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Experimentation

The group is involved with a broad spectrum of experimental work on the dynamics and control of epidemics.

We work at a range of scales that extend from:

• the spread of fungal colonies through soil;
• pathozone dynamics and disease transmission between individual plants;
• disease spread through plant populations using microcosms;
• large scale field experiments.

The experimental programme is designed:

• to answer specific questions about the epidemiology and control of soil-borne plant disease;
• to use these plant systems as experimental models to test hypotheses about more generic epidemiological mechanisms that control the spatial and temporal dynamics and efficiency of control in a broad range of pathogens including aerial pathogens and certain animal and even human diseases.

Fungal colonies

We use a combination of immunological techniques and soil physics to analyse the dynamics of spread of Rhizoctonia solani through soil

The epidemiological challenges are:

• to quantify the dynamics of colony behaviour in a porous medium;
• to identify how soil physical conditions affect the spread of saprotrophic and parasitic fungi and microbial antagonists;
• to visualise fungal spread on and through soil;
• to identify criteria to prevent invasion of harmful organisms and to promote the spread of beneficial organisms.

				Hyphae of Rhizoctonia solani growing through soil. By analysing thin sections of soil, it is possible to examine hyphal behaviour down to the scale of the individual hyphae. The soil is first encased in resin so that the structure remains constant when it is cut; the sections are stained and examined under a microscope and analysed by computer. (Credits W. Otten, K. Harris, I. Young, K. Ritz, C.A. Gilligan)
Immunoblot showing the growth of Rhizoctonia solani on a sand surface. This immunological method detects surface antigens on fungal hyphae. (Credits C.R. Thornton, F.M. Dewey, D.J. Bailey, C.A. Gilligan)	Growth of a fungal colony of R. solani showing branching at the hyphal scale.

Pathozone dynamics

The pathozone is the region of soil surrounding a host target within which a pathogen must lie in order to be able to infect the host. It can be quantified using ‘placement’ experiments, in which discrete units of inoculum are placed at different distances in soil from the host. The proportion of infected hosts at each distance in then used as an estimator of the probability of infection.

The epidemiological challenges are to quantify:

• the spatial and temporal dynamics of the pathozone;
• the effect of disease control measures as well as soil type and other environmental variables on pathozone dynamics;
• the relationships between colony dynamics and pathozone behaviour;
• how it can be used to predict epidemic behaviour at the large (patch to field) scale.

Most of our work has been focused on the pathozone for Rhizoctonia solani, and the way that this changes when a biological control agent (Trichoderma viride) or a fungicide is added in different soil types. Other work has been directed towards the wheat take-all fungus, Gaeumannomyces graminis, as well as the oomycetes, Pythium ultimum ( a widely occurring damping-off disease) and Polymyxa betae (the vector of rhizomania disease of sugar beet) and the parasitic Nematode, Meloidogyne incognita.

Adding a biocontrol agent (right figure) ‘shrinks’ the pathozone for primary infection of Rhizoctonia solani and radish (Credits D.J. Bailey, A. Kleczkowski, D. Long, C.A. Gilligan)	Computer tomography scan of soil surrounding a cotton root. The scan shows how moisture availability changes through the pathozone, which in turn affects microbial dynamics and the probability of infection. (Credits M.J. Grose, D. Spenser, B.V.D. Goddard, C.A. Gilligan)

Microcosm experiments

Collecting epidemiological data on the spatial and temporal dynamics of disease in the field is expensive and difficult. Experiments are difficult to replicate and the underlying dynamics of disease are often hidden by incomplete sampling, local variation of global fluctuations in temperature or other variables.

We therefore use laboratory microcosms experiments to help us to understand the underlying principles that drive epidemics. Microcosms allow fast, highly replicated epidemics under controlled environmental conditions. For example, by using microcosms of radish or other seedlings exposed to known amounts of initial inoculum of Rhizoctonia solani, it is possible to observe and map entire epidemics within 20 d periods.

Epidemiological challenges are:

• to analyse the relative importance of primary infection (driven by resident inoculum) and secondary infection (driven by transmission from infected to susceptible individuals) on the dynamics of epidemics;
• to analyse the effects of demographic stochasticity (chance effects in transmission from infected to susceptible individuals under otherwise identical conditions) from environmental stochasticity (when transmission parameters are influenced by local or global changes in environmental variables);
• to scale from individual to population to metapopulation behaviour.

Radish plants in microcosm		Before and after a virulent epidemic of Pythium on cress seedlings. The dots represent sites of primary infection

Spatial maps of epidemics derived from microcosms, showing site of initial inoculum (lines), previously infected plants (grey) and newly infected plants. (Credits W. Otten, J.A.N. Filipe, C.A. Gilligan)		Microcosm experiments can also be used to analyse transient dynamics of plant and weed populations (Credits S. Mertens)

Field experiments

Field experiments form an important test of epidemiological theory for the control of disease. The group uses data from collaborators as well as our own field experiments for this purpose. Current work is focused on the take-all fungus of wheat and on the epidemiology control of damping-off diseases of horticultural crops. Collaborative work with Rothamsted Research is also looking at the transient dynamics of weed populations.

Epidemiological challenges are:

• to test the epidemiological principles derived from microcosm and other small scale experiments under field conditions;
• to derive criteria for invasion and persistence of disease under field conditions;
• to provide growers and advisors with epidemiological advice about how to optimise the control of disease at the field and larger (regional scale).

Field experiment to quantify and analyse the balance of primary and secondary infection on damping-off disease of radish in fen soils near Cambridge. (Credits I. Moltini, D.J. Bailey, C. Pillinger, C.A. Gilligan)	Experiment near Cambridge on heat treatment of soil as a means of controlling epidemics of damping-off. (Credits D.J. Bailey and Soil Sterilizers U.K.)

Map such as these (left) showing extent of Citrus Canker Disease on amenity trees in Miami enable estimation of dispersal kernels for disease in order to improve efficiency of disease control. The picture (right) shows eradication of the disease in Sao Paulo. (Credits T. Gottwald, USDA)