Particle size distribution and optimal capture of aqueous macrobial eDNA

Methods in Ecology and Evolution

Volumn 5, Issue 7, 2014, Pages 676-684

  Turner, Cameron R ^a   Barnes, Matthew A ^a   Xu, Charles C Y ^a   Jones, Stuart E ^a   Jerde, Christopher L ^a   Lodge, David M ^a  

^a UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

Aquatic ecosystems; Ecological monitoring; Environmental DNA; Genetic monitoring; Particle size analysis; Rare species; Sampling methods

Indexed keywords

EID: 84904345282     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12206     Document Type: Article

References (78)

1. Barnes, M.A., Turner, C.R., Jerde, C.L., Renshaw, M.A., Chadderton, W.L. & Lodge, D.M. (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environmental Science & Technology, 48, 1819-1827.
2. Bloesch, J. (1995) Mechanisms, measurement and importance of sediment resuspension in lakes. Marine and Freshwater Research, 46, 295-304.
3. Brewin, R.J.W., Sathyendranath, S., Lange, P.K. & Tilstone, G. (2014) Comparison of two methods to derive the size-structure of natural populations of phytoplankton. Deep Sea Research Part I: Oceanographic Research Papers, 85, 72-79.
4. Buffle, J. & Lepard, G.G. (1995) Characterization of aquatic colloids and macromolecules. 2. Key role of physical structures on analytical results. Environmental Science & Technology, 29, 2176-2184.
5. Burd, A.B. & Jackson, G.A. (2009) Particle aggregation. Annual Review of Marine Science, 1, 65-90.
6. Caldwell, J., Payment, P. & Villemur, R. (2011). Mitochondrial DNA as source tracking markers of fecal contamination. Microbial Source Tracking: Methods, Applications, and Case Studies (eds C. Hagedorn, A.R. Blanch & V.J. Harwood ), pp. 229-250. Springer, New York, NY.
7. Cary, S.C., Hicks, B.J., Coyne, K.J., Rueckert, A., Gemmill, C.E.C. & Barnett, C.M.E. (2007). A sensitive genetic-based detection capability for Didymosphenia geminata (Lyngbye) M. Schmidt: Phases Two and Three. Hamilton, New Zealand. http://cber.bio.waikato.ac.nz/PDFs/CBER_62_Early_detection_Cary_Hicks_2007_10_19_final_approved_by_MAFBNZ.pdf
8. Collins, R.A., Armstrong, K.F., Holyoake, A.J. & Keeling, S. (2013) Something in the water: biosecurity monitoring of ornamental fish imports using environmental DNA. Biological Invasions, 15, 1209-1215.
9. Corinaldesi, C., Danovaro, R. & Dell'Anno, A. (2005) Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Applied Environmental Microbiology, 71, 46-50.
10. Corinaldesi, C., Barucca, M., Luna, G.M. & Dell'Anno, A. (2011) Preservation, origin and genetic imprint of extracellular DNA in permanently anoxic deep-sea sediments. Molecular Ecology, 20, 642-654.
11. Coyne, K.J., Handy, S.M., Demir, E., Whereat, E.B., Hutchins, D.A., Portune, K.J., Doblin, M.A. & Cary, S.C. (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.
12. Danielsson, L.G. (1982) On the use of filters for distinguishing between dissolved and particulate fractions in natural waters. Water Research, 16, 179-182.
13. Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P. & Miaud, C. (2011) Persistence of environmental DNA in freshwater ecosystems. PLoS ONE, 6, e23398.
14. 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.
15. Douville, M., Gagné, F., Blaise, C. & André, C. (2007) Occurrence and persistence of Bacillus thuringiensis (Bt) and transgenic Bt corn cry1Ab gene from an aquatic environment. Ecotoxicology and Environmental Safety, 66, 195-203.
16. Droppo, I.G. (2006). Filtration in particle size analysis. Encyclopedia of Analytical Chemistry (ed R.A. Meyers ), pp. 1-16. John Wiley & Sons, Ltd, Hoboken, NJ.
17. Ellison, S.L.R., English, C.A., Burns, M.J. & Keer, J.T. (2006). Routes to improving the reliability of low level DNA analysis using real-time PCR. BMC Biotechnology, 6, 33.
18. Ficetola, G.F., Miaud, C., Pompanon, F. & Taberlet, P. (2008) Species detection using environmental DNA from water samples. Biology Letters, 4, 423-425.
19. Flindt, R. (2006). Amazing Numbers in Biology, 6th edn. (ed. D. Czeschlik ). Springer-Verlag, Berlin, Heidelberg, Germany.
20. Foppen, J.W., Orup, C., Adell, R., Poulalion, V. & Uhlenbrook, S. (2011) Using multiple artificial DNA tracers in hydrology. Hydrological Processes, 25, 3101-3106.
21. Gallup, J. (2011). qPCR inhibition and amplification of difficult templates. PCR Troubleshooting and Optimization: The Essential Guide (eds S. Kennedy & N. Oswald ), pp. 23-65. Caister Academic Press, Norfolk, UK.
22. Gibson, K.E., Schwab, K.J., Spencer, S.K. & Borchardt, M.A. (2012) Measuring and mitigating inhibition during quantitative real time PCR analysis of viral nucleic acid extracts from large-volume environmental water samples. Water Research, 46, 4281-4291.
23. Goldberg, C.S., Pilliod, D.S., Arkle, R.S. & Waits, L.P. (2011) Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS ONE, 6, e22746.
24. Håkanson, L. (2006) Suspended Particulate Matter in Lakes, Rivers, and Marine Systems. The Blackburn Press, Caldwell, New Jersey, USA.
25. Hartman, L.J., Coyne, S.R. & Norwood, D.A. (2005) Development of a novel internal positive control for Taqman based assays. Molecular and Cellular Probes, 19, 51-59.
26. Hata, A., Katayama, H., Kitajima, M., Visvanathan, C., Nol, C. & Furumai, H. (2011) Validation of internal controls for extraction and amplification of nucleic acids from enteric viruses in water samples. Applied and Environmental Microbiology, 77, 4336-4343.
27. Hedman, J. & Rådström, P. (2013). Overcoming inhibition in real-time diagnostic PCR. PCR Detection of Microbial Pathogens (ed M. Wilks ), pp. 17-48. Humana Press, Totowa, NJ.
28. Hickel, W. (1984) Seston retention by Whatman GF/C glass-fiber filters. Marine Ecology Progress Series, 16, 185-191.
29. Hochmeister, M.N., Budowle, B., Jung, J., Borer, U.V., Comey, C.T. & Dirnhofer, R. (1991) PCR-based typing of DNA extracted from cigarette butts. International Journal of Legal Medicine, 104, 229-233.
30. Hofreiter, M., Mead, J.I., Martin, P. & Poinar, H.N. (2003) Molecular caving. Current Biology, 13, R693-R695.
31. Isao, K., Hara, S., Terauchi, K. & Kogure, K. (1990) Role of sub-micrometre particles in the ocean. Nature, 345, 242-244.
32. Jerde, C.L., Mahon, A.R., Chadderton, W.L. & Lodge, D.M. (2011) "Sight-unseen" detection of rare species using environmental DNA. Conservation Letters, 4, 150-157.
33. Kibbe, W.A. (2007) OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Research, 35, W43-W46.
34. Knefelkamp, B., Carstens, K. & Wiltshire, K.H. (2007) Comparison of different filter types on chlorophyll-a retention and nutrient measurements. Journal of Experimental Marine Biology and Ecology, 345, 61-70.
35. Kortbaoui, R., Locas, A., Imbeau, M., Payment, P. & Villemur, R. (2009) Universal mitochondrial PCR combined with species-specific dot-blot assay as a source-tracking method of human, bovine, chicken, ovine, and porcine in fecal-contaminated surface water. Water Research, 43, 2002-2010.
36. Lee, S., Kang, Y. & Fuhrman, J. (1995) Imperfect retention of natural bacterioplankton cells by glass fiber filters. Marine Ecology Progress Series, 119, 285-290.
37. Liang, Z. & Keeley, A. (2013) Filtration recovery of extracellular DNA from environmental water samples. Environmental Science & Technology, 47, 9324-9331.
38. Lloyd, K.G., Macgregor, B.J. & Teske, A. (2010). Quantitative PCR methods for RNA and DNA in marine sediments: maximizing yield while overcoming inhibition. FEMS Microbiology Ecology, 72, 143-151.
39. Lodge, D.M., Turner, C.R., Jerde, C.L., Barnes, M.A., Chadderton, L., Egan, S.P., Feder, J.L., Mahon, A.R. & Pfrender, M.E. (2012) Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Molecular Ecology, 21, 2555-2558.
40. Lowe, S., Browne, M., Boudjelas, S. & De Poorter, M. (2004). 100 of the World's Worst Invasive Alien Species, a Selection From the Global Invasive Species Database. World Conservation Union (IUCN), Auckland, New Zealand. http://www.issg.org/pdf/publications/worst_100/english_100_worst.pdf
41. Maggi, F. (2013) The settling velocity of mineral, biomineral, and biological particles and aggregates in water. Journal of Geophysical Research: Oceans, 118, 2118-2132.
42. Martellini, A., Payment, P. & Villemur, R. (2005) Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Research, 39, 541-548.
43. Maruyama, F., Tani, K., Kenzaka, T., Yamaguchi, N. & Nasu, M. (2008) Application of real-time long and short polymerase chain reaction for sensitive monitoring of the fate of extracellular plasmid DNA introduced into river waters. Microbes and Environments, 23, 229-236.
44. Matsui, K., Honjo, M. & Kawabata, Z. (2001) Estimation of the fate of dissolved DNA in thermally stratified lake water from the stability of exogenous plasmid DNA. Aquatic Microbial Ecology, 26, 95-102.
45. Matsui, K., Ishii, N., Honjo, M. & Kawabata, Z. (2004) Use of the SYBR Green I fluorescent dye and a centrifugal filter device for rapid determination of dissolved DNA concentration in fresh water. Aquatic Microbial Ecology, 36, 99-105.
46. McDevitt, J.J., Lees, P.S.J., Merz, W.G. & Schwab, K.J. (2007) Inhibition of quantitative PCR analysis of fungal conidia associated with indoor air particulate matter. Aerobiologia, 23, 35-45.
47. Minamoto, T., Yamanaka, H., Takahara, T., Honjo, M.N. & Kawabata, Z. (2011) Surveillance of fish species composition using environmental DNA. Limnology, 13, 193-197.
48. Morán, X., Gasol, J., Arin, L. & Estrada, M. (1999) A comparison between glass fiber and membrane filters for the estimation of phytoplankton POC and DOC production. Marine Ecology Progress Series, 187, 31-41.
49. Murgia, M., Pizzo, P., Sandona, D., Zanovello, P., Ruzzuto, R. & Virgilioll, F.Di. (1992) Mitochondrial DNA is not fragmented during apoptosis. Journal of Biological Chemistry, 267, 10939-10941.
50. Ogram, A., Sayler, G.S. & Barkay, T. (1987) The extraction and purification of microbial DNA from sediments. Journal of Microbiological Methods, 7, 57-66.
51. Paul, J.H., Cazares, L.H., David, A.W., DeFlaun, M.F. & Jeffrey, W.H. (1991) The distribution of dissolved DNA in an oligotrophic and a eutrophic river of Southwest Florida. Hydrobiologia, 218, 53-63.
52. Piaggio, A.J., Engeman, R.M., Hopken, M.W., Humphrey, J.S., Keacher, K.L., Bruce, W.E. & Avery, M.L. (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.
53. Pilliod, D., Goldberg, C., Arkle, R.S. & Waits, L.P. (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.
54. Pilliod, D.S., Goldberg, C.S., Arkle, R.S. & Waits, L.P. (2014) Factors influencing detection of eDNA from a stream-dwelling amphibian. Molecular Ecology Resources, 14, 109-116.
55. Poté, J., Mavingui, P., Navarro, E., Rosselli, W., Wildi, W., Simonet, P. & Vogel, T.M. (2009) Extracellular plant DNA in Geneva groundwater and traditional artesian drinking water fountains. Chemosphere, 75, 498-504.
56. Rickwood, D. & Chambers, J.A. (1981) Evidence for protected regions of DNA in the mitochondrial nucleoid of Saccharomyces cerevisiae. Fems Microbiology Letters, 12, 187-190.
57. Robison, B.H. & Bailey, T. (1981) Sinking rates and dissolution of midwater fish fecal matter. Marine Biology, 65, 135-142.
58. Rosin, P. & Rammler, E. (1933) The laws governing the fineness of powdered coal. Journal of the Institute of Fuel, 7, 29-36.
59. Sabir, I.H., Torgersen, J., Haldorsen, S. & Aleström, P. (2002) DNA tracers with information capacity and high detection sensitivity tested in groundwater studies. Hydrogeology Journal, 7, 264-272.
60. Saeki, K., Ihyo, Y., Sakai, M. & Kunito, T. (2011) Strong adsorption of DNA molecules on humic acids. Environmental Chemistry Letters, 9, 505-509.
61. Schmidt, B.R., Kéry, M., Ursenbacher, S., Hyman, O.J. & Collins, J.P. (2013) Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods in Ecology and Evolution, 4, 646-653.
62. Schrader, C., Schielke, A., Ellerbroek, L. & Johne, R. (2012). PCR inhibitors - occurrence, properties and removal. Journal of Applied Microbiology, 113, 1014-1026.
63. Sheldon, R.W. (1972) Size separation of marine seston by membrane and glass-fiber filters. Limnology and Oceanography, 17, 494-498.
64. Sutherland, W.J., Bardsley, S., Clout, M., Depledge, M.H., Dicks, L.V., Fellman, L. et al. (2013) A horizon scan of global conservation issues for 2013. Trends in Ecology & Evolution, 28, 16-22.
65. Suzuki, H., Daimon, M., Awano, T., Umekage, S., Tanaka, T. & Kikuchi, Y. (2009) Characterization of extracellular DNA production and flocculation of the marine photosynthetic bacterium Rhodovulum sulfidophilum. Applied Microbiology and Biotechnology, 84, 349-356.
66. 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.
67. Takahara, T., Minamoto, T., Yamanaka, H., Doi, H. & Kawabata, Z. (2012) Estimation of fish biomass using environmental DNA. PLoS ONE, 7, e35868.
68. Tepper, C.G. & Studzinski, G.P. (1993) Resistance of mitochondrial DNA to degradation characterizes the apoptotic but not the necrotic mode of human leukemia cell death. Journal of Cellular Biochemistry, 52, 352-361.
69. Thompson, D.E., Rajal, V.B., De Batz, S. & Wuertz, S. (2006) Detection of Salmonella spp. in water using magnetic capture hybridization combined with PCR or real-time PCR. Journal of Water and Health, 4, 67-75.
70. Thomsen, P.F., Kielgast, J., Iversen, L.L., Wiuf, C., Rasmussen, M., Gilbert, M.T.P., Orlando, L. & Willerslev, E. (2012a) Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 2565-2573.
71. Thomsen, P.F., Kielgast, J., Iversen, L.L., Møller, P.R., Rasmussen, M. & Willerslev, E. (2012b) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE, 7, e41732.
72. Widmer, F., Seidler, R.J., Donegan, K.K. & Reed, G.L. (1997) Quantification of transgenic plant marker gene persistence in the field. Molecular Ecology, 6, 1-7.
73. Wilcox, T.M., McKelvey, K.S., Young, M.K., Jane, S.F., Lowe, W.H., Whiteley, A.R. & Schwartz, M.K. (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS ONE, 8, e59520.
74. Willerslev, E., Hansen, A.J., Binladen, J., Brand, T.B., Gilbert, M.T.P., Shapiro, B. et al. (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science, 300, 791-795.
75. Wotton, R.S. (ed.) (1994) The Biology of Particles in Aquatic Systems, 2nd edn. CRC Press, Boca Raton, Florida, USA.
76. Wotton, R.S. & Malmqvist, B. (2001) Feces in aquatic ecosystems. BioScience, 51, 537-544.
77. Zhan, A., Hulák, M., Sylvester, F., Huang, X., Adebayo, A.A., Abbott, C.L. et al. (2013) High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods in Ecology and Evolution, 4, 558-565.
78. Zobeck, T.M., Gill, T.E. & Popham, T.W. (1999) A two-parameter Weibull function to describe airborne dust particle size distributions. Earth Surface Processes and Landforms, 24, 943-955.