Multidimensional mapping of root responses to soil environmental cues using a luminescence-based imaging system

Multidimensional mapping of root responses to soil environmental cues using a luminescence-based imaging system

Root systems develop different root types that individually sense cues from their local environment and integrate them with systemic signals. This complex multi-dimensional amalgam of inputs leads to continuous adjustment of root growth rates, direction and metabolic activity to define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties such as soil moisture with root traits. We propose GLO-Roots as a system that has great utility in both presenting environmental stimuli to roots in ways that evoke natural adaptive responses, and in providing tools for developing a multi-dimensional understanding of such processes.

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Rubén Rellán Álvarez

April 05, 2015
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  1. Multidimensional mapping of root responses to soil environmental cues ubén

    Rellán Álvarez bit.ly/glo-roots-preprint bit.ly/glo-roots-slides www.rrlab.org/glo_roots @rubenrellan rrellan@langebio.cinvestav.mx www.rrlab.org
  2. Aaron Escobar: http://www.flickr.com/photos/aaronescobar/2569091622/

  3. Aaron Escobar: http://www.flickr.com/photos/aaronescobar/2569091622/ water

  4. Aaron Escobar: http://www.flickr.com/photos/aaronescobar/2569091622/ water Phosphate

  5. Roots integrate a variety of signals and adjust function and

    shape accordingly Drew et al. 1978 JXB 109:435 Lima et al. 2011 PMID: 21119058 Tabata et al. 2014PMID: 25324386 AMT1:GFP
  6. None
  7. Yun et al. 2014 PMID: 24927545 From metabolite in vivo

    imaging to 3D in soil root architecture Grossman et al. 2011 PMID: 22186371 Soil Artificial Substrate
  8. Yun et al. 2014 PMID: 24927545 From metabolite in vivo

    imaging to 3D in soil root architecture Grossman et al. 2011 PMID: 22186371 Soil Artificial Substrate
  9. Soil A multidimensional map of root responses to soil environmental

    cues
  10. Soil Time A multidimensional map of root responses to soil

    environmental cues
  11. Soil Soil Properties Time A multidimensional map of root responses

    to soil environmental cues
  12. Soil Soil Properties Time Gene Expression A multidimensional map of

    root responses to soil environmental cues
  13. Soil Soil Properties Time Root Structure Gene Expression A multidimensional

    map of root responses to soil environmental cues
  14. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression

    A multidimensional map of root responses to soil environmental cues
  15. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression

    A multidimensional map of root responses to soil environmental cues
  16. Transpiring environment Roots protected from light

  17. 30 cm 15 cm 2 mm 100 cm3 of soil

    Rhizotrons: a 2D sample of soil
  18. 30 cm 15 cm 2 mm 100 cm3 of soil

    Rhizotrons: a 2D sample of soil
  19. The expression profile of roots grown in pots and rhizotrons

    is very similar Fresh Weight FW (mg) 0 60 120 180 240 MS Pot Rhizotron
  20. Aaron Escobar: http://www.flickr.com/photos/aaronescobar/2569091622/ water Phosphate

  21. Different environmental cues can be recreated and quantified in rhizotrons

    water
  22. Different environmental cues can be recreated and quantified in rhizotrons

    water
  23. Different environmental cues can be recreated and quantified in rhizotrons

    water
  24. Different environmental cues can be recreated and quantified in rhizotrons

    water 80 60 40 20 0 moisture content (%)
  25. Different environmental cues can be recreated and quantified in rhizotrons

    water 80 60 40 20 0 moisture content (%)
  26. Different environmental cues can be recreated and quantified in rhizotrons

    water Phosphate 80 60 40 20 0 moisture content (%)
  27. Different environmental cues can be recreated and quantified in rhizotrons

    water Phosphate 80 60 40 20 0 moisture content (%)
  28. Different environmental cues can be recreated and quantified in rhizotrons

    water Phosphate 80 60 40 20 0 moisture content (%)
  29. None
  30. None
  31. We use luciferase to visualize roots in soil www.firefly.org/firefly-pictures.html Luciferase

    is great! • Does not require any light excitation • No background luminescence • LUC can be used in temporal studies • Dynamic response to gene expression • Multiple color reporters are possible luciferin + ATP + O2 → oxyluciferin +
  32. Roots are visualized with the GLO1 imaging system

  33. Roots are visualized with the GLO1 imaging system

  34. Both sides of the rhizotron are combined visualize the full

    root system
  35. Both sides of the rhizotron are combined visualize the full

    root system
  36. Root system architecture can be studied until late stages of

    development
  37. Root system architecture can be studied until late stages of

    development
  38. Images are data

  39. Images are data

  40. GLO-RIA is an ImageJ plugin developed to analyze root traits

    www.guillaumelobet.be
  41. GLO-RIA is an ImageJ plugin developed to analyze root traits

    GLO-RIA Demo www.guillaumelobet.be
  42. GLO-RIA enables semi-automatic quantification of RSA traits 11 12 13

    14 15 16 17 18 19 20 21 Angle Count 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 0 45 90 Root system area
  43. Different accessions show distinct root traits including lateral root angle

  44. Different accessions show distinct root traits including lateral root angle

  45. X Y DAS 0 21 Soil Soil Properties Time Root

    Structure water Phosphate
  46. Root system architecture is light regulated

  47. Root system architecture is light regulated

  48. Root system architecture is light regulated

  49. Root system architecture is light regulated

  50. P-deficient plants have wider RSA and invest more resources in

    root growth 22 DAS 27 P P
  51. Several degrees of water deficit can be induced

  52. Several degrees of water deficit can be induced

  53. Several degrees of water deficit can be induced

  54. Early withdrawal of water may affect lateral root emergence

  55. Early withdrawal of water may affect lateral root emergence

  56. Early withdrawal of water may affect lateral root emergence

  57. Early withdrawal of water may affect lateral root emergence

  58. Early withdrawal of water may affect lateral root emergence

  59. + 24 h Early withdrawal of water may affect lateral

    root emergence
  60. If water deprivation starts later there is an induction of

    lateral root growth and a higher proliferation of tertiary roots
  61. Lateral root angle is affected differently in different ecotypes in

    response to water deprivation
  62. This response is different from hydrotropism and auxin dependent

  63. Root system architecture can be revealed days after luciferin addition

    16 17 18 19 20 21 22 23 24
  64. Root system architecture can be revealed days after luciferin addition

    16 17 18 19 20 21 22 23 24
  65. Root system architecture can be revealed days after luciferin addition

    16 17 18 19 20 21 22 23 24
  66. Root direction can be locally correlated with soil moisture content

    WW WD
  67. 500 540 580 620 660 700 UBQ10:vLUC2 ACT2:PpyREo We have

    generated a golden gate ready collection of different luciferases Intensity 1005 1064 1123 1182 1241 1300 UBQ10:CBRo Intensity 1005 1064 1123 1182 1241 1300 500 540 580 620 660 700 UBQ10:LUC2o 500 540 580 620 660 700 UBQ10:CBGo LUC2o Maximum Intensity vLUC CBG99o PpyRE8o CBRo λ (nm)
  68. Microbe interactions imaged using luminescence emitting bacteria

  69. Simultaneous imaging of root structure and gene is expression is

    possible ProACT2:PPyRE8o ProDR5rev:LUC+
  70. Rapid changes in gene expression can be imaged ProACT2:PPyRE8o x

    ProZAT12:LUC ProZAT12:LUC
  71. Rapid changes in gene expression can be imaged ProACT2:PPyRE8o x

    ProZAT12:LUC ProZAT12:LUC
  72. Rapid changes in gene expression can be imaged ProACT2:PPyRE8o x

    ProZAT12:LUC ProZAT12:LUC GLO-RIA Demo
  73. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression

    A multidimensional map of root responses to soil environmental cues
  74. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression

    A multidimensional map of root responses to soil environmental cues
  75. Soil Microbe Colonization Soil Properties Time Root Structure Gene Expression

    A multidimensional map of root responses to soil environmental cues
  76. Dinneny Lab Muh-Ching Yee Geng Yu Emilie Winfield Pierre-Luc Pradier

    Charlotte Trontin Thérèse LaRue Heike Lindner Guillaume Lobet Image Analysis Jose Sebastian John Vogel Julin Maloof Other Species Cara Haney
  77. None
  78. None
  79. Other species can also be imaged : Dual Color Tomato

  80. Other species can also be imaged: Brachypodium dystachion