Metabarcoding Phytophtora

The increasing international trade in rooted plants and the continual introduction of new varieties and/or species exposes nurseries, with particular emphasis on the potted ornamentals, to new host−pathogen combinations and creates new disease threats. Invasive pathogens have been frequently found on ornamental plants and their trade is considered a primary driver of new disease outbreaks since it causes large-scale distribution of pathogens beyond their natural endemic ranges with severe socio-economic impact

The water mold genus Phytophthora contains 140 species that are pathogens of dicotyledons. They are plant pathogens of considerable economic importance capable of causing enormous economic losses on crops worldwide, as well as environmental damage in natural ecosystems. 

Both the identification of known and the discovery of new Phytophthora speces is difficult due to the limits of conventional culturing and bating methods. As a consequence, several invasive and previously unknown species have been identified only when it was too late and they already caused severe damage in nonnative environments.

In a recent study, Phytophthora diversity was analyzed in potted ornamental plant nurseries using genus specific primers combined with the Sanger sequencing of cloned amplicons. The analyses highlighted a complex assemblage of Phytophthora species with new host−pathogen combinations, evidence of species previously unreported in the investigated area, and phylotypes representative of species that remain to be taxonomically defined

A new study now investigated the power and reliability of a metabarcoding approach based on genus-specific primers and the 454 platform as it is considered more powerful and less costly which is needed if one is looking at broad testing. The colleagues used soil and root samples from potted ornamental nurseries, already analyzed as part of the former study. 

The study indicates that the use of genus-specific primers combined with 454 is a very useful approach to investigate Phytophthora diversity in different ecosystems. Compared to the Sanger approach, it enabled deeper sequencing at a fraction of the time and cost. According to the authors several aspects confirmed the reliability of the method: 

• many identical sequence types were identified independently in different nurseries, 
• most sequence types identified with 454 pyrosequencing were identical to those from the cloning/Sanger sequencing approach and/or perfectly matched GenBank deposited sequences, and 
• the divergence noted between sequence types of putative new Phytophthora species and all other detected sequences was sufficient to rule out sequencing errors.