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New Insights Into Nematode DNA-metabarcoding as Revealed by the Characterization of Artificial and Spiked Nematode Communities

1
ILVO-Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
2
Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
*
Author to whom correspondence should be addressed.
Diversity 2019, 11(4), 52; https://doi.org/10.3390/d11040052
Received: 15 March 2019 / Revised: 26 March 2019 / Accepted: 27 March 2019 / Published: 2 April 2019
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Abstract

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. View Full-Text
Keywords: amplicon PCR; correction factors; DNA-extraction efficiency; DNA-metabarcoding; Nematoda amplicon PCR; correction factors; DNA-extraction efficiency; DNA-metabarcoding; Nematoda
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Waeyenberge, L.; de Sutter, N.; Viaene, N.; Haegeman, A. New Insights Into Nematode DNA-metabarcoding as Revealed by the Characterization of Artificial and Spiked Nematode Communities. Diversity 2019, 11, 52.

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