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.
Eleven golf courses and eight football pitches, located in Belgium, were surveyed for plant-parasitic nematodes. This revealed a remarkably high diversity: 52 different species/taxa were identified morphologically, belonging to 23 genera and nine families. Among the most prevalent nematodes on both sports field types were Helicotylenchus pseudorobustus and Meloidogyne naasi (> 85% and > 45% of the analysed samples, respectively). Golf greens contained a higher density and diversity of cyst nematodes than football fields. Cyst nematode species included Punctodera punctata, Heterodera mani, H. ustinovi, H. bifenestra and H. hordecalis. Multivariate statistics of the first three species showed that they could be separated based on morphometrical characters of juveniles, but not on values based on the vulva! pattern. Several detected species, e.g., Meloidogyne minor, are a potential source of infestation of agricultural fields. This study shows the importance of plant-parasitic nematodes in turf grass in temperate Europe. In addition, a comparison between two extraction methods revealed that significantly more nematodes were extracted with the zonal centrifuge than after 2 weeks extraction with the Baermann method, except for juveniles of Meloidogyne spp. and cyst-forming specie
Summary1. Although biotic legacies of past agricultural practices are widespread and increasing in contemporary ecosystems, our understanding of the mechanisms driving such legacies is still poor. Forest understories on former agricultural land show low frequencies and abundance of typical woodland species when compared with ancient forests. 2. These community shifts have been ascribed to the effects of dispersal limitation. A rarely considered mechanism is that post-dispersal processes driven by plant-associated communities determine the poor performance and recruitment of woodland indicators. Given the strong alterations in soil conditions due to former agricultural practices, we hypothesized that (abiotic) plant-soil feedbacks could be a major factor in community shifts. 3. We addressed this hypothesis by comparing plant-associated communities in the soil and above the ground in ancient and post-agricultural alluvial forests; then, we experimentally tested whether the changes in biotic and abiotic soil properties could affect above-ground herbivore abundance and pressure and plant performance. 4. Ancient and post-agricultural communities clearly differed in composition at different levels of the food web. Besides the plant community, we also observed the differences in the microbial and nematode community with increased abundance of root-feeding nematodes in postagricultural soils. The composition of the above-ground invertebrate community did not differ in ancient and post-agricultural forest parcels; however, plants growing in post-agricultural sites showed higher abundance of invertebrate herbivores and suffered more herbivory. Nutrient analyses of soil and plants showed that increased levels of phosphorus (and to a lesser extent, nitrogen) made plants more nutritious for insect herbivores. Laboratory experiments further pointed to this mechanism as an explanation of the poorer performance of woodland indicators in post-agricultural woodlands. 5. Our results point to biotic and abiotic plant-soil feedbacks coupled with herbivory as a new mechanism to explain the legacy effects in temperate forests. The modification of the belowground community and soil abiotic characteristics by previous agricultural activity affects not only the plant growth but also the plant nutrient content in the compared understorey species, making them more susceptible to above-ground herbivory. Our results provide one of the first examples of integrating plant-soil feedback and above-and below-ground interactions to explain land-use legacies.
The food specificity of nematodes, their high number of species and high abundance in every habitat where decomposition takes place, indicate that the structure of the nematode assemblage has a high information content. Since nematodes respond quickly to changes in soil management and since the nematode fauna can be efficiently analysed, the structure of the nematode assemblage offers an interesting instrument to assess changes in soil conditions. We studied the effect of five organic amendments on the shortterm nematode population dynamics and compared them to minerally fertilised and unfertilised plots. The experiment was started in 2005, and samples were taken in spring and autumn 2006 and spring 2007. In spring 2006, no clear differences among treatments in the diversity of free-living nematodes were observed, probably since the organic amendments were applied only twice, of which the last application was carried out 7 months before the sampling. At the second and third sampling, the enrichment index in the organically amended plots was higher than in the unamended plots, owing to the organic matter application. However, in plots amended with farmyard manure and cattle slurry the number of bacterivores increased significantly, while in the compost plots the fungivorous nematodes tended to be higher. This resulted in a low channel index for the manure and slurry plots, indicating a predominant bacterial decomposition pathway, and a higher channel index in the compost plots, suggesting a greater proportion of fungal decomposition. These assumptions on the decomposition of the applied organic matter were strongly supported by the composition of the soil microbial community, determined through PLFA analysis: in the compost plots the bacteria to fungi ratio was lower than in the manure and slurry plots. At all sampling occasions there was a remarkably lower abundance of plant-parasitic nematodes in plots amended with slurry and manure, indicating a negative impact of both amendments on plant-parasitic nematodes. We can conclude from this study that the fertiliser regimes affected the nematode assemblage, but that more samplings in the future are certainly necessary to assess adequately the impact of the different organic amendments.
The root-knot nematodes (RKN), Meloidogyne spp., represent an important threat to yam (Dioscorea spp.) production in West Africa. With the aim to establish the diversity of RKN species affecting yam tubers, for control and resistance screening purposes, surveys were conducted in the main yam producing areas of Nigeria. Galled tubers (N = 48) were collected from farmers' stores and markets in nine states in Nigeria and in one district in Ghana. RKN isolated from yam tubers were identified using enzyme phenotyping (esterase and malate dehydrogenase) and mitochondrial DNA (mtDNA) NADH dehydrogenase subunit 5 (Nad5) barcoding. Examination of 48 populations revealed that yam tubers were infested by Meloidogyne incognita (69%), followed by M. javanica (13%), M. enterolobii (2%), and M. arenaria (2%). Most of the tubers sampled (86%) were infected by a single species, and multiple species of RKN were detected in 14% of the samples. Results of both identification methods revealed the same species, confirming their accuracy for the identification of these tropical RKN species. In addition to M. incognita, M. javanica, and M. enterolobii, we report for the first time M. arenaria infecting yam tubers in Nigeria. This finding extends the list of yam pests and calls for caution when developing practices for yam pest management.
In glasshouses practising monoculture of butterhead lettuce in Belgium, high densities of pin nematodes (Paratylenchus spp.) are frequently associated with reduced plant growth. Growers currently apply chemical soil disinfestation measures to manage this problem, although stricter phytosanitary regulations are forcing a shift towards integrated management. Efficient implementation of such management requires knowledge about the factors influencing nematode population dynamics, and the damage threshold for lettuce. The nematode populations in five Belgian glasshouses were monitored for at least 1 year by frequently soil sampling at 0-30 cm and 30-60 cm depth. An undescribed species of Paratylenchus was identified in all glasshouses based on morphological and molecular features. High nematode densities (>20,000 (100 ml soil) −1) occurred in winter and spring. Chemical soil disinfestation lowered these populations greatly, although up to 14% survived in the deeper soil layer. After soil steaming under negative pressure, no pin nematodes were found. After 2 months of black fallow pin nematode densities were reduced by 50%-76%. Lamb's lettuce, parsley and wild rocket were found to be poor hosts in a pot experiment, while reproduction factors (P f /P i) on lettuce cultivars varied between 1 and 3. In three experiments with butterhead lettuce 'Cosmopolia' in pots with a series of 9 or 10 densities of Paratylenchus sp. [up to 35,000 (100 ml soil) −1 ], no damage to lettuce heads was observed. However, root weight and root quality were reduced, and the corresponding damage thresholds were rather low [1,754 and 362 Paratylenchus sp. (100 ml soil) −1 , respectively]. Management strategies such as crop rotation, soil disinfestation or fallow are recommended to avoid pin nematode population build-up.
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