Meloidogyne species pose a significant threat to crop production in Africa due to the losses they cause in a wide range of agricultural crops. The direct and indirect damage caused by various Meloidogyne species results in delayed maturity, toppling, reduced yields and quality of crop produce, high costs of production and therefore loss of income. In addition, emergence of resistance-breaking Meloidogyne species has partly rendered various pest management programmes already in place ineffective, therefore putting food security of the continent at risk. It is likely that more losses may be experienced in the future due to the on-going withdrawal of nematicides. To adequately address the threat of Meloidogyne species in Africa, an accurate assessment and understanding of the species present, genetic diversity, population structure, parasitism mechanisms and how each of these factors contribute to the overall threat posed by Meloidogyne species is important. Thus, the ability to accurately characterize and identify Meloidogyne species is crucial if the threat of Meloidogyne species to crop production in Africa is to be effectively tackled. This review discusses the use of traditional versus molecular-based identification methods of Meloidogyne species and how accurate identification using a polyphasic approach can negate the eminent threat of root knot nematodes in crop production. The potential threat to Africa posed by highly damaging and resistance-breaking populations of 'emerging' Meloidogyne species is also examined.

The asexual root-knot nematodes (RKNs) (Meloidogyne spp.) exemplified by Meloidogyne incognita are widespread and damaging pests in tropical and subtropical regions worldwide. Comparison of amplification products of two adjacent polymorphic regions of the mitochondrial genome using DNA extracts of characterized RKN strains, including 15 different species, indicate that several species are derived from the same or closely related female lineages. Nevertheless, M. javanica, M. enterolobii, M. incognita, and other key species could each be assigned unique mitochondrial haplotypes based on polymerase chain reaction fragment size and restriction cleavage patterns. M. arenaria isolates did not group as a single haplotype, consistent with other reports of diversity within this species. To test the utility of this assay, we characterized ethanol-preserved samples from 103 single-species isolates from four countries in sub-Saharan Africa (Benin, Nigeria, Kenya, and Tanzania). Mitochondrial haplotypes corresponding to M. javanica and M. incognita were the most prevalent. Samples from western Africa included several instances of M. enterolobii but this species was not detected in samples from East Africa. This protocol provides progress toward a standardized strategy for identification of RKN species from small, preserved samples and a rational starting point for classifying species present in regions where previous knowledge has been limited.

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The significance of fungal endophytes in African agriculture, particularly Kenya, has not been well investigated. Therefore, the objective of the present work was isolation, multi-gene phylogenetic characterization and biocontrol assessment of endophytic fungi harbored in tomato roots for nematode infection management. A survey was conducted in five different counties along the central and coastal regions of Kenya to determine the culturable endophytic mycobiota. A total of 76 fungal isolates were obtained and characterized into 40 operational taxonomic units based on the analysis of ITS, β-tubulin and tef1α gene sequence data. Among the fungal isolates recovered, the most prevalent species associated with tomato roots were members of the Fusarium oxysporum and F. solani species complexes. Of the three genes utilized for endophyte characterization, tef1α provided the best resolution. A combination of ITS, β-tubulin and tef1α resulted in a better resolution as compared to single gene analysis. Biotests demonstrated the ability of selected non-pathogenic fungal isolates to successfully reduce nematode penetration and subsequent galling as well as reproduction of the root-knot nematode Meloidogyne incognita. Most Trichoderma asperellum and F. oxysporum species complex isolates reduced root-knot nematode egg densities by 35-46 % as compared to the nonfungal control and other isolates. This study provides first insights into the culturable endophytic mycobiota of tomato roots in Kenya and the potential of some isolates for use against the root-knot nematode M. incognita. The data can serve as a framework for fingerprinting potential beneficial endophytic fungal isolates which are optimized for abiotic and biotic environments and are useful in biocontrol strategies -016-1169-9 against nematode pests in Kenyan tomato cultivars. This information would therefore provide an alternative or complementary crop protection component.

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