1. 1st February 2013 – Agrocampus Ouest
Modelling and experimentation of the spatio-temporal spread of soilborne pathogens: Rhizoctonia solani on sugar beet as an example pathosystem
Leclerc Melen
PhD defence
1st February 2013 – Agrocampus Ouest
UMR – IGEPP
Cifre I.T.B
Reporters: Joël Chadoeuf, Christian Lannou
Examiners: Yannick Outreman, Marc Richard-Molard
Supervisors: Philippe Lucas, Thierry Doré, João Filipe

2. General context – current problems
Introduction
50% reduction in pesticide use (Grenelle de l’environnement  Ecophyto)
Find alternatives to pesticide use
Keep crop production levels and growers’ incomes

3. Proposed approaches
Introduction
Necessity of considering the complexity of agro-ecosystems (e.g. using system approaches)
Understand ecological and epidemiological processes involved in the dynamics of pathogens
Use ecological and epidemiological knowledge to improve pest management and design efficient crop protection strategies
Combine several controls with partial effects (there is no ‘one fits all’ solution)
SysPID Casdar Project: Reduce the impact of soilborne diseases in crop systems towards an integrated and sustainable pest management
Action n°2: Epidemiological processes in field crop systems

4. Soilborne disease epidemics
Introduction
Soilborne disease epidemics
Soilborne diseases
Wide range of pathogenic organisms (fungi, bacteria, viruses, nematodes, protozoa)
Cause substantial damage to crops worldwide (up to 50 % of crop loss in the US (Lewis & Papaizas, 1991) )
Pathogens often survive for many years in soils (5-7 years for Pythium)
Difficult to detect, predict and control
Epidemiology
External source of inoculum X(t) : dynamic pathogen population
Primary infections : external inoculum epidemic initiation
Secondary infections : spread of the pathogen within the crop/population
General points on soilborne disease and epidemiology of these disease
Susceptible
hosts S I
Infected/Infectious
hosts X

5. Rhizoctonia solani on sugar beet as an example pathosystem
Introduction
The host
The pathogen

6. The host : sugar beet The plant Cultivated Beta vulgaris
Introduction
The plant
Cultivated Beta vulgaris
High production of sucrose
The crop
Grown for sugar production
France is one of the largest producer (33 Mt in 2009)
Introduce briefly sugar beet: plant and crop

7. The pathogen : Rhizoctonia solani
Introduction
The pathogen : Rhizoctonia solani
R. solani fungi
Basidiomycetes
Polyphagous saprotrophic fungi
Anastomisis Groups (AG)
R. solani AG2-2 IIIB
Parasites maize, rice, sugar beet, ginger …
Important optimal temperature range for growth
Develops late in the growing season
Infects mostly mature plants
Introduce R. solani fungi, characteristics of R. solani AG2-2IIIB
Aoyagi et al., 1998

8. The disease : the brown root rot disease of sugar beet
Introduction
Present the root rot disease at different levels: field, individual, above-ground and belowground symptoms

9. Rhizoctonia root rot disease control
Introduction
Current management strategies
Think crop rotations (host & non-host crops)
Resistant varieties
Biological controls ?
Antagonists (e.g. Trichoderma fungi)
Biofumigation

10. Our system Visible epidemic: symptomatic plants Hidden epidemic:
Introduction
Visible epidemic:
symptomatic plants
Above-ground
Hidden epidemic:
Cryptic infections
Source of inoculum :
R. solani
Temporal scale : growing season of sugar beet
 Spatial scale : field
Belowground

11. Research questions and structure of the presentation
Introduction
Research questions and structure of the presentation
1. How does R. solani spread in field conditions ? (Understand epidemiology of R. solani in field conditions)
2. How to infer hidden infections from observations of the disease ?
3. How does biofumigation affect epidemic development ?
Study 1 : R. solani spread
Experimentation
Modelling
Study 2 : Incubation period
Experimentation
Modelling
Study 3 : Effects of biofumigation
2007 data (Motisi, 2009)
Modelling

12. How does R. solani spread in field conditions ?
Part 1
How does R. solani spread in field conditions ?

13. Pathozone concept and spread of soilborne pathogens
Part 1
Pathozone concept and spread of soilborne pathogens
Difficult to asses R. solani growth in soils  use of pathozone concept
“Pathozone means the region of soil surrounding a host unit within which the centre of a propagule must lie for infection of the host unit to be possible” (Gilligan, 1985)
Probability of infection
Placement experiment
Inoculum(donor)-host(recipient)
n replicates at distance x
ni number of infected recipients at time t
 P(x,t) = ni / n
Time exposed
to inoculum
Contact distance

14. Results of the experiments (Pathozone profiles)
Part 1
Results of the experiments (Pathozone profiles)
Field experiments in 2011 (Le Rheu)
Primary inoculum
(5 infested barley seeds)
Secondary inoculum
(an infected plant)
Localised spread (nearest neigbour plants) (Filipe et al., 2004, Gibson et al.,2006)
Infections occurs further with secondary inoculum ( Kleczkowski et al.,1997)
The fungus translocates nutrients from the parasited host to other parts of the mycelium

15.  Host growth may increase pathogen transmission at individual level
Part 1
 Host-plant growth decreases the contact distance between neighbouring plants
 Host growth may increase pathogen transmission at individual level

16. Host growth can trigger the development of epidemics
Part 1
Static contact distance
Dynamic contact distance
xcc= 11 cm
 Host growth can cause a switch from non-invasive to invasive behaviour
Non-invasive behaviour (linear trend)
xcc= 14 cm
xcc= 17 cm
Invasive behaviour (non-linear trend)

17. Conclusion (Part 1) First Pathozone profiles measured in a real soil
Locality of pathogen spread in field conditions
Importance of considering space : mean-field approximation/homogeneous mixing assumption may fail when predicting the spread of soilborne pathogens (Dieckmann et al., 2000 ; Filipe & Gibson, 2001)
Host growth can trigger the development of epidemics by decreasing contact distances
 Need to take into account host growth for epidemic thresholds – conditions for invasive spread of plant population by pathogens (Grassberger, 1983 ; Brown & Bolker, 2004)

18. How to infer hidden infections from observations ?
Part 2
How to infer hidden infections from observations ?

19. Problem
Part 2
From belowground infections to above-ground detection of the disease

20. A problem of incubation period
Part 2
Time between hidden infection and appearance of detectable symptoms of pathology
Incubation period (Kern, 1956 ; Keeling & Rohani, 2008)
Incubation period distributions are often described by non-negative probability distributions with a pronounced mode (Keeling & Rohani, 2008 ; Chan & Johansson, 2012)
Incubation period data are rare …

21. Compartmental models an incubation period distributions
How to describe cryptic infections with compartmental models ?
Compartmental Markovian models
The time spent in each state is exponentially distributed
In a simple SID model the incubation period is exponentially distributed
How to introduce realistic distributions in classical compartmental models ?
A tractable way: by subdividing compartments (i.e. introducing transient states)
Sum of exponentialy distributed random variables =
Erlang (or Gamma) distributed random variable
Susceptible hosts
Infected/infectious hosts
Detectable/symptomatic hosts
Realistic distribution
Distribution in classical Markovian models
Introduce the issue of realistic nonexponential distribution in compartmental models
One solution  Erlang distribution

22. Working hypothesis and methodology
Part 2
Hypothesis: the distribution (e.g. mean and range) of the incubation period is age-dependent
Methodology:
Experimental measures for various ages of infection
Statistical analysis (is Gamma distribution robust enough ?)
Build a model for age-varying distribution of the incubation period
Incorporate it into an SID compartmental model

23. Experimental measures of the incubation period
Part 2
Experiments
Plant inoculated with 3 infested barley seeds (inoculum)
9 ages of plants (14, 32, 46, 60, 74, 88, 102, 116, 130 days)
For each individual the time of first above-ground symptom was recorded
At least 45 individual observations for each age  distributions of the incubation period

24. Raw data (results of the experiments)
Part 2
Inubation period calculated in degree- days
Present raw data and general tendencies

25. number of transient states (=19)
Part 2
Age-varying model of the incubation period distribution
Age by age distribution analysis  Gamma distribution (general case of Erlang) can reasonably describe incubation period distributions
Age-varying model of the incubation period T(t)
k : shape parameter =
number of transient states (=19)
λ: time dependent rate parameter
Compartmental model with realistic incubation distribution (19 transient non-symptomatic states)
Present our model and how we can introduce it in a simple compartmental model

26. Hidden infections and observations
Part 2
Hidden infections and observations
Simulations of cryptic epidemics (individual-based spatial model with stochastic continuous time)
Illustrate i) difference in infected and detected dynamics, ii) importance of considering realistic distributions (Exp vs Erlang)
 Infected and detectable/symptomatic individuals have different dynamics

27. Conclusion (Part 2)
Part 2
One of the first epidemiological model for soilborne disease with data-supported incubation period
Link hidden processes and observations of disease
Estimate rates of infections and cryptic infections from observations
Test management strategies based on the detection of symptomatic individuals
This end of the incubation period corresponds to a visual detectability
May change with other detection/survey methods, e.g. molecular techniques, remote sensing
Variability ? (soils, human error, strains, environmental conditions …)

28. How does biofumigation affect epidemic development?
Part 3
How does biofumigation affect epidemic development?

29. Background Previous work
Part 3
Previous work
The effect of biofumigation on the root rot disease has been analysed using a simple epidemiological model (Motisi, 2009 ; Motisi et al., 2012)
Observations of symptomatic plants for 3 treatments :
1) without control, 2) with complete biofumigation, 3) with partial biofumigation
Biofumigation affects mostly primary infections
Biofumigation can affect secondary infections with a variable pattern
Force of infection

30. Aim of the current study
Part 3
Integrate new epidemiological knowledge and data
Improve existing epidemiological models
Re-analyse the effects of biofumigation
Investigate the variability of epidemics to estimate uncertainty in the outcome of treatments

31. Improved epidemiological model : epidemic predictions
Part 3
Improved epidemiological model : epidemic predictions
Spatial individual-based model with stochastic spread of the pathogen
Spatial component : better description of epidemics
Stochastic model : introduce variability in outcomes  predictions of uncertainty
Stochastic infections
Rate of primary infection
Rate of secondary infection

32. Estimate parameter for each treatment from observations of disease
Part 3
Introduce a more realistic incubation period for inferring epidemiological parameters
Statistical inferrence of spatio-temporal can be difficult and time consuming…
Estimate spatial rates of infection using a semi-spatial model (Filipe et al., 2004)
Localized spread of infections (see Part 1)
Pair approximation (Matsuda et al., 1992 ; Filipe & Gibson, 1998 ; van Baalen, 2000)
Need to describe the dynamics of all pairs of the system (i.e. SS, SI II for an SI model)
 Tractability : necessity to simplify the incubation period…

33. Model fitting and estimated rates of infection
Part 3
Model fitting and estimated rates of infection
Rate of primary infection
Symptomatic plants (2007 data)
Rate of secondary infection
 Biofumigation reduced rates of primary and secondary infection in this trial (2007)

34. Distributions of infected plants at harvest (%)
Spatial model predictions
Part 3
Distributions of infected plants at harvest (%)
Biofumigation allows a partial control of epidemics
Biofumigation seems to reduce the uncertainty in epidemic outcome
Marginal differences between partial and complete biofumigation in 2007

35. Conclusion (Part 3)
Part 3
Analyses are consistent with previous results on the effect of biofumigation on the spread of R. solani, but
We predict less primary infections and more secondary infections than in the previous study
New vision of epidemic : different disease progress curves
Biofumigation seems to reduce the uncertainty in epidemic outcome
Take these results with care
More statistical analyses are required to assess model fitting and conclude on the effects of treatments on epidemic development
Assess the effects of incubation period simplification – Pairwise vs temporal model …
Isotropic space (may overestimate epidemics ?)
Re-analyse 2008 data

36. General conclusion

37. Soilborne disease epidemics
General conclusion
This work provide insights into root rot disease epidemics
spread of R. solani
incubation period
Data-supported studies – field experiments
We still need to improve knowledge on the epidemiology of this disease
May apply to others pathosystems : perennial and non-perennial plants

38. Incubation period  improve disease survey
Control of soilborne disease epidemics
General conclusion
Biofumigation
partial control of the root rot disease (Motisi et al., 2009 , 2010, 2012)
can reduce the uncertainty in epidemic outcome
This work points out important epidemiological parameters for disease management
Design and test new strategies
Plant growth  use crop mixing, precise key phenological stages to select for resistances
Incubation period  improve disease survey
Locality of pathogen spread  optimize the effects of treatments, use local treatments ?
Combine partial controls (new and conventional)  improve the control of epidemics
Models may help to test disease management strategies

39. Perspectives
General conclusion
Mutltiple perspectives (theoretical, applied, epidemiological, ecological…)
Consider main environmental parameters (temperature, moisture)
Investigate pathogen dynamic at the crop rotation scale
Understand ecological functionning of soils (pathogenic and non pathogenic communities)

40. Merci… Doug Bailey Philipe Lucas – Thierry Doré – João Filipe
Françoise Montfort
Les anciens membres de l’équipe EPSOS
UMR IGEPP
Les Unités Expérimentales de Dijon et de Le Rheu
L’Institut Technique de la Betterave
Christian Lannou – Joël Chadoeuf – Marc Richard Molard – Yannick Outreman (jury)
Pauline Ezanno – Marie Gosme – Christian Steinberg – Agnès Champeil – Étienne Rivot (comité de thèse)
Chris Gilligan et l’Epidemiology and Modelling Group
Les membres du projet Casdar SysPID
Le portakabin (qui a eu chaud…)
Et tous ceux qui m’ont supporté…
Mon bureau…avant-hier

41. Introduction
Evolution of symptoms

42. The pathogen: R. solani Rate of primary infection
Introduction
Rate of primary infection
Rate of secondary infection
Rates of infection and pathozones
Pathozones P(x,t)
x: contact distance
t: time of exposure
Infer parameters from pair experiment data
ninf: number of infected recipients
ntot: number of replicates (25)

43. Incubation period ?
Part 2
Periods in Natural history of disease in a host – these are incorporated as compartments in epidemiological models
Introduce period in epidemiology : infectious statess vs pathological states
Link between infections and detection  incubation period
Incubation period:
"time required for multiplication of a parasitic organism within a host organism up to the threshold point at which the parasite population is large enough to produce detectable symptoms of pathology“ (Kern, 1956)

44. Host growth and dynamic contact distances
Introduction
Host growth and dynamic contact distances
Increase in the radius h(t)
Radial growth measured with Pepista tools (ITB)
Simple empirical model
Dynamic of the contact distance between nearest neighbours xee(t)
Static centre-centre distance xcc
Spatial population model
30*30 square lattice
t0= 30 days
5% infected

45. Rate of primary infection
Part 3
First results
Previous epidemiological model
Detectable/
symptomatic
Force of infection
Infected
Assumptions
Mean field mass action/homogeneous mixing assumption
Epidemics initiated too soon
Pre-emergence damping off
Unrealistic incubation period
Rate of primary infection
Motisi et al., 2012