Plant and Soil

, Volume 432, Issue 1–2, pp 373–387 | Cite as

Involvement of auxin in the regulation of ammonium tolerance in rice (Oryza sativa L.)

  • Dong-Wei Di
  • Li Sun
  • Xiaonan Zhang
  • Guangjie Li
  • Herbert J. Kronzucker
  • Weiming ShiEmail author
Regular Article


Background and aims

Ammonium (NH4+) is an important nitrogen source and is widely used as a fertilizer in agricultural systems. However, excess NH4+ inhibits root growth, and, subsequently, vegetative shoot growth and yield. This study examines whether auxin is involved in differential NH4+ tolerance in rice (Oryza sativa L.), and how auxin is regulated under high-NH4+ conditions in rice.


An NH4+-sensitive (Kasalath, Kas) and an NH4+-insensitive (Koshihikari, Kos) rive cultivar were cultured hydroponically with or without exogenous indole-3-acetic acid (IAA) and auxin biosynthesis inhibitors. Root growth, root area, tissue IAA content, and transcription of genes involved in auxin biosynthesis, conjugation and degradation were determined.


pDR5::GUS staining and auxin measurement show that high NH4+ can decrease free IAA content in roots. In addition, quantitative RT-PCR, pharmacology, and genetics analysis suggest that Kos possesses a higher capacity for auxin biosynthesis and a weaker capacity for auxin metabolism compared to Kas under high-NH4+ stress.


We conclude that the NH4+-tolerant cultivar possesses a higher capacity to maintain auxin homeostasis under high-NH4+ stress, and that this advantage is incurred by promotion of auxin biosynthesis and a suppression of auxin metabolism.


Ammonium toxicity Auxin level Nitrogen fertilizer Rice Root development 



Dioxygenase for Auxin Oxidation


Group II GRETCHEN HAGEN3 acyl amido synthetases


indole-3-acetic acid




indole-3-pyruvate acid






2-oxoindole-3-acetic acid








5-(4-chlorophenyl)-4H-1, 2, 4-triazole-3-thiol



We thank Prof. Shiping Wang (Huazhong Agricultural University) and Prof. Jianmin Wan (Nanjing Agricultural University) for kindly providing the OsGH3.2ox and Osdao mutant, respectively. This work was supported by grants from the National Natural Science Foundation of China [31430095, 31601823 and 31471948.], China Postdoctoral Science Foundation [2015 M58048 and 2017 T100411] and the University of Melbourne.

Supplementary material

11104_2018_3813_MOESM1_ESM.docx (1.2 mb)
ESM 1 (DOCX 1246 kb)
11104_2018_3813_MOESM2_ESM.xls (34 kb)
Table S1 Genes and rice cultivars used in this study. (XLS 33 kb)
11104_2018_3813_MOESM3_ESM.xls (37 kb)
Table S2 Primers used in qRT-PCR. (XLS 37 kb)
11104_2018_3813_MOESM4_ESM.xls (32 kb)
Table S3 Quantitative data of of shoots and roots in 25 cultivars under NA and HA. (XLS 32 kb)


  1. Abu-Zaitoon YM (2014) Phylogenetic analysis of putative genes involved in the tryptophan-dependent pathway of auxin biosynthesis in rice. Appl Biochem Biotechnol 172:2480–2495. CrossRefPubMedGoogle Scholar
  2. Balkos KD, Britto DT, Kronzucker HJ (2010) Optimization of ammonium acquisition and metabolism by potassium in rice (Oryza sativa L. cv. IR-72). Plant Cell Environ 33:23–34. CrossRefPubMedGoogle Scholar
  3. Barth C, Gouzd ZA, Steele HP, Imperio RM (2010) A mutation in GDP-mannose pyrophosphorylase causes conditional hypersensitivity to ammonium, resulting in Arabidopsis root growth inhibition, altered ammonium metabolism, and hormone homeostasis. J Exp Bot 61:379–394. CrossRefPubMedGoogle Scholar
  4. Britto DT, Kronzucker HJ (2002) NH4 + toxicity in higher plants: a critical review. J Plant Physiol 159:567–584. CrossRefGoogle Scholar
  5. Britto DT, Siddiqi MY, Glass AD, Kronzucker HJ (2001) Futile transmembrane NH4 + cycling: a cellular hypothesis to explain ammonium toxicity in plants. Proc Natl Acad Sci U S A 98:4255–4258. CrossRefPubMedPubMedCentralGoogle Scholar
  6. Cao Y, Glass AD, Crawford NM (1993) Ammonium inhibition of Arabidopsis root growth can be reversed by potassium and by auxin resistance mutations aux1, axr1, and axr2. Plant Physiol 102:983–989. CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chaillou S, Vessey JK, Morotgaudry JF, Raper CD, Henry LT, Boutin JP (1991) Expression of characteristics of ammonium nutrition as affected by pH of the root medium. J Exp Bot 42:189–196. CrossRefPubMedGoogle Scholar
  8. Chen G, Guo SW, Kronzucker HJ, Shi WM (2013) Nitrogen use efficiency (NUE) in rice links to NH4 + toxicity and futile NH4 + cycling in roots. Plant Soil 369:351–363. CrossRefGoogle Scholar
  9. Coskun D, Britto DT, Li M, Becker A, Kronzucker HJ (2013) Rapid ammonia gas transport accounts for futile transmembrane cycling under NH3/ NH4 + toxicity in plant roots. Plant Physiol 163:1859–1867. CrossRefPubMedPubMedCentralGoogle Scholar
  10. Di DW, Zhang C, Luo P, An CW, Guo GQ (2016a) The biosynthesis of auxin: how many paths truly lead to IAA? Plant Growth Regul 78:275–285. CrossRefGoogle Scholar
  11. Di DW et al (2016b) Functional roles of Arabidopsis CKRC2/YUCCA8 gene and the involvement of PIF4 in the regulation of auxin biosynthesis by cytokinin. Sci Rep 6:36866. CrossRefPubMedPubMedCentralGoogle Scholar
  12. Ding ZJ, Yan JY, Li CX, Li GX, Wu YR, Zheng SJ (2015) Transcription factor WRKY46 modulates the development of Arabidopsis lateral roots in osmotic/salt stress conditions via regulation of ABA signaling and auxin homeostasis. Plant J 84:56–69. CrossRefPubMedGoogle Scholar
  13. Dominguez-Valdivia MD, Aparicio-Tejo PM, Lamsfus C, Cruz C, Martins-Loucao MA, Moran JF (2008) Nitrogen nutrition and antioxidant metabolism in ammonium-tolerant and -sensitive plants. Physiol Plant 132:359–369. CrossRefPubMedGoogle Scholar
  14. Du H, Wu N, Fu J, Wang SP, Li XH, Xiao JH, Xiong LZ (2012) A GH3 family member, OsGH3-2, modulates auxin and abscisic acid levels and differentially affects drought and cold tolerance in rice. J Exp Bot 63:6467–6480. CrossRefPubMedPubMedCentralGoogle Scholar
  15. Esteban R, Ariz I, Cruz C, Moran JF (2016a) Review: mechanisms of ammonium toxicity and the quest for tolerance. Plant Sci 248:92–101. CrossRefPubMedGoogle Scholar
  16. Esteban R, Royo B, Urarte E, Zamarreno AM, Garcia-Mina JM, Moran JF (2016b) Both free indole-3-acetic acid and photosynthetic performance are important players in the response of Medicago truncatula to urea and ammonium nutrition under axenic conditions. Front Plant Sci 7:140. CrossRefPubMedPubMedCentralGoogle Scholar
  17. Finnemann J, Schjoerring JK (1999) Translocation of NH4 + in oilseed rape plants in relation to glutamine synthetase isogene expression and activity. Physiol Plant 105:469–477. CrossRefGoogle Scholar
  18. Fu J, Liu H, Li Y, Yu H, Li X, Xiao J, Wang S (2011) Manipulating broad-spectrum disease resistance by suppressing pathogen-induced auxin accumulation in rice. Plant Physiol 155:589–602. CrossRefPubMedGoogle Scholar
  19. Fujino K, Matsuda Y, Ozawa K, Nishimura T, Koshiba T, Fraaije MW, Sekiguchi H (2008) NARROW LEAF 7 controls LEAF shape mediated by auxin in rice. Mol Gen Genomics 279:499–507. CrossRefGoogle Scholar
  20. Groot CCD, Marcelis LFM, Boogaard RVD, Kaiser WM, Lambers H (2003) Interaction of nitrogen and phosphorus nutrition in determining growth. Plant Soil 248:257–268. CrossRefGoogle Scholar
  21. He W et al (2011) A small-molecule screen identifies L-kynurenine as a competitive inhibitor of TAA1/TAR activity in ethylene-directed auxin biosynthesis and root growth in Arabidopsis. Plant Cell 23:3944–3960. CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kakei Y et al (2017) Biochemical and chemical biology study of rice OsTAR1 revealed that tryptophan aminotransferase is involved in auxin biosynthesis: identification of a potent OsTAR1 inhibitor, Pyruvamine 2031. Plant Cell Physiol 58:598–606. CrossRefPubMedGoogle Scholar
  23. Kiba T, Kudo T, Kojima M, Sakakibara H (2011) Hormonal control of nitrogen acquisition: roles of auxin, abscisic acid, and cytokinin. J Exp Bot 62:1399–1409. CrossRefGoogle Scholar
  24. Korasick DA, Enders TA, Strader LC (2013) Auxin biosynthesis and storage forms. J Exp Bot 64:2541–2555. CrossRefPubMedPubMedCentralGoogle Scholar
  25. Kronzucker HJ, Siddiqi MY, Glass ADM (1997) Conifer root discrimination against soil nitrate and the ecology of forest succession. Nature 385:59–61. CrossRefGoogle Scholar
  26. Kronzucker HJ, Adm SM, Britto DT (2003) Root ammonium transport efficiency as a determinant in forest colonization patterns: an hypothesis. Physiol Plant 117:164–170. CrossRefGoogle Scholar
  27. Kronzucker HJ, Glass ADM, Siddiqi MY, Kirk GJD (2010) Comparative kinetic analysis of ammonium and nitrate acquisition by tropical lowland rice: implications for rice cultivation and yield potential. New Phytol 145:471–476. CrossRefGoogle Scholar
  28. Li Q, Li BH, Kronzucker HJ, Shi WM (2010) Root growth inhibition by NH4 + in Arabidopsis is mediated by the root tip and is linked to NH4 + efflux and GMPase activity. Plant Cell Environ 33:1529–1542. CrossRefPubMedGoogle Scholar
  29. Li B et al (2011) Shoot-supplied ammonium targets the root auxin influx carrier AUX1 and inhibits lateral root emergence in Arabidopsis. Plant Cell Environ 34:933–946. CrossRefPubMedGoogle Scholar
  30. Li B, Li G, Kronzucker HJ, Baluska F, Shi W (2014) Ammonium stress in Arabidopsis: signaling, genetic loci, and physiological targets. Trends Plant Sci 19:107–114. CrossRefPubMedGoogle Scholar
  31. Li XZ, Yang DL, Sun L, Li Q, Mao BZ, He ZH (2016) The systemic acquired resistance regulator OsNPR1 attenuates growth by repressing auxin signaling through promoting IAA-amido synthase expression. Plant Physiol 172:546–558. CrossRefPubMedPubMedCentralGoogle Scholar
  32. Liu Y, Lai NW, Gao K, Chen FJ, Yuan LX, Mi GH (2013) Ammonium inhibits primary root growth by reducing the length of meristem and elongation zone and decreasing elemental expansion rate in the root apex in Arabidopsis thaliana. PLoS One 8:e61031. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Liu G, Gao S, Tian H, Wu W, Robert HS, Ding Z (2016) Local transcriptional control of YUCCA regulates auxin promoted root-growth inhibition in response to aluminium stress in Arabidopsis. PLoS Genet 12:e1006360. CrossRefPubMedPubMedCentralGoogle Scholar
  34. Luo XT, Cai BD, Chen X, Feng YQ (2017) Improved methodology for analysis of multiple phytohormones using sequential magnetic solid-phase extraction coupled with liquid chromatography-tandem mass spectrometry. Anal Chim Acta 983:112–120. CrossRefPubMedGoogle Scholar
  35. Magalhaes JR, Huber DM (1991) Response of ammonium assimilation enzymes to nitrogen form treatments in different plant-species. J Plant Nutr 14:175–185. CrossRefGoogle Scholar
  36. Nishimura T et al (2014) Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis. Plant J 77:352–366. CrossRefPubMedGoogle Scholar
  37. Qin C, Qian W, Wang W, Wu Y, Yu C, Jiang X, Wang D, Wu P (2008) GDP-mannose pyrophosphorylase is a genetic determinant of ammonium sensitivity in Arabidopsis thaliana. Proc Natl Acad Sci USA 105(47):18308–18313. CrossRefGoogle Scholar
  38. Qin H, Zhang ZJ, Wang J, Chen XB, Wei PC, Huang RF (2017) The activation of OsEIL1 on YUC8M transcription and auxin biosynthesis is required for ethylene-inhibited root elongation in rice early seedling development. PLoS Genet 13:e1006955. CrossRefPubMedPubMedCentralGoogle Scholar
  39. Raven JA, Wollenweber B, Handley LL (1993) The quantitative role of ammonia/ammonium transport and metabolism by plants in the global nitrogen cycle. Physiol Plant 89:512–518. CrossRefGoogle Scholar
  40. Siddiqi MY, Malhotra B, Min XJ, Glass ADM (2002) Effects of ammonium and inorganic carbon enrichment on growth and yield of a hydroponic tomato crop. J Plant Nutr Soil Sci 165:191–197.;2-D CrossRefGoogle Scholar
  41. Song W et al (2013) Auxin distribution is differentially affected by nitrate in roots of two rice cultivars differing in responsiveness to nitrogen. Ann Bot 112:1383–1393. CrossRefPubMedPubMedCentralGoogle Scholar
  42. Staswick PE, Serban B, Rowe M, Tiryaki I, Maldonado MT, Maldonado MC, Suza W (2005) Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell 17:616–627. CrossRefPubMedPubMedCentralGoogle Scholar
  43. Tamura W et al (2010) Reverse genetics approach to characterize a function of NADH-glutamate synthase1 in rice plants. Amino Acids 39:1003–1012. CrossRefPubMedGoogle Scholar
  44. Tian QY, Chen FJ, Liu JX, Zhang FS, Mi GH (2008) Inhibition of maize root growth by high nitrate supply is correlated with reduced IAA levels in roots. J Plant Physiol 165:942–951. CrossRefGoogle Scholar
  45. Tobin AK, Yamaya T (2001) Cellular compartmentation of ammonium assimilation in rice and barley. J Exp Bot 52:591–604. CrossRefPubMedGoogle Scholar
  46. Wang MY, Siddiqi MY, Ruth TJ, Glass A (1993a) Ammonium uptake by rice roots (I. fluxes and subcellular distribution of 13NH4 +). Plant Physiol 103:1249–1258. CrossRefPubMedPubMedCentralGoogle Scholar
  47. Wang MY, Siddiqi MY, Ruth TJ, Glass A (1993b) Ammonium uptake by rice roots (II. Kinetics of 13NH4 + influx across the plasmalemma). Plant Physiol 103:1259–1267. CrossRefPubMedPubMedCentralGoogle Scholar
  48. Wang YD, Zhang T, Wang RC, Zhao YD (2018) Recent advances in auxin research in rice and their implications for crop improvement. J Exp Bot 69:255–263. CrossRefPubMedGoogle Scholar
  49. Yamamoto Y, Kamiya N, Morinaka Y, Matsuoka M, Sazuka T (2007) Auxin biosynthesis by the YUCCA genes in rice. Plant Physiol 143:1362–1371. CrossRefPubMedPubMedCentralGoogle Scholar
  50. Yang ZB, Geng XY, He CM, Zhang F, Wang R, Horst WJ, Ding ZJ (2014) TAA1-regulated local auxin biosynthesis in the root-apex transition zone mediates the aluminum-induced inhibition of root growth in Arabidopsis. Plant Cell 26:2889–2904. CrossRefPubMedPubMedCentralGoogle Scholar
  51. Yoshikawa T et al (2014) The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin-related processes. Plant J 78:927–936. CrossRefPubMedGoogle Scholar
  52. Zhang SW et al (2009) Altered architecture and enhanced drought tolerance in rice via the down-regulation of indole-3-acetic acid by TLD1/OsGH3.13 activation. Plant Physiol 151:1889–1901. CrossRefPubMedPubMedCentralGoogle Scholar
  53. Zhao ZG et al (2013) A role for a dioxygenase in auxin metabolism and reproductive development in rice. Dev Cell 27:113–122. CrossRefPubMedGoogle Scholar
  54. Zhao Y et al (2018) Overexpression of the maize ZmAMT1;1a gene enhances root ammonium uptake efficiency under low ammonium nutrition. Plant Biotechnol Rep 12:47–56. CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.School of Agriculture and Food, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleAustralia

Personalised recommendations