Pathogens share their host plant with many other microbes, some of which being also pathogenic. We hereafter consider as “multiple infection” or “co-infection” when a host plant is infected by many pathogen species, or pathogen genotypes.
This phenomenon can have strong effects on symptom expression and within-plant multiplication, but the population-scale consequences, in terms of pathogen multiplication and epidemics are still unexplored, in spite of the considerable consequences for managing crop diseases. EVCOPAR project aims at verifying the following hypothesis: co-infection affects pathogen evolutionary pathways and disease dynamics.
This project focuses on rice in Sub-Saharan Africa, becoming a major crop because of the demographic growth and changing in food habits. Rice in Africa is threatened by two major pathogens: the Rice Yellow Mottle Virus (RYMV) and the bacteria Xanthomonas oryzae (Xo). Our preliminary results have shown within-plant interactions between these two pathogens in co-infection context: the virus RYMV causes an increase in the bacterial symptoms, while the Xo bacteria reduces the viral load. Spacio-temporal monitoring of these two diseases have been performed in Burkina Faso (VIRBIARF, E-SPACE, RiPABIOME, CRP-RICE projects), so that samples and detailed information on disease epidemiology are available. EVCOPAR project will study the consequences on pathogen populations of inter-species co-infections (RYMV-Xo) but also intra-species co-infections (various Xo or RYMV genotypes). The project offers an original approach combining field work, experimental infections, viral and bacterial genomics and epidemiological and evolutionary modelling.
In the first task, we will describe the genetic structures of the RYMV and the Xo populations in areas where this disease is prevalent, through innovative sequencing approaches, in order to test the hypothesis that co-infection affects the genetic structure of pathogen populations.
The second task will apply an experimental evolution approach. Viral populations (RYMV) having evolved in a context of a single infection will be compared with those that evolved in co-infection (presence of Xo bacteria or of another RYMV genotype), both in terms of genomics and phenotypes (viral load and virulence on sensitive rice and capacity to bypass rice resistance.
Ultimately, task 3 will integrate the data generated in the two first tasks and develop an epidemiological modelling approach of the pathosystem including the effect of co-infection.
Globally, the EVCOPAR project encompass the “Pathobiome” approach, which integrated each pathogen in its host’s microbe community. The original nature of the project lies in a population-based approach, mainly focused on evolution and epidemiology, and in an application to pathosystem very important for food safety. The expected results will, not only enable to proceed with academic valuing, but also will provide more very important teachings for an integrated management of crops and therefore plant health, which puts food security at stake in Sub-Saharan Africa.
The project is coordinated by Charlotte TOLLENAERE (IRD) and involves INERA’s partners (Issa WONNI, Drissa SEREME, Abalo Itolou KASSANKOGNO), as well as IRD and INRAE.