Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

K. Andersen; K.L. Bird; M. Rasmussen; J. Haile; H. Breuning-Madsen; K.H. Kjaer; L. Orlando; M.T.P. Gilbert; E. Willerslev

doi:10.1111/j.1365-294X.2011.05261.x

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Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

Journal article

Peer reviewed

Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity

K. Andersen, K.L. Bird, M. Rasmussen, J. Haile, H. Breuning-Madsen, K.H. Kjaer, L. Orlando, M.T.P. Gilbert and E. Willerslev

Molecular Ecology, Vol.21(8), pp.1966-1979

2012

DOI: https://doi.org/10.1111/j.1365-294X.2011.05261.x

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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.

Details

Title: Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity
Authors/Creators: K. Andersen (Author/Creator) - University of Copenhagen
K.L. Bird (Author/Creator) - Geocenter Denmark
M. Rasmussen (Author/Creator) - University of Copenhagen
J. Haile (Author/Creator) - Murdoch University
H. Breuning-Madsen (Author/Creator) - Geocenter Denmark
K.H. Kjaer (Author/Creator)
L. Orlando (Author/Creator) - University of Copenhagen
M.T.P. Gilbert (Author/Creator) - University of Copenhagen
E. Willerslev (Author/Creator) - University of Copenhagen
Publication Details: Molecular Ecology, Vol.21(8), pp.1966-1979
Publisher: Blackwell Publishing
Identifiers: 991005539571407891
Copyright: © 2011 Blackwell Publishing Ltd.
Murdoch Affiliation: School of Biological Sciences and Biotechnology
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.64 Phylogenetics & Genomics; 3.64.2564 Environmental DNA
Web Of Science research areas: Biochemistry & Molecular Biology; Ecology; Evolutionary Biology
ESI research areas: Environment/Ecology