How Complexity Affects

Structural Stability: Using

Protist Microcosms and
Mathematical Modeling to
Navigate Realism in
Theoretical Ecology

Sylvia Gimbel
Oak Park and River Forest High School
Junior Science and Humanities Symposium
2022
Inspiration
Inspiration
 The Question

How does ecosystem

complexity
complexity affect its
stability?
https://en.wikipedia.org/wiki/Brown_marmorated_stink_bug
https://en.wikipedia.org/wiki/Taraxacum
https://www.insider.com/squirrel-went-on-vicious-christmas-rampage-in-wales-attacking-18-2021-12
https://www.gardeningknowhow.com/plant-problems/pests/insects/beneficial-insects.htm
https://home.howstuffworks.com/grass.htm
https://pixabay.com/photos/field-mouse-mouse-nature-animal-3311668/
 The Question

complexity

https://en.wikipedia.org/wiki/Brown_marmorated_stink_bug
https://en.wikipedia.org/wiki/Taraxacum
https://www.insider.com/squirrel-went-on-vicious-christmas-rampage-in-wales-attacking-18-2021-12
https://www.gardeningknowhow.com/plant-problems/pests/insects/beneficial-insects.htm
https://home.howstuffworks.com/grass.htm
https://pixabay.com/photos/field-mouse-mouse-nature-animal-3311668/
 The Question

complexity

https://en.wikipedia.org/wiki/Brown_marmorated_stink_bug
https://en.wikipedia.org/wiki/Taraxacum
https://www.insider.com/squirrel-went-on-vicious-christmas-rampage-in-wales-attacking-18-2021-12
https://www.gardeningknowhow.com/plant-problems/pests/insects/beneficial-insects.htm
https://home.howstuffworks.com/grass.htm
https://pixabay.com/photos/field-mouse-mouse-nature-animal-3311668/
The Question

Structural
Stability

https://commons.wikimedia.org/wiki/File:Skull_%26_Crossbones_BW.png
http://www.fao.org/fileadmin/templates/SOFO/2020/src/images/share.jpg
https://learnenglishteens.britishcouncil.org/sites/teens/files/styles/article/public/field/image/rs930_135120665-low.jpg?itok=g5LI5W4C
 Gap in Research
Mathematical Model

https://matlabgeeks.com/wp-content/uploads/2011/08/lv-plot.png
https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcT_OlrCFUekMKBLAwK1L6VqP-3FP80wqBMtGA&usqp=CAU
https://vivadifferences.com/wet-lab-vs-dry/
https://americangardener.net/wp-content/uploads/2020/11/IMG_20201101_202019.jpg
https://learnenglishteens.britishcouncil.org/sites/teens/files/styles/article/public/field/image/rs930_135120665-low.jpg?itok=g5LI5W4C
 OBJECTIVE

Add to research on the relationship

between complexity and structural stability
using an experimentally informed model
Experimental Workflow

1 Chose a 2 Collected 3 Quantified

Mathematical Data to Fit Structural
Model the Model Stability
The Model

zi = 𝛾i + ⅀𝜏 z (k)
ij j
(k
i≠j

http://gppreview.com/wp-content/uploads/2018/07/data-1.jpg
The Model
The Model
Parameters

&
Interaction
Populations Growth Rates
Strengths
https://miro.medium.com/max/692/1*SfZpl4HO9BVcze999KVIYA.png
 Collecting Data

Protist Microcosms

https://microscopeclarity.com/protozoa-explained/
 Collecting Data

2
1 3
x3
Cosmarium sp. Paramecium
caudatum
Chilomonas sp. Blepharisma sp.

9 days
5 7
6
https://www.wetroyes.com/uploads/wetroyes-4oz-crystal-mason-jar53.jpg
Model Fit

R2 = 0.70
Species
Predicted

Observed
Calculating Structural Stability
Novel Method of Calculating Structural Stability

Does not Coexist

Coexists (Feasibility Domain)

(Blepharisma)
Growth Rate

(28.82, -1.32)

Growth Rate (Cosmarium)

Novel Method of Calculating Structural Stability
Interaction Strength (Cosmarium  Blepharisma)

Interaction Strength (Blepharisma  Cosmarium)

 Novel Method of Calculating Structural Stability

Note. Not an Accurate Representation of a Feasibility Domain

https://sketchfab.com/3d-models/stellated-icosahedron-62c3e249ddf64972a8034ed90f2943a1
Results

r = -0.65 r = -0.60 r = -0.53

Growth Rates
Structural Stability

Interaction Strengths
r = -0.94 r = -0.92 r = -0.75

Species Richness (Complexity)

 Positive Impact

More Less
Vulnerable VS Vulnerable

https://images.squarespace-cdn.com/content/v1/53308523e4b0bce3b676cb5d/1562166784798-J3O8AW7KCUX80B2ROV2O/hand-3035665_1920.jpg?format=1000w
https://www.greenqueen.com.hk/wp-content/uploads/2020/12/Veganic-Farming.png
 Positive Impact

https://image.shutterstock.com/image-photo/-260nw-1574578603.jpg
https://www.mentalfloss.com/article/88720/10-freezing-facts-about-arctics-ecosystem
https://www.macmillandictionary.com/external/slideshow/thumb/134503_thumb.jpg
https://www.azocleantech.com/news.aspx?newsID=26805
https://greatplainstravel.com/wp-content/uploads/2021/01/Great-Plains-General-5-Cropped-1024x623.jpg
https://media.istockphoto.com/vectors/search-magnifying-glass-icon-symbol-vector-id1221635138?k=20&m=1221635138&s=170667a&w=0&h=d2MqIxeYYJC5D_Bo-YB_LIYUwHCNyyo-r0iVI8ya7ak=
 Positive Impact

https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcQrl393OBxiaW6aDDSCgFYklbaPJ94lin4uiw&usqp=CAU
https://media.istockphoto.com/photos/seven-pebbles-pyramid-picture-id98730752?k=20&m=98730752&s=612x612&w=0&h=M2M_UeM2Z-iKgIR5GuOHvB-lA1pO3vp0hKCPPri73ms=
 Acknowledgements
Mentors:
- Paula Lemos-Costa, Ph.D., Allesina Lab, University of Chicago
- Canan Karakoç, Ph.D., Lennon Lab, Indiana University
Supervisor: Allison Hennings, R.N., B.S.N., M.A.T., OPRFHS
Amber Hooper, MLIS, OPRFHS
Mr. Cain & Mr. Bernthal, OPRFHS
Gimbel Family
Friends & Peers
 References
References
1. Altermatt, F., Fronhofer, E., Garnier, A., Giometto, A., Hammes, F., Klecka, J., Legrand, D., Mächler, E., Massie, T., Pennekamp, F., Plebani, M., Pontarp, M.,
Schtickzelle, M., Thullier, V., & Petchey, O. (2015). Big answers from small worlds: A user's guide for protist microcosms as a model system in ecology and
evolution. Methods in Ecology and Evolution, 6(1), 218–231. https://doi.org/10.1111/2041-210X.12312
2. Bartomeus, I., Saavedra, S., Rohr, R., & Godoy, O. (2021). Experimental evidence of the importance of multitrophic structure for species persistence.
Proceedings of the National Academy of Sciences, 118(12), 1–7. https://doi.org/10.1073/pnas.2023872118
3. Center for Sustainable Systems, University of Michigan. (2021). Biodiversity factsheet. https://css.umich.edu/factsheets/biodiversity-factsheet
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ecological systems in a changing world. Ecosphere, 4(2), 1–12. https://doi.org/10.1890/ES12-00178.1
5. Fox, J. & McGrady-Steed, J. (2002). Stability and complexity in microcosm communities. Journal of Animal Ecology, 71(5), 749–756.
https://doi.org/10.1046/J.1365-2656.2002.00640.X
6. Geary, W. L., Bode, M., Doherty, T. S., Fulton, E. A., Nimmo, D. G., Tulloch, A. I. T., Tulloch, V. J. D., & Ritchie, E. G. (2020). A guide to ecosystem models and
their environmental applications. Nature Ecology & Evolution, 4(11), 1459–1471. https://doi.org/10.1038/s41559-020-01298-8
7. Grilli, J., Adorisio, M., Suweis, S., Barabás, G., Banavar, J., Allesina, S., & Maritan, A. (2017). Feasibility and coexistence of large ecological communities.
Nature Communications, 8, 1–9. https://doi.org/10.1038/ncomms14389 
8. Gross, T., Rudolf, L., Levin, S. A., & Dieckmann, U. (2009). Generalized models reveal stabilizing factors in food webs. Science, 325(5941), 747–750.
https://doi.org/10.1126/science.1173536
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Population Ecology, 60(4), 319–345. https://doi.org/10.1007/s10144-018-0628-3
10. Maynard, D., Miller, Z., & Allesina, S. (2020). Predicting coexistence in experimental ecological communities. Nature Ecology & Evolution, 4, 91–100.
https://doi.org/10.1038/s41559-019-1059-z
 References
References
11. Pennekamp, F., Pontarp, M., Tabi, A., Altermatt, F., Alther, R., Choffat, Y., Fronhofer, E., Ganesanandamoorthy, P., Garnier, A., Griffiths, J., Greene, S.,
Horgan, K., Massie, T., Mächler, E., Palamara, G.-M., Saymour, M., & Petchey, O. (2018). Biodiversity increases and decreases ecosystem stability. Nature,
563(7729), 109–112. https://doi.org/10.1038/s41586-018-0627-8
12. Plitzko, S., Drossel, B., & Guill, C. (2012). Complexity-stability relations in generalized food-web models with realistic parameters. Journal of Theoretical
Biology, 306, 7–14. https://doi.org/10.1016/j.jtbi.2012.04.008
13. Rohr, R., Saavedra, S., & Bascompte, J. (2014). On the structural stability of mutualistic systems. Science, 345(6195), 1–9.
https://doi.org/10.1126/science.1253497
14. Shade, A., Peter, H., Allison, S. D., Baho, D. L., Berga, M., Bürgmann, H., Huber, D. H., Langenheder, S., Lennon, J. T., Martiny, J. B. H., Matulich, K. L.,
Schmidt, T. M., & Handelsman, J. (2012). Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology, 3, 1–19.
https://doi.org/10.3389/fmicb.2012.00417
15. Song, C. (2020). Structural stability: Concepts, methods, and applications. Biodiversity Science, 28(11), 1345–1361.
https://doi.org/10.17520/biods.2020110
16. Voit, E. O., Davis, J. D., & Olivença, D. V. (2021). Inference and validation of the structure of lotka-volterra models. BioRxiv.
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17. Wieczynski, D. J., Singla, P., Doan, A., Singleton, A., Han, Z.-Y., Votzke, S., Yammine, A., & Gibert, J. P. (2021). Linking species traits and demography to
explain complex temperature responses across levels of organization. Proceedings of the National Academy of Sciences, 118(42), 1–10.
https://doi.org/10.1073/pnas.2104863118
18. Yang, X., Tan, J., Sun, K. H., & Jiang, L. (2020). Experimental demonstration of the importance of keystone communities for maintaining metacommunity
biodiversity and ecosystem functioning. Oecologia, 193(2), 437–447. https://doi.org/10.1007/s00442-020-04693-x
19. Yonatan, Y., Amit, G., Friedman, J., & Bashan, A. (2021). Complexity-stability relationship in empirical microbial ecosystems. BioRxiv.
https://doi.org/10.1101/2021.07.29.454345
 Thank
You!
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The Model

zi = 𝛾i +
(k)
i≠j

⅀𝜏ijzj (k)

= + ×
Grass  Mouse
The Model

zi = 𝛾i +
(k)
i≠j

⅀𝜏ijzj (k)

= + ×
Mouse  Grass
The Model

-1 = B z (k) (k)

-1 -1/𝛾1 𝜏12/𝛾1 𝜏13/𝛾1 . . . 𝜏ij/𝛾i z1(k)

-1 𝜏21/ z2(k)

=
-1/𝛾2 𝜏23/𝛾2 . . . 𝜏ij/𝛾i
-1 𝛾2
z3(k)
. 𝜏31/𝛾i 𝜏32/𝛾3 -1/𝛾3 . . . 𝜏ij/𝛾i
.
. . .
. . . .
. . .
. . . .
. . . . .
-1 zn(k)
𝜏ij/𝛾i 𝜏ij/𝛾i 𝜏ij/𝛾i . . . -1/𝛾i
The Model

-1 = B z (k) (k)
-1 -1 z1(k)
-1/𝛾1 𝜏12/𝛾1 𝜏13/𝛾1 . . . 𝜏ij/𝛾i
𝜏21/ -1 z2(k)
-1/𝛾2 𝜏23/𝛾2 . . . 𝜏ij/𝛾i

=
𝛾2
-1 z3(k)
𝜏31/𝛾i 𝜏32/𝛾3 -1/𝛾3 . . . 𝜏ij/𝛾i
. .
. . . . . . .
. . . . . . .
. . . . .
-1 zn(k)
𝜏ij/𝛾i 𝜏ij/𝛾i 𝜏ij/𝛾i . . . -1/𝛾i
Using R

x1000
Maintenance
Maintenance
Maintenance
Maintenance
Pre-Experiment: Observing Species

01 Easily Countable

02 Easily Differentiable

03 Clean Culture
Pre-Experiment: Testing Coexistence

Cosmarium sp. Euglena sp. Paramecium Chilomonas sp. Blepharisma sp.

caudatum
Experimental Design

Cosmarium Paramecium & Chilomonas Blepharisma & Chilomonas

Experimental Design
Community Paramecium & Blepharisma &
Cosmarium
Composition Chilomonas Chilomonas
1
2
3
4
5
6
7
 Collecting Data

https://cdn-tp2.mozu.com/27776-44382/cms/44382/files/5d953ff6-e60e-4a5a-ad5a-acd7910f4121?maxWidth=350&_mzcb=
Collecting Data
Collecting Data
Mean Species Abundance
32.07 ± 11.48
Cosmarium sp.
35

20.47 ± 9.11
Number per 20ul

30

25
8.47 ± 15.24 13.00 ± 11.68
20

15

10

0
co-bl-pc-ch co-pc-ch co-bl-ch co

Community Composition
Mean Species Abundance
6.27 ± 2.74
Paramecium caudatum
7

6
2.87 ± 3.38 3.93 ± 1.74
Number per 20ul

5
3.13 ± 1.60
4

0
co-bl-pc-ch bl-pc-ch co-pc-ch pc-ch

Community Composition
Mean Species Abundance
22.10 ± 23.05

Blepharisma sp.
25
14.73 ± 16.05
17.80 ± 5.96
Number per 20ul

20

13.47 ± 5.22
15

10

0
co-bl-pc-ch bl-pc-ch co-bl-ch bl-ch

Community Composition
Mean Species Abundance
247.33 ± 359.4

Chilomonas sp.
300
137.50 ± 310.36
250
Number per 20ul

200

150
85.17 ± 82.78 85.17 ± 66.01
93.50 ± 23.66
100 76.83 ± 31.03

50

0
co-bl-pc-ch bl-pc-ch co-bl-ch co-pc-ch pc-ch bl-ch

Community Composition
Fitted Model Parameters
Growth Rates Interaction Strengths

Cosmarium 28.82 Cosmarium Blepharisma Paramecium Chilomonas

Blepharisma -1.32 Cosmarium -1.70 -5.65 0.16

Paramecium 3.31 Blepharisma 0.69 0.95 0.098

Chilomonas 690.13 Paramecium -0.098 -0.22 0.030

Chilomonas -13.17 -22.21 -97.94

Calculated Structural Stabilities
3.5

3
Structural Stability

2.5

1.5

0.5

0
co-bl-pc-ch bl-pc-ch co-pc-ch co-bl-ch co-bl-pc pc-ch co-ch co-bl bl-pc co-pc bl-ch

6 5 4 3 2 1

Interaction Strengths
Calculated Structural Stabilities
70

60
Structural Stability

50

40

30

20

10

0
co-bl-pc- bl-pc-ch co-pc-ch co-bl-ch co-bl-pc pc-ch co-ch co-bl bl-pc co-pc bl-ch co pc ch
ch

60 50 40 30 20 10

Growth Rates
Minimum Lengths
0.7

0.6
Minimum Length

0.5

0.4

0.3

0.2

0.1

0
co-bl-pc-ch bl-pc-ch co-pc-ch co-bl-ch co-bl-pc pc-ch co-ch co-bl bl-pc co-pc bl-ch

Community Composition

Interaction Strengths
Minimum Lengths
35

30
Minimum Length

25

20

15

10

0
co-bl-pc- bl-pc-ch co-pc-ch co-bl-ch co-bl-pc pc-ch co-ch co-bl bl-pc co-pc bl-ch co pc ch
ch

Community Composition

Growth Rates
Future Research
 Bacteria

https://www.news-medical.net/news/20210208/Scientists-produce-active-antigen-in-bacteria-to-help-combat-SARS-CoV-2.aspx
 Bacteria

8 9

10 11
https://assets.thermofisher.com/TFS-Assets/MBD/product-images/Escherichia-coli-ATCC%2035218-on-Mueller-Hinton-Agar-Plate-white-background.jpg-650.jpg
 Bacteria
a b

600
600nm
nm
https://www.vernier.com/wp-content/uploads/2019/11/video.svis-pl.labq2_._tech-tips._jmelville.001-1-768x432.jpg
Bacteria
0.17 ± 0.23

0.15 ± 0.14 p = 0.25

0.18
0.11 ± 0.097
0.12 ± 0.063 0.12 ± 0.10 0.13 ± 0.052
A b s o rb a n c e %

0.16
0.13 ± 0.03
0.14 0.093 ± 0.083
0.11 ± 0.031
0.12
0.076 ± 0.086
0.1

0.08 0.065 ± 0.031

0.06

0.04

0.02

0
co-bl-pc-ch bl-pc-ch co-bl-ch co-pc-ch pc-ch bl-ch co
Community Composition

Not Treated with Antibiotics Treated with Antibiotics

Novel Method of Calculating Structural Stability
Does not Coexist
Growth Rate (Mouse)

Coexists

Growth Rate (Grass)

https://pixabay.com/illustrations/axis-graph-chart-analytics-6007272/
Real Feasibility Domains

Coexistence

One negative
abundance

Interaction Two negative

Growth Rates abundances
Strengths

Original Graphs Created Using Desmos