, 226:839 | Cite as

Rhizobacterial volatile emissions regulate auxin homeostasis and cell expansion in Arabidopsis

  • Huiming Zhang
  • Mi-Seong Kim
  • Venkat Krishnamachari
  • Paxton Payton
  • Yan Sun
  • Mark Grimson
  • Mohamed A. Farag
  • Choong-Min Ryu
  • Randy Allen
  • Itamar S. Melo
  • Paul W. ParéEmail author
Original Article


Certain plant growth-promoting rhizobacteria (PGPR), in the absence of physical contact with a plant stimulate growth via volatile organic compound (VOC) emissions, through largely unknown mechanisms. To probe how PGPR VOCs trigger growth in plants, RNA transcript levels of Arabidopsis seedlings exposed to Bacillus subtilus (strain GB03) were examined using oligonucleotide microarrays. In screening over 26,000 protein-coded transcripts, a group of approximately 600 differentially expressed genes related to cell wall modifications, primary and secondary metabolism, stress responses, hormone regulation and other expressed proteins were identified. Transcriptional and histochemical data indicate that VOCs from the PGPR strain GB03 trigger growth promotion in Arabidopsis by regulating auxin homeostasis. Specifically, gene expression for auxin synthesis was up regulated in aerial regions of GB03-exposed plants; auxin accumulation decreased in leaves and increased in roots with GB03 exposure as revealed in a transgenic DR5::GUS Arabidopsis line, suggesting activation of basipetal auxin transport. Application of the auxin transport inhibitor 1-naphthylphthalamic acid (NPA) restricted auxin accumulation to sites of synthesis thereby preventing GB03-mediated decreases in shoot auxin levels as well as thwarting GB03-mediated growth promotion. In addition, microarray data revealed coordinated regulation of cell wall loosening enzymes that implicated cell expansion with GB03 exposure, which was confirmed by comparative cytological measurements. The discovery that bacterial VOCs, devoid of auxin or other known plant hormones regulate auxin homeostasis and cell expansion provides a new paradigm as to how rhizobacteria promote plant growth.


Auxin transport Bacillus subtilus GB03 Cell expansion Plant growth promotion Transcriptional profiling Rhizobacterial signaling 



Indole acetic acid


1-Naphthylphthalamic acid


Plant growth promotion rhizobacteria


Real time PCR


Reverse transcriptase PCR


Volatile organic compounds



We especially want to thank Drs. Rangasamy Elumalai for technical expertise with microarray analyses; Mary Catherine Hastert for technical expertise with microscopic analyses; and Tom Guilfoyle for the DR5::GUS line. This research was funded in part by the Welch Foundation (Grant D1478), The Frasch Foundation for Chemical Research, Biogreen 21 and Technology Development Programs for Agriculture and Forestry, Ministry of Agriculture and Forestry, Republic of Korea.

Supplementary material


  1. Alonso JM, Hirayama T, Roman G, Nourizadeh S, Ecker JR (1999) EIN2, a bifunctional transducer of ethylene and stress responses in Arabidopsis. Science 284:2148–2152PubMedCrossRefGoogle Scholar
  2. Andro T, Chambost JP, Kotoujansky A, Cattaneo J, Bertheau Y, Barras F, Van Gijsegem F, Coleno A (1984) Mutants of Erwinia chrysanthemi defective in secretion of pectinase and cellulase. J Bacteriol 160:1199–1203PubMedGoogle Scholar
  3. Anterola AM, Lewis NG (2002) Trends in lignin modification: a comprehensive analysis of the effects of genetic manipulations/mutations on lignification and vascular integrity. Phytochemistry 61:221–294PubMedCrossRefGoogle Scholar
  4. Baskin TI, Betzner AS, Hoggart R, Cork A, Williamson RE (1992) Root morphology mutants in Arabidopsis thaliana. Aust J Plant Physiol 19:427–437CrossRefGoogle Scholar
  5. Bernards MA, Susag LM, Bedgar DL, Anterola AM, Lewis NG (2000) Induced phenylpropanoid metabolism during suberization and lignification: a comparative analysis. J Plant Physiol 157:601–607PubMedGoogle Scholar
  6. Bernasconi P (1996) Effect of synthetic and natural protein tyrosine kinase inhibitors on auxin efflux in zucchini (Cucurbita pepo) hypocotyls. Physiol Plant 96:205–510CrossRefGoogle Scholar
  7. Bhalerao RP, Eklof J, Ljung K, Marchant A, Bennett M, Sandberg G (2002) Shoot-derived auxin is essential for early lateral root emergence in Arabidopsis seedlings. Plant J 29:325–332PubMedCrossRefGoogle Scholar
  8. Boerjan W, Cervera MT, Delarue M, Beeckman T, Dewitte W, Bellini C, Caboche M, Van Onckelen H, Van Montagu M, Inze D (1995) Superroot, a recessive mutation in Arabidopsis, confers auxin overproduction. Plant Cell 7:1405–1419PubMedCrossRefGoogle Scholar
  9. Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546PubMedCrossRefGoogle Scholar
  10. Buchanan BB, Gruissem W, Jones RL (2000) The cell wall (in biochemistry and molecular biology of plants). American Society of Plant Physiologists, pp 52–89Google Scholar
  11. Campbell P, Braam J (1999) Xyloglucan endotransglycosylases: diversity of genes, enzymes and potential wall-modifying functions. Trends Plant Sci 4:361–366PubMedCrossRefGoogle Scholar
  12. Carey AT, Smith DL, Harrison E, Bird CR, Gross KC, Seymour GB, Tucker GA (2001) Down-regulation of a ripening-related beta-galactosidase gene (TBG1) in transgenic tomato fruits. J Exp Bot 52:663–668PubMedGoogle Scholar
  13. Cartieaux F, Thibaud MC, Zimmerli L, Lessard P, Sarrobert C, David P, Gerbaud A, Robaglia C, Somerville S, Nussaume L (2003) Transcriptome analysis of Arabidopsis colonized by a plant-growth promoting rhizobacterium reveals a general effect on disease resistance. Plant J 36:177–188PubMedCrossRefGoogle Scholar
  14. Dubrovsky JG, Rost TL, Colon-Carmona A, Doerner P (2001) Early primordium morphogenesis during lateral root initiation in Arabidopsis thaliana. Planta 214:30–36PubMedCrossRefGoogle Scholar
  15. Faulkner IJ, Rubery PH (1992) Flavonoids and flavonoid sulphates as probes of auxin-transport regulation in Cucurbita pepo hypocotyl segments and vesicles. Planta 186:618–625CrossRefGoogle Scholar
  16. Glick BR, Patten CN, Holguin G, Penrose DM (1999) Biochemical and genetic mechanisms used by plant growth promotion bacteria. Imperial College Press, London, pp 1–13Google Scholar
  17. Goujon T, Sibout R, Pollet B, Maba B, Nussaume L, Bechtold N, Lu F, Ralph J, Mila I, Barriere Y, Lapierre C, Jouanin L (2003) A new Arabidopsis thaliana mutant deficient in the expression of O-methyltransferase impacts lignins and sinapoyl esters. Plant Mol Biol 51:973–989PubMedCrossRefGoogle Scholar
  18. Guo H, Ecker JR (2004) The ethylene signaling pathway: new insights. Curr Opin Plant Biol 7:40–49PubMedCrossRefGoogle Scholar
  19. Halitschke R, Baldwin IT (2003) Antisense LOX expression increases herbivore performance by decreasing defense responses and inhibiting growth-related transcriptional reorganization in Nicotiana attenuata. Plant J 36:794–807PubMedCrossRefGoogle Scholar
  20. Hass C, Lohrmann J, Albrecht V, Sweere U, Hummel F, Yoo SD, Hwang I, Zhu T, Schafer E, Kudla J, Harter K (2004) The response regulator 2 mediates ethylene signaling and hormone signal integration in Arabidopsis. EMBO J 23:3290–3302PubMedCrossRefGoogle Scholar
  21. Hillebrand H, Bartling D, Weiler EW (1998) Structural analysis of the nit2/nit1/nit3 gene cluster encoding nitrilases, enzymes catalyzing the terminal activation step in indole-acetic acid biosynthesis in Arabidopsis thaliana. Plant Mol Biol 36:89–99PubMedCrossRefGoogle Scholar
  22. Hruba P, Honys D, Twell D, Capkova V, Tupy J (2005) Expression of beta-galactosidase and beta-xylosidase genes during microspore and pollen development. Planta 220:931–940PubMedCrossRefGoogle Scholar
  23. Humphreys JM, Chapple C (2002) Rewriting the lignin roadmap. Curr Opin Plant Biol 5:224–229PubMedCrossRefGoogle Scholar
  24. Inan G, Zhang Q, Li P, Wang Z, Cao Z, Zhang H, Zhang C, Quist TM, Goodwin SM, Zhu J, Shi H, Damsz B, Charbaji T, Gong Q, Ma S, Fredricksen M, Galbraith DW, Jenks MA, Rhodes D, Hasegawa PM, Bohnert HJ, Joly RJ, Bressan RA, Zhu JK (2004) Salt stress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophiles. Plant Physiol 135:1718–1737PubMedCrossRefGoogle Scholar
  25. Jones DL, Dennis PG, Owen AG, van Hees PAW (2003) Organic acid behavior in soils-misconceptions and knowledge gaps. Plant Soil 248:31– 41CrossRefGoogle Scholar
  26. Keller CP, Stahlberg R, Barkawi LS, Cohen JD (2004) Long-term inhibition by auxin of leaf blade expansion in bean and Arabidopsis. Plant Physiol 134:1217–1226PubMedCrossRefGoogle Scholar
  27. Klee HJ, Horsch RB, Hinchee MA, Hein MB, Hoffman NL (1987) The effects of overproduction of two Agrobacterium tumefaciens T-DNA auxin biosynthetic gene products in transgenic petunia plants. Genes Dev 1:86–96CrossRefGoogle Scholar
  28. Kloepper JW, Rodriguez-Kabana R, Zehnder GW, Murphy J, Sikora E, Fernandez C (1999) Plant root–bacterial interactions in biological control of soil borne diseases and potential extension to systemic and foliar diseases. Aust J Plant Pathol 28:27–33CrossRefGoogle Scholar
  29. Kloepper JW, Ryu CM, Zhang S (2004) Induced systemic resistance and promotion of plant growth by Bacillus spp. Phytopathology 94:1259–1266CrossRefPubMedGoogle Scholar
  30. Kokalis-Burelle N, Kloepper JW, Reddy MS (2006) Plant growth-promotion rhizobacteria as transplant amendments and their effects on indigenous rhizosphere microorganisms. Appl Soil Ecol 31:91–100CrossRefGoogle Scholar
  31. Lin W, Okon Y, Hardy RWF (1983) Enhanced mineral uptake by Zea mays and sorghum bicolor roots inoculated with Azospirillum brasilense. Appl Environ Microbiol 45:1775–1779PubMedGoogle Scholar
  32. Ljung K, Hull AK, Kowalczyk M, Marchant A, Celenza J, Cohen JD, Sandberg G (2002) Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in Arabidopsis thaliana. Plant Mol Biol 49:249–272PubMedCrossRefGoogle Scholar
  33. Ljung K, Hull AK, Celenza J, Yamada M, Estelle M, Normanly J, Sandberg G (2005) Sites and regulation of auxin biosynthesis in Arabidopsis roots. Plant Cell 17:1090–1104PubMedCrossRefGoogle Scholar
  34. Loper JE, Schroth MN (1986) Influence of bacterial sources of indole-3-acetic acid on root elongation of sugar beet. Phytopathology 76:386–389Google Scholar
  35. Luschnig C, Gaxiola RA, Grisafi P, Fink GR (1998) EIR1, a root-specific protein involved in auxin transport, is required for gravitropism in Arabidopsis thaliana. Genes Dev 12:2175–2187PubMedGoogle Scholar
  36. MacDonald EMS, Powell GK, Regier DA, Glass NL, Roberto F, Kosuge T, Morris RO (1986) Secretion of zwatin, Ribosylzeatin, and ribosyl-1″-methylzeatin by Pseudomonas savastanoi plasmid-coded cytokinin biosynthesis. Plant Physiol 82:742–747PubMedCrossRefGoogle Scholar
  37. Marita JM, Ralph J, Hatfield RD, Guo D, Chen F, Dixon RA (2003) Structural and compositional modifications in lignin of transgenic alfalfa down-regulated in caffeic acid 3-O-methyltransferase and caffeoyl coenzyme A 3-O-methyltransferase. Phytochemistry 62:53–65PubMedCrossRefGoogle Scholar
  38. Mattsson J, Ckurshumova W, Berleth T (2003) Auxin signaling in Arabidopsis leaf vascular development. Plant Physiol 131:1327–1339PubMedCrossRefGoogle Scholar
  39. Murphy A, Peer WA, Taiz L (2000) Regulation of auxin transport by aminopeptidases and endogenous flavonoids. Planta 211:315–324PubMedCrossRefGoogle Scholar
  40. Murphy AS, Hoogner KR, Peer WA, Taiz L (2002) Identification, purification, and molecular cloning of N-1-naphthylphthalmic acid-binding plasma membrane-associated aminopeptidases from Arabidopsis. Plant Physiol 128:935–950PubMedCrossRefGoogle Scholar
  41. Nishitani K (1997) The role of endoxyloglucan transferase in the organization of plant cell walls. Int Rev Cytol 173:157–206PubMedCrossRefGoogle Scholar
  42. Paré PW, Farag MA, Krishnamachari V, Zhang H, Ryu CM, Kloepper JW (2005) Elicitors and priming agents initiate plant defense responses. Photosynth Res 85:149–159PubMedCrossRefGoogle Scholar
  43. Peer WA, Bandyopadhyay A, Blakeslee JJ, Makam SN, Chen RJ, Masson PH, Murphy AS (2004) Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis thaliana. Plant Cell 16:1898–1911PubMedCrossRefGoogle Scholar
  44. Reid JSG (1997) Carbohydrate metabolism: structural carbohydrates. In: Dey PM, Harborne JB (eds) Plant biochemistry. Academic, San Diego, pp 205–236Google Scholar
  45. Reid JSG, Edwards M, Gidley MJ, Clark AH (1995) Enzyme specificity in galactomannan biosynthesis. Planta 195:489–495Google Scholar
  46. Ryu CM, Farag MA, Hu CH, Reddy MS, Wei HX, Pare PW, Kloepper JW (2003) Bacterial volatiles promote growth in Arabidopsis. Proc Natl Acad Sci USA 100:4927–4932PubMedCrossRefGoogle Scholar
  47. Ryu CM, Farag MA, Hu CH, Reddy MS, Kloepper JW, Pare PW (2004) Bacterial volatiles induce systemic resistance in Arabidopsis. Plant Physiol 134:1017–1026PubMedCrossRefGoogle Scholar
  48. Salzman RA, Brady JA, Finlayson SA, Buchanan CD, Summer EJ, Sun F, Klein PE, Klein RR, Pratt LH, Cordonnier-Pratt MM, Mullet JE (2005) Transcriptional profiling of Sorghum induced by methyl jasmonate, salicylic acid, and aminocyclopropane carboxylic acid reveals cooperative regulation and novel gene responses. Plant Physiol 138:352–368PubMedCrossRefGoogle Scholar
  49. Schiefelbein JW, Somerville C (1990) Genetic control of root hair development in Arabidopsis thaliana. Plant Cell 2:235–243PubMedCrossRefGoogle Scholar
  50. Sieberer T, Seifert GJ, Hauser MT, Grisafi P, Fink GR, Luschnig C (2000) Post-transcriptional control of the Arabidopsis auxin efflux carrier EIR1 requires AXR1. Curr Biol 10:1595–1598PubMedCrossRefGoogle Scholar
  51. Sweere U, Eichenber K, Lohrmann J, Mira-Rodado V, Baurle I, Kudla J, Nagy F, Schafer E, Harter K (2001) Interaction of the response regulator ARR4 with phytochrome B in modulating red light signaling. Science 294:1108–1111PubMedCrossRefGoogle Scholar
  52. Timmusk S, Nicander B, Granhall U, Tillberg E (1999) Cytokinin production by Paenibacillus polymyxa. Soil Biol Biochem 31:1847–1852CrossRefGoogle Scholar
  53. To JPC, Haberer G, Ferreira FJ, Deruere J, Mason MG, Schaller GE, Alonso JM, Ecker JR, Kieber JJ (2004) Type-A Arabidopsis response regulators are partially redundant negative regulators of cytokinin signaling in Arabidopsis. Plant Cell 16:658–671PubMedCrossRefGoogle Scholar
  54. Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ (1997) Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9:1963–1971PubMedCrossRefGoogle Scholar
  55. Vercauteren I, de Almeida Engler J, De Groodt R, Gheysen G (2002) An Arabidopsis thaliana pectin acetylesterase gene is upregulated in nematode feeding sites induced by root-knot and cyst nematodes. Mol Plant Microbe Interact 15:404–407PubMedCrossRefGoogle Scholar
  56. Vincent D, Lapierre C, Pollet B, Cornic G, Negroni L, Zivy M (2005) Water deficits affect caffeate O-methyltransferase, lignification, and related enzymes in maize leaves: a proteomic investigation. Plant Physiol 137:949–960PubMedCrossRefGoogle Scholar
  57. Winicur ZM, Zhang GF, Staehelin LA (1998) Auxin deprivation induces synchronous golgi differentiation in suspension-cultured tobacco BY-2 cells. Plant Physiol 117:501–513PubMedCrossRefGoogle Scholar
  58. Woodward AW, Bartel B (2005) Auxin: regulation, action, and interaction. Ann Bot 95:707–735PubMedCrossRefGoogle Scholar
  59. Zazimalova E, Opatrny Z, Brezinova A (1995) The effect of auxin starvation on the growth of auxin-dependent tobacco cell culture-dynamics of auxin binding activity and endogenous free IAA content. J Exp Bot 46:1205–1213CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Huiming Zhang
    • 1
  • Mi-Seong Kim
    • 1
  • Venkat Krishnamachari
    • 1
  • Paxton Payton
    • 2
  • Yan Sun
    • 1
  • Mark Grimson
    • 1
  • Mohamed A. Farag
    • 1
  • Choong-Min Ryu
    • 3
  • Randy Allen
    • 1
  • Itamar S. Melo
    • 4
  • Paul W. Paré
    • 1
    Email author
  1. 1.Departments of Chemistry/Biochemistry and BiologyTexas Tech UniversityLubbockUSA
  2. 2.USDA-ARS Cropping Systems LabLubbockUSA
  3. 3.Microbial Genomics LabKorean Research Institute of Biosci/Biotech, YusongTaejonSouth Korea
  4. 4.EMBRAPA Meio AmbienteJaguariúnaBrazil

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