Abstract
With an estimated 1.5 million species in the biosphere, fungi represent one of the most diverse eukaryotic lineages. Fungi are found in almost all ecosystems and are spread throughout the globe exhibiting huge diversity in form and function. The global mycological community faces a daunting task in morphology-based species definition and identification, particularly in dealing with the overlap in cultural, pathological and ecological characteristics exhibited by closely related fungal species groups and populations. Recent advances in the application of DNA-based methodologies are revolutionising fungal systematics. At Warwick HRI, we have been using a combination of molecular and biological markers to characterise populations and species of major fungal pathogens. Fungal genus Fusarium is hugely important in the context of human well being as it includes several major plant pathogens and mycotoxin producers. Fusarium species have also emerged as opportunistic pathogens causing life-threatening infections in immuno-compromised patients. This genus has had a confusing and unstable taxonomic history as it includes a large number of species and sub-species. For example, the F. oxysporum (FO) species complex reportedly contains more than 150 host-specific forms. Members of the FO complex include pathogens that cause economically important diseases as well as non-pathogenic (saprophytic) isolates that could act as disease suppressors and it is not uncommon for both these forms to co-exist in cropping systems. In the UK, basal rot of onion has been recognised as an increasing problem and a high research priority by the British Onion Producers Association and we often receive requests for pathogen diagnosis from the growers. Preliminary work at Warwick HRI suggests that in addition to Fusarium oxysporum f. sp. cepae, other Fusarium species are also associated with onion crops in the UK. A recent study also reported a complex of Fusarium species isolates from onion in Netherlands and Uruguay. This clearly highlights the need to characterise the diversity and the species and sub-species level identity of Fusarium species populations associated with onion crops in the UK and understand their role in the basal rot disease. Similarly, basal rot of Narcissus caused by F. oxysporum has been a difficult disease to control in the UK and serious outbreaks of the Fusarium crown and root rot in tomato have also been reported; other FOs of importance include those on basil, asparagus and lettuce. New diseases and species of Fusarium and invasion of new geographic locations by these pathogens are constantly encountered. Fusaria that pose plant health problems include F. circinatum (pitch pine canker), F. foetens (begonia), F. lactis (pepper), F. sambucinum and F. coeruleum (potato dry rot) and F. albedinis (listed disease affecting date palms). For example, F. oxysporum f. sp. rapae has recently been described as a new pathogen on rape in Japan. Similarly, in addition to previously recognised pathogen F. begoniae, a new species F. foetens has been identified as the causal agent of a new disease on begonia in Europe and diseased material was also encountered in the UK. In these studies, various research groups have tended to use different sets of DNA markers such as AFLPs and gene sequences. The international FUSARIUM-ID database is mainly based on the use of a single gene sequence, but the need to use data from other genes to resolve taxonomic conflicts has been recognised. Multigene DNA barcoding is emerging as a power tool in taxonomy research with potential applications in biodiversity, ecology and epidemiology. The main aim of the current project is to develop a framework integrating DNA barcoding and biotyping methodologies to attain a synergy of resolution that neither can provide separately in modern Fusarium taxonomy. The project will utilise the Fusarium species populations associated with the basal rot of onion in the UK as a model to develop the methodologies. The generic approaches will be tested with a range of other key sub-species and species representing the diversity encountered within this major fungal genus. The proposed activities will involve establishing a collection of Fusarium species isolates associated with the onion crops in the UK through surveys and by receiving samples from growers. Some reference isolates from onion in other geographic locations will also be obtained from other researchers. Isolates of other major Fusarium pathogens available at Warwick HRI will be also be included in the study. In addition, isolates representing different species complexes, those posing plant health problems and mycotoxigenic species will be obtained from other UK, European and International Fusarium research groups. Comparative analysis of these diverse collections of isolates will enhance the robustness of the approaches. Potential DNA barcoding genes applicable for species and sub-species level differentiation in Fusarium will be identified and the data will be generated from the various sets of isolates referred to above. A range of biotyping methods will be tested and used for characterising the Fusarium species isolates from onion as well as with a selection of isolates representing other species. These two datasets will then be utilised to test the integrated use of the DNA barcoding and biotyping approaches for species and sub-species level differentiation of Fusaria. Close interaction with and benefit to British onion growers as well as the international Fusarium community will be ensured through various dissemination activities. Overall this work relates to Defra’s policy objectives in sustainable farming and food and the UK government initiative to develop capability in modern taxonomic approaches.
United Kingdom