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Background  Progressive yield decline in Philippine aerobic rice fields has been recently associated with three closely related  Pythium  spp.,  P. arrhenomanes ,  P. graminicola  and  P. inflatum . To understand their differential virulence towards rice seedlings, we conducted a comparative survey in which three isolates each of  P. arrhenomanes ,  P. graminicola  and  P. inflatum  were selected to investigate host colonization, host responses and carbon utilization profiles using histopathological analyses, phenoarrays, DNA quantifications and gene expression studies.    Results  The isolate of the most virulent species,  P. arrhenomanes , quickly colonized the outer and inner root tissues of rice seedlings, including the xylem, by which it possibly blocked the water transport and induced severe stunting, wilting and seedling death. The lower virulence of the tested  P. graminicola  and  P. inflatum  isolates seemed to be reflected in slower colonization processes, limited invasion of the vascular stele and less systemic spread, in which cell wall fortification appeared to play a role. Progressive hyphal invasions triggered the production of reactive oxygen species (ROS) and phenolic compounds, which was the strongest for the  P. arrhenomanes  isolate and was delayed or much weaker upon inoculation with the  P. inflatum  isolate. The necrosis marker  OsJamyb  seemed faster and stronger induced by the most virulent isolates. Although the isolate of  P. inflatum  was nutritionally the most versatile, the most virulent  Pythium  isolate appeared physiologically more adapted to its host, evidenced by its broad amino acid utilization profile, including D-amino acids, L-threonine and hydroxyl-L-proline. The latter two compounds have been implicated in plant defense and their use by  P. arrhenomanes  could therefore represent a part of its virulence strategy.    Conclusions  This study illustrates that the differential virulence of rice-pathogenic  P. arrhenomanes, P. graminicola  and  P. inflatum  isolates is related to their root colonization capacity, the intensity of induced root responses and their ability to utilize amino acids in their colonization niche. Accordingly, this paper presents important knowledge concerning rice root infections by oomycetes, which could be helpful to further disentangle virulence tactics of soil-borne pathogens.

Pythium species from rice roots differ in virulence, host colonization and nutritional profile