title: Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity.
abstract: DNA molecules originating from animals and plants can be retrieved directly from sediments and have been used for reconstructing both contemporary and past ecosystems. However, the extent to which such 'dirt' DNA reflects taxonomic richness and structural diversity remains contentious. Here, we couple second generation high-throughput sequencing with 16S mitochondrial DNA (mtDNA) meta-barcoding, to explore the accuracy and sensitivity of 'dirt' DNA as an indicator of vertebrate diversity, from soil sampled at safari parks, zoological gardens and farms with known species compositions. PCR amplification was successful in the full pH range of the investigated soils (6.2 ± 0.2 to 8.3 ± 0.2), but inhibition was detected in extracts from soil of high organic content. DNA movement (leaching) through strata was evident in some sporadic cases and is influenced by soil texture and structure. We find that DNA from the soil surface reflects overall taxonomic richness and relative biomass of individual species. However, one species that was recently introduced was not detected. Furthermore, animal behaviour was shown to influence DNA deposition rates. The approach potentially provides a quick methodological alternative to classical ecological surveys of biodiversity, and most reliable results are obtained with spatial sample replicates, while relative amounts of soil processed per site is of less importance.
authors.affiliation: Centre for GeoGenetics, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Andersen
authors.forename: Karen Lise
authors.initials: KL
authors.lastname: Bird
authors.forename: Morten
authors.initials: M
authors.lastname: Rasmussen
authors.forename: James
authors.initials: J
authors.lastname: Haile
authors.forename: Henrik
authors.initials: H
authors.lastname: Breuning-Madsen
authors.forename: Kurt H
authors.initials: KH
authors.lastname: Kjaer
authors.forename: Ludovic
authors.initials: L
authors.lastname: Orlando
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
mesh_terms: D000818:Animals; D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004272:DNA, Mitochondrial / Q000032:analysis*; D059014:High-Throughput Nucleotide Sequencing; D010944:Plants / Q000145:classification / Q000235:genetics; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012680:Sensitivity and Specificity; D012987:Soil / Q000032:analysis*; D014714:Vertebrates / Q000145:classification / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial; D012336:RNA, Ribosomal, 16S; D012987:Soil