Expanding the Paradigms of Plant Pathogen Life History and Evolution of Parasitic Fitness beyond Agricultural Boundaries

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The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain

[EN] Phytophthora is one of the most important and aggressive plant pathogenic genera in agriculture and forestry. Early detection and identification of its pathways of infection and spread are of high importance to minimize the threat they pose to natural ecosystems. eDNA was extracted from soil and water from forests and plantations in the north of Spain. Phytophthora-specific primers were adapted for use in high-throughput Sequencing (HTS). Primers were tested in a control reaction containing eight Phytophthora species and applied to water and soil eDNA samples from northern Spain. Different score coverage threshold values were tested for optimal Phytophthora species separation in a custom-curated database and in the control reaction. Clustering at 99% was the optimal criteria to separate most of the Phytophthora species. Multiple Molecular Operational Taxonomic Units (MOTUs) corresponding to 36 distinct Phytophthora species were amplified in the environmental samples. Pyrosequencing of amplicons from soil samples revealed low Phytophthora diversity (13 species) in comparison with the 35 species detected in water samples. Thirteen of the MOTUs detected in rivers and streams showed no close match to sequences in international sequence databases, revealing that eDNA pyrosequencing is a useful strategy to assess Phytophthora species diversity in natural ecosystems.This project has been supported by the Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (EUPHRESCO-CEP: "Current and Emerging Phytophthoras: Research Supporting Risk Assessment And Risk Management"). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Català, S.; Pérez Sierra, AM.; Abad Campos, P. (2015). The Use of Genus-Specific Amplicon Pyrosequencing to Assess Phytophthora Species Diversity Using eDNA from Soil and Water in Northern Spain. 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Phytophthora gallica sp. nov., a new species from rhizosphere soil of declining oak and reed stands in France and Germany

A non-papillate, slow-growing Phytophthora species, which could not be assigned to any existing taxon, was isolated from rhizosphere soil of a declining oak in Northeast France, and from the rhizosphere of Phragmites australis at Lake Constance in south-west Germany in 1998 and 2004, respectively. We describe this species, previously informally designated Phytophthora taxon ‘G’, as Phytophthora gallica sp. nov. Morphology, growth rates, and pathogenicity against cuttings of riparian tree species and leaves of reed are described and compared with those of morphologically and phylogenetically similar Phytophthora species. P. gallica produces colonies with limited aerial mycelium and variable growth patterns. Gametangia are not formed in single or mixed cultures with tester strains of known mating types. P. gallica produces globose and elongated irregular chlamydospores, of which a high proportion is abortive. In water culture irregular hyphal swellings and non-papillate persistent sporangia are formed abundantly. P. gallica is moderately aggressive to Alnus glutinosa and Fagus sylvatica, weakly aggressive to Quercus robur and Salix alba and non-pathogenic to Fraxinus excelsior and Phragmites australis. According to ITS and mtDNA sequence data P. gallica belongs to a distinct Phytophthora clade, with P. boehmeriae and P. kernoviae being the closest relatives. The origin of P. gallica and its ecological role in wet ecosystems remain unclear