Plant and Soil

, Volume 376, Issue 1–2, pp 95–110 | Cite as

Quantifying coupled deformation and water flow in the rhizosphere using X-ray microtomography and numerical simulations

  • Jazmín E. Aravena
  • Markus Berli
  • Siul Ruiz
  • Francisco Suárez
  • Teamrat A. Ghezzehei
  • Scott W. Tyler
Regular Article


Background and aims

The rhizosphere, the soil immediately surrounding roots, provides a critical bridge for water and nutrient uptake. The rhizosphere is influenced by various forms of root–soil interactions of which mechanical deformation due to root growth and its effects on the hydraulics of the rhizosphere are the least studied. In this work, we focus on developing new experimental and numerical tools to assess these changes.


This study combines X-ray micro-tomography (XMT) with coupled numerical simulation of fluid and soil deformation in the rhizosphere. The study provides a new set of tools to mechanistically investigate root-induced rhizosphere compaction and its effect on root water uptake. The numerical simulator was tested on highly deformable soil to document its ability to handle a large degree of strain.


Our experimental results indicate that measured rhizosphere compaction by roots via localized soil compaction increased the simulated water flow to the roots by 27 % as compared to an uncompacted fine-textured soil of low bulk density characteristic of seed beds or forest topsoils. This increased water flow primarily occurred due to local deformation of the soil aggregates as seen in the XMT images, which increased hydraulic conductivity of the soil. Further simulated root growth and deformation beyond that observed in the XMT images led to water uptake enhancement of ~50 % beyond that due to root diameter increase alone and demonstrated the positive benefits of root compaction in low density soils.


The development of numerical models to quantify the coupling of root driven compaction and fluid flow provides new tools to improve the understanding of plant water uptake, nutrient availability and agricultural efficiency. This study demonstrated that plants, particularly during early growth in highly deformable low density soils, are involved in active mechanical management of their surroundings. These modeling approaches may now be used to quantify compaction and root growth impacts in a wide range of soils.


Rhizosphere Growth Mechanical deformation Uptake X-ray microtomography 



This material is based upon work supported by the National Science Foundation under Grants No. DEB-0816726 and DEB-0817073. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional support for SWT was provided by the Centre for Ecohydrology at the University of Western Australia. The authors would like to thank Ajay Mandava and Emma Regentova for providing preliminary segmentations of the geometries of the rhizosphere and M. Menon for contributions toward the direction of this research. The authors also greatly appreciate the comments and suggestions of two anonymous reviewers whose insight and questions greatly improved the manuscript.


  1. Alaoui A, Lipiec J, Gerke HH (2011) A review of the changes in the soil pore system due to soil deformation: a hydrodynamic perspective. Soil Tillage Res 115–116:1–15. doi: 10.1016/j.still.2011.06.002 CrossRefGoogle Scholar
  2. Aravena JE (2011) Root-induced compaction and its effects on soil microstructure and soil hydraulic properties using x-ray micro-tomography and numerical simulations, PhD Dissertation, Depart. Civil Environ. Eng., Univ. Nevada, Reno, Reno, Nevada, United StatesGoogle Scholar
  3. Aravena JE, Berli M, Ghezzehei TA, Tyler SW (2011) Effects of root-induced compaction on rhizosphere hydraulic properties—X-ray microtomography imaging and numerical simulations. Environ Sci Technol 45:425–431. doi: 10.1021/es102566j PubMedCrossRefGoogle Scholar
  4. Aravena JE, Berli M, Menon M, Ghezzehei TA, Mandava AK, Regentova EE, Young MH, Nico PS, Tyler SW (2012) Synchrotron X-ray Microtomography (XMT)—new means to quantify root induced changes of rhizosphere physical properties. In: Anderson SH, Hopmans JW (eds) Tomography and imaging of soil-water-root processes. SSSA Special Publication 61, Soil Science Society of America. Madison, WI, 289 ppGoogle Scholar
  5. Augeard B, Bresson LM, Assouline S, Kao C, Vauclin M (2008) Dynamics of soil surface bulk density: role of water table elevation and bulk density. Soil Sci Soc Am J. doi: 10.2136/sssaj2006.0429 Google Scholar
  6. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM (2006) The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 57:233–266. doi: 10.1146/annurev.arplant.57.032905.105159 PubMedCrossRefGoogle Scholar
  7. Bengough AG, McKenzie BM, Hallett PD, Valentine TA (2011) Root elongation, water stress, and mechanical impedance: a review of limiting stresses and beneficial root tip traits. J Exp Bot 62:59–68. doi: 10.1093/jxb/erq350 PubMedCrossRefGoogle Scholar
  8. Berli M, Or D (2006) Deformation of pores in viscoplastic soil material. Int J Geomech 6:108–118. doi: 10.1061/(ASCE)1532-3641(2006)6:2(108) CrossRefGoogle Scholar
  9. Berli M, Accorsi ML, Or D (2006) Size and shape evolution of pores in viscoplastic matrix under compression. Int J Numer Anal Methods Geomech 30:1259–1281. doi: 10.1002/nag.529 CrossRefGoogle Scholar
  10. Berli M, Carminati A, Ghezzehei TA, Or D (2008) Evolution of unsaturated hydraulic conductivity of aggregated soils due to compressive forces. Water Resour Res 44:W00C09. doi: 10.1029/2007WR006501 Google Scholar
  11. Bezdek JC (1981) Pattern recognition with fuzzy objective function algorithms plenum. Press, New YorkCrossRefGoogle Scholar
  12. Carminati A, Kaestner P, Lehmann R, Flühler H (2008) Unsaturated water flow across soil aggregate contacts. Adv Water Res 31:1221–1232. doi: 10.1016/j.advwatres.2008.01.008 CrossRefGoogle Scholar
  13. Carminati A, Moradi AB, Vetterlein D, Vontobel P, Lehmann E, Weller U, Vogel HJ, Oswald SE (2010) Dynamics of soil water content in the rhizosphere. Plant Soil 332:163–176. doi: 10.1007/s11104-010-0283-8 CrossRefGoogle Scholar
  14. Carminati A, Schneider CL, Moradi AB, Zarebanadkouki M, Vetterlein D, Vogel HJ, Hildebrandt A, Weller U, Schüler L, Oswald SE (2011) How the rhizosphere may favor water availability to roots. Vadose Zone J 10:988–998. doi: 10.2136/vzj2010.0113 CrossRefGoogle Scholar
  15. Carminati A, Vetterlein D, Koebernick N, Blaser S, Weller U, Vogel H-J (2012) Do roots mind the gap? Plant Soil. doi: 10.1007/s11104-012-1496-9 Google Scholar
  16. Dexter AR (1987) Compression of soil around roots. Plant and Soil 97:401–406Google Scholar
  17. Doussan C, Pierret A, Garrigues E, Pages L (2006) Water uptake by plant roots: II—modelling of water transfer in the soil root-system with explicit account of flow within the root system—comparison with experiments. Plant Soil 283:99–117. doi: 10.1007/s11104-004-7904-z CrossRefGoogle Scholar
  18. Dunn JC (1973) A fuzzy relative of the isodata process and its use in detecting compact well-separated clusters. J Cybern 3:32–57CrossRefGoogle Scholar
  19. Eggers CG, Berli M, Accorsi ML, Or D (2006) Deformation and permeability of aggregated soft earth materials. J Geophys Res 111:B10204. doi: 10.1029/2005JB004123 CrossRefGoogle Scholar
  20. Eggers CG, Berli M, Accorsi ML, Or D (2007) Permeability of deformable soft aggregated earth materials: from single pore to sample cross section. Water Resour Res 43:W08424. doi: 10.1029/2005WR004649 Google Scholar
  21. Entry J, Rygiewicz P, Watrud L, Donnelly P (2002) Influence of adverse soil conditions on the formation and function of Arbuscular mycorrhizas. Adv Environ Res 7:123–138CrossRefGoogle Scholar
  22. Ghezzehei TA, Or D (2000) Dynamics of soil aggregate coalescence governed by capillary and rheological processes. Water Resour Res 36:367–379CrossRefGoogle Scholar
  23. Ghezzehei TA, Or D (2001) Rheological properties of wet soils and clays under steady and oscillatory stresses. Soil Sci Soc Am J 65:624–637CrossRefGoogle Scholar
  24. Ghezzehei TA, Or D (2003) Stress-induced volume reduction of isolated pores in wet soil. Water Resour Res 39:1067. doi: 10.1029/2001WR001137 Google Scholar
  25. Goss MJ (1991) Consequences of the activity of roots on soil. In: Atkinson D (ed) Plant root growth: an ecological perspective. pp 161–186Google Scholar
  26. Graecen EL, Farrell DA, Cockroft B (1968) Soil resistance to metal probes and plant roots. 9th International Congress of Soil Science, Angus and Roberton, Adelaide, pp 769–779Google Scholar
  27. Gregory PJ (2006) Roots, rhizosphere and soil: the route to a better understanding of soil science? Eur J Soil Sci 57:2–12. doi: 10.1111/j.1365-2389.2005.00778.x CrossRefGoogle Scholar
  28. Gregory PJ, Hinsinger P (1999) New approaches to studying chemical and physical changes in the rhizosphere: an overview. Plant Soil 211:1–9CrossRefGoogle Scholar
  29. Hallett PD, Gordon DC, Bengough AG (2003) Plant influence on rhizosphere hydraulic properties: direct measurements using a miniaturized infiltrometer. New Phytol 157:597–603. doi: 10.1046/j.1469-8137.2003.00690.x CrossRefGoogle Scholar
  30. Hamamoto S, Moldrup P, Kawamoto K, Komatsu T (2009) Effect of particle size and soil compaction on gas transport parameters in variably saturated, sandy soils. Vadose Zone J 8:986–995. doi: 10.2136/vzj2008.0157 CrossRefGoogle Scholar
  31. Hamza M, Anderson W (2005) Soil compaction in cropping systems—a review of the nature, causes and possible solutions. Soil Tillage Res 82:121–145CrossRefGoogle Scholar
  32. Hargreaves CE, Gregory PJ, Bengough AG (2009) Measuring root traits in barley (Hordeum vulgare ssp. vulgare and ssp. spontaneum) seedlings using gel chambers, soil sacs and X-ray microtomography. Plant Soil 316:285–297. doi: 10.1007/s11104-008-9780-4 CrossRefGoogle Scholar
  33. Hettiaratchi DRP, Goss MJ, Harris JA, Nye PH, Smith KA (1990) Soil compaction and plant root growth. Phil Trans R Soc B 329:343–355CrossRefGoogle Scholar
  34. Kozlowski T (1999) Soil compaction and growth of woody plants. Scand J For Res 14:596–619CrossRefGoogle Scholar
  35. Misra RK, Dexter AR, Alston AM (1986) Maximum axial and radial growth pressures of plant roots. Plant Soil 95:315–326CrossRefGoogle Scholar
  36. Or D, Ghezzehei TA (2002) Modeling post-tillage soil structural dynamics: a review. Soil Tillage Res 64:41–59. doi: 10.1016/S0167-1987(01)00256-2 CrossRefGoogle Scholar
  37. Perzyna P (1966) Fundamental problems in viscoplasticity. In: Kuerti G (ed) Advances in applied mechanics. Academic, New York, pp 243–377Google Scholar
  38. Peth S, Nellesen J, Fischer G, Horn R (2010) Non-invasive 3D analysis of local soil deformation under mechanical and hydraulic stresses by μCT and digital image correlation. Soil Tillage Res 111:3–18. doi: 10.1016/j.still.2010.02.007 CrossRefGoogle Scholar
  39. Pfeffer W (1893) Druck und Arbeitsleistung durch Wachsende Pflanzen. Abhandlungen der mathematisch-physischen Classe de Königlich Sächsischen Gesellschaft der Wissenschaften, Leipzig, 33, 235–474Google Scholar
  40. Pierret A, Doussan C, Capowiez Y, Bastardie F, Pages L (2007) Root functional architecture: a framework for modeling the interplay between roots and soil. Vadose Zone J 6:269–281. doi: 10.2136/vzj2006.0067 CrossRefGoogle Scholar
  41. Romaneckas K, Piipavicius V, Sarauskis E (2010) Impact of seedbed density on sugar beet seed germination, yield and quality of roots. J Food Agric Environ 8(2):599–601Google Scholar
  42. Schmidt S, Bengough AG, Gregory PJ, Grinev DV, Otten W (2012) Estimating root–soil contact from 3D X-ray microtomographs. Eur J Soil Sci 63:776–786. doi: 10.1111/j.1365-2389.2012.01487.x CrossRefGoogle Scholar
  43. Schöder T, Javaux M, Vanderborght J, Körfgen B, Vereecken H (2009) Implementation of a microscopic soil-root hydraulic conductivity drop function in a three-dimensional soil-root architecture water transfer model. Vadose Zone J 8:783–792. doi: 10.2136/vzj2008.0116 CrossRefGoogle Scholar
  44. Segal E, Kushnir T, Mualem Y, Shani U (2008) Microsensing of water dynamics and root distributions in sandy soils. Vadose Zone J 7:1018–1026. doi: 10.2136/vzj2007.0121 CrossRefGoogle Scholar
  45. Shames IH, Cozzarellli FA (1997) Elastic and inelastic stress analysis. Taylor and Francis, WashingtonGoogle Scholar
  46. Steudle E (2000) Water uptake by plant roots: an integration of views. Plant Soil 226:45–56CrossRefGoogle Scholar
  47. Taylor HM (1974) Root behavior as affected by soil structure and strength. In: Carson EW (ed) The plant root and its environment. University Press of Virginia, Charlottesville, pp 271–291Google Scholar
  48. Tracy SR, Black CR, Roberts JA, Mooney SJ (2013) Exploring the interacting effect of soil texture and bulk density on root system development in tomato (Solanum lycopersicum L.). Environ Exp Bot 91:38–47. doi: 10.1093/jxb/erp386 CrossRefGoogle Scholar
  49. van Genuchten MT (1980) A closed-form equation for predicting the hydraulic conductivity of unsaturated soils. Soil Sci Soc Am J 44:892–898CrossRefGoogle Scholar
  50. Vollsnes AV, Futsaether CM, Bengough AG (2010) Quantifying rhizosphere particle movement around mutant maize roots using time-lapse imaging and particle image velocimetry. Eur J Soil Sci 61:926–939. doi: 10.1111/j.1365-2389.2010.01297.x CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Jazmín E. Aravena
    • 1
  • Markus Berli
    • 2
  • Siul Ruiz
    • 2
  • Francisco Suárez
    • 3
  • Teamrat A. Ghezzehei
    • 4
  • Scott W. Tyler
    • 1
  1. 1.Department of Geological Sciences and EngineeringUniversity of Nevada, RenoRenoUSA
  2. 2.Division of Hydrologic SciencesDesert Research InstituteLas VegasUSA
  3. 3.Department of Hydraulic and Environmental EngineeringPontificia Universidad Católica de ChileSantiagoChile
  4. 4.School of Natural SciencesUniversity of California, MercedMercedUSA

Personalised recommendations