Residual soil DNA extraction increases the discriminatory power between samples
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TECHNICAL REPORT
Residual soil DNA extraction increases the discriminatory power between samples Jennifer M. Young • Laura S. Weyrich Laurence J. Clarke • Alan Cooper
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Accepted: 5 February 2015 Ó Springer Science+Business Media New York 2015
Abstract Forensic soil analysis relies on capturing an accurate and reproducible representation of the diversity from limited quantities of soil; however, inefficient DNA extraction can markedly alter the taxonomic abundance. The performance of a standard commercial DNA extraction kit (MOBIO PowerSoil DNA Isolation kit) and three modified protocols of this kit: soil pellet re-extraction (RE); an additional 24-h lysis incubation step at room temperature (RT); and 24-h lysis incubation step at 55 °C (55) were compared using high-throughput sequencing of the internal transcribed spacer I ribosomal DNA. DNA yield was not correlated with fungal diversity and the four DNA extraction methods displayed distinct fungal community profiles for individual samples, with some phyla detected exclusively using the modified methods. Application of a 24 h lysis step will provide a more complete inventory of fungal biodiversity, and re-extraction of the residual soil pellet offers a novel tool for increasing discriminatory power between forensic soil samples. Keywords Soil Forensics Metagenomics DNA extraction High-throughput sequencing
Electronic supplementary material The online version of this article (doi:10.1007/s12024-015-9662-z) contains supplementary material, which is available to authorized users. J. M. Young (&) L. S. Weyrich L. J. Clarke A. Cooper Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, Australia e-mail: [email protected]
Introduction Soil is a powerful form of contact trace evidence that can link a suspect to a location, object or victim [1], or provide information on the likely origin of an unknown sample [2]. Soil microbial DNA fingerprinting methods, such as T-RFLP, have limited resolution and individual taxa cannot be identified [3]. In contrast, high-throughput sequencing (HTS) can detect a more detailed picture of the soil community, in particular, fungal diversity can provide better discrimination between soil samples than bacterial profiles [4, 5]. However, obtaining an accurate representation of soil communities has proven problematic due to difficulties in recovering DNA from complex soil matrices [6–9]. Studies have shown that portions of the endogenous DNA are not captured using standard extraction kit protocols [10, 11]. For example, previous studies indicate poor DNA recovery rates from commercial kits when soils are spiked with known amounts of DNA [12–14] and successive extraction from the residual soil pellet has shown increased DNA yield and diversity [10, 15]; however, the effect of such approach on discriminatory power remains unknown. Using HTS of the internal transcribed spacer I (ITS1) ribosomal DNA, DNA yield, fungal diversity and discriminatory power using a standard
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