Abstract
Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.
Highlights
Soil can be found on items submitted for forensic analysis, there is currently no reliable method to compare the DNA content of soils for forensic purposes
Along with standard metagenomic approaches such as shotgun and whole genome amplification (WGA), which are widely accepted as the most comprehensive sources of data for studying complex microbial communities, we evaluated AP-PCR as a method for generation of random metagenomic DNA profiles of soils that were analysed by high throughput DNA sequencing
In the research presented here we investigated the ability of whole metagenome analysis techniques to discriminate soil samples of similar land use and vegetation type but collected from different geographical locations
Summary
Soil can be found on items submitted for forensic analysis, there is currently no reliable method to compare the DNA content of soils for forensic purposes. Soil, owing to its inherent features, adheres under fingernails, to cars, tools, weapons or items of clothing and can transfer during the commission of a criminal act [1]. Soil can be useful associative evidence in the investigation of wildlife crimes, such as poaching. The presence of soil is often recorded during the forensic examination of exhibits. Due to the lack of a validated analytical method, or set of techniques for meaningful comparison of soil samples, this evidential type provides only limited value in investigations. There is a need to develop such comparative methodologies
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