title: Random whole metagenomic sequencing for forensic discrimination of soils.
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.
authors.affiliation: School of Biological Sciences, Flinders University, Adelaide, Australia.
authors.forename: Anastasia S
authors.initials: AS
authors.lastname: Khodakova
authors.affiliation: School of Biological Sciences, Flinders University, Adelaide, Australia.
authors.forename: Renee J
authors.initials: RJ
authors.lastname: Smith
authors.affiliation: School of Biological Sciences, Flinders University, Adelaide, Australia.
authors.forename: Leigh
authors.initials: L
authors.lastname: Burgoyne
authors.affiliation: School of Biological Sciences, Flinders University, Adelaide, Australia; Forensic Science South Australia, Adelaide, Australia.
authors.forename: Damien
authors.initials: D
authors.lastname: Abarno
authors.affiliation: School of Biological Sciences, Flinders University, Adelaide, Australia.
authors.forename: Adrian
authors.initials: A
authors.lastname: Linacre
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D004247:DNA / Q000032:analysis / Q000235:genetics; D056890:Eukaryota / Q000235:genetics*; D053803:Forensic Genetics / Q000379:methods*; D005843:Geography; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods; D021141:Nucleic Acid Amplification Techniques; D017422:Sequence Analysis, DNA; D012987:Soil / Q000145:classification*; D012988:Soil Microbiology
chemical_list: D012987:Soil; D004247:DNA
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