Molecular identification and characterisation of Meloidogyne and Pratylenchus species

Plant-parasitic nematodes devastate a wide range of plant species across the world including many economically important crops such as coffee. Determining the mechanisms that underpin nematode entry and parasitism of the root is of great interest for the design of control strategies. The first aspect of crop protection is to accurately and reliably diagnose the nematode species of concern. A molecular pipeline is described in this thesis that utilises PCR to rapidly detect and quantify the major Meloidogyne and Pratylenchus nematode species that are capable of parasitising coffee. This methodology assessed the prevalence of these species across the major coffee growing regions in Brazil, Vietnam and Indonesia. Distinct profiles of Meloidogyne species were detected across the regions whereas congruent Pratylenchus species were associated with coffee in all three countries. Furthermore, the pathogens were more numerous around intercropped plants such as banana and black pepper compared to coffee, suggesting that these crops may aggravate the issue. There was a high abundance of Meloidogyne in soil in which Pratylenchus was low, suggesting that the success of one genus may deter another. There is a clear widespread, yet differential nematode problem within coffee plantations that is likely to be effecting production and the issue is compounded by local practices and choices of intercrops. The global scale of the problem and the cost to coffee production could be elucidated with wider application of the approach. Plant-nematode interactions must be defined in order to act upon diagnoses from the field. As obligate plant parasites, Meloidogyne and Pratylenchus nematodes must be able to locate and feed from their host in order to survive. The plant cell wall provides protection and support to plant cells and is a major barrier that the nematode must overcome to initiate feeding. This projects shows that Pratylenchus coffeae, a key species detected in the field, regulates the expression of selected cell-wall degrading enzyme genes relative to the abundance of substrate in root exudates, thereby tailoring gene expression to maximise the chances of successful parasitism. Treatment with the substrates directly or with root exudates deficient in the substrates conferred a specific gene expression response with no effect on expression of another cell wall degrading enzyme gene. This indicates that host-specific gene expression in this plant-parasitic nematode is influenced by cell wall components that derive from plant secretion or degradation of root tissue. The illustrated transcriptional plasticity may have evolved as an adaptation for recognition and increased root invasion of a wider range of host species.