Presentation made during a public seminar during the hiring process for a professorship position between the Université catholique de Louvain and the Forschungszentrum Jülich in the domain of soil-plant-atmosphere modelling

1. Guillaume Lobet |
UNDERSTANDING
COMPLEX
PLANT PROCESSES
IN
HETEROGENEOUS
ENVIRONMENTS
Guillaume Lobet
@guillaumelobet

2. Guillaume Lobet | 2Yves Lobet
PLANTS ARE
FASCINATING

3. Guillaume Lobet | 3Wayne Stadler Jane Kahler Eric Hossinger

4. Guillaume Lobet | 4

5. Guillaume Lobet | 4
H2O

6. Guillaume Lobet | 4
H2O
N, P, …

7. Guillaume Lobet | 4
H2O C
N, P, …

8. Guillaume Lobet |
Water uptake
Carbon fluxes
Nutrient uptake
Plant development
5
f(time)
f(space)
f(species)
f(soil)
…
H2O
C

9. Guillaume Lobet |
Water uptake
Carbon fluxes
Nutrient uptake
Plant development
5
SYSTEMS BIOLOGY
f(time)
f(space)
f(species)
f(soil)
…
H2O
C

10. Guillaume Lobet | 6Lobet et al. 2014b
biological
model

11. Guillaume Lobet | 6Lobet et al. 2014b
biological
model
functional
structural
plant
model

12. Guillaume Lobet |
plant
level
organ
level
sub-organ
level
7

13. Guillaume Lobet |
Question NEW
Insights
8
Experiment
in vivo
Data
analysis
DATA-CENTERED SCIENCE PIPELINE

14. Guillaume Lobet | 9
Question NEW
Insights
in vivo data model
MODEL-ASSISTED SCIENCE PIPELINE
Guillaume Lobet |
Using models to help understand your data

15. Guillaume Lobet |Ge et al. 2000 10
MODEL
ASSISTED
BREEDING
Ideotype
analysis

16. Guillaume Lobet | 11
MY OWN
RESEARCH

17. Guillaume Lobet | 12
2 0 0 3
2 0 0 8
2 0 1 3
M AST ER IN BIO - ENGINEERING
PHD AGRONO M IC AL S CIENCE S
P O ST- DOC TOR AL F EL L OW
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É DE L IÈ GE
2 0 1 6 VI SI T ING S CIEN T I ST
F OR S CH UNG S Z EN T RU M
J UL ICH
PLANT
M
O
DELS
IM
AGE
ANALYSIS
PL AN T
PH YS I O L O G Y
me

18. Guillaume Lobet | 12
2 0 0 3
2 0 0 8
2 0 1 3
M AST ER IN BIO - ENGINEERING
PHD AGRONO M IC AL S CIENCE S
P O ST- DOC TOR AL F EL L OW
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É DE L IÈ GE
2 0 1 6 VI SI T ING S CIEN T I ST
F OR S CH UNG S Z EN T RU M
J UL ICH
PLANT
M
O
DELS
IM
AGE
ANALYSIS
PL AN T
PH YS I O L O G Y
me
OPEN
S CIENCE
S CIENCE
CO M M .

19. Guillaume Lobet | 12
2 0 0 3
2 0 0 8
2 0 1 3
M AST ER IN BIO - ENGINEERING
PHD AGRONO M IC AL S CIENCE S
P O ST- DOC TOR AL F EL L OW
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É C AT HOL IQUE DE
L O UVAIN
UNI VER SI T É DE L IÈ GE
2 0 1 6 VI SI T ING S CIEN T I ST
F OR S CH UNG S Z EN T RU M
J UL ICH
PLANT
M
O
DELS
IM
AGE
ANALYSIS
PL AN T
PH YS I O L O G Y
me
OPEN
S CIENCE
S CIENCE
CO M M .
www.guillaumelobet.be

20. Guillaume Lobet |
Question NEW
Insights
in vivo data model
Mathieu et al. 2015
Rellan-Alvarez et al. 2015
13
Lobet et al. 2014a
Rellan-Alvarez et al. 2016
Bouché et al. 2016
Lobet et al. 2014b
Périlleux et al. 2014
Hill et al. 2013
Draye et al. 2010
Lobet et al. 2015a
Delory et al. 2015
Lobet et al. 2013a
Lobet et al. 2013b
Lobet et al. 2011
Guillaume Lobet |
MY CONTRIBUTIONS
(SO FAR)

21. Guillaume Lobet |
Question NEW
Insights
in vivo data model
14Guillaume Lobet |Guillaume Lobet | 14
Water uptake is a
multi-dimensional
and highly
heterogeneous
process along the
root-soil domain
Lobet et al. 2014a
PMID: 24515834

22. Guillaume Lobet | 15Guillaume Lobet |
Question NEW
Insights
in vivo data model
Guillaume Lobet | 15
GLO-ROOT: Tracking root
system architecture and
specific gene expression in
the root system in response
to local environmental clues
Rellan-Alvarez et al. 2015
PMID: 26287479
http://bit.ly/glo-root

23. Guillaume Lobet |
in vivo
16Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 16
Referencing 140 plant
image analysis tools
in a searchable web
database
Lobet et al. 2013
PMID: 24107223
www.plant-image-analysis.org
ǡ +10 000 page views / months

24. Guillaume Lobet |
in vivo
17Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 17
Root System
Markup Language:
A common format for
root system architecture
data
Lobet et al. 2015
PMID: 25614065
http://rootsystemml.github.io/
SmartRoot
RootNav
RootSystem
Analyser
RhizoScan
RSML MTG
Open
Alea
IMAGE ANALYSIS
MODELLING
Root
Box
R
DATA ANALYSIS

DIRT
RSWMS
Excel
ImageJ
Plant
Ontologies
XML
RooTrak
RootTrace
ArchiSimple
C#
EZ-Rhizo
archi
DART
GLORIA
RooTyp
PlaNet

25. Guillaume Lobet |
in vivo
18Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 18
PlaNet-Maize:
a whole functional
structural plant
model for water
flows in the SPAC
Lobet et al. 2014
DOI: 10.1016/j.ecolmodel.2013.11.025
☠

26. Guillaume Lobet |
ɏ
ɏ
ɏ
ɏ
ɏ
ɏ
ɏɏ
ɏ
MY SCIENTIFIC
NETWORK
ɏ Plant Biology
ɏ Phenotyping
ɏ Modelling
19

27. Guillaume Lobet | 20
RESEARCH
PROJECT

28. Guillaume Lobet | 21
H2O C
Whole plant
FSPM
Late
developmental
stages
Complex processes
(H20, C, Nutr.)
Heterogeneous
environments

29. Guillaume Lobet |
Question NEW
Insights
in vivo data model
22Guillaume Lobet |Guillaume Lobet |
VEGETATIVE PHASE
LEAVES
ROOT
STEM

30. Guillaume Lobet |
Question NEW
Insights
in vivo data model
22Guillaume Lobet |Guillaume Lobet |
VEGETATIVE PHASE
LEAVES
ROOT
STEM
REPRODUCTIVE PHASE
LEAVES
ROOT
STEM GRAIN

31. Guillaume Lobet |
data
23Guillaume Lobet |
Question NEW
Insights
in vivo model
Guillaume Lobet | 23
MAIZE AS A MODEL PLANT
RIL population [Palomero Tolequeno x B73]
Large phenotypic variability
 R. Rellan-Alvarez & R. Sawers (Cinvestav, Mexico)

32. Guillaume Lobet |
in vivo
AEROPONIC
AGRASIM
LYSIMETERS
GLO-ROOT
PET-SCAN
RHIZOTRONS
Question NEW
Insights
data model
24Guillaume Lobet |Guillaume Lobet | 24
UNIQUE
INFRASTRUCTURES
 J. Dinneny (Carnegie Institution for Sciences, Stanford)
UCL
IBG3
IBG2
Carnegie
Complementary systems
Integrated approach

33. Guillaume Lobet |
in vivo
25Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 25
SimRoot RootMap RootBox
L-Peach Cut-Rose L-Py
WHOLE PLANT
FSPM

34. Guillaume Lobet |
in vivo
26Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 26
H2O
DuMuX
Water transport Soil

35. Guillaume Lobet |
in vivo
26Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 26
H2O
DuMuX
PlaNet-Maize
Water transport Soil

36. Guillaume Lobet |
in vivo
26Guillaume Lobet |
Question NEW
Insights
data model
Guillaume Lobet | 26
H2O C
DuMuX
Atmosphere
Carbon transport
PlaNet-Maize
Water transport Soil

37. Guillaume Lobet | 27
?
MODEL-ASSISTED SCIENCE …
Guillaume Lobet |

38. Guillaume Lobet | 27
?
MODEL-ASSISTED SCIENCE …
Guillaume Lobet |

39. Guillaume Lobet | 27
?
MODEL-ASSISTED SCIENCE …
Guillaume Lobet |

40. Guillaume Lobet | 27
?
MODEL-ASSISTED SCIENCE …
Guillaume Lobet |
? ?
? ?
…FOR THE COMMUNITY

41. ANY
QUESTIONS ?
Presentation
available on figshare
bit.ly/lobet-ucl-fzj

42. Guillaume Lobet | 29
REFERENCES
•Band LR, Wells DM, Fozard JA, Ghetiu T, French AP, Pound MP,
Wilson MH, Yu L, Li W, Hijazi HI, et al. 2014. The Plant Cell.
•Bouché F, Lobet G, Tocquin P, Périlleux C. 2016. Nucleic Acids
Research 44: D1167–D1171.
•Delory BM, Baudson C, Brostaux Y, Lobet G, Jardin du P, Pagès
L, Delaplace P. 2015. Plant and Soil: 1–15.
•Draye X, Kim Y, Lobet G, Javaux M. 2010. Journal of
Experimental Botany 61: 2145–2155.
•Ge Z, Rubio G, Lynch JP. 2000. Plant and Soil 218: 159–171.
•Hill K, Porco S, Lobet G, Zappala S, Mooney S, Draye X,
Bennett MJ. 2013. Plant Physiology 163: 1487–1503.
•Lobet G, Draye X. 2013. Plant Methods 9: 2–10.
•Lobet G, Couvreur V, Meunier F, Javaux M, Draye X. 2014a.
Plant Physiology 164: 1619–1627.
•Lobet G, Draye X, Périlleux C. 2013. Plant Methods 9: 1–7.
• Lobet G, Pagès L, Draye X. 2011. Plant Physiology 157: 29–39.
• Lobet G, Pagès L, Draye X. 2014b. Ecological Modelling 290:
65–75.
• Lobet G, Pound MP, Diener J, Pradal C, Draye X, Godin C,
Javaux M, Leitner D, Meunier F, Nacry P, et al. 2015. Plant
Physiology 167: 617–627.
• Mathieu L, Lobet G, Tocquin P, Périlleux C. 2015. Plant Methods
11: 1–7.
• Périlleux C, Lobet G, Tocquin P. 2014. Frontiers in Plant
Sciences 5: 1–12.
• Rellán-Álvarez R, Lobet G, Lindner H, Pradier P-L, Sebastian
J, Yee M-C, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A,
et al. 2015. eLife 4: e07597.
• Xuan W, Band LR, Kumpf RP, Van Damme D, Parizot B, De Rop
G, Opdenacker D, Möller BK, Skorzinski N, Njo MF, et al. 2016.
Science 351: 384–387.

43. Guillaume Lobet | 30
COLOPHON (1/3)
This presentation was made on Keynote.
The fonts used are Glode (text) and Font Awesome (glyphs)
Main colors are: #28353A #70BF42
#52A8F9
#F6D428 #F48F18

44. Guillaume Lobet | 31
COLOPHON (2/3)
Figures and illustrations were made using a mixture of:
- r plot (slide 18)
- ggplot2 (simulated plants, slides 6, 7, 15, 21, 22, 25, 26)
- Omnigraffle (slides 14, 17)
- GIMP (slides 11, 23, 25)
- Keynote (everything else)

45. Guillaume Lobet | 32
COLOPHON (3/3)
Images are coming from:
- Flickr (slide 3)
- www.lobet.eu (slide 2)
- My own library