Extracting DNA from whole organism homogenates and the risk of false positives in PCR based diet studies: A case study using spiny lobster larvae

Journal of Experimental Marine Biology and Ecology

Volumn 441, Issue , 2013, Pages 1-6

  O'Rorke, R ^a   Jeffs, A G ^a   Fitzgibbon, Q ^b   Chow, S ^c   Lavery, S ^a,d  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF TASMANIA   (Australia)

^c FISHERIES RESEARCH AGENCY   (Japan)

^d UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Contamination; Diet; Larvae; PCR; Phyllosoma; Plankton

Indexed keywords

ARTIFICIAL DIET; BLEACHING; COMMERCIALIZATION; DNA; HOMOGENEITY; LARVA; LOBSTER; POLYMERASE CHAIN REACTION; PREDATOR; RISK; ZOOPLANKTON;

ANIMALIA; PALINURIDAE;

EID: 84873301534     PISSN: 00220981     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jembe.2013.01.003     Document Type: Article

References (53)

1. Albaina A., Fox C.J., Taylor N., Hunter E., Maillard M., Taylor M.I. A TaqMan real-time PCR based assay targeting plaice (Pleuronectes platessa L.) DNA to detect predation by the brown shrimp (Crangon crangon L.) and the shore crab (Carcinus maenas L.) - assay development and validation. J. Exp. Mar. Biol. Ecol. 2010, 391(1-2):178-189.
2. Beja-Pereira A., Oliveira R., Alves P.C., Schwartz M.K., Luikart G. Advancing ecological understandings through technological transformations in noninvasive genetics. Mol. Ecol. Resour. 2009, 9(5):1279-1301. (Blackwell Publishing Ltd). 10.1111/j.1755-0998.2009.02699.x.
3. Blankenship L., Yayanos A. Universal primers and PCR of gut contents to study marine invertebrate diets. Mol. Ecol. 2005, 14(3):891-899.
4. Bonnet D., Lindeque P.K., Harris R.P. Sagitta setosa predation on Calanus helgolandicus in the English Channel. J. Plankton Res. 2010, 32(5):725-737. 10.1093/plankt/fbq008.
5. Chen Y., Giles K.L., Payton M.E., Greenstone M.H. Identifying key cereal aphid predators by molecular gut analysis. Mol. Ecol. 2000, 9(11):1887-1898. 10.1046/j.1365-294x.2000.01100.x.
6. Chittleborough R.G., Thomas L.R. Larval ecology of the Western Australian marine crayfish, with notes upon other palinurid larvae from the eastern Indian Ocean. Aust. J. Mar. Freshw. Res. 1969, 20:199-223.
7. Chow S., Suzuki S., Matsunaga T., Lavery S., Jeffs A.G., Takeyama H. Investigation on natural diets of larval marine animals using peptide nucleic acid-directed polymerase chain reaction clamping. Mar. Biotechnol. 2010, 13(2):305-313. 10.1007/s10126-010-9301-3.
8. Cox S., Bruce M. Feeding behaviour and associated sensory mechanisms of stage I-III phyllosoma of Jasus edwardsii and Jasus verreauxi. J. Mar. Biol. Assoc. U. K. 2003, 83(3):465-468.
9. Dennis D.M., Pitcher C.R., Skewes T.D. Distribution and transport pathways of Panulirus ornatus (Fabricius, 1776) and Panulirus spp. larvae in the Coral Sea, Australia. Mar. Freshw. Res. 2001, 52:1175-1185.
10. Durbin E., Casas M., Rynearson T., Smith D. Measurement of copepod predation on nauplii using qPCR of the cytochrome oxidase I gene. Mar. Biol. 2008, 153(4):699-707.
11. Fitzgibbon Q.P., Battaglene S.C. Effect of water temperature on the development and energetics of early, mid and late-stage phyllosoma of spiny lobster Sagmariasus verreauxi. Aquaculture 2012, 344-349:153-160.
12. Fitzgibbon Q.P., Battaglene S.C. Effect of photoperiod on the culture of early-stage phyllosoma and metamorphosis of spiny lobster (Sagmariasus verreauxi). Aquaculture 2012, 368-369:48-54.
13. Fournier V., Hagler J., Daane K., León J., Groves R. Identifying the predator complex of Homalodisca vitripennis (Hemiptera: Cicadellidae): a comparative study of the efficacy of an ELISA and PCR gut content assay. Oecologia 2008, 157(4):629-640. 10.1007/s00442-008-1095-x.
14. Greenstone M.H., Weber D.C., Coudron T.A., Payton M.E., Hu J.S. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis. Mol. Ecol. Res. 2012, 12:464-469. 10.1111/j.1755-0998.2012.03112.x.
15. Haond C., Charmantier G., Flik G., Bonga S.E.W. Identification of respiratory and ion-transporting epithelia in the phyllosoma larvae of the slipper lobster Scyllarus arctus. Cell Tissue Res. 2001, 305:445-455.
16. Hoogendoorn M., Heimpel G.E. PCR based gut content analysis of insect predators: using ribosomal ITS1 fragments from prey to estimate predation frequency. Mol. Ecol. 2001, 10:2059-2067.
17. Inoue M. Studies on the cultured phyllosoma larvae of the Japanese spiny lobster, Panulirus japonicus (V. Siebold). Spec. Rep. Kanagawa Prefect. Fish. Exp. Stn. 1981, 1:1-91.
18. Jarman S.N. Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics 2004, 20(10):1644-1645.
19. Jeffs A.G. Revealing the natural diet of the phyllosoma larvae of spiny lobster. Bull. Fish. Res. Agen. 2007, 20:9-14.
20. Jeffs A.G. Status and challenges of advancing lobster aquaculture globally. J. Mar. Biol. Assoc. India 2010, 52:320-326.
21. Jeffs A.G., Chiswell S.M., Booth J.D. Spiny lobster puerulus condition in the Wairarapa Eddy off New Zealand. Mar. Freshw. Res. 2001, 52:1211-1216.
22. Juen A., Traugott M. Detecting predation and scavenging by DNA gut-content analysis: a case study using a soil insect predator-prey system. Oecologia 2005, 142(3):344-352.
23. King R., Read D., Traugott M., Symondson W. Molecular analysis of predation: a review of best practice for DNA-based approaches. Mol. Ecol. 2008, 17(4):947-963.
24. King R.A., Davey J.S., Bell J.R., Read D.S., Bohan D.A., Symondson W.O.C. Suction sampling as a significant source of error in molecular analysis of predator diets. Bull. Entomol. Res. 2012, 102(3):261-266. 10.1017/S0007485311000575.
25. Kittaka J. Culture of larval spiny lobsters: a review of work done in northern Japan. Mar. Freshw. Res. 1997, 48:923-930.
26. Kittaka J., Ono K., Booth J.D. Complete development of the green rock lobster, Jasus verreauxi from egg to juvenile. Bull. Mar. Sci. 1997, 61:57-71.
27. Lesser J.H.R. Phyllosoma larvae of Jasus edwardsii (Hutton) (Crustacea: Decapoda: Palinuridae) and their distribution off the east coast of the North Island, New Zealand. N. Z. J. Mar. Freshw. Res. 1978, 12:357-370.
28. Lewis J.B. The phyllosoma larvae of the spiny lobster Panulirus argus. Bull. Mar. Sci. Gulf Caribb. 1951, 1:89-103.
29. Linville J., Wells J. Surface sterilization of a maggot using bleach does not interfere with mitochondrial DNA analysis of crop contents. J. Forensic Sci. 2002, 47(5):1055-1061.
30. Maloy A.P., Culloty S.C., Bolton-Warberg M., Fitzgerald R., Slater J.W. Molecular identification of laser-dissected gut contents from hatchery-reared larval cod, Gadus morhua: a new approach to diet analysis. Aquacult. Nutr. 2010, 17:1-6. 10.1111/j.1365-2095.2010.00836.x.
31. Matsuda H., Takenouchi T. Larval molting and growth of the Japanese spiny lobster Panulirus japonicus under laboratory conditions. Fish. Sci. 2006, 72(4):767-773.
32. Meyer J., Hoy M. Removal of fungal contaminants and their DNA from the surface of Diaphorina citri (Hemiptera: Psyllidae) prior to a molecular survey of endosymbionts. Fla. Entomol. 2008, 91(4):702-705.
33. Nelson M.M., Cox S.L., Ritz D.A. Function of mouthparts in feeding behavior of phyllosoma larvae of the packhorse lobster, Jasus verreauxi (Decapoda: Palinuridae). J. Crustac. Biol. 2002, 22:595-600.
34. Nishida S., Kittaka J. Integumental organs of the phyllosoma larva of the rock lobster Jasus edwardsii (Hutton). J. Plankton Res. 1992, 14(4):563-573.
35. O'Rorke R., Lavery S., Chow S., Takeyama H., Tsai P., Beckley L.E., Thompson P., Waite A.M., Jeffs A.G. Determining the diet of larvae of western rock lobster (Panulirus cygnus) using high-throughput DNA sequencing techniques. PLoS One 2012, 7(8):e42757.
36. Oberholster P., Botha A., Cloete T. Use of molecular markers as indicators for winter zooplankton grazing on toxic benthic cyanobacteria colonies in an urban Colorado lake. Harmful Algae 2006, 5(6):705-716.
37. O'Rorke R., Lavery S., Jeffs A.G. PCR enrichment techniques to identify the diet of predators. Mol. Ecol. Resour. 2012, 12:5-17. 10.1111/j.1755-0998.2011.03091.x.
38. Phillips B.F., Booth J.D., Cobb J.S., Jeffs A.G., McWilliam P. Larval and postlarval ecology. Lobsters: Biology, Management, Aquaculture and Fisheries 2006, Blackwell Publishing, Oxford. B.F. Phillips (Ed.).
39. Pliru A., van der Kooij J., Engelhard G.H., Fox C.J., Milligan S.P., Hunter E. Sprat feeding behaviour, selective predation, and impact on plaice egg mortality. ICES J. Mar. Sci. 2012, 69(6):1019-1029. 10.1093/icesjms/fss081.
40. Remén C., Krüger M., Cassel-Lundhagen A. Successful analysis of gut contents in fungal-feeding oribatid mites by combining body-surface washing and PCR. Soil Biol. Biochem. 2010, 42:1952-1957.
41. Rodriguez Souza J.C., Strussmann C.A., Takashima F., Sekine S., Shima Y. Absorption of dissolved and dispersed nutrients from sea-water by Panulirus japonicus phyllosoma larvae. Aquacult. Nutr. 1999, 5:41-51.
42. Rodriguez Souza J.C., Strüssmann C.A., Takashima F., Satoh H., Sekine S., Shima Y., Matsuda H. Oral and integumental uptake of free exogenous glycine by the Japanese spiny lobster Panulirus japonicus phyllosoma larvae. J. Exp. Biol. 2010, 213(11):1859-1867.
43. Schielke E., Costantini C., Carchini G., Sagnon N., Powell J., Caccone A. Development of a molecular assay to detect predation on Anopheles gambiae complex larval stages. Am.J.Trop. Med. Hyg. 2007, 77(3):464-466.
44. Simonelli P., Troedsson C., Nejstgaard J.C., Zech K., Larsen J.B., Frischer M.E. Evaluation of DNA extraction and handling procedures for PCR-based copepod feeding studies. J. Plankton Res. 2009, 31(12):1465-1474. 10.1093/plankt/fbp087.
45. Smith G., Lyall L., Ritar A. The effect of predator/prey density and water dynamics on feed intake and growth in spiny lobster larvae (Jasus edwardsii). Aquaculture 2007, 263:122-129.
46. Smith G.G., Hall M.W., Salmon M. Use of microspheres, fresh and microbound diets to ascertain dietary path, component size, and digestive gland functioning in phyllosoma of the spiny lobster Panulirus ornatus. N. Z. J. Mar. Freshw. Res. 2009, 43:205-215.
47. Suzuki N., Murakami K., Takeyama H., Chow S. Molecular attempt to identify prey organisms of lobster phyllosoma larvae. Fish. Sci. 2006, 72:342-349.
48. Suzuki N., Murakami K., Takeyama H., Chow S. Eukaryotes from the hepatopancreas of lobster phyllosoma larvae. Bull. Fish. Res. Agen. 2007, 20:1-7.
49. Suzuki N., Hoshino K., Murakami K., Takeyama H., Chow S. Molecular diet analysis of phyllosoma larvae of the Japanese spiny lobster Panulirus japonicus (Decapoda: Crustacea). Mar. Biotechnol. 2008, 10(1):49-55.
50. Thornhill D.J., Wiley A.A., Campbell A.L., Bartol F.F., Teske A., Halanych K.M. Endosymbionts of Siboglinum fiordicum and the phylogeny of bacterial endosymbionts in Siboglinidae (Annelida). Biol. Bull. 2008, 214(2):135-144.
51. Troedsson C., Simonelli P., Nägele V., Nejstgaard J., Frischer M. Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR). Mar. Biol. 2009, 156(3):253-259.
52. Vestheim H., Jarman S.N. Blocking primers to enhance PCR amplification of rare sequences in mixed samples - a case study on prey DNA in Antarctic krill stomachs. Front. Zool. 2008, 5(1):12.
53. Vestheim H., Kaartvedt S. Vertical migration, feeding and colouration in the mesopelagic shrimp Sergestes arcticus. J. Plankton Res. 2009, 31(11):1427-1435.