New environmental metabarcodes for analysing soil DNA: Potential for studying past and present ecosystems

Molecular Ecology

Volumn 21, Issue 8, 2012, Pages 1821-1833

  Epp, Laura S ^a   Boessenkool, Sanne ^a   Bellemain, Eva P ^a   Haile, James ^b,c   Esposito, Alfonso ^a,i   Riaz, Tiayyba ^d   Erséus, Christer ^e   Gusarov, Vladimir I ^a   Edwards, Mary E ^f   Johnsen, Arild ^a   Stenøien, Hans K ^g   Hassel, Kristian ^g   Kauserud, Håvard ^a   Yoccoz, Nigel G ^h   Bråthen, Kari Anne ^h   Willerslev, Eske ^b   Taberlet, Pierre ^d   Coissac, Eric ^d   Brochmann, Christian ^a  

^a UNIVERSITY OF OSLO   (Norway)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c MURDOCH UNIVERSITY   (Australia)

^d UNIVERSITÉ JOSEPH FOURIER   (France)

^e UNIVERSITY OF GOTHENBURG   (Sweden)

^f UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^g NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^h UNIVERSITY OF TROMSØ   (Norway)

ⁱ FREE UNIVERSITY OF BOZEN BOLZANO   (Italy)

Author keywords

ancient DNA; Arctic; environmental DNA; metabarcoding; primers

Indexed keywords

DNA; PRIMER DNA;

ANIMAL; ARTICLE; BIOLOGY; CHEMISTRY; DNA BARCODING; ECOSYSTEM; ENVIRONMENT; FOSSIL; ISOLATION AND PURIFICATION; METHODOLOGY; MICROBIOLOGY; NORWAY; POLYMERASE CHAIN REACTION; RUSSIAN FEDERATION; SEDIMENT; SOIL;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA; DNA BARCODING, TAXONOMIC; DNA PRIMERS; ECOSYSTEM; ENVIRONMENT; FOSSILS; GEOLOGIC SEDIMENTS; NORWAY; POLYMERASE CHAIN REACTION; SIBERIA; SOIL; SOIL MICROBIOLOGY;

AVES; BRYOPHYTES; COLEOPTERA; ENCHYTRAEIDAE; FUNGI;

EID: 84859621660     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05537.x     Document Type: Article

References (66)

1. Alfimov AV, Berman DI, Sher AV, (2003) Tundra-steppe insect assemblages and reconstruction of Late Pleistocene climate in the lower reaches of the Kolyma River. Zoologichesky Zhurnal, 82, 281-300 (in Russian).
2. Bellemain EP, Carlsen T, Brochmann C, Coissac E, Taberlet P, Kauserud H, (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.
3. Beutel RG, Friedrich F, Leschen RAB, (2009) Charles Darwin, beetles and phylogenetics. Naturwissenschaften, 96, 1293-1312.
4. Birkemoe T, Coulson SJ, Somme L, (2000) Life cycles and population dynamics of enchytraeids (Oligochaeta) from the High Arctic. Canadian Journal of Zoology-Revue Canadienne De Zoologie, 78, 2079-2086.
5. Blinnikov MS, Gaglioti BV, Walker DA, Wooller MJ, Zazula GD, (2011) Pleistocene graminoid-dominated ecosystems in the Arctic. Quaternary Science Reviews, 30, 2906-2929.
6. Boessenkool S, Epp LS, Haile J, et al. (2012) Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Molecular Ecology, 21, 1806-1815.
7. Briones MJI, Ineson P, Heinemeyer A, (2007) Predicting potential impacts of climate change on the geographical distribution of enchytraeids: a meta-analysis approach. Global Change Biology, 13, 2252-2269.
8. Callaghan TV, Bjorn LO, Chernov Y, et al. (2004) Biodiversity, distributions and adaptations of arctic species in the context of environmental change. Ambio, 33, 404-417.
9. Cochrane G, Akhtar R, Bonfield J, et al. (2009) Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Research, 37, D19-D25.
10. Coolen MJL, Saenz JP, Giosan L, et al. (2009) DNA and lipid molecular stratigraphic records of haptophyte succession in the Black Sea during the Holocene. Earth and Planetary Science Letters, 284, 610-621.
11. Coolen MJL, van de Giessen J, Zhu EY, Wuchter C, (2011) Bioavailability of soil organic matter and microbial community dynamics upon permafrost thaw. Environmental Microbiology, 13, 2299-2314.
12. Creer S, Fonseca VG, Porazinska DL, et al. (2010) Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19, 4-20.
13. De Rijk P, Robbrecht E, de Hoog S, Caers A, Van de Peer Y, De Wachter R, (1999) Database on the structure of large subunit ribosomal RNA. Nucleic Acids Research, 27, 174-178.
14. Denayer FO, Van Haluwyn C, de Foucault B, Schumacker R, Colein P, (1999) Use of bryological communities as a diagnostic tool of heavy metal soil contamination (Cd, Pb, Zn) in northern France. Plant Ecology, 140, 191-201.
15. Dieffenbach CW, Lowe TM, Dveksler GS, (1993) General concepts for PCR primer design. Genome Research, 3, S30-S37.
16. Dunbar J, Takala S, Barns SM, Davis JA, Kuske CR, (1999) Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning. Applied and Environmental Microbiology, 65, 1662-1669.
17. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R, (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27, 2194-2200.
18. Elias SA, (2006) Quaternary beetle research: the state of the art. Quaternary Science Reviews, 25, 1731-1737.
19. Epp LS, Stoof-Leichsenring KR, Trauth MH, Tiedemann R, (2011) Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC). Molecular Ecology Resources, 11, 842-853.
20. Ficetola GF, Coissac E, Zundel S, et al. (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics, 11, 434.
21. Gangneux C, Akpa-Vinceslas M, Sauvage H, Desaire S, Houot S, Laval K, (2011) Fungal, bacterial and plant dsDNA contributions to soil total DNA extracted from silty soils under different farming practices: relationships with chloroform-labile carbon. Soil Biology & Biochemistry, 43, 431-437.
22. Gigli E, Rasmussen M, Civit S, et al. (2009) An improved PCR method for endogenous DNA retrieval in contaminated Neandertal samples based on the use of blocking primers. Journal of Archaeological Science, 36, 2676-2679.
23. Haile J, Holdaway R, Oliver K, et al. (2007) Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution, 24, 982-989.
24. Haile J, Froese DG, MacPhee RDE, et al. (2009) Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences of the United States of America, 106, 22352-22357.
25. Hajibabaei M, Smith MA, Janzen DH, Rodriguez JJ, Whitfield JB, Hebert PDN, (2006) A minimalist barcode can identify a specimen whose DNA is degraded. Molecular Ecology Notes, 6, 959-964.
26. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ, (2011) Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using River Benthos. PLoS ONE, 6, e17497.
27. Hebert PDN, Cywinska A, Ball SL, DeWaard JR, (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences, 270, 313-321.
28. Hibbett DS, Binder M, Bischoff JF, et al. (2007) A higher-level phylogenetic classification of the Fungi. Mycological Research, 111, 509-547.
29. Hickson RE, Simon C, Copper A, Spicer GS, Sullivan J, Penny D, (1996) Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Molecular Biology and Evolution, 13, 150-169.
30. Hofreiter M, Mead JI, Martin P, Poinar HN, (2003) Molecular caving. Current Biology, 13, R693-R695.
31. Jaensch S, Rombke J, Didden W, (2005) The use of enchytraeids in ecological soil classification and assessment concepts. Ecotoxicology and Environmental Safety, 62, 266-277.
32. Kalendar R, Lee D, Schulman AH, (2009) FastPCR software for PCR primer and probe design and repeat search. Genes, Genomes and Genomics, 3, 1-14.
33. Kuzmina SA, Sher AV, Edwards ME, et al. (2011) The late Pleistocene environment of the Eastern West Beringia based on the principal section at the Main River, Chukotka. Quaternary Science Reviews, 30, 2091-2106.
34. Leonard JA, Shanks O, Hofreiter M, et al. (2007) Animal DNA in PCR reagents plagues ancient DNA research. Journal of Archaeological Science, 34, 1361-1366.
35. Levy-Booth DJ, Campbell RG, Gulden RH, et al. (2007) Cycling of extracellular DNA in the soil environment. Soil Biology & Biochemistry, 39, 2977-2991.
36. Lewis K, Epstein S, Godoy VG, Hong SH, (2008) Intact DNA in ancient permafrost. Trends in Microbiology, 16, 92-94.
37. Lindo Z, Gonzalez A, (2010) The Bryosphere: an integral and influential component of the earth's biosphere. Ecosystems, 13, 612-627.
38. Lydolph MC, Jacobsen J, Arctander P, et al. (2005) Beringian paleoecology inferred from permafrost-preserved fungal DNA. Applied and Environmental Microbiology, 71, 1012-1017.
39. Mäki-Petäys H, Corander J, Aalto J, Liukkonen T, Helle P, Orell M, (2007) No genetic evidence of sex-biased dispersal in a lekking bird, the capercaillie (Tetrao urogallus). Journal of Evolutionary Biology, 20, 865-873.
40. Meusnier I, Singer GAC, Landry JF, Hickey DA, Hebert PDN, Hajibabaei M, (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics, 9, 214.
41. Meyerhans A, Vartanian JP, Wainhobson S, (1990) DNA recombination during PCR. Nucleic Acids Research, 18, 1687-1691.
42. Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R, (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology, 57, 750-757.
43. Nimis PL, Fumagalli F, Bizzotto A, Codogno M, Skert N, (2002) Bryophytes as indicators of trace metals pollution in the River Brenta (NE Italy). Science of the Total Environment, 286, 233-242.
44. Ozerskaya S, Kochkina G, Ivanushkina N, Gilichinsky DA, (2009) Fungi in permafrost. Soil Biology, 16, 85-95.
45. Pääbo S, Poinar H, Serre D, et al. (2004) Genetic analyses from ancient DNA. Annual Review of Genetics, 38, 645-679.
46. Pietramellara G, Ascher J, Borgogni F, Ceccherini MT, Guerri G, Nannipieri P, (2009) Extracellular DNA in soil and sediment: fate and ecological relevance. Biology and Fertility of Soils, 45, 219-235.
47. Pompanon F, Coissac E, Taberlet P, (2011) Metabarcoding, a new way to analyze biodiversity. Biofutur, 30, 30-32.
48. Rappé MS, Giovannoni SJ, (2003) The uncultured microbial majority. Annual Review of Microbiology, 57, 369-394.
49. Raupach MJ, Astrin JJ, Hannig K, Peters MK, Stoeckle MY, Wagele JW, (2010) Molecular species identification of Central European ground beetles (Coleoptera: Carabidae) using nuclear rDNA expansion segments and DNA barcodes. Frontiers in Zoology, 7, 26.
50. Ravolainen VT, Bråthen KA, Ims RA, Yoccoz NG, Henden J-A, Killengreen ST, (2011) Rapid, landscape scale responses in riparian tundra vegetation to exclusion of small and large mammalian herbivores. Basic and Applied Ecology, 12, 643-653.
51. Regnaut S, Lucas FS, Fumagalli L, (2006) DNA degradation in avian faecal samples and feasibility of non-invasive genetic studies of threatened capercaillie populations. Conservation Genetics, 7, 449-453.
52. Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E, (2011) ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Research, 39, e145.
53. Sher AV, Kuzmina SA, Kuznetsova TV, Sulerzhitsky LD, (2005) New insights into the Weichselian environment and climate of the East Siberian Arctic, derived from fossil insects, plants, and mammals. Quaternary Science Reviews, 24, 533-569.
54. Shokralla S, Zhou X, Janzen DH, et al. (2011) Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS ONE, 6, e21252.
55. Sonnenberg R, Nolte AW, Tautz D, (2007) An evaluation of LSU rDNA D1-D2 sequences for their use in species identification. Frontiers in Zoology, 4, 6.
56. Sønstebø JH, Gielly L, Brysting AK, et al. (2010) Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate. Molecular Ecology Resources, 10, 1009-1018.
57. Stackebrandt E, Liesack W, Goebel BM, (1993) Bacterial diversity in a soil sample from a subtropical australian environment as determined by 16S rDNA analysis. FASEB Journal, 7, 232-236.
58. Taberlet P, Coissac E, Pompanon F, et al. (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research, 35, e14.
59. Ullman JD, Aho AV, Hirschberg DS, (1976) Bounds on the complexity of the longest common subsequence problem. Journal of the ACM, 23, 1-12.
60. Valentini A, Miquel C, Nawaz MA, et al. (2009a) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Resources, 9, 51-60.
61. Valentini A, Pompanon F, Taberlet P, (2009b) DNA barcoding for ecologists. Trends in Ecology & Evolution, 24, 110-117.
62. Vestheim H, Jarman SN, (2008) Blocking primers to enhance PCR amplification of rare sequences in mixed samples-a case study on prey DNA in Antarctic krill stomachs. Frontiers in Zoology, 5, 12.
63. White T, Bruns T, Lee S, Taylor J, (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR-Protocols A Guide to Methods and Applications (eds, Innis MA, Gelfand DH, Sninski JJ, and, White TJ,), pp. 315-322. Academic Press, San Diego.
64. Willerslev E, Hansen AJ, Binladen J, et al. (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300, 791-795.
65. Willerslev E, Cappellini E, Boomsma W, et al. (2007) Ancient biomolecules from deep ice cores reveal a forested Southern Greenland. Science, 317, 111-114.
66. Xie CF, Lou HX, (2009) Secondary metabolites in Bryophytes: an ecological aspect. Chemistry & Biodiversity, 6, 303-312.