Nematodes are ideal biological indicators to monitor soil biodiversity and ecosystem functioning. For this reason, they have been receiving increasing attention from a broad range of scientists. The main method to characterize soil nematode communities until at least genus level is still based on microscopic observations of nematode morphology. Such an approach is time-consuming, labor-intensive, and requires specialized personnel. The first studies on the potential use of DNA-metabarcoding to characterize nematode communities showed some shortcomings: under- or overestimation of species richness caused by failure to detect a number of nematode species or caused by intraspecific sequence variants increasing the number of OTUs (operational taxonomic units) or ‘molecular’ species, and flaws in quantification. We set up experiments to optimize this metabarcoding approach. Our results provided new insights such as the drastic effect of different DNA-extraction methods on nematode species richness due to variation in lysis efficacy. Our newly designed primer set (18S rRNA gene, V4-V5 region) showed in silico an improved taxonomic coverage compared with a published primer set (18S rRNA gene, V6-V8 region). However, results of DNA-metabarcoding with the new primer set showed less taxonomic coverage, and more non-nematode reads. Thus, the new primer set might be more suitable for whole soil faunal analysis. Species-specific correction factors calculated from a mock community with equal amounts of different nematode species were applied on another mock community with different amounts of the same nematode species and on a biological sample spiked with four selected nematode species. Results showed an improved molecular quantification. In conclusion, DNA-metabarcoding of soil nematode communities is useful for monitoring shifts in nematode composition but the technique still needs further optimization to enhance its precision.

The influence of both host and temperature on the vertical migration of Pratylenchus penetrans was examined in a series of experiments using maize, carrot, black salsify, pea, bean and potato. Plants were grown in a pot placed on top of a plastic pipe of variable length in a growth chamber. This pipe was planted into a second pot to maintain the humidity in the pipe. Nematodes were inoculated at the bottom of the pipe and were allowed to migrate upwards for 14 days after which the pipe was cut into 5 cm sectors from which the nematodes were extracted and counted. More nematodes migrated at 21°C than at 16 or 11°C. Migration of P. penetrans towards a host decreased with increasing distance between the nematodes and all hosts, with maize and bean eliciting the most attraction. They were the only hosts able to stimulate nematode migration up to the distal end of 31 cm pipes. Potato and carrot were the least influential hosts. Hosts differently influenced the migration only of second-stage juveniles (J2), with a greater percentage of J2 moving under maize and bean than under carrot. Under all hosts, adults migrated in greater proportions with increasing distance than did other stages. The attractiveness of hosts was age dependent. Generally, infectivity decreased with distance travelled by the nematode.

Visual assessment surveys were carried out between November 2012 and February 2013 in order to identify nematodes and to establish the damage caused on yam (Dioscorea spp.) in different agro-ecological zones in Nigeria. Galled tubers were collected and used for root-knot nematode (RKN) population increase on susceptible tomato cultivar and species identification after maturation of nematodes. Nematode species were then identified using the PhastSystem and sequence analysis of the mitochondrial gene COX2 mtDNA, based on pure populations of the associated nematode species. The results unequivocally identified the root-knot nematode Meloidogyne enterolobii. Inoculation of M. enterolobii onto white yam D. rotundata cv. Makakusa under screen house conditions resulted in severe galling damage of tubers and roots. To our knowledge, this is the first record of M. enterolobii infecting yam, which is known for its aggressive nature and damage to a range of crops in various locations. The present report extends the ...