The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction

Molecular Ecology Resources

Volumn 15, Issue 1, 2015, Pages 168-176

  Renshaw, Mark A ^a   Olds, Brett P ^a,b   Jerde, Christopher L ^a,b   Mcveigh, Margaret M ^a   Lodge, David M ^a,b  

^a UNIVERSITY OF NOTRE DAME   (United States)

^b Unit 117   (United States)

Author keywords

Lepomis macrochirus; eDNA extraction; eDNA preservation; Environmental DNA

Indexed keywords

LEPOMIS MACROCHIRUS;

ALCOHOL DERIVATIVE; DNA; PHENOL;

FILTRATION; ISOLATION AND PURIFICATION; METAGENOMICS; PRESERVATION; PROCEDURES; TEMPERATURE;

ALCOHOLS; DNA; FILTRATION; METAGENOMICS; PHENOL; PRESERVATION, BIOLOGICAL; TEMPERATURE;

EID: 84923079413     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/1755-0998.12281     Document Type: Article

References (39)

1. Ahmed W, Goonetilleke A, Gardner T (2010) Human and bovine adenoviruses for the detection of source-specific fecal pollution in coastal waters in Australia. Water Research, 44, 4662-4673.
2. Ahmed W, Yusuf R, Hasan I et al. (2013) Fecal indicators and bacterial pathogens in bottled water from Dhaka, Bangladesh. Brazilian Journal of Microbiology, 44, 97-103.
3. Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science and Technology, 48, 1819-1827.
4. Converse RR, Griffith JF, Noble RT, Haugland RA, Schiff KC, Weisberg SB (2012) Correlation between quantitative PCR and culture-based methods for measuring Enterococcus spp. over various temporal scales at three California marine beaches. Applied and Environmental Microbiology, 78, 1237-1242.
5. Coyne KJ, Handy SM, Demir E et al. (2005) Improved quantitative real-time PCR assays for enumeration of harmful algal species in field samples using an exogenous DNA reference standard. Limnology and Oceanography: Methods, 3, 381-391.
6. Deiner K, Altermatt F (2014) Transport distance of invertebrate environmental DNA in a natural river. PLoS ONE, 9, e88786.
7. Dejean T, Valentini A, Miquel C, Taberlet P, Bellemain E, Miaud C (2012) Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology, 49, 953-959.
8. Foote AD, Thomsen PF, Sveegaard S et al. (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE, 7, e41781.
9. Goldberg CS, Pilliod DS, Arkle RS, Waits LP (2011) Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS ONE, 6, e22746.
10. Goldberg CS, Sepulveda A, Ray A et al. (2013) Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshwater Science, 32, 792-800.
11. Herath P, Hoover GA, Angelini E, Moorman GW (2010) Detection of elm yellows phytoplasma in elms and insects using real-time PCR. Plant Disease, 94, 1355-1360.
12. Jerde CL, Chadderton WL, Mahon AR et al. (2013) Detection of Asian carp DNA as part of a Great Lakes basin-wide surveillance program. Canadian Journal of Fisheries and Aquatic Sciences, 70, 522-526.
13. Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using environmental DNA to census marine fishes in a large mesocosm. PLoS ONE, 9, e86175.
14. Kilpatrick CW (2002) Noncryogenic preservation of mammalian tissues for DNA extraction: an assessment of storage methods. Biochemical Genetics, 40, 53-62.
15. Liang Z, Keeley A (2013) Filtration recovery of extracellular DNA from environmental water samples. Environmental Science and Technology, 47, 9324-9331.
16. Lodge DM, Turner CR, Jerde CL et al. (2012) Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Molecular Ecology, 21, 2555-2558.
17. Longmire JL, Maltbie M, Baker RJ (1997) Use of 'lysis buffer' in DNA isolation and its implications for museum collections. Museum of Texas Tech University, 163, 1-3.
18. Lu H, Schmidt MA, Jensen KF (2005) A microfluidic electroporation device for cell lysis. Lab on a Chip, 5, 23-29.
19. Mahon AR, Rohly A, Budny M et al. (2010) Environmental DNA monitoring and surveillance: standard operation procedures. Report to the United States Army Corps of Engineers, Environmental Laboratories, Cooperative Environmental Studies Unit, Vicksburg, Mississippi.
20. Miller HC (2006) Cloacal and buccal swabs are a reliable source of DNA for microsatellite genotyping of reptiles. Conservation Genetics, 7, 1001-1003.
21. Miller BF, DeYoung RW, Campbell TA, Laseter BR, Ford WM, Miller KV (2010) Fine-scale genetic and social structuring in a central Appalachian white-tailed deer herd. Journal of Mammalogy, 91, 681-689.
22. Minamoto T, Yamanaka H, Takahara T, Honjo MN, Kawabata Z (2012) Surveillance of fish species composition using environmental DNA. Limnology, 13, 193-197.
23. Olson ZH, Briggler JT, Williams RN (2012) An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water. Wildlife Research, 39, 629-636.
24. Piaggio AJ, Engeman RM, Hopken MW et al. (2014) Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA. Molecular Ecology Resources, 14, 374-380.
25. Pilliod DS, Goldberg CS, Arkle RS, Waits LP (2013) Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Canadian Journal of Fisheries and Aquatic Sciences, 70, 1123-1130.
26. Pilliod DS, Goldberg CS, Arkle RS, Waits LP (2014) Factors influencing detection of eDNA from a stream-dwelling amphibian. Molecular Ecology Resources, 14, 109-116.
27. Rhodes KL, Lewis RI, Chapman RW, Sadovy Y (2003) Genetic structure of camouflage grouper, Epinephelus polyphekadion (Pisces: Serranidae), in the western central Pacific. Marine Biology, 142, 771-776.
28. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Harbor Laboratory Press, Cold Spring Harbor, New York.
29. Seutin G, White BN, Boag PT (1991) Preservation of avian blood and tissue samples for DNA analyses. Canadian Journal of Zoology, 69, 82-90.
30. Siuda W, Gude H (1996) Determination of dissolved deoxyribonucleic acid concentration in lake water. Aquatic Microbial Ecology, 11, 193-202.
31. Smith S, Hughes J (2008) Microsatellite and mitochondrial DNA variation defines island genetic reservoirs for reintroductions of an endangered Australian marsupial, Perameles bougainville. Conservation Genetics, 9, 547-557.
32. Stark KDC, Nicolet J, Frey J (1998) Detection of Mycoplasma hyopneumoniae by air sampling with a nested PCR assay. Applied and Environmental Microbiology, 64, 543-548.
33. Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z (2012) Estimation of fish biomass using environmental DNA. PLoS ONE, 7, e35868.
34. Takahara T, Minamoto T, Doi H (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS ONE, 8, e56584.
35. Thomsen PF, Kielgast J, Iversen LL et al. (2012a) Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 2565-2573.
36. Thomsen PF, Kielgast J, Iversen LL, Moller PR, Rasmussen M, Willerslev E (2012b) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE, 7, e41732.
37. Turner CR, Barnes MA, Xu CCY, Jones SE, Jerde CL, Lodge DM (2014) Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods in Ecology and Evolution, doi: 10.1111/2041-210X.12206, in press.
38. Wilcox TM, McKelvey KS, Young MK et al. (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE, 8, e59520.
39. Wirgin I, Grunwald C, Stabile J, Waldman JR (2010) Delineation of discrete population segments of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequence analysis. Conservation Genetics, 11, 689-708.