Highlights
- •DNA-based methods for bacterial differentiation of soil samples were compared.
- •RISA, 16S-rRNA TRFLP and 16S-rRNA MiSeq performed best.
- •TRFLP methodology was optimized for forensic usage.
Abstract
The ubiquity and transferability of soil makes it a resource for the forensic investigator,
as it can provide a link between agents and scenes. However, the information contained
in soils, such as chemical compounds, physical particles or biological entities, is
seldom used in forensic investigations; due mainly to the associated costs, lack of
available expertise, and the lack of soil databases. The microbial DNA in soil is
relatively easy to access and analyse, having thus the potential to provide a powerful
means for discriminating soil samples or linking them to a common origin. We compared
the effectiveness and reliability of multiple methods and genes for bacterial characterisation
in the differentiation of soil samples: ribosomal intergenic spacer analysis (RISA),
terminal restriction fragment length polymorphism (TRFLP) of the rpoB gene, and five methods using the 16S rRNA gene: phylogenetic microarrays, TRFLP,
and high throughput sequencing with Roche 454, Illumina MiSeq and IonTorrent PGM platforms.
All these methods were also compared to long-chain hydrocarbons (n-alkanes) and fatty alcohol profiling of the same soil samples. RISA, 16S TRFLP and
MiSeq performed best, reliably and significantly discriminating between adjacent,
similar soil types. As TRFLP employs the same capillary electrophoresis equipment
and procedures used to analyse human DNA, it is readily available for use in most
forensic laboratories. TRFLP was optimized for forensic usage in five parameters:
choice of primer pair, fluorescent tagging, concentrating DNA after digestion, number
of PCR amplifications per sample and number of capillary electrophoresis runs per
PCR amplification. This study shows that molecular microbial ecology methodologies
are robust in discriminating between soil samples, illustrating their potential usage
as an evaluative forensic tool.
Keywords
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Article info
Publication history
Published online: October 06, 2016
Accepted:
October 6,
2016
Received in revised form:
September 20,
2016
Received:
April 16,
2016
Identification
Copyright
© 2016 Elsevier Ireland Ltd. All rights reserved.
