title: New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems.
abstract: Metabarcoding approaches use total and typically degraded DNA from environmental samples to analyse biotic assemblages and can potentially be carried out for any kinds of organisms in an ecosystem. These analyses rely on specific markers, here called metabarcodes, which should be optimized for taxonomic resolution, minimal bias in amplification of the target organism group and short sequence length. Using bioinformatic tools, we developed metabarcodes for several groups of organisms: fungi, bryophytes, enchytraeids, beetles and birds. The ability of these metabarcodes to amplify the target groups was systematically evaluated by (i) in silico PCRs using all standard sequences in the EMBL public database as templates, (ii) in vitro PCRs of DNA extracts from surface soil samples from a site in Varanger, northern Norway and (iii) in vitro PCRs of DNA extracts from permanently frozen sediment samples of late-Pleistocene age (~16,000-50,000 years bp) from two Siberian sites, Duvanny Yar and Main River. Comparison of the results from the in silico PCR with those obtained in vitro showed that the in silico approach offered a reliable estimate of the suitability of a marker. All target groups were detected in the environmental DNA, but we found large variation in the level of detection among the groups and between modern and ancient samples. Success rates for the Pleistocene samples were highest for fungal DNA, whereas bryophyte, beetle and bird sequences could also be retrieved, but to a much lesser degree. The metabarcoding approach has considerable potential for biodiversity screening of modern samples and also as a palaeoecological tool.
authors.affiliation: National Centre for Biosystematics, Natural History Museum, University of Oslo, Oslo, Norway. laura.epp@nhm.uio.no
authors.forename: Laura S
authors.initials: LS
authors.lastname: Epp
authors.forename: Sanne
authors.initials: S
authors.lastname: Boessenkool
authors.forename: Eva P
authors.initials: EP
authors.lastname: Bellemain
authors.forename: James
authors.initials: J
authors.lastname: Haile
authors.forename: Alfonso
authors.initials: A
authors.lastname: Esposito
authors.forename: Tiayyba
authors.initials: T
authors.lastname: Riaz
authors.forename: Christer
authors.initials: C
authors.lastname: Erséus
authors.forename: Vladimir I
authors.initials: VI
authors.lastname: Gusarov
authors.forename: Mary E
authors.initials: ME
authors.lastname: Edwards
authors.forename: Arild
authors.initials: A
authors.lastname: Johnsen
authors.forename: Hans K
authors.initials: HK
authors.lastname: Stenøien
authors.forename: Kristian
authors.initials: K
authors.lastname: Hassel
authors.forename: Håvard
authors.initials: H
authors.lastname: Kauserud
authors.forename: Nigel G
authors.initials: NG
authors.lastname: Yoccoz
authors.forename: Kari Anne
authors.initials: KA
authors.lastname: Bråthen
authors.forename: Eske
authors.initials: E
authors.lastname: Willerslev
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.forename: Eric
authors.initials: E
authors.lastname: Coissac
authors.forename: Christian
authors.initials: C
authors.lastname: Brochmann
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000032:analysis* / Q000302:isolation & purification; D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D017931:DNA Primers; D017753:Ecosystem; D004777:Environment; D005580:Fossils; D019015:Geologic Sediments / Q000737:chemistry*; D009664:Norway; D016133:Polymerase Chain Reaction / Q000379:methods; D012800:Siberia; D012987:Soil / Q000737:chemistry*; D012988:Soil Microbiology
chemical_list: D017931:DNA Primers; D012987:Soil; D004247:DNA