Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA. (May 2016)

• Record Type: Journal Article
• Authors: Zinger, Lucie; Chave, Jérôme; Coissac, Eric; Iribar, Amaia; Louisanna, Eliane; Manzi, Sophie; Schilling, Vincent; Schimann, Heidy; Sommeria-Klein, Guilhem; Taberlet, Pierre
• Is Part Of: Soil biology and biochemistry. Volume 96(2016)
• Page Start: 16
• Page End: 19
• Publication Date: 2016-05
• Subjects: DNA metabarcoding -- DNA extraction protocol -- Tropical forest -- Multi-taxa biodiversity; Soil biochemistry -- Periodicals; Soil biology -- Periodicals; Sols -- Biochimie -- Périodiques; Sols -- Biologie -- Périodiques; Sols -- Microbiologie -- Périodiques; Bodembiologie; Biochemie; 631.46
• DOI: 10.1016/j.soilbio.2016.01.008
• Languages: English
• ISSNs: 0038-0717

Abstract

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. Highlights: A multi-taxa diversity survey was done from DNA contained in 10 g soil samples. DNA extraction protocols focusing on extracellular or total DNA were compared. Few differences were observed between the two protocols. The extracellular DNA extraction protocol was more time/cost effective. It is appropriate for broad taxonomic and large-scale DNA-based surveys.