Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA

Abstract : DNA metabarcoding on soil samples is increasingly used for large-scale and multi-taxa biodiversity studies. However, DNA extraction may be a major bottleneck for such wide uses. It should be cost/time effective and allow dealing with large sample volumes so as to maximise the representativeness of both micro- and macro-organisms diversity. Here, we compared the performances of a fast and cheap extracellular DNA extraction protocol with a total DNA extraction method in retrieving bacterial, eukaryotic and plant diversity from tropical soil samples of ca. 10 g. The total DNA extraction protocol yielded more high-quality DNA. Yet, the extracellular DNA protocol provided similar diversity assessments although it presented some differences in clades relative abundance and undersampling biases. We argue that extracellular DNA is a good compromise between cost, labor, and accuracy for high throughput DNA metabarcoding studies of soil biodiversity.
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https://hal.archives-ouvertes.fr/hal-01532638
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Submitted on : Friday, June 2, 2017 - 8:10:24 PM
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Lucie Zinger, Jérôme Chave, Eric Coissac, Amaia Iribar, Eliane Louisanna, et al.. Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA. Soil Biology and Biochemistry, Elsevier, 2016, 96, pp.16-19. ⟨10.1016/j.soilbio.2016.01.008⟩. ⟨hal-01532638⟩

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