Molecular detection of oomycetes species in water courses

In Poland, about 20% of forest nurseries use irrigation water coming from natural superficial reservoirs, presumed to be the first source of infection caused by harmful pathogens belonging to the Oomycota class, especially Phytophthora genus and Pythium genus. The forest nursery is the only place where forest managers can react before pathogens leave it with asymptomatic plants or soil attached to their roots. The aim of this research was detection and identification phytopathogens in water samples. In order to recognise genus Phytophthora or Pythium in water collected from 33 places in five different forest districts in Poland, two DNA-based approaches of identification were applied: (i) the TaqMan probes, and (ii) sequencing of the ITS6/4 region. The genomic DNA was obtained from 17 of 33 investigated water samples. TaqMan probes helped to identify 8 oomycetes present in 17 water samples. Based on ITS rDNA sequencing data, pathogens were identified in 17 cases, and this to the genus level (6 cases) and to the species level (11 cases). In total five Oomycetes species were identified, i.e. 3 Pythium species (Py. citrinum, Py. angustatum, Py. helicoides) and two Phytophthora species (P. lacustris sp. nov. – former taxon Salixsoil, P. gallica sp. nov.).