, Volume 254, Issue 5, pp 1867–1877 | Cite as

Regulation of root development in Arabidopsis thaliana by phytohormone-secreting epiphytic methylobacteria

  • Jana Klikno
  • Ulrich KutscheraEmail author
Original Article


In numerous experimental studies, seedlings of the model dicot Arabidopsis thaliana have been raised on sterile mineral salt agar. However, under natural conditions, no plant has ever grown in an environment without bacteria. Here, we document that germ-free (gnotobiotic) seedlings, raised on mineral salt agar without sucrose, develop very short root hairs. In the presence of a soil extract that contains naturally occurring microbes, root hair elongation is promoted; this effect can be mimicked by the addition of methylobacteria to germ-free seedlings. Using five different bacterial species (Methylobacterium mesophilicum, Methylobacterium extorquens, Methylobacterium oryzae, Methylobacterium podarium, and Methylobacterium radiotolerans), we show that, over 9 days of seedling development in a light-dark cycle, root development (hair elongation, length of the primary root, branching patterns) is regulated by these epiphytic microbes that occur in the rhizosphere of field-grown plants. In a sterile liquid culture test system, auxin (IAA) inhibited root growth with little effect on hair elongation and significantly stimulated hypocotyl enlargement. Cytokinins (trans-zeatin, kinetin) and ethylene (application of the precursor ACC) likewise exerted an inhibitory effect on root growth but, in contrast to IAA, drastically stimulated root hair elongation. Methylobacteria are phytosymbionts that produce/secrete cytokinins. We conclude that, under real-world conditions (soil), the provision of these phytohormones by methylobacteria (and other epiphytic microbes) regulates root development during seedling establishment.


Arabidopsis Auxin Cytokinin Epiphytic microbes Methylobacteria Root development 



This work was supported by the Alexander von Humboldt Foundation (Bonn, Germany) (AvH Stanford 2013/2014 to UK). We thank Dr. Z.Y. Wang for the provision of plant material and consultation.


  1. Abanda-Nkpwatt D, Müsch M, Tschiersch J, Boettner M, Schwaab W (2006) Molecular interaction between Methylobacteria extorquens and seedlings: growth promotion, methanol consumption, and localization of the methanol emission site. J Exp Bot 57:4025–4032CrossRefPubMedGoogle Scholar
  2. Aloni R, Aloni E, Lanhans M (2006) Role of cytokinin and auxin in shaping root architecture: regulating vascular differentiation, lateral root initiation, root apical dominance and root gravitropism. Ann Bot 97:883–893CrossRefPubMedPubMedCentralGoogle Scholar
  3. Baluska F, Mancuso S, Volkmann D, Barlow PM (2010) Root apex transition zone: a signalling-response nexus in the root. Trends Plant Sci 15:402–408CrossRefPubMedGoogle Scholar
  4. Barazani O, Friedman J (1999) Is IAA the major root growth factor secreted from plant-growth-mediating bacteria? J Chem Ecol 25:2397–2406CrossRefGoogle Scholar
  5. Bresson J, Vasseur F, Dauzat M, Labadie M, Varoquaux F, Touraine B, Vile D (2014) Interact to survive: Phyllobacterium brassicacearum improves Arabidopsis tolerance to severe water deficit and growth recovery. PLoS One 9:e107607CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bulgarelli D, Schlaeppi K, Spaepen S, van Themaat EVL, Schulze-Lefert P (2013) Structure and function of the bacterial microbiota of plants. Annu Rev Plant Biol 64:807–838CrossRefPubMedGoogle Scholar
  7. Chaiwanon J, Wang Z-Y (2015) Spatiotemporal brassinosteroid signalling and antagonism with auxin pattern stem cell dynamics in Arabidopsis roots. Curr Biol 25:1031–1042CrossRefPubMedPubMedCentralGoogle Scholar
  8. Datta S, Kim CM, Pernas M, Pires ND, Proust H, Tam T, Vijayakumar P, Dolan L (2011) Root hairs: development, growth and the evolution at the plant-soil interface. Plant Soil 364:1–14CrossRefGoogle Scholar
  9. Deng Z, Oses-Prieto JA, Kutschera U, Tseng T-S, Hao L, Burlingame AL, Wang Z, Briggs WR (2014) Blue light-induced proteomic changes in etiolated Arabidopsis seedlings. J Proteome Res 13:2524–2533Google Scholar
  10. Doerges L, Kutschera U (2014) Assembly and loss of the polar flagellum in plant-associated methylobacteria. Naturwissenschaften 101:339–346CrossRefPubMedGoogle Scholar
  11. Galland M, Gamet L, Varoquaux F, Touraine B, Touraine B, Desbrosses G (2012) The ethylene pathway contributes to root hair elongation induced by the beneficial bacteria Phyllobacterium brassicacearum STM196. Plant Sci 190:74–81CrossRefPubMedGoogle Scholar
  12. Garcia-Fraile P, Menendex E, Rivas P (2015) Role of bacterial biofertilizers in agriculture and forestry. AIMS Bioengineering 2:183–205CrossRefGoogle Scholar
  13. Hornschuh M, Grotha R, Kutschera U (2002) Epiphytic bacteria associated with the bryophyte Funaria hygrometrica: effects of Methylobacterium strains on protonema development. Plant Biol 4:682–687CrossRefGoogle Scholar
  14. Hornschuh M, Grotha R, Kutschera U (2006) Moss-associated methylobacteria as phytosymbionts: an experimental study. Naturwissenschaften 93:480–486CrossRefPubMedGoogle Scholar
  15. Jucknischke A, Kutschera U (1998) The role of the cotyledons and primary leaves during seedling etablishment in sunflower. J Plant Physiol 153:700–705CrossRefGoogle Scholar
  16. Jung JKH, McCouch S (2013) Getting to the roots of it: genetic and hormonal control of root architecture. Front Plant Sci 4/186:1–32Google Scholar
  17. Kazan K (2013) Auxin and the integration of environmental signals into plant root development. Ann Bot 112:1655–1665CrossRefPubMedPubMedCentralGoogle Scholar
  18. Kircher T, Schopfer P (2012) Photosynthetic sucrose acts as cotyledon-derived long-distance signal to control root growth during early seedling development in Arabidopsis. Proc Natl Acad Sci U S A 109:11217–11221CrossRefPubMedPubMedCentralGoogle Scholar
  19. Koopmann V, Kutschera U (2005) In-vitro regeneration of sunflower plants: effects of a Methylobacterium strain on organ development. J Appl Bot 79:59–62Google Scholar
  20. Kutschera U (2002) Bacterial colonization of sunflower cotyledons during seed germination. J Appl Bot 76:96–98Google Scholar
  21. Kutschera U (2007) Plant-associated methylobacteria as co-evolved phytosymbionts: a hypothesis. Plant Signal Behav 2:74–78CrossRefPubMedPubMedCentralGoogle Scholar
  22. Kutschera U (2011) From the scala naturae to the symbiogenetic and dynamic tree of life. Biol Direct 6/33:1–20Google Scholar
  23. Kutschera U (2015a) Comment: 150 years of an integrative plant physiology. Nature Plants 1/15131:1–3Google Scholar
  24. Kutschera U (2015b) Basic versus applied research: Julius Sachs (1832–1897) and the experimental physiology of plants. Plant Signal Behav 10/9 e1062958:1–9Google Scholar
  25. Kutschera U, Khanna R (2016) Plant gnotogiology: epiphytic microbes and sustainable agriclture. Plant Signal Behav 11/e1256529:1–4Google Scholar
  26. Kutschera U, Koopmann V (2005) Growth in liverworts of the Marchantiales is promoted by epiphytic methylobacteria. Naturwissenschaften 92:347–349CrossRefPubMedGoogle Scholar
  27. Kutschera U, Niklas KJ (2016) The evolution of the plant genome-to-morphology auxin circuit. Theory Biosci 135:175–186CrossRefPubMedGoogle Scholar
  28. Kutschera U, Wang Z-Y (2012) Brassinosteroid action in flowering plants: a Darwinian perspective. J Exp Bot 63:3511–3522CrossRefPubMedPubMedCentralGoogle Scholar
  29. Kutschera U, Wang Z-Y (2016) Growth-limiting proteins in maize coleoptiles and the auxin-brassinosteroid hypothesis of mesocotyl elongation. Protoplasma 253:3–14CrossRefPubMedGoogle Scholar
  30. Lidstrom ME, Chistoserdova L (2002) Plants in the pink: cytokinin production by methylobacterium. J Bacteriol 184:1818CrossRefPubMedPubMedCentralGoogle Scholar
  31. Lugtenberg BJ, Kamilova F (2009) Plant-growth-promoting rhizobacteria. Annu Rev Microbiol 53:541–556CrossRefGoogle Scholar
  32. Marschner H (1995) Mineral nutrition of higher plants, 2. edn. Academic Press, LondonGoogle Scholar
  33. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio-assays with tobacco tissue cultures. Physiol Plant 15:473–497Google Scholar
  34. Niklas KJ, Kutschera U (2017) From Goethe’s plant archetype via Haeckel’s biogenetic law to plant evo-devo 2016. Theory Biosci. doi: 10.1007/s12064-016-0237-7
  35. Overvoorde P, Fukaki H, Beeckman T (2010) Auxin control of root development. Cold Spring Harb Perspect Biol 2(6):a001537CrossRefPubMedPubMedCentralGoogle Scholar
  36. Petricka JJ, Winter CM, Benfey PN (2012) Control of Arabidopsis root development. Annu Rev Plant Biol 63:563–590CrossRefPubMedPubMedCentralGoogle Scholar
  37. Pitts RJ, Cernac A, Estelle M (1998) Auxin and ethylene promote root-hair elongation in Arabidopsis. Plant J 16:553–560CrossRefPubMedGoogle Scholar
  38. Redei GP (1962) Supervital mutants of Arabidopsis. Genetics 47:443–460PubMedPubMedCentralGoogle Scholar
  39. Requena N, Jimenez I, Toro M, Barea JM (1997) Interaction between plant-growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi and Rhizobium spp. in the rhizosphere of Anthyllis cytisoides, a model legume for revegetation in Mediterranean semi-arid ecosystems. New Phytol 136:667–766CrossRefGoogle Scholar
  40. Sachs J (1865) Handbuch der Experimental-Physiologie der Pflanzen. Verlag Wilhelm Engelmann, LeipzigGoogle Scholar
  41. Sachs J (1882) Vorlesungen über Pflanzen-Physiologie. Verlag Wilhelm Engelmann, LeipzigGoogle Scholar
  42. Schauer S, Kutschera U (2008) Methylotrophic bacteria on the surfaces of field-grown sunflower plants: a biogeographic perspective. Theory Biosci 127:23–29CrossRefPubMedGoogle Scholar
  43. Schauer S, Kutschera U (2011) A novel growth-promoting microbe, Methylobacterium funariae sp. nov., isolated from the leaf surface of a common moss. Plant Signal Behav 6:510–515CrossRefPubMedPubMedCentralGoogle Scholar
  44. Schauer S, Kämpfer P, Wellner S, Spröer C, Kutschera U (2011) Methylobacterium marchantiae sp. nov., a pink-pigmented, facultatively methylotrophic bacterium isolated from the thallus of a liverwort. Internat J Syst Evol Microbiol 61:870–876Google Scholar
  45. Slovak R, Ogura T, Satbhai SB, Ristova D, Busch W (2015) Genetic control of root growth: from genes to networks. Ann Bot 117:9–24CrossRefPubMedPubMedCentralGoogle Scholar
  46. Tanaka N, Kato M, Tomioka R, Kurata R, Fukao Y, Aoyama T, Maeshima M (2014) Characteristics of a root hair-less line of Arabidopsis thaliana under physiological stresses. J Exp Bot 65:1497–1512CrossRefPubMedPubMedCentralGoogle Scholar
  47. Vacheron J, Desbrosses G (2013) Plant growth-promoting rhizobacteria and root system functioning. Front Plant Sci 4/356:166–176Google Scholar
  48. Went FW, Thimann KV (1937) Phytohormones. The MacMillan Company, New YorkGoogle Scholar
  49. Zamioudis C, Mastranesti P, Dhonukshe P, Blilou I, Pieterse CM (2013) Unraveling root developmental programs initiated by beneficial Pseudomonas spp. bacteria. Plant Physiol 162:304–318CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag Wien 2017

Authors and Affiliations

  1. 1.Institute of BiologyUniversity of KasselKasselGermany

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