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.
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References
Concheri G. Chemical elemental distribution and soil DNA fingerprints provide the critical evidence in murder case investigation. PLoS ONE. 2011;6:e20222.
Fitzpatrick RW, Raven MD, Forrester ST. A systematic approach to soil forensics: criminal case studies involving transference from crime scene to forensic evidence. In: Ritz K, Dawson L, Miller L, editors. Criminal and environmental soil forensics. Dordrecht: Springer; 2009. p. 105–27.
Sensabaugh GF. Microbial community profiling for the characterisation of soil evidence: forensic considerations. In: Ritz K, Dawson L, Miller L, editors. Criminal and environmental soil forensics. Dordrecht: Springer; 2009. p. 49–60.
Macdonald LM, Singh BK, Thomas N, Brewer MJ, Campbell CD, Dawson LA. Microbial DNA profiling by multiplex terminal restriction fragment length polymorphism for forensic comparison of soil and the influence of sample condition. J Appl Microbiol. 2008;105:813–21.
Young JM, Weyrich LS, Cooper A. Forensic soil DNA analysis using high-throughput sequencing: a comparison of four molecular markers. Forensic Sci Int Genet. 2014;13:176–84.
Delmont TO, Robe P, Clark I, Simonet P, Vogel TM. Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods. 2011;86:397–400.
Robe P, Nalin R, Capellano C, Vogel TA, Simonet P. Extraction of DNA from soil. Eur J Soil Biol. 2003;39:183–90.
Courtois S, Frostegård A, Göransson P, Depret G, Jeannin P, Simonet P. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ Microbiol. 2001;3:431–9.
Frostegård A, Courtois S, Ramisse V, Clerc S, Bernillon D, Le Gall F, Jeannin P, Nesme X, Simonet P. Quantification of bias related to the extraction of DNA directly from soils. Appl Environ Microbiol. 1999;65:5409–20.
Feinstein LM, Sul WJ, Blackwood CB. Assessment of bias associated with incomplete extraction of microbial DNA from soil. Appl Environ Microbiol. 2009;75:5428–33.
Jiang YX, Wu JG, Yu KQ, Ai CX, Zou F, Zhou HW. Integrated lysis procedures reduce extraction biases of microbial DNA from mangrove sediment. J Biosci Bioeng. 2011;111:153–7.
Zhou JZ, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 1996;62:316–22.
Mumy KL, Findlay RH. Convenient determination of DNA extraction efficiency using an external DNA recovery standard and quantitative-competitive PCR. J Microbiol Methods. 2004;57:259–68.
Lloyd-Jones G, Hunter DWF. Comparison of rapid DNA extraction methods applied to contrasting New Zealand soils. Soil Biol Biochem. 2001;33:2053–9.
Jones MD, Singleton DR, Sun W, Aitken MD. Multiple DNA extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil. Appl Environ Microbiol. 2011;77:2984–91.
Berry D, Mahfoudh KB, Wagner M, Loy A. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl Environ Microbiol. 2011;77:7846–9.
Epp LS, Boessenkool S, Bellemain EP, Haile J, Esposito A, Riaz T, et al. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol Ecol. 2012;21:1821–33.
Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010;(6):pdb.prot5448.
Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Bioinformatics in Action. 2012;17:10–2.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Eisenman HC, Casadevall A. Synthesis and assembly of fungal melanin. Appl Microbiol Biotechnol. 2012;93:931–40.
Acknowledgments
This work was supported by an ARC Linkage Grant between the University of Adelaide and the Australian Federal Police. We thank Alla Marchuk for collecting the soil samples and members of the Australian Centre for Ancient DNA for helpful comments on previous versions of the manuscript.
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Young, J.M., Weyrich, L.S., Clarke, L.J. et al. Residual soil DNA extraction increases the discriminatory power between samples. Forensic Sci Med Pathol 11, 268–272 (2015). https://doi.org/10.1007/s12024-015-9662-z
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DOI: https://doi.org/10.1007/s12024-015-9662-z