The plant nursery industry has become an ideal reservoir for Phytophthora species and other soilborne pathogens. In this context, isolation from tissues and soil of ornamental and forest plants from nurseries in four regions of Spain was carried out. A high diversity of Phytophthora species was confirmed. Fourteen Phytophthora phylotypes (P. cactorum, P. cambivora, P. cinnamomi, P. citrophthora, P. crassamura, P. gonapodyides, P. hedraiandra, P. nicotianae, P. niederhauserii, P. palmivora, P. plurivora, P. pseudocryptogea, P. sansomeana, and Phytophthora sp. tropicalis-like 2) were isolated from over 500 plant samples of 22 species in 19 plant genera. Nine species were detected in water sources, two of them (P. bilorbang and P. lacustris) exclusively from water samples. P. crassamura was detected for the first time in Spain. This is the first time P. pseudocryptogea is isolated from Chamaecyparis lawsoniana and Yucca rostrata in Spain.

The diversity of Phytophthora species in declining Fagaceae forests in Europe is increasing in the last years. The genus Quercus is one of the most extended Fagaceae genera in Europe, and Q. ilex is the dominant tree in Spain. The introduction of soil-borne pathogens, such as Phytophthora in Fagaceae forests modifies the microbial community present in the rhizosphere, and has relevant environmental and economic consequences. A better understanding of the diversity of Phytophthora spp. associated with Q. ilex is proposed in this study by using Next Generation Sequencing (NGS) in six Q. ilex stands located in three regions in Spain. Thirty-seven Phytophthora phylotypes belonging to clades 1 to 12, except for clades 4, 5 and 11, are detected in this study, which represents a high diversity of Phytophthora species in holm oak Spanish forests. Phytophthora chlamydospora, P. citrophthora, P. gonapodyides, P. lacustris, P. meadii, P. plurivora, P. pseudocryptogea, P. psychrophila and P. quercina were present in the three regions. Seven phylotypes could not be associated with known Phytophthora species, so they were putatively named as Phytophthora sp. Most of the detected phylotypes corresponded to terrestrial Phytophthora species but aquatic species from clades 6 and 9 were also present in all regions.

Between 2010 and 2015, an extensive survey of Phytophthora diversity was performed across Portugal. Baiting and direct isolation tests obtained 48 Phytophthora taxa in 62 of 70 forest stands (89%) from 148 of 302 rhizosphere soil samples (49%) and 25 of 29 tree species (86%), and from bark cankers of Alnus lusitanica and Fagus sylvatica ; from 33 of 34 rivers and forest streams (97%); and in 12 of 13 forest nurseries (92%) from 54 of 87 root ball samples (61%) and 16 of 21 tree species (76%). The 799 Phytophthora isolates belonged to 28 known and three recently described species; one designated and two new non‐hybrid taxa; and five designated and nine new hybrid taxa. The majority, 34 Phytophthora taxa (71%), are introduced aliens in Europe while nine (19%) and five (10%) taxa are of cryptic and native origin, respectively. Phytophthora cinnamomi was the most common species in forests (56%) and forest nurseries (61%). Multiple first records for Portugal and partly Europe of both Phytophthora taxa and tree declines and new host– Phytophthora associations were found. Isolation rates from forest soil differed considerably between declining (65%) and healthy trees (10%), regardless of the tree species. The widespread infestations of nurseries with aggressive wide‐host range pathogens like P . cinnamomi , P . pseudocryptogea , P . × cambivora , P . multivora and P . plurivora , and host‐specific pathogens like P . alticola , P . quercetorum and P . quercina , will inevitably cause their further spread to the wider environment, exacerbating pathogen threats to forest ecosystems and thus weakening their resilience to climatic extremes.

The struggling Spanish holm oak woodland situation associated with Phytophthora root rot has been studied for a long time. Phytophthora cinnamomi is considered the main, but not the only species responsible for the decline scenario. This study verifies the presence and/or detection of Phytophthora species in two holm oak areas of Spain (southwestern “dehesas” and northeastern woodland) using different isolation and detection approaches. Direct isolation and baiting methods in declining and non-declining holm oak trees revealed Phytophthora cambivora, Phytophthora cinnamomi, Phytophthora gonapodyides, Phytophthora megasperma, and Phytophthora pseudocryptogea in the dehesas, while in the northeastern woodland, no Phytophthora spp. were recovered. Statistical analyses indicated that there was not a significant relationship between the Phytophthora spp. isolation frequency and the disease expression of the holm oak stands in the dehesas. Phytophthora quercina and P. cinnamomi TaqMan real-time PCR probes showed that both P. cinnamomi and P. quercina are involved in the holm oak decline in Spain, but P. quercina was detected in a higher frequency than P. cinnamomi in both studied areas. Thus, this study demonstrates that molecular approaches complement direct isolation techniques in natural and seminatural ecosystem surveys to determine the presence and distribution of Phytophthora spp. This is the first report of P. pseudocryptogea in Europe and its role in the holm oak decline should be further studied.