Molecular diagnostics of soilborne fungal pathogens.

Abstract

Abstract Microbes underpin most of the soil ecosystem functions and studying plant pathogens amongst the incredible soil biodiversity is a challenge. Soilborne plant pathogens are, most often, within taxonomically difficult genera, but fortunately, this also means that they have been included in many comprehensive phylogenetic studies of fungi, including oomycetes. Such databases are being used for the development of molecular diagnostic tools that can provide qualitative or quantitative data on specific taxa. More than two decades after its invention, polymerase chain reaction (PCR) and its many derived applications remain the core technology for soil molecular studies. There are two general kinds of approaches to study soil with PCR. Universal primers of various taxonomic resolution are used to generate a broad mixture of amplicons that are analysed further through a range of techniques. Alternatively, species-specific PCR reactions are performed to detect and/or quantify the target species. Both approaches can be amenable to the detection of a range of pathogens and beneficials. Molecular techniques can resolve many of the taxonomic difficulties that more traditional approaches need to confront, but the crucial issue of soil sampling in ecological studies remains. Molecular detection uncovered and compounded another problem. Many fungi that are being characterized by direct DNA processing of soil are supposedly unculturable, whereas molecular detection is reducing the need for isolation of the culturable ones. There is a need to try to find ways to grow and describe unculturable species and maintain reference collections of live cultures. The stability of DNA in dead organisms and a bias towards detecting non-living organisms does not appear to be a broad issue in microbiologically active soil. Testing for regulatory purposes is an important niche for DNA-based soil assays, but routine usage of these techniques on a commercial scale has not yet been achieved. The availability of on-site testing devices that can provide a resolution at the pathotype or race level of the pathogens and detect the beneficial species that reduce the impact of pathogens would greatly encourage the wide adoption of DNA-base techniques for soilborne disease management. The biosecurity initiatives supporting the sequencing of many genomes of soilborne pathogens and the DNA barcode initiatives targeting the sequencing of the largest possible number of species will greatly help to achieve this goal.