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.
Highlights
Nematodes are among the most diverse and highly specialized multicellular eukaryotes on earth
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
(i) nematodes can be extracted from the soil using simple extraction procedures; (ii) they are more sensitive to changes in the soil environment than other organisms due to their permeable cuticle; (iii) numerous species can withstand anaerobic conditions and desiccation which benefits their survival; (iv) they can be detected in all seasons [2,3]; and (v) their generation time is longer than metabolically active
Summary
Nematodes are among the most diverse and highly specialized multicellular eukaryotes on earth. Diversity 2019, 11, 52 microbes (hours to days), making them more temporally stable and less fluctuating with nutrient flushes [4] These arguments assure nematodes to be ideal biological indicators suited for monitoring soil biodiversity and ecosystem functioning as recently confirmed by a panel of approximately 50. Far less is known about the majority of the nematode species that play beneficial roles in soil environments and together form a nematode community, holding valuable information for soil health assessment. The fact that these nematodes are microscopically small and live hidden between soil particles can only partially explain this paucity of knowledge
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