Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Strategies and methods for studying the rhizosphere—the plant science toolbox


This review summarizes and discusses methodological approaches for studies on the impact of plant roots on the surrounding rhizosphere and for elucidation of the related mechanisms, covering a range from simple model experiments up to the field scale. A section on rhizosphere sampling describes tools and culture systems employed for analysis of root growth, root morphology, vitality testing and for monitoring of root activity with respect to nutrient uptake, water, ion and carbon flows in the rhizosphere. The second section on rhizosphere probing covers techniques to detect physicochemical changes in the rhizosphere as a consequence of root activity. This comprises compartment systems to obtain rhizosphere samples, visualisation techniques, reporter gene approaches and remote sensing technologies for monitoring the conditions in the rhizosphere. Approaches for the experimental manipulation of the rhizosphere by use of molecular and genetic methods as tools to study rhizosphere processes are discussed in a third section. Finally it is concluded that in spite of a wide array of methodological approaches developed in the recent past for studying processes and interactions in the rhizosphere mainly under simplified conditions in model experiments, there is still an obvious lack of methods to test the relevance of these findings under real field conditions or even on the scale of ecosystems. This also limits reliable data input and validation in current rhizosphere modelling approaches. Possible interactions between different environmental factors or plant-microbial interactions (e.g. mycorrhizae) are frequently not considered in model experiments. Moreover, most of the available knowledge arises from investigations with a very limited number of plant species, mainly crops and studies considering also intraspecific genotypic differences or the variability within wild plant species are just emerging.

This is a preview of subscription content, log in to check access.

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


  1. Alvarez JP, Pekkera I, Goldshmidt A, Blum E, Amsellem Z, Eshed Y (2006) Endogenous and synthetic MicroRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell 18:1134–1151. doi:10.1105/tpc.105.040725

  2. Asmar F, Gahoonia TS, Nielsen NE (1995) Barley genotypes differ in activity of soluble extracellular phosphatase and depletion of organic phosphorus in the rhizosphere soil. Plant Soil 172:117–122. doi:10.1007/BF00020865

  3. Asseng S, Aylmore LAG, MacFall JS, Hopmanns JW, Gregory PJ (2000) Computer-assisted tomography and magnetic resonance imaging. In: Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (eds) Root methods. A handbook. Springer, Heidelberg, Germany, pp 343–364

  4. Aviani I, Laor Y, Raviv M (2006) Limitations and potential of in situ rhizobox sampling for assessing microbial activity in fruit tree rhizosphere. Plant Soil 279:327–332. doi:10.1007/s11104-005-2189-4

  5. Baret F, Fourty T (1997) Radiometric estimates of nitrogen status of leaves and canopies. In: Lemaire G (ed) Diagnosis of the nitrogen status in crops. Springer, Heidelberg, pp 201–227

  6. Bienfait HF, van den Briel W, Mesland-Mul NT (1985) Free space iron pools in roots: generation and mobilization. Plant Physiol 78:596–600. doi:10.1104/pp. 78.3.596

  7. Blackmer TM, Schepers JS (1996) Aerial photography to detect nitrogen stress in corn. J Plant Physiol 148:440–444

  8. Blossfeld S, Gansert D (2007) A novel non-invasive optical method for quantitative visualization of pH dynamics in the rhizosphere of plants. Plant Cell Environ 30:176–186. doi:10.1111/j.1365-3040.2006.01616.x

  9. Bobowski BR, Hole D, Wolfs PG, Bryant L (1999) Identification of roots of woody species using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Mol Ecol 8:485–491. doi:10.1046/j.1365-294X.1999.00603.x

  10. Boukcim H, Pages L, Plassard C, Mousain D (2001) Root system architecture and receptivity to mycorrhizal infection in seedlings of Cedrus atlantica as affected by nitrogen source and concentration. Tree Physiol 21:109–115

  11. Boukcim H, Pages L, Mousain D (2006) Local NO 3 - or NH 4 + supply modifies the root system architecture of Cedrus atlantica seedlings grown in a split-root device. J Plant Physiol 163:1293–1304. doi:10.1016/j.jplph.2005.08.011

  12. Briones AM, Okabe S, Umemiya Y, Ramsing NW, Reichardt-Okuyama H (2002) Influence of different cultivars on populations of ammonia-oxidising bacteria in the root environment of rice. Appl Environ Microbiol 68:3067–3075. doi:10.1128/AEM.68.6.3067-3075.2002

  13. Brunner I, Brodbeck S, Büchler U, Sperisen C (2001) Molecular identification of fine roots of trees from the alps: reliable and fast DNA extraction and PCR-RFLP analyses of plastid DNA. Mol Ecol 10:2079–2087. doi:10.1046/j.1365-294X.2001.01325.x

  14. Buchanan CD, Lim S, Salzman RA, Kagiampakis I, Morishige DT (2005) Sorghum bicolor’s transcriptome response to dehydration, high salinity and ABA. Plant Mol Biol 58:699–720. doi:10.1007/s11103-005-7876-2

  15. Bucher M (2006) Aeroponic culture. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmersdorf, pp 119–120

  16. Buso GSC, Bliss FA (1988) Variability among lettuce cultivars grown at two levels of available phosphorus. Plant Soil 111:67–73. doi:10.1007/BF02182038

  17. Cardon ZG, Gage DJ (2006) Resource exchange in the rhizosphere: molecular tools and the microbial perspective. Annu Rev Ecol Evol Syst 37:459–488. doi:10.1146/annurev.ecolsys.37.091305.110207

  18. Cardon ZG, Herron PM (2005) Sweeping water, oozing carbon: Long distance transport and patterns of rhizosphere resource exchange. In: Holbrook NM, Zwieniecki MA (eds) Vascular transport in plants. San Diego Academic, USA, pp 257–76

  19. Chaignon V, Hinsinger P (2003) A biotest for evaluating copper availability to plants in a contaminated soil. J Environ Qual 32:824–833

  20. Chao DY, Luo YH, Shi M, Luo D, Lin HX (2005) Salt responsive genes in rice revealed by cDNA microarray analysis. Cell Res 15:796–810. doi:10.1038/sj.cr.7290349

  21. Cheng W, Gershenson A (2007) Carbon fluxes in the rhizosphere. In: Cardon CG, Whitbeck JL (eds) The rhizosphere. An ecological perspective. Elsevier Academic, Burlington, USA, pp 31–56

  22. Ciarelli DM, Furlani AMC, Dechen AR, Lima M (1998) Genetic variation among maize genotypes for phosphorus uptake and phosphorus-use efficiency in nutrient solution. J Plant Nutr 21:2219–2229. doi:10.1080/01904169809365556

  23. Cieslinski G, Rees KCJ, van Szmigielska AM, Krishnamurti GSR, Huang PM (1998) Low molecular weight organic acids in rhizosphere soils of durum wheat and their effect on cadmium bioaccumulation. Plant Soil 203:109–117. doi:10.1023/A:1004325817420

  24. Comas LH, Eissenstat DM (2004) Linking fine root traits to maximum potential growth rate among 11 mature temperate tree species. Funct Ecol 18:388–397. doi:10.1111/j.0269-8463.2004.00835.x

  25. Cutler DF, Rudall PJ, Gasson PE, Gale RMO (1987) Root identification manual of trees and shrubs. A guide to the anatomy of trees and shrubs hardy in Britain and Northern Europe. Chapman & Hall, London

  26. Danjon F, Reubens B (2008) Assessing and analyzing 3D architecture of woody root systems, a review of methods and applications in tree and soil stability, resource acquisition and allocation. Plant Soil 303:1–34. doi:10.1007/s11104-007-9470-7

  27. Darwent MJ, Paterson E, James A, McDonald S, Deri Tomos A (2003) Biosensor reporting of root exudation from Hordeum vulgare in relation to shoot nitrate concentration. J Exp Bot 54:325–334. doi:10.1093/jxb/54.381.325

  28. de la Fuente-Martínez JM, Ramirez-Rodriguez V, Cabrera-Ponce JL, Herrera-Estrella L (1997) Aluminum tolerance in transgenic plants by alteration of citrate synthesis. Science 276:1566–1588. doi:10.1126/science.276.5318.1566

  29. Delhaize E, Ryan PR (2006) Aluminium-induced malate exudation. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmersdorf, pp 285–286

  30. Delhaize E, Ryan PR, Randall PJ (1993) Aluminium tolerance in wheat (Triticum aestivum L.) 2. Aluminium stimulated excretion of malic acid from root apices. Plant Physiol 103:695–702

  31. Delhaize E, Hebb DM, Ryan PR (2001) Expression of a Pseudomonas aeruginosa citrate synthase gene is not associated with either enhanced citrate accumulation or efflux. Plant Physiol 125:2059–2067. doi:10.1104/pp. 125.4.2059

  32. Delhaize E, Ryan PR, Hocking PJ, Richardson AE (2003) Effects of altered citrate synthase and isocitrate dehydrogenase expression on internal citrate concentrations in tobacco (Nicotiana tabacum L.). Plant Soil 248:137–144. doi:10.1023/A:1022352914101

  33. Delhaize E, Ryan PR, Hebb DM, Yamamoto Y, Sasaki T, Matsumoto H (2004) Engineering high level aluminum tolerance in barley with the ALMT1 gene. Proc Natl Acad Sci USA 101:15249–15254. doi:10.1073/pnas.0406258101

  34. Dessureault-Rompré J, Nowack B, Schulin R, Luster J (2006) Modified microsuction cup/rhizobox approach for the in-situ detection of organic acids in rhizosphere soil solution. Plant Soil 286:99–107. doi:10.1007/s11104-006-9029-z

  35. Dinkelaker B, Hahn G, Römheld V, Wolf GA (1993) Non-destructive methods for demonstrating chemical changes in the rhizosphere I. Description of methods. Plant Soil 155/156:67–74. doi:10.1007/BF00024985

  36. Dinkelaker B, Hengeler C, Neumann G, Eltrop L, Marschner H (1997) Root exudates and mobilization of nutrients. In: Rennenberg H, Eschrich W, Ziegler H (eds) Trees—contributions to modern tree physiology. Backhuys, Leiden, The Netherlands, pp 441–452

  37. Eapen S, D’Souza SF (2005) Prospects of genetic engineering of plants for phytoremediation of toxic metals. Biotechnol Adv 23:97–114. doi:10.1016/j.biotechadv.2004.10.001

  38. Engels C, Neumann G, Gahoonia T, George E, Schenk M (2000) Assessment of the ability of roots for nutrient acquisition. In: Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (eds) Root methods. A handbook. Springer, Heidelberg, Germany, pp 403–459

  39. Fageria NK, Baligar VC (1997a) Phosphorus use efficiency by corn genotypes. J Plant Nutr 20:1267–1277. doi:10.1080/01904169709365334

  40. Fageria NK, Baligar VC (1997b) Upland rice genotypes evaluation for phosphorus use efficiency. J Plant Nutr 20:499–509. doi:10.1080/01904169709365270

  41. Fageria NK, Wright RJ, Baligar VC (1988) Rice cultivar evaluation for phosphorus use efficiency. Plant Soil 111:105–109. doi:10.1007/BF02182043

  42. Fernandez JE, Clothier BE, van Noordwijk M (2000) Water uptake. In: Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (eds) Root Methods. A Handbook. Springer, Heidelberg, Germany, pp 461–507

  43. Fiedler S, Fischer WR (1994) Automatic device for longtime measurements of redox potentials under field condition. Z Pflanzenernahr Bodenk 157:305–308. doi:10.1002/jpln.19941570410

  44. Fischer WR, Schaller G (1980) Ein Elektrodensystem zur Messung des Redoxpotentials im Kontaktbereich Boden/Wurzel. Z Pflanzenernaehr Bodenk 143:344–348. doi:10.1002/jpln.19801430312

  45. Frey B, Turnau K (2006) Elemental analysis of roots and fungi. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 200–213

  46. Gahoonia TS, Nielsen NE (1996) Variation in acquisition of soil phosphorus among wheat and barley genotypes. Plant Soil 178:223–230. doi:10.1007/BF00011587

  47. Gahoonia TS, Nielsen NE, Lyshede OB (1999) Phosphorus acquisition of cereal cultivars in the field at three levels of P fertilization. Plant Soil 211:269–281. doi:10.1023/A:1004742032367

  48. Gahoonia TS, Nielsen NE, Joshi PA, Jahoor A (2004) A root hairless barley mutant for elucidating genetic of root hairs and phosphorus uptake. Plant Soil 235:211–219. doi:10.1023/A:1011993322286

  49. Garnett TP, Shabala SN, Smethurst PJ, Newman IA (2001) Simultaneous measurements of ammonium, nitrate and proton fluxes along the length of eucalypt roots. Plant Soil 236:55–62. doi:10.1023/A:1011951413917

  50. Garrigues E, Doussan C, Pierret A (2006) Water uptake by plant roots: I—Formation and propagation of a water extraction front in mature root systems as evidenced by 2D light transmission imaging. Plant Soil 283:83–98. doi:10.1007/s11104-004-7903-0

  51. Gaume A, Machler F, Deleon C, Narro L, Frossard E (2001) Low-P tolerance by maize (Zea mays L.) genotypes: significance of root growth, and organic acids and acid phosphatase root exudation. Plant Soil 228:253–264. doi:10.1023/A:1004824019289

  52. Geelhoed JS, van Riemsdijk WH, Findenegg GR (1999) Simulation of the effect of citrate exudation from roots on the plant availability of phosphate adsorbed on goethite. Eur J Soil Sci 50:379–390. doi:10.1046/j.1365-2389.1999.00251.x

  53. George TS, Richardson AE, Hadobas PA, Simpson RJ (2004) Characterisation of transgenic Trifolium subterraneum L. which expresses phyA and releases extracellular phytase: growth and phosphorus nutrition in laboratory media and soil. Plant Cell Environ 27:1351–1361. doi:10.1111/j.1365-3040.2004.01225.x

  54. George TS, Richardson AE, Simpson RJ (2005a) Behaviour of plant-derived extracellular phytase upon addition to soil. Soil Biol Biochem 37:977–988. doi:10.1016/j.soilbio.2004.10.016

  55. George TS, Simpson RJ, Hadobas PA, Richardson AE (2005b) Expression of a fungal phytase gene in Nicotiana tabacum improves phosphorus nutrition in plants grown in amended soil. Plant Biotechnol J 3:129–140. doi:10.1111/j.1467-7652.2004.00116.x

  56. George TS, Richardson AE, Smith JB, Hadobas PA, Simpson J (2005c) Limitations to the potential of transgenic Trifolium subterraneum L. plants that exude phytase, when grown in soils with a range of organic phosphorus content. Plant Soil 278:263–274. doi:10.1007/s11104-005-8699-2

  57. George TS, Gregory PJ, Hocking PJ, Richardson AE (2008) Variation in root-associated phosphatase activities in wheat contributes to the utilisation of organic P substrates in vitro, but does not effectively predict P-nutrition in different soils. Environ Exp Bot 64:239–249. doi:10.1016/j.envexpbot.2008.05.002

  58. Gleason C, Chaudhuri S, Yang T, Muňoz A, Poovaiah BW, Oldroyd GED (2006) Nodulation independent of rhizobia induced by a calcium-activated kinase lacking autoinhibition. Nature 441:1149–1152. doi:10.1038/nature04812

  59. Gobert A, Plassard C (2002) Differential NO 3 - dependent patterns of NO 3 - uptake in Pinus pinaster, Rhizopogon roseolus and their ectomycorrhizal association. New Phytol 154:509–516. doi:10.1046/j.1469-8137.2002.00378.x

  60. Göttlein A, Hell U, Blasek R (1996) A system for microscale tensiometry and lysimetry. Geoderma 69:147–156. doi:10.1016/0016-7061(95)00059-3

  61. Grayston SJ, Vaughan D, Jones D (1996) Rhizosphere carbon flow in trees, in comparison with annual plants: the importance of root exudation and its impact on microbial activity and nutrient availability. Appl Soil Ecol 5:29–56. doi:10.1016/S0929-1393(96)00126-6

  62. Haase S, Ruess L, Neumann G, Marhan S, Kandeler E (2007a) Low-level herbivory by root-knot nematodes (Meloidogyne incognita) modifies root hair morphology and rhizodeposition in host plants (Hordeum vulgare). Plant Soil 301:151–164. doi:10.1007/s11104-007-9431-1

  63. Haase S, Neumann G, Kania A, Kuzyakov Y, Römheld V, Kandeler E (2007b) Atmospheric CO2 and the N-nutritional status modifies nodulation, nodule-carbon supply and root exudation of Phaseolus vulgaris L. Soil Biol Biochem 39:2208–2221. doi:10.1016/j.soilbio.2007.03.014

  64. Hacin JI, Ben Bohlool B, Singleton PW (1997) Partitioning of 14C-labelled photosynthate to developing nodules and roots of soybean (Glycine max). New Phytol 137:257–265. doi:10.1046/j.1469-8137.1997.00812.x

  65. Hainsworth JM, Aylmore LAG (1989) Non-uniform soil water extraction by plant roots. Plant Soil 113:121–124. doi:10.1007/BF02181929

  66. Häussling M, Leisen E, Marschner H, Römheld V (1985) An improved method for non-destructive measurements of the pH at the root-soil interface (rhizosphere). J Plant Physiol 117:371–375

  67. Hawkins HJ, George E (1999) Effect of plant nitrogen status on the contribution of arbuscular mycorrhizal hyphae to plant nitrogen uptake. Physiol Plant 105:694–700. doi:10.1034/j.1399-3054.1999.105414.x

  68. Hazan SP, Pathan MS, Sanchez A, Baxter I, Dunn M, Estes B, Chang HS, Zhu T, Kreps JA, Nguyen HT (2005) Expression profiling of rice segregating for drought tolerance QTLs using a rice genome array. Funct Integr Genomics 5:104–116. doi:10.1007/s10142-004-0126-x

  69. Helmisaari HS, Makkonen K (2006) Root biomass and necromass. In: Finlay R, Luster J (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 153–164

  70. Henriksen GH, Raman DR, Walker LP, Spanwick RM (1992) Measurement of net fluxes of ammonium and nitrate at the surface of barley roots using ion-selective microelectrodes. II-Patterns of uptake along the root axis and evaluation of the microelectrode flux estimation technique. Plant Physiol 99:734–747. doi:10.1104/pp. 99.2.734

  71. Herrmann AM, Ritz K, Nunan N, Clode PL, Pett-Ridge J, Kilburn MR, Murphy DV, O’Donnell AG, Stockdale EA (2007) Nano-scale secondary ion mass spectrometry—a new analytical tool in biogeochemistry and soil ecology. UCRL-JRNL-225506, Lawrence Livermore National Laboratory, CA, USA

  72. Hinsinger P, Gilkes RJ (1996) Mobilization of phosphate from phosphate rock and alumina-sorbed phosphate by the roots of ryegrass and clover as related to rhizosphere pH. Eur J Soil Sci 47:533–544. doi:10.1111/j.1365-2389.1996.tb01853.x

  73. Hirano Y, Walthert L, Brunner I (2006) Callose in root apices of European chestnut seedlings: a physiological indicator of aluminum stress. Tree Physiol 26:431–440

  74. Hodge A, Robinson D, Griffiths B, Fitter AH (1999) Why plants bother: root proliferation results in increased nitrogen capture from an organic patch when two grasses compete. Plant Cell Environ 22:811–820. doi:10.1046/j.1365-3040.1999.00454.x

  75. Hoffland E (1992) Quantitative evaluation of the role of organic acid exudation in the mobilization of rock phosphate by rape. Plant Soil 140:279–289. doi:10.1007/BF00010605

  76. Hoffland E, Findenegg GR, Nelemans JA (1989) Solubilization of rock phosphorus by rape II. Local root exudation of organic acids in response to P-starvation. Plant Soil 113:161–165. doi:10.1007/BF02280176

  77. Hossain AK, Zakir M, Subbarao GV, Pearse SJ, Gopalakrishnan S, Ito O, Ishikawa T, Kawano N, Nakahara K, Yoshihashi T, Ono H, Yoshida M (2008) Detection, isolation and characterization of a root-exuded compound methyl 3-(4-hydroxyphenyl) propionate, responsible for biological nitrification inhibition by sorghum (Sorghum bicolor). New Phytol 180:442451

  78. Iizumi Z, Mizumoto M, Nakamura K (1998) A bioluminescence assay using Nitrosomonas europaea for rapid and sensitive detection of nitrification inhibitors. Appl Environ Microbiol 64:3656–3662

  79. Ishikawa S, Adu-Gyamfi JJ, Nakamura T, Yoshihara T, Watanabe T, Wagatsuma T (2002) Genotypic variability in phosphorus solubilising activity of root exudates by pigeon pea grown in low-nutrient environments. Plant Soil 245:71–81. doi:10.1023/A:1020659227650

  80. Jaeger CHIII, Lindow SE, Miller W, Clark E, Firestone MK (1999) Mapping of sugar and amino acid availability in soil around roots with bacterial sensors of sucrose and tryptophan. Appl Environ Microbiol 65:2685–2690

  81. Jaillard B, Ruiz L, Arvieu JC (1996) pH mapping in transparent gel using color indicator videodensitometry. Plant Soil 183:1–11. doi:10.1007/BF02185568

  82. Jefferies SP, Pallotta MA, Paull JG, Katakousis A, Kretchmer JM, Manning S, Islam AKMR, Langridge P, Chalmers KJ (2000) Mapping and validation of chromosome regions conferring boron toxicity tolerance in wheat (Triticum aestivum). Theor Appl Genet 101:767–777. doi:10.1007/s001220051542

  83. Johnson F, Allan DL, Vance CP, Weiblen G (1996) Root carbon dioxide fixation by phosphorus-deficient Lupinus albus (Contribution to organic acid exudation by proteoid roots). Plant Physiol 112:19–30

  84. Jones DL (1998) Organic acids in the rhizosphere—a critical review. Plant Soil 205:25–44

  85. Kamh M, Horst WJ, Amer F, Mostafa H, Maier P (1999) Mobilization of soil and fertilizer phosphate by cover crops. Plant Soil 211:19–27

  86. Kania A, Langlade N, Martinoia E, Neumann G (2003) Phosphorus deficiency-induced modifications in citrate catabolism and in cytosolic pH as related to citrate exudation in cluster roots of white lupin. Plant Soil 248:117–127

  87. Kawasaki S, Borchert C, Deyholos M, Wang H, Brazile S, Kawai K, Galbraith D, Bohnert HJ (2001) Gene expression profiles during the initial phase of salt stress in rice. Plant Cell 13:889–905

  88. Kawaura K, Mochida K, Yamazaki Y, Ogihara Y (2006) Transcriptome analysis of salinity stress responses in common wheat using a 22 k oligo-DNA microarray. Funct Integr Genomics 6:132–142

  89. Keerthisinghe G, Hooking PJ, Ryan PR, Delhaize E (1998) Effect of phosphorus supply on the formation and function of proteoid roots of white lupin (Lupinus albus L.). Plant Cell Environ 21:467–478

  90. Killham K, Yeomans C (2001) Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes. Plant Soil 232:91–96

  91. Kirk GJD, Santos EE, Findenegg GR (1999) Phosphate solubilization by organic anion secretion from rice (Oryza sativa L.) growing in aerobic soil. Plant Soil 211:11–18

  92. Kitchen NR (2007) Incorporating nutrient sensing technology in production agriculture. Fluid Fertilizer Forum, February 18–20, 2007, Scottsdale. AZ, pp 35–40

  93. Knipfer T, Steudle E (2008) Root hydraulic conductivity measured by pressure clamp is substantially affected by internal unstirred layers. J Exp Bot 59:2071–2084

  94. Kojima S, Bohner A, von Wirén N (2006) Molecular mechanisms of urea transport in plants. J Membr Biol 212:83–91

  95. Koyama H, Kanamura A, Kihara T, Hara T, Takita E, Shibata D (2000) Overexpression of mitochondrial citrate synthase in Arabidopsis thaliana improved growth on a phosphorus limited soil. Plant Cell Physiol 41:1030–1037

  96. Kragelund L, Hosond C, Nybroe O (1997) Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere. Appl Environ Microbiol 63:4920–4928

  97. Kuchenbuch R, Jung A (1982) A method for determining concentration profiles at the root-soil interface by thin slicing rhizospheric soil. Plant Soil 68:391–394

  98. Kuzyakov Y, Domanski G (2000) Carbon input by plants into the soil. Review. Journal of Plant Nutr Soil Sci 163:421–431

  99. Lan L, Li M, Lai Y, Xu W, Kong Z, Ying K, Han B, Xue Y (2005) Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.). Plant Mol Biol 59:151–164

  100. Li M, Osaki M, Rao IM, Tadano T (1997) Secretion of phytase from the roots of several plant species under phosphorus-deficient conditions. Plant Soil 195:161–169

  101. Li L, Zhang F, Li X, Christie P, Sun J, Yang S, Tang C (2003) Interspecific facilitation of nutrient uptake by intercropped maize and faba bean. Nutrient Cycling in Agroecosystems 65:61–71

  102. Li SM, Li L, Zhang FS, Tang C (2004) Acid phosphatase role in Chickpea/Maize intercropping. Annals of Botany 94:297–202

  103. Lian X, Wang S, Zhang J, Feng Q, Zhang L, Fan D, Li X, Yuan D, Han B, Zhang Q (2006) Expression profiles of 10,422 genes at early stages of low nitrogen stressing rice assayed using a cDNA microarray. Plant Mol Biol 60:617–631

  104. Liao MT, Fillery IRP, Palta JA (2004) Early vigorous growth is a major factor influencing nitrogen uptake in wheat. Funct Plant Biol 31:121–129

  105. Liao M, Hocking PJ, Dong B, Delhaize E, Richardson AE, Ryan PR (2008) Variation in early phosphorus-uptake efficiency among wheat genotypes grown on two contrasting Australian soils. Aust J Agric Res 59:157–166

  106. Liew OW, Ching P, Chong J, Li B, Asundi AK (2008) Signature optical cues: emerging technologies for monitoring plant health. Sensors 8:3205–3239

  107. Lilienthal H, Schnug E (2007) New issues for remote sensing in agriculture—a critical overview. Dahlia Greidinger Symposium—advanced technologies for monitoring nutrient and water availability to plants, March 2007. Haifa, Israel, pp 87–104

  108. Lopez-Buccio J, de la Vega OM, Guevara-Garcia A, Herrera-Estrella L (2000) Enhanced phosphorus uptake in transgenic tobacco plants that overproduce citrate. Nature Biotech 18:450–453

  109. Lung SC, Chan WL, Yip W, Wang L, Yeung EC, Lim BL (2005) Secretion of beta-propeller phytase from tobacco and Arabidopsis roots enhances phosphorus utilisation. Plant Sci 169:341–349

  110. Luster J, Finlay R (eds) (2006) Handbook of methods used in rhizosphere research. Swiss Federal Institute for Forest, Snow, and Landscape Research, Birmensdorf, Switzerland, online at www.rhizo.at/handbook

  111. Luster J, Göttlein A, Nowack B, Sarret G (2009) Sampling, defining, characterising and modeling the rhizosphere—the soil science tool box. Plant Soil (This volume), in press. doi:10.1007/s11104-008-9781-3

  112. Lynch JP, Brown KM (2001) Topsoil foraging—an architectural adaptation of plants to low phosphorus availability. Plant Soil 237:225–237

  113. Lynch JM, Whipps JM (1990) Substrate flow in the rhizosphere. Plant Soil 129:1–10

  114. Macfall JS, Johnson GA, Kramer PJ (1990) Observation of a water-depletion region surrounding lobolly pine roots by magnetic resonance imaging. Proc Natl Acad Sci USA 87:1203–1207

  115. Majdi H (1996) Root sampling methods-applications and limitations of the minirhizotron technique. Plant and Soil 185:255–258

  116. Makkonen K, Helmisaari HS (1999) Assessing fine-root biomass and production in a Scots pine stand—comparison of soil core and ingrowth core methods. Plant Soil 210:43–50

  117. Maniero R (2006) Fine root dynamics. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 165–166

  118. Manske GGB, Ortiz-Monasterio JI, Van Grinkel M, Rajaram S, Molina E, Vlek PLG (2000) Traits associated with improved P-uptake efficiency in CIMMYT’s semidwarf spring bread wheat grown on an acid andisol in Mexico. Plant Soil 221:189–204

  119. Markandeya G, Babu PR, Lachagari VBR, Feltus FA, Paterson AH, Reddy AR (2005) Functional genomics of drought-stress response in rice: transcript mapping of annotated unigenes of an indica rice (Oryza sativa L. cv. Nagina 22). Curr Sci 89:496–514

  120. Marshall Porterfield D (2002) Use of microsensors for studying the physiological activity of plant roots. In: Waisel Y, Eshel A, Kafkafi U (eds) Plant roots the hidden half, 3rd edn. Marcel Dekker, New York, USA, pp 333–347

  121. Miki D, Shimamoto K (2004) Simple RNAi vectors for stable and transient suppression of gene function in rice. Plant Cell Physiol 45:490–495

  122. Mudge SR, Smith FW, Richardson AE (2003) Root-specific and phosphate-regulated expression of phytase under the control of a phosphate transporter promoter enables Arabidopsis to grow on phytate as a sole phosphorus source. Plant Sci 165:871–878

  123. Munns R, Hare RA, James RA, Rebetzke GJ (2000) Genetic variation for improving the salt tolerance of durum wheat. Aust J Agric Res 51:69–74

  124. Nakaji T, Noguchi K, Oguma H (2008) Classification of rhizosphere components using visible-near infrared spectral images. Plant Soil 310:245–261

  125. Negishi T, Nakanishi H, Yazaki J, Kishimoto N, Fujii F, Shimbo K et al (2002) cDNA microarray analysis of gene expression during Fe-deficiency stress in barley suggests that polar transport of veiscles is implicated in phytosiderophore secretion in Fe-deficient barley roots. Plant J 30:83–94

  126. Neumann G (2006a) Construction and setup of rhizoboxes. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 143–144

  127. Neumann G (2006b) Collection of root exudates and rhizosphere soil solution from soil-grown plants. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 317–318

  128. Neumann G, Römheld V (2007) The release of root exudates as affected by the plant physiological status. In: Pinton R, Varanini Z, Nannipieri Z (eds) The rhizosphere: biochemistry and organic substances at the soil-plant interface, 2nd edn. CRC, Boca Raton, Florida, USA, pp 23–72

  129. Newman IA (2001) Ion transport in roots: measurement of fluxes using ion-selective microelectrodes to characterize transporter function. Plant Cell Environm 24:1–14

  130. Newman IA, Kochian LV, Grusak MA, Lucas WJ (1987) Fluxes of H+ and K+ in corn roots: characterization and stoichiometries using ion-selective microelectrodes. Plant Physiol 84:1177–1184

  131. Oh SJ, Kwon CW, Choi DW, Song SI, Kim JK (2007) Expression of barley HvCBF4 enhances tolerance to abiotic stress in transgenic rice. Plant Biotechnol J 5:646–656

  132. Oliveira MG, van Noordwijk M, Gaze SR, Brouwer G, Bona S, Mosca G, Hairiah K (2000) Auger sampling, ingrowth cores and pinboard methods. In: Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (eds) Root methods. A handbook. Springer, Heidelberg, Germany, pp 175–210

  133. Osborne LD, Rengel Z (2002) Screening cereals for genotypic variation in the efficiency of phosphorus uptake and utilization. Aust J Agric Res 53:295–303

  134. Ozturk ZN, Talame V, Deyholos M, Michalowski CB, Galbraith DW, Gozukirmizi N, Tuberosa R, Bohnert HJ (2002) Monitoring large-scale changes in transcript abundance in drought-and salt-stressed barley. Plant Mol Biol 48:551–573

  135. Pearse SJ, Venaklaas EJ, Cawthray G, Bolland MDA, Lambers H (2006) Carboxylate composition of root exudates does not relate consistently to a crop species’ ability to use phosphorus from aluminium, iron or calcium phosphate sources. New Phytol 173:181–190

  136. Pearse SJ, Venaklaas EJ, Cawthray G, Bolland MDA, Lambers H (2008) Lupinus albus landraces from different ecogeographical origins vary in their ability to use phosphorus from sparingly soluble forms. Austr J Agr Res 59:626–623

  137. Plassard C, Meslem M, Souche G, Jaillard B (1999) Localization and quantification of net fluxes of H+ along maize roots by combined use of pH-indicator dye videodensitometry and H+-selective microelectrodes. Plant Soil 211:29–39

  138. Plassard C, Guérin-Laguette A, Véry AA, Casarin V, Thibaud TB (2002) Local measurements of nitrate and potassium fluxes along roots of maritime pine. Effects of ectomycorrhizal symbiosis. Plant Cell Environm 25:75–84

  139. Polomski J, Kuhn N (2002) Root research methods. In: Waisel Y, Eshel A, Kafkafi U (eds) Plant roots the hidden half, 3rd edn. Marcel Dekker, New York, USA, pp 295–321

  140. Pratt LH, Liang C, Shah M, Sun F, Wang H, Reid SP et al (2005) Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16 801 unique transcripts. Plant Physiol 139:869–884

  141. Rabbani MA, Maruyama K, Abe H, Khan MA, Katsura K, Ito Y, Yoshiwara K, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2003) Monitoring expression profiles of rice genes under cold, drought and high salinity stresses and abscisic acid application using cDNA microarray and RNA gel blot analyses. Plant Physiol 133:1755–1767

  142. Raghothama KG (1999) Phosphate acquisition. Ann Rev Plant Physiol Plant Mol Biol 50:665–693

  143. Raman H, Zhang K, Cakir M, Appels R, Garvin DF, Maron LG, Kochian LV, Moroni JS, Raman R, Imtiaz M, Drake-Brockman F, Waters I, Martin P, Sasaki T, Yamamoto Y, Matsumoto H, Hebb DM, Delhaize E, Ryan PR (2005) Molecular characterisation and mapping of ALMT1, the aluminium tolerance gene in bread wheat (Triticum aestivum L.). Genome 48:781–791

  144. Rengel Z, Marschner P (2005) Nutrient availability and management in the rhizosphere: exploiting genotypic differences. New Phytol 168:305–312

  145. Rengel Z, Ross G, Hirsch P (1998) Plant genotype and micronutrient status influence colonization of wheat roots by soil bacteria. J Plant Nutr 21:99–113

  146. Rensink WA, Lobst S, Hart A, Stegalkina S, Liu J, Buell CR (2005) Gene expression profiling of potato responses to cold heat and salt stress. Funct Integr Genomics 5:201–207

  147. Richards RA, Watt M, Rebetzke GJ (2007) Physiological traits and cereal germplasm for sustainable agricultural systems. Euphytica 154:409–425

  148. Richardson AE, Hadobas PA, Hayes JE (2001) Extracellular secretion of Aspergillus phytase from Arabidopsis roots enables plants to obtain phosphorus from phytate. Plant J 25:641–649

  149. Richardson AE, George TS, Jakobsen I, Simpson RJ (2007) Plant utilization of inositol phosphates. In: Turner BL, Richardson AE, Mullaney EJ (eds) Inositol phosphates: linking agriculture and the environment. CAB International, Wallingford, pp 242–260

  150. Richter AK, Frossard E, Brunner I (2007) Polyphenols in woody roots of Norway spruceand European beech reduce TTC. Tree Physiol 27:155–160

  151. Ruiz L, Arvieu JC (1990) Measurements of pH gradients in the rhizosphere. Symbiosis 9:71–75

  152. Ryan PR, Delhaize E, Randall PJ (1995) Malate efflux from root apices and tolerance to aluminium are highly correlated in wheat. Aust J Plant Phys 22:531–536

  153. Sasaki T, Yamomoto Y, Ezaki B, Katsuhara M, Ahn SJ, Ryan PR, Delhaize E, Matsumoyo H (2004) A wheat gene encoding an aluminium-activated malate transporter. Plant J 37:645–653

  154. Schilling G, Gransee A, Deubel A, Lezovic G, Ruppel S (1998) Phosphorus availability, root exudates, and microbial activity in the rhizosphere. Z Pflanzenernähr Bodenk 161:465–478

  155. Schmidhalter U, Jungert S, Bredemeier C, Gutser R, Manhart R, Mistele B et al (2003) Field-scale validation of a tractor-based multispectral crop scanner to determine biomass and nitrogen uptake of winter wheat. In: Stafford J, Werner A (eds) Precision agriculture: Papers from the 4th European Conference on Precision Agriculture, Berlin, pp 615–619

  156. Schünmann PHD, Richardson AE, Smith FW, Delhaize E (2004) Characterization of promoter expression patterns derived from the Pht1 phosphate transporter genes of barley (Hordeum vulgare L.). J Exp Bot 55:855–865

  157. Shen J, Hoffland E (2007) In situ sampling of small volumes of soil solution using modified micro cups. Plant Soil 292:161–169

  158. Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (2000a) Root methods. A handbook. Springer, Heidelberg, Germany

  159. Smit AL, George E, Groenwold J (2000b) Root observations and measurements at (transparent) interfaces with soil. In: Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (eds) Root methods. A handbook. Springer, Heidelberg, Germany, pp 236–271

  160. Smith DM, Allen SJ (1996) Measurement of sap flow in plant stems. J Exp Bot 47:1833–1844

  161. Steudle E (1994) Water transport across roots. Plant Soil 167:79–90

  162. Strasser O, Köhl K, Römheld V (1999) Overestimation of apoplastic Fe in roots of soil grown plants. Plant Soil 210:179–187

  163. Stromberg N (2006) Imaging optodes. Dept. of Chemistry Analytical Chemistry, Goteborg University, Sweden

  164. Stromberg N (2008) Determination of ammonium turnover and flow patterns close to roots using imaging optodes. Environm. Sci Technol 42:1630–1637

  165. Subbarao GV, Ae N, Otani T (1997) Genotypic variation in the iron- and aluminium-phosphate solubilising activity of pigeon pea root exudates under P deficient conditions. Soil Sci Plant Nutr 43:295–305

  166. Subbarao GV, Ishikawa T, Ito O, Nakahara K, Wang HY, Berry WL (2006) A bioluminescence assay to detect nitrification inhibitors released from plant roots: a case study with Brachiaria humidicola. Plant Soil 288:101–112

  167. Tadano T, Ozawa K, Sakai H, Osaki M, Matsui H (1993) Secretion of acid phosphatase by the roots of crop plants under phosphorus-deficient conditions and some properties of the enzyme secreted by lupin roots. Plant Soil 155(156):95–98

  168. Takahashi M, Nakanishi H, Kawasaki NK, Mori S (2001) Enhanced tolerance of rice to low iron availability in alkaline soils using barley nicotinamine aminotransferase genes. Nat Biotechnol 19:466–469

  169. Tesfaye M, Temple SJ, Allan DL, Vance CP, Samac DA (2001) Overexpression of malate dehydrogenase in transgenic alfalfa enhances organic acid synthesis and confers tolerance to aluminium. Plant Physiol 127:1836–1844

  170. Thorup-Kristensen K (2006) Root density and rooting depth, root turnover, short term root growth responses. In: Luster J, Finlay R (eds) Handbook of methods used in rhizosphere research. Swiss Federal Research Institute WSL, Birmensdorf, pp 177–178

  171. Tirichine L, Imaizumi-Anraku H, Yoshida S, Murakami Y, Madsen LH, Miwa H, Nakagawa T, Sandal N, Albrektsen AS, Kawaguchi M, Downie A, Sato S, Tabata S, Kouchi H, Parniske M, Kawasaki S, Stougaard J (2006) Deregulation of a Ca2+/calmodulin-dependent kinase leads to spontaneous nodule development. Nature 441:1153–1156

  172. Turpault MP, Utérano C, Boudot JP, Ranger J (2005) Influence of mature Douglas fir roots on the solid phase of the rhizosphere and its solution chemistry. Plant Soil 275:327–336

  173. Turpault MP, Gobran GR, Bonnaud P (2007) Temporal variations of rhizosphere and bulk soil chemistry in a Douglas fir stand. Geoderma 137:490–496

  174. Uhde-Stone C, Zinn KE, Ramirez-Yáñez M, Li A, Vance CP, Allan DL (2003) Nylon filter arrays reveal differential gene expression in proteoid roots of white lupin in response to P deficiency. Plant Physiol 131:1064–1079

  175. Van Noordwijk M, Brouwer G, Meijboom F, Oliveira MG, Bengough AG (2000) Trench profile techniques and core break methods. In: Smit AL, Bengough AG, Engels C, Van Noordwijk M, Pellerin S, Van de Geijn SC (eds) Root methods. A handbook. Springer, Heidelberg, Germany, pp 211–233

  176. Van Veen JA, Kay E, Vogel TM, Simonet P (2007) Methodological approaches to the study of carbon flow and the associated microbial population dynamics in the rhizosphere. In: Pinton R, Varanini Z, Nannipieri Z (eds) The rhizosphere: biochemistry and organic substances at the soil-plant interface, 2nd edn. CRC, Boca Raton, Florida, USA, pp 371–399

  177. Vance CP, Uhde-Stone C, Allan DL (2003) Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. New Phytol 157:423–447

  178. Vanguelova E, Hirano Y, Eldhuset TD, Sas-Paszt L, Bakker MR, Püttsepp U et al (2007) Tree fine root Ca/Al molar ratio—indicator of Al and acidity stress. Plant Biosyst 141:460–480

  179. Vetterlein D, Jahn R (2004) Combination of micro suction cups and time-domain reflectometry to measure osmotic potential gradients between bulk soil and rhizosphere at high resolution in time and space. Eur J Soil Sci 55:497–504

  180. Vetterlein D, Marschner H, Horn R (1993) Microtensiometer technique to study hydraulic lift in a sandy soil planted with pearl millet (Pennisetum americanum L. Leeke). Plant Soil 149:275–282

  181. Vij S, Tyagi AK (2007) Emerging trends in the functional genomics of the abiotic stress response in crop plants. Plant Biotechnol J 5:361–380

  182. Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ (2005) Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol 139:822–835

  183. Wang QR, Li JY, Li ZS, Christie P (2005) Screening Chinese wheat germplasm for phosphorus efficiency in calcareous soils. J Plant Nutr 28:489–505

  184. Wichern F, Eberhardt E, Mayer J, Joergensen RG, Müller T (2008) Nitrogen rhizodeposition in agricultural crops: methods, estimates and future prospects. Soil Biol Biochem 40:30–48

  185. Williams RF (1948) The effects of phosphorus supply on the rates of intake of phosphorus and nitrogen and upon certain aspects of phosphorus metabolism in graminaceous plants. Aust J Sci Res B1:333–361

  186. Wissuwa M (2003) How do plants achieve tolerance to phosphorus deficiency? Small causes with big effects. Plant Physiol 133:1947–1958

  187. Wissuwa M, Ae N (2001a) Further characterization of two QTLs that increase phosphorus uptake of rice (Oryza sativa L.) under phosphorus deficiency. Plant Soil 237:275–286

  188. Wissuwa M, Ae N (2001b) Genotypic variation for tolerance to phosphorus deficiency in rice and the potential for its exploitation in rice improvement. Plant Breeding 120:43–48

  189. Wissuwa M, Mazzola M, Picard C (2009) Novel approaches in plant breeding for rhizosphere-related traits. Plant Soil (This volume), in press. doi:10.1007/s11104-008-9693-2

  190. Xiao K, Harrison MJ, Wang ZY (2005) Transgenic expression of a novel Medicago truncatula phytase gene results in improved acquisition of organic phosphorus by Arabidopsis. Planta 222:27–36

  191. Yan X, Liao H, Beebe SE, Blair MW, Lynch JP (2004) QTL mapping of root hair and acid exudation traits and their relationship to phosphorus uptake in common bean. Plant Soil 265:17–29

  192. Yeomans C, Porteous F, Paterson E, Meharg AA, Killham K (1999) Assessment of lux-marked Pseudomonas fluorescent for reporting on organic compounds. FEMS Microbiol Letters 176:79–83

  193. Yu LX, Setter TL (2003) Comparative transcriptional profiling of placenta and endosperm in developing maize kernels in response to water deficit. Plant Physiol 131:568–582

  194. Yuan L, Loque D, Kojima S, Rauch S, Ishiyama K, Inoue E, Takahashi H, von Wiren N (2007) The organization of high-affinity ammonium uptake in Arabidopsis roots depends on the spatial arrangement and biochemical properties of AMT1-type transporters. Plant Cell 19:2636–2652

  195. Zhang WH, Ryan PR, Tyerman SD (2004) Citrate-permeable channels in the plasma membrane of cluster roots from white lupin. Plant Physiol 136:3771–3783

  196. Zhu J, Kaeppler SM, Lynch JP (2005) Mapping of QTL controlling root hair length in maize (Zea mays L.) under phosphorus deficiency. Plant Soil 270:299–310

  197. Zimmermann U, Meinzer FC, Benker R, Zhu JJ, Schneider H, Goldstein G, Kuchenbrod E, Haase A (1994) Xylem water transport: ist the available evidence consistent with the cohesion theory? Plant Cell Environ 17:1169–1181

  198. Zimmermann P, Zardi G, Lehmann M, Zeder C, Amrhein N, Frossard E, Bucher M (2003) Engineering the root-soil interface via targeted expression of a synthetic phytase gene in trichoblasts. Plant Biotech J 1:353–360

Download references

Author information

Correspondence to Günter Neumann.

Additional information

Responsible Editor: Philippe Hinsinger.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Neumann, G., George, T.S. & Plassard, C. Strategies and methods for studying the rhizosphere—the plant science toolbox. Plant Soil 321, 431–456 (2009). https://doi.org/10.1007/s11104-009-9953-9

Download citation


  • Genotypic variation
  • Imaging
  • Ion uptake
  • Nutrient acquisition
  • Rhizosphere management
  • Root exudates
  • Root growth