Yin ZY, Kang ZS (2014) MicroRNAs involving in cold, wounding and salt stresses in Triticum aestivum L. Plant Physiol Biochem 80:90–96PubMedCrossRefGoogle Scholar
  173. Wang H, Miyazaki S, Kawai K, Deyholos M, Galbraith DW, Bohnert HJ (2003) Plant Mol Biol 52(4):873–891PubMedCrossRefGoogle Scholar
  174. Wang Y, Wang M, Li Y, Wu A, Huang J (2018) Effects of arbuscular mycorrhizal fungi on growth and nitrogen uptake of Chrysanthemum morifolium under salt stress. PLoS One 13:e0196408PubMedPubMedCentralCrossRefGoogle Scholar
  175. Waśkiewicz A, Gładysz O, Goliński P (2016) Participation of phytohormones in adaptation to salt stress. In: Ahammed G, Yu JQ (eds) Plant hormones under challenging environmental factors. Springer, Dordrecht, pp 75–115Google Scholar
  176. Wu YH, Wang T, Wang K, Liang QY, Bai ZY, Liu QL, Pan YZ, Jiang BB, Zhang L (2016) Comparative analysis of the chrysanthemum leaf transcript profiling in response to salt stress. PLoS One 11:e0159721PubMedPubMedCentralCrossRefGoogle Scholar
  177. Xia K, Wang R, Ou X, Fang Z, Tian C, Duan J, Wang Y, Zhang M (2012) OsTIR1 and OsAFB2 downregulation via OsmiR393 over expression leads to more tillers, early flowering and less tolerance to salt and drought in rice. PLoS One 7:e30039PubMedPubMedCentralCrossRefGoogle Scholar
  178. Xie Z, Khanna K, Ruan S (2010) Expression of microRNAs and its regulation in plants. Semin Cell Devel Biol 21:790–797CrossRefGoogle Scholar
  179. Xu R, Wang Y, Zheng H, Lu W, Wu C, Huang J, Yan K, Yang G, Zheng C (2015) Salt-induced transcription factor MYB74 is regulated by the RNA-directed DNA methylation pathway in Arabidopsis. J Exp Bot 66:5997–6008PubMedPubMedCentralCrossRefGoogle Scholar
  180. Yan H, Kikuchi S, Neumann P, Zhang W, Wu Y, Chen F, Jiang J (2010) Genome-wide mapping of cytosine methylation revealed dynamic DNA methylation patterns associated with genes and centromeres in rice. Plant J 63:353–365PubMedCrossRefGoogle Scholar
  181. Yan K, Liu P, Wu CA, Yang GD, Xu R, Guo QH, Huang JG, Zheng CC (2012) Stress-induced alternative splicing provides a mechanism for the regulation of microRNA processing in Arabidopsis thaliana. Mol Cell 48:521–531PubMedCrossRefGoogle Scholar
  182. Yang T, Zhang L, Hao H, Zhang P, Zhu H, Cheng W, Wang Y, Wang X, Wang C (2015) Nuclear-localized at HSPR links abscisic acid-dependent salt tolerance and antioxidant defense in Arabidopsis. Plant J 84:1274–1294PubMedCrossRefGoogle Scholar
  183. Yin YG, Kobayashi Y, Sanuki A, Kondo S, Fukuda N, Ezura H, Sugaya S, Matsukura C (2009) Salinity induces carbohydrate accumulation and sugar-regulated starch biosynthetic genes in tomato (Solanum lycopersicum L. cv. ‘Micro-Tom’) fruits in an ABA-and osmotic stress-independent manner. J Exp Bot 61:563–574PubMedPubMedCentralCrossRefGoogle Scholar
  184. Zhang X (2008) The epigenetic landscape of plants. Science 320:489–492PubMedCrossRefGoogle Scholar
  185. Zhang B, Wang Q, Pan X (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210:279–289PubMedCrossRefGoogle Scholar
  186. Zhang H, Han B, Wang T, Chen S, Li H, Zhang Y, Dai S (2011) Mechanisms of plant salt response: insights from proteomics. J Proteome Res 11:49–67PubMedCrossRefGoogle Scholar
  187. Zhang X, Lii Y, Wu Z, Polishko A, Zhang H, Chinnusamy V, Lonardi S, Zhu JK, Liu R, Jin H (2013) Mechanisms of small RNA generation from cis-NATs in response to environmental and developmental cues. Mol Plant 6:704–715PubMedPubMedCentralCrossRefGoogle Scholar
  188. Zhao YL, Yu SX, Ye WW, Wang HM, Wang JJ, Fang BX (2010) Study on DNA cytosine methylation of cotton (Gossypium hirsutum L.) genome and its implication for salt tolerance. Agric Sci China 9:783–791CrossRefGoogle Scholar
  189. Zhu JK (2001) Plant salt tolerance. Trends Plant Sci 6:66–71PubMedCrossRefGoogle Scholar
  190. Zhu JK (2003) Regulation of ion homeostasis under salt stress. Curr Opin Plant Biol 6:441–445PubMedCrossRefGoogle Scholar
  191. Zhu JK, Bressan RA, Hasegawa PM, Pardo JM, Bohnert HJ (2005) Salt and crops: salinity tolerance. Success Stories in Agriculture. Council for Agricultural Science and Technology, Autumn/Winter 32:13Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Department of BiotechnologyMagadh UniversityBodh GayaIndia
  2. 2.Department of BotanyGandhi Faiz-e-Aam CollegeShahjahanpurIndia

Personalised recommendations