Investigating the diversity of plant-parasitic nematodes associated with coffee in Kenya, using morphological and molecular approaches

Comprehensive surveys in nine coffee-growing counties in Kenya, involving 53 farms and comprising 116 soil and 63 root samples, revealed a total of 12 genera of plant-parasitic nematodes, including: Meloidogyne, Paratylenchus, Pratylenchus, Helicotylenchus, Rotylenchus, Rotylenchulus, Scutellonema, Trophotylenchulus, Xiphinema, Trichodorus, Aphelenchoides and Hemicycliophora. Meloidogyne was the most abundant genus, with densities of up to 210 juveniles (100 ml soil)− 1. Morphological and molecular characterisation enabled the identification of several nematode species including Meloidogyne javanica, M. africana, Rotylenchulus borealis and Trophotylenchulus obscurus. For T. obscurus, the 18S rDNA sequences obtained in this study are the first ever reported for the genus. Additionally, the 18S and D2-D3 of 28S, as well as ITS sequences, marked first for this species. In total, six partial 18S, seven D2-D3 of 28S, four ITS sequences of rDNA, ten COI, and two nad5 gene sequences were generated in this study. In conclusion, our study reveals that our knowledge of plant-parasitic nematode occurrence on important crops even, such as coffee, remains poorly documented and understood, highlighting the potential for new discoveries in such areas.