A soil-free root observation system for the study of root-microorganism interactions in maize


Background and aims

The root surface of a plant usually exceeds the leaf area and is constantly exposed to a variety of soil-borne microorganisms. Root pathogens and pests, as well as belowground interactions with beneficial microbes, can significantly influence a plants' performance. Unfortunately, the analysis of these interactions is often limited because of the arduous task of accessing roots growing in soil. Here, we present a soil-free root observation system (SF-ROBS) designed to grow maize (Zea mays) plants and to study root interactions with either beneficial or pathogenic microbes.


The SF-ROBS consists of pouches lined with wet filter paper supplying nutrient solution.


The aspect of maize grown in the SF-ROBS was similar to soil-grown maize; the plant growth was similar for the shoot but different for the roots (biomass and length increased in the SF-ROBS). SF-ROBS-grown roots were successfully inoculated with the hemi-biotrophic maize fungal pathogen Colletotrichum graminicola and the beneficial rhizobacteria Pseudomonas putida KT2440. Thus, the SF-ROBS is a system suitable to study two major belowground phenomena, namely root fungal defense reactions and interactions of roots with beneficial soil-borne bacteria.


This system contributes to a better understanding of belowground plant microbe interactions in maize and most likely also in other crops.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5



soil-free root observation system




maize nutrient solution


green fluorescent protein


day(s) post infection




colony-forming unit(s)


  1. Ahn IP, Lee SW, Kim MG, Park SR, Hwang DJ, Bae SC (2011) Priming by rhizobacterium protects tomato plants from biotrophic and necrotrophic pathogen infections through multiple defense mechanisms. Mol Cells 32:7–14. doi:10.1007/s10059-011-2209-6

    PubMed  Article  CAS  Google Scholar 

  2. Boeuf-Tremblay V, Plantureux S, Guckert A (1995) Influence of mechanical impedance on root exudation of maize seedlings at two development stages. Plant Soil 172:279–287. doi:10.1007/BF00011330

    Article  CAS  Google Scholar 

  3. Deshmukh S, Hückelhoven R, Schäfer P, Imani J, Sharma M, Weiss M, Waller F, Kogel KH (2006) The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley. Proc Natl Acad Sci USA 103:18450–18457. doi:10.1073/pnas.0605697103

    PubMed  Article  CAS  Google Scholar 

  4. De Vleesschauwer D, Höfte M (2009) Rhizobacteria-induced systemic resistance. Adv Bot Res 51:223–281. doi:10.1016/S0065-2296(09)51006-3

    Article  Google Scholar 

  5. Djonovic S, Vargas W, Kolomiets M, Horndeski M, Wiest A, Kenerley C (2007) A proteinaceous elicitor Sm1 from the beneficial fungus Trichoderma virens is required for induced systemic resistance in maize. Plant Physiol 145:875–889. doi:10.1104/pp. 107.103689

    PubMed  Article  CAS  Google Scholar 

  6. Erb M, Flors V, Karlen D, de Lange E, Planchamp C, d’Alessandro M, Turlings TCJ, Ton J (2009) Signal signature of aboveground-induced resistance upon belowground herbivory in maize. Plant J 59:292–302. doi:10.1111/j.1365-313X.2009.03868.x

    PubMed  Article  CAS  Google Scholar 

  7. Erb M, Balmer D, De Lange ES, Von Merey G, Planchamp C, Robert CAM, Röder G, Sobhy I, Zwahlen C, Mauch-Mani B, Turlings TCJ (2011) Synergies and trade-offs between insect and pathogen resistance in maize leaves and roots. Plant Cell Environ 34:1088–1103. doi:10.1111/j.1365-3040.2011.02307.x

    PubMed  Article  CAS  Google Scholar 

  8. Gewin V (2010) Food: an underground revolution. Nature 466:552–553

    PubMed  Article  CAS  Google Scholar 

  9. Gibeaut DM, Hulett J, Cramer GR, Seemann JR (1997) Maximal biomass of Arabidopsis thaliana using a simple, low-maintenance hydroponic method and favorable environmental conditions. Plant Physiol 115:317–319

    PubMed  Article  CAS  Google Scholar 

  10. Gunning T, Cahill DM (2009) A soil-free plant growth system to faciliate analysis of plant pathogen interactions in roots. J Phytopathol 157:497–501. doi:10.1111/j.1439-0434.2008.01503.x

    Article  Google Scholar 

  11. Hétu MF, Tremblay LJ, Lefebvre DD (2005) High root biomass production in anchored Arabidopsis plants grown in axenic sucrose supplemented liquid culture. Biotechniques 39:345–349

    PubMed  Article  Google Scholar 

  12. Huang CJ, Yang KH, Liu YH, Lin YJ, Chen CY (2010) Suppression of southern corn leaf blight by a plant growth-promoting rhizobacterium Bacillus cereus C1L. Ann Appl Biol 157:45–53. doi:10.1111/j.1744-7348.2012.00408.x

    Article  Google Scholar 

  13. Hund A, Reimer R, Stamp P, Walter A (2012) Can we improve heterosis for root growth of maize by selecting parental inbred lines with different temperature behavior? Philos Trans R Soc B-Biol Sci 367:1580–1588. doi:10.1098/rstb.2011.0242

    Article  CAS  Google Scholar 

  14. Hund A, Ruta N, Liedgens M (2009a) Rooting depth and water use efficiency of tropical maize inbred lines, differing in drought tolerance. Plant Soil 318:311–325. doi:10.1007/s11104-008-9843-6

    Article  CAS  Google Scholar 

  15. Hund A, Trachsel S, Stamp P (2009b) Growth of axile and lateral roots of maize: I development of a phenotyping platform. Plant Soil 325:335–349. doi:10.1007/s111104-009-9984-2

    Article  CAS  Google Scholar 

  16. Ishiga Y, Ishiga T, Uppalapati SR, Mysore KS (2011) Arabidopsis seedling flood-inoculation technique: a rapid and reliable assay for studying plant-bacterial interactions. Plant Methods 7:32. doi:10.1186/1746-4811-7-32

    PubMed  Article  CAS  Google Scholar 

  17. Kaplan I, Halitschke R, Kessler A, Rehill BJ, Sardanelli S, Denno RF (2008) Physiological integration of roots and shoots in plant defense strategies links above- and belowground herbivory. Ecol Lett 11:841–851. doi:10.1111/j.1461-0248.2008.01200.x

    PubMed  Article  Google Scholar 

  18. Kim DW, Rakwal R, Agrawal GK, Jung YH, Shibato J, Jwa NS, Iwahashi Y, Iwahashi H, Kim DH, Shim IS, Usui K (2005) A hydroponic rice seedling culture model system for investigating proteome of salt stress in rice leaf. Electrophoresis 26:4521–4539. doi:10.1002/elps.200500334

    PubMed  Article  CAS  Google Scholar 

  19. Matilla MA, Ramos JL, Bakker PAHM, Doornbos R, Badri DV, Vivanco JM, Ramos-González MI (2010) Pseudomonas putida KT2440 causes induced systemic resistance and changes in Arabidopsis root exudation. Environ Microbiol Rep 2:381–388. doi:10.1111/j.1758-2229.2009.00091.x

    Article  CAS  Google Scholar 

  20. Nadeem SM, Zahir ZA, Naveed M, Arshad M (2009) Rhizobacteria containing ACC-deaminase confer salt tolerance in maize grown on salt-affected fields. Can J Microbiol 55:1302–1309. doi:10.1139/w11-044

    PubMed  Article  CAS  Google Scholar 

  21. Neal AL, Ahmad S, Gordon-Weeks R, Ton J (2012) Benzoxazinoids in root exudates of maize attract Pseudomonas putida to the rhizosphere. PLoS ONE 7(4):e35498. doi:10.1371/journal.pone.0035498

    PubMed  Article  CAS  Google Scholar 

  22. Okubara PA, Paulitz TC (2005) Root defense responses to fungal pathogens: a molecular perspective. Plant Soil 274:215–226. doi:10.007/s11104-004-7328-9

    Article  CAS  Google Scholar 

  23. Pineda A, Zheng SJ, van Loon JJA, Pieterse CMJ, Dicke M (2010) Helping plants to deal with insects: the role of beneficial soil-borne microbes. Trends Plant Sci 15:507–514. doi:10.1016/j.tplants.2010.05.007

    PubMed  Article  CAS  Google Scholar 

  24. Raaijmakers JM, Leeman M, van Oorschot MMP, van der Sluis I, Schippers B, Bakker PAHM (1995) Dose–response relationships in biological control of Fusarium wilt of radish by Pseudomonas spp. Phytopathology 85:1075–1081. doi:10.1094/Phyto-85-1075

    Article  Google Scholar 

  25. Rasmann S, Agrawal AA (2008) In defense of roots: a research agenda for studying plant resistance to belowground herbivory. Plant Physiol 146:875–880. doi:10.1104/pp. 107.112045

    PubMed  Article  CAS  Google Scholar 

  26. Ruta N, Liedgens M, Fracheboud Y, Stamp P, Hund A (2009) QTLs for the elongation of axile and lateral roots of maize in response to low water potential. Theor Appl Genet 120:621–631. doi:10.1007/s00122-009-1180-5

    PubMed  Article  Google Scholar 

  27. Sambrook J, Russell DW (2001) Molecular cloning. Cold Spring Harbor, NY

  28. Schulze J, Pöschel G (2004) Bacterial inoculation of maize affects carbon allocation to roots and carbon turnover in the rhizosphere. Plant Soil 267:235–241. doi:10.1007/s11104-005-4980-7

    Article  CAS  Google Scholar 

  29. Simons M, van der Bij AJ, de Weger LA, Wijffelman CA, Lugtenberg BJJ (1996) Gnotobiotic system for studying rhizosphere colonization by plant growth-promoting Pseudomonas bacteria. Mol Plant Microbe In 9:600–607

    Article  CAS  Google Scholar 

  30. Smith GS, Johnston CM, Cornforth IS (1983) Comparison of nutrient solutions for growth of plants in sand culture. New Phytol 94:537–548. doi:10.1111/j.1469-8137.1983.tb04863.x

    Article  CAS  Google Scholar 

  31. Sukno SA, Garcia VM, Shaw BD, Thon MR (2008) Root infection and systemic colonization of maize by Colletotrichum graminicola. Appl Environ Microbiol 74:823–832. doi:10.1128/AEM.01165-07

    PubMed  Article  CAS  Google Scholar 

  32. Trachsel S, Stamp P, Hund A (2010) Effect of high temperatures, drought and aluminum toxicity on root growth of tropical maize (Zea mays l.) Seedlings. Maydica 55:249–260

    Google Scholar 

  33. Vaughan MM, Tholl D, Tokuhisa JG (2011) An aeroponic culture system for the study of root herbivory on Arabidopsis thaliana. Plant Methods 7:5. doi:10.1186/1746-4811-7-5

    PubMed  Article  Google Scholar 

Download references


We thank Natacha Fleury and Daniela Villacres de Papajewski for their technical help, Christophe Weider (Syngenta Crop Protection) for technical advices and Felix Mauch for critical reading of the manuscript. Partial funding of this project by the National Center of competence in Research, Plant Survival, is gratefully acknowledged.

Author information



Corresponding author

Correspondence to Brigitte Mauch-Mani.

Additional information

Chantal Planchamp and Dirk Balmer contributed equally.

Responsible Editor: Bernard Glick.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

(MPG 76116 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Planchamp, C., Balmer, D., Hund, A. et al. A soil-free root observation system for the study of root-microorganism interactions in maize. Plant Soil 367, 605–614 (2013). https://doi.org/10.1007/s11104-012-1497-8

Download citation


  • Corn
  • Zea mays
  • Root infection
  • Pathogen
  • Rhizobacteria
  • Colletotrichum graminicola
  • Pseudomonas putida