Test Allelopathy Model

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WHAT IS IT?

This model allows users to design experiments to explore the phenomenon of allelopathy, in which chemicals secreted by certain plants impede the germination of seeds or growth of other plants.

BACKGROUND

Allelopathy is a mechanism by which plants, which generally can't move from where they germinate, compete with other plants using chemicals. An alleopathic chemical is usually defined by these characteristics:

1) the chemical mediates competition with other plants by providing an advantage to the plant secreting it and a disadvantage to the competitor, and

2) it is not necessary for the growth or reproduction of the plant producing it. These are called secondary metabolites.

Allelopathic chemicals are typically released into the soil and impede the germination of competing seeds or slows the growth of seedlings. Garlic Mustard, Alliaria petiolata, an herbaceous forest plant, for example releases one or more chemicals from its roots that inhibits the germination of seeds of potential competitors (1.) The same or other chemicals released into the soil disrupts the relationship between mycorrhizal fungi and canopy tree seedlings which may reduce forest regeneration 2.) Some allelopathic chemicals are contained in the leaves of the plant and enter the soil as the leaves fall and decay. One of the most widely known allelopathic chemicals is juglone which is found in the leaves, fruit husks, shell, and bark of Black Walnut and related trees (3.) While many plants are tolerant of juglone, many of the ones people grow for food are very sensitive to it and will die if planted in soil contaminated with juglone. In other words, don't plant your tomatoes under a Black Walnut tree or use any compost made with Black Walnut trees on garden plants.

Testing water-soluble extracts from plants for allelopathic properties is a relatively easy lab experiment for students in K-12 and undergraduate college biology courses. Seeds of plants to be tested may be placed in pots with seed-starting mix or simply on paper towels in a petri dish. Water is usually used as a control and failed germination of the seeds is a primary indicator of allelopathic properties of the plant extracts. Secondary indicators include stunted growth and/or discoloration of seedlings.

HOW IT WORKS

"Place Pots" is the setup button and sets up the world.

The choosers are used to provide the true/false input for multiple nested ifelse statements.

The "Add to Pot#" and "Treat Pot#" buttons implement multiple ifelse statements with inputs from the choosers.

The "Go" button performs a single run. Additional runs require the user repeat the process from the beginning.

HOW TO USE IT

Users must first set up 4 pots by pressing the "Place Pots" button. Before continuing, the user should develop a hypothesis and the predictions they want to test with their experiment based on background research and observations.
The users then place seeds in the pots according to their experimental desig, selecting specific seeds using the chooser and then clicking on the appropriate "Add to Pot# button. Different pots can have different seeds or they can all have the same type of seed, but only one type of seed per pot.
The users then choose the chemical(s) for treating the seeds using the "Choose-Chemical" chooser, and treat the seeds in each pot by clicking the "Treat Pot" buttons. The pots may all be treated with the same chemical or with different chemicals in any combination, but only one chemical per pot.
Once the pots are loaded with seeds and treated with the chemical(s), the user presses "Go" and records the results: A. Germination of healthy seedlings (tall and green) B. Germination of stunted but otherwise healthy seedlines (short and green) C. Germination, but stunted and discolored plants (brown and/or small plants) B. No germination (shriveled black dots)

THINGS TO NOTICE

Germination is all-or-none but post germination effects do occur. That is to say, either all the seeds germinate or none of them do, but the size and colo of the seedlings, both indicators of plant health may vary.

If you don't treat a pot at all, the seeds die. This simulates what happens when the seeds aren't watered.

THINGS TO TRY

Initially test only one type of seed with the different chemicals or test different seeds with only one chemical.

One of the chemicals is known to be allelopathic to many plants and one of the seeds is known to be sensitive to allelopathic chemicals. These are good starting points for making comparisons

EXTENDING THE MODEL

It would be fun to add code using random numbers to simulate variability in germination rates and plant health making the model more natural. Were this combined with a way to repeat the same run, automatically resetting the pots and reloading them with the user's initial selections and then reporting the output to monitors would make the simulation work more like real lab expriments.

CREDITS AND REFERENCES

Created by: Chris Caprette

(1) Patri, D.P. and O. Bossdorf. 2004. Allelopathic inhibition of germination by Alliaria petiolata (Brassicaceae.) Am. J. Bot., 91(2): 285-288. DOI: 10.3732/ajb.91.2.285

(2) Stinson, K.A., et al. 2006. Invasive plant suppresses the growth of native tree seedlings by disrupting belowground mutualisms. PLOS Biology, 12(2) DOI: 10.1371/journal.pbio.0040140

(3) Soderquist, C.J. 1973. Juglone and allelopathy. J. Chem. Educ. 50(11) 782. DOI: 10.1021/ed050p782

Comments and Questions

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Click to Run Model

breed [ Pot1seeds Pot1seed ]
breed [ Pot2seeds Pot2seed ]
breed [ Pot3seeds Pot3seed ]
breed [ Pot4seeds Pot4seed ]
breed [ seedlings seedling ]

patches-own
[ pot-id  chemical-type ]

turtles-own
[
  growth-rate
  A_tol ;; seed tolerant of soln-A
  B_tol ;; seed tolerant of soln-B
  C_tol ;; seed tolerant of soln-C
  D_tol ;; seed tolerant of soln-D
  P_tol ;; seed tolerant of allelopath
]

globals
[ selected-pot-id selected-seeds selected-soln ]

;; soln-A color 137 (light pink)
;; soln-B color 47 (light yellow)
;; soln-C color 118 (light violet)
;; soln-D color 58 (light green)
;; allelopath color 15 (red)
;; water color 98 (light blue)

;********* PRESSING THE PLACE POTS BUTTON INITIATES SETUP *********

to setup
  clear-all
  setup-pots ; calls the setup-pots procedure
;  setup-seeds
;  load-pots
  reset-ticks
end 

;*************** SETS THE POT POSITION AND COLOR ******************

to setup-pots
  ask patches
  [
    set pcolor 0 ; background is black
  ]

  ;; pot 1 is in the upper left corner and colored white
  ask patches with [ pxcor >= -12 and pxcor < -2 and pycor >= 2 and pycor < 12 ]
  [
    set pcolor white
    set pot-id "pot1"

  ]

  ;; pot 2 is in the upper right corner and colored white
  ask patches with [ pxcor >= 2 and pxcor < 12 and pycor >= 2 and pycor < 12 ]
  [
    set pcolor white
    set pot-id "pot2"
  ]

  ;; pot 3 is in the lower left corner and colored white
  ask patches with [ pxcor >= -12 and pxcor < -2 and pycor >= -12 and pycor < -2 ]
  [
    set pcolor white
    set pot-id "pot3"
  ]

  ;; pot 4 is in the lower right corner and colored white
  ask patches with [ pxcor >= 2 and pxcor < 12 and pycor >= -12 and pycor < -2 ]
  [
    set pcolor white
    set pot-id "pot4"
  ]
end 

;*********** ADD SEEDS TO POTS USING THE SEED CHOOSER AND POT BUTTONS ************

to add-to-pot1
  create-Pot1seeds 10
  ask Pot1seeds
      [
        ifelse Choose-Seeds = "spiny" ; spiny seeds selected
          [
            set xcor (-10 + random-float 6)  ; x-axis scatter from the center of pot
            set ycor (4 + random-float 6) ; y-axis scatter from the center of pot
            set shape "spiny_seed" ; use the spiny seed shape
            set color 55 ; dark green
            set size 2 ; base shape is small so make it bigger
          ]
          [
            ifelse Choose-Seeds = "egg" ; egg-shaped seeds selected
              [
                set xcor (-10 + random-float 6)
                set ycor (4 + random-float 6)
                set shape "egg_seed"
                set color 38 ; pale brown
                set size 1.5
                  ]
                  [
                    ifelse Choose-Seeds = "spindle" ; spindle-shaped seeds selected
                      [
                        set xcor (-10 + random-float 6)
                        set ycor (4 + random-float 6)
                        set shape "spindle_seed"
                        set color 43 ; olive
                        set size 1.5
                      ]
                      [
                        ifelse Choose-Seeds = "wafer" ; flat heart-shaped seeds selected
                          [
                            set xcor (-10 + random-float 6)
                            set ycor (4 + random-float 6)
                            set shape "wafer_seed"
                            set color 6 ; medium grey
                            set size 1.5
                          ]
          ; ***** LAST SEED SHAPE IS LONG SAMARA *****
          [
            set xcor (-10 + random-float 6)
            set ycor (4 + random-float 6)
            set shape "long_samara"
            set color 24 ; dark orange
            set size 1.5
         ]
    ]   ]   ]   ]
end 

to add-to-pot2
  create-Pot2seeds 10
  ask Pot2seeds
      [
        ifelse Choose-Seeds = "spiny" ; SPINY SEEDS SELECTED
          [
            set xcor (4 + random-float 6)
            set ycor (4 + random-float 6)
            set shape "spiny_seed"
            set color 55 ; dark green
            set size 2
          ]
          [
            ifelse Choose-Seeds = "egg" ; EGG SEEDS SELECTED
              [
                set xcor (4 + random-float 6)
                set ycor (4 + random-float 6)
                set shape "egg_seed"
                set color 38 ; pale brown
                set size 1.5
                  ]
                  [
                    ifelse Choose-Seeds = "spindle" ; SPINDLE SEEDS SELECTED
                      [
                        set xcor (4 + random-float 6)
                        set ycor (4 + random-float 6)
                        set shape "spindle_seed"
                        set color 43 ; olive
                        set size 1.5
                      ]
                      [
                        ifelse Choose-Seeds = "wafer" ; WAFER SEEDS SELECTED
                          [
                            set xcor (4 + random-float 6)
                            set ycor (4 + random-float 6)
                            set shape "wafer_seed"
                            set color 6 ; medium grey
                            set size 1.5
                          ]
          ; ***** LAST SEED SHAPE IS LONG SAMARA *****
          [
            set xcor (4 + random-float 6)
            set ycor (4 + random-float 6)
            set shape "long_samara"
            set color 24 ; dark orange
            set size 1.5
         ]
    ]   ]   ]   ]
end 

to add-to-pot3
  create-Pot3seeds 10
  ask Pot3seeds
      [
        ifelse Choose-Seeds = "spiny" ; SPINY SEEDS SELECTED
          [
            set xcor (-10 + random-float 6)
            set ycor (-10 + random-float 6)
            set shape "spiny_seed"
            set color 55 ; dark green
            set size 2
          ]
          [
            ifelse Choose-Seeds = "egg" ; EGG SEEDS SELECTED
              [
                set xcor (-10 + random-float 6)
                set ycor (-10 + random-float 6)
                set shape "egg_seed"
                set color 38 ; pale brown
                set size 1.5
                  ]
                  [
                    ifelse Choose-Seeds = "spindle" ; SPINDLE SEEDS SELECTED
                      [
                        set xcor (-10 + random-float 6)
                        set ycor (-10 + random-float 6)
                        set shape "spindle_seed"
                        set color 43 ; olive
                        set size 1.5
                      ]
                      [
                        ifelse Choose-Seeds = "wafer" ; WAFER SEEDS SELECTED
                          [
                            set xcor (-10 + random-float 6)
                            set ycor (-10 + random-float 6)
                            set shape "wafer_seed"
                            set color 6 ; medium grey
                            set size 1.5
                          ]
          ; ***** LAST SEED SHAPE IS LONG SAMARA *****
          [
            set xcor (-10 + random-float 6)
            set ycor (-10 + random-float 6)
            set shape "long_samara"
            set color 24 ; medium-dark orange
            set size 1.5
         ]
    ]   ]   ]   ]
end 

to add-to-pot4
  create-Pot4seeds 10
  ask Pot4seeds
      [
        ifelse Choose-Seeds = "spiny" ; SPINY SEEDS SELECTED
          [
            set xcor (4 + random-float 6)
            set ycor (-10 + random-float 6)
            set shape "spiny_seed"
            set color 55 ; dark green
            set size 2
          ]
          [
            ifelse Choose-Seeds = "egg" ; EGG SEEDS SELECTED
              [
                set xcor (4 + random-float 6)
                set ycor (-10 + random-float 6)
                set shape "egg_seed"
                set color 38 ; pale brown
                set size 1.5
                  ]
                  [
                    ifelse Choose-Seeds = "spindle" ; SPINDLE SEEDS SELECTED
                      [
                        set xcor (4 + random-float 6)
                        set ycor (-10 + random-float 6)
                        set shape "spindle_seed"
                        set color 43 ; olive
                        set size 1.5
                      ]
                      [
                        ifelse Choose-Seeds = "wafer" ; WAFER SEEDS SELECTED
                          [
                            set xcor (4 + random-float 6)
                            set ycor (-10 + random-float 6)
                            set shape "wafer_seed"
                            set color 6 ; medium grey
                            set size 1.5
                          ]
          ; ***** LAST SEED SHAPE IS LONG SAMARA *****
          [
            set xcor (4 + random-float 6)
            set ycor (-10 + random-float 6)
            set shape "long_samara"
            set color 24 ; medium dark orange
            set size 1.5
         ]
    ]   ]   ]   ]
end 

to treat-pot1
  ask patches with [ pxcor >= -12 and pxcor < -2 and pycor >= 2 and pycor < 12 ]
    [ ifelse Choose-Chemical = "soln-A"
      [set pcolor 139]
       [ ifelse Choose-Chemical = "soln-B"
         [set pcolor 119]
           [ ifelse Choose-Chemical = "soln-C"
             [set pcolor 109]
               [ ifelse Choose-Chemical = "soln-D"
                 [set pcolor 89]
                   [ ifelse Choose-Chemical = "allelopath"
                     [set pcolor 29]
      [set pcolor 9]
  ]]]]]
end 

to treat-pot2
  ask patches with [ pxcor >= 2 and pxcor < 12 and pycor >= 2 and pycor < 12 ]
    [ ifelse Choose-Chemical = "soln-A"
      [set pcolor 139]
       [ ifelse Choose-Chemical = "soln-B"
         [set pcolor 119]
           [ ifelse Choose-Chemical = "soln-C"
             [set pcolor 109]
               [ ifelse Choose-Chemical = "soln-D"
                 [set pcolor 89]
                   [ ifelse Choose-Chemical = "allelopath"
                     [set pcolor 29]
      [set pcolor 9]
  ]]]]]
end 

to treat-pot3
  ask patches with [ pxcor >= -12 and pxcor < -2 and pycor >= -12 and pycor < -2 ]
    [ ifelse Choose-Chemical = "soln-A"
      [set pcolor 139]
       [ ifelse Choose-Chemical = "soln-B"
         [set pcolor 119]
           [ ifelse Choose-Chemical = "soln-C"
             [set pcolor 109]
               [ ifelse Choose-Chemical = "soln-D"
                 [set pcolor 89]
                   [ ifelse Choose-Chemical = "allelopath"
                     [set pcolor 29]
      [set pcolor 9]
  ]]]]]
end 

to treat-pot4
  ask patches with [ pxcor >= 2 and pxcor < 12 and pycor >= -12 and pycor < -2 ]
    [ ifelse Choose-Chemical = "soln-A"
      [set pcolor 139]
       [ ifelse Choose-Chemical = "soln-B"
         [set pcolor 119]
           [ ifelse Choose-Chemical = "soln-C"
             [set pcolor 109]
               [ ifelse Choose-Chemical = "soln-D"
                 [set pcolor 89]
                   [ ifelse Choose-Chemical = "allelopath"
                     [set pcolor 29]
      [set pcolor 9]
  ]]]]]
end 

;*************************** RUN PROCEDURE ******************************
; pots need to be set up with seeds and treatments first
; pressing go initiates germination of seeds based on their chemical sensitivity (_tol)
; solutions B 119 and C 109 are not allelopathic for any of the seeds
; spiny_seeds are tolerant of all solutions and the known allelopath
; spindle_seeds are sensitive to solution A 139 only and allelopath 29
; egg_seeds are sensitive to allelopath 29 only
; wafer_seeds are sensitive to solutions partly to A 139, partly to D 89, and fully to allelopath 29
; long_samara seeds also are sensitive to solutions A 139, D 89, and allelopath 29

to go
  ;***************** APPLIES TO SPINY SEEDS **********************
  ask turtles with [ color = 55 ] ; affects only spiny seeds
    [
      set shape "plant"
      set size 3
      set color 64
    ]

    ; ***************** APPLIES TO EGG SEEDS *********************
    ask turtles with [ color = 38 ] ; affects only egg seeds
    [ ifelse pcolor = 9 ; water
        [
          set shape "plant"
          set color 64
          set size 3
         ]
      [ ifelse pcolor = 119 ; soln_B
        [
          set shape "plant"
          set color 64
          set size 3
        ]
        [ ifelse pcolor = 109 ; soln_C
          [
            set shape "plant"
            set color 64
            set size 3
          ]
          [ ifelse pcolor = 139 ; soln_A
             [
               set shape "plant"
               set color 64
               set size 1.5
             ]
             [  ifelse pcolor = 89 ; soln_D
                [
                  set shape "plant"
                  set color 64
                  set size 3
                ]
    [
      set shape "dot"
      set size 1
      set color 0
  ]  ]  ]  ]  ] ]

   ;********************** APPLIES TO SPINDLE SEEDS ***********************
    ask turtles with [ color = 43 ] ; affects only spindle seeds
    [ ifelse pcolor = 9 ; water
        [
          set shape "plant"
          set color 64
          set size 3
         ]
      [ ifelse pcolor = 119 ; soln_B
        [
          set shape "plant"
          set color 64
          set size 3
        ]
        [ ifelse pcolor = 109 ; soln_C
          [
            set shape "plant"
            set color 64
            set size 3
          ]
          [  ifelse pcolor = 89 ; soln_D
             [
               set shape "plant"
               set color 64
               set size 3
          ]
    [
      set shape "dot"
      set size 1
      set color 0
  ]  ]  ]  ]  ]

   ;********************** APPLIES TO WAFER SEEDS ***********************
  ask turtles with [ color = 6 ] ; affects only wafer seeds
    [ ifelse pcolor = 9 ; water
        [
          set shape "plant"
          set color 64
          set size 3
         ]
      [ ifelse pcolor = 119 ; soln_B
        [
          set shape "plant"
          set color 64
          set size 3
        ]
        [ ifelse pcolor = 109 ; soln_C
          [
            set shape "plant"
            set color 64
            set size 3
          ]
          [ ifelse pcolor = 139 ; soln_A
          [
            set shape "plant"
            set color 35
            set size 1
          ]
          [ ifelse pcolor = 89 ; soln_D
            [
              set shape "plant"
              set color 64
              set size 0.75
            ]
       [
         set shape "plant"
         set size 1
         set color 35
  ]  ]  ]  ] ] ]

  ;********************** APPLIES TO LONG SAMARA SEEDS ***********************
  ask turtles with [ color = 24 ] ; affects only long samara seeds
    [ ifelse pcolor = 9 ; water
        [
          set shape "plant"
          set color 64
          set size 3
         ]
      [ ifelse pcolor = 119 ; soln_B
        [
          set shape "plant"
          set color 64
          set size 3
        ]
        [ ifelse pcolor = 109 ; soln_C
          [
            set shape "plant"
            set color 64
            set size 3
          ]
          [ ifelse pcolor = 89 ; soln_D
          [
            set shape "plant"
            set color 35
            set size 1
          ]
          [
             set shape "dot"
             set size 1
             set color 0
  ]  ]  ]  ] ]
end

There is only one version of this model, created 6 days ago by Chris Caprette.

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