A High-Throughput Molecular Pipeline Reveals the Diversity in Prevalence and Abundance of Pratylenchus and Meloidogyne Species in Coffee Plantations

Coffee yields are adversely affected by plant-parasitic nematodes and the pathogens are largely under-reported because a simple and reliable identification method is not available. We describe a PCR-based approach to rapidly detect and quantify the major Pratylenchus and Meloidogyne nematode species that are capable of parasitising coffee. The procedure was applied to soil samples obtained from a number of coffee farms in Brazil, Vietnam and Indonesia to assess the prevalence of these species associated both with coffee (Coffea arabica and C. canephora) and its intercropped species Musa acuminata (banana) and Piper nigrum (black pepper). Pratylenchus coffeae and P. brachyurus were associated with coffee in all three countries, but there were distinct profiles of Meloidogyne species. Meloidogyne incognita, M. exigua and M. paranaensis were identified in samples from Brazil and M. incognita and M. hapla were detected around the roots of coffee in Vietnam. No Meloidogyne species were detected in samples from Indonesia. There was a high abundance of Meloidogyne in soil samples in which Pratylenchus were low or not detected, suggesting that the success of one genus may deter another. Meloidogyne species in Vietnam and Pratylenchus species in Indonesia were more numerous around intercropped plants than in association with coffee. The data suggest a wide-spread but differential nematode problem associated with coffee production across the regions studied. The issue is compounded by the current choice of intercrops that support large nematode populations. Wider application of the approach would elucidate the true global scale of the nematode problem and the cost to coffee production.