Effectiveness of Annealing Blocking Primers versus Restriction Enzymes for Characterization of Generalist Diets: Unexpected Prey Revealed in the Gut Contents of Two Coral Reef Fish Species

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Leray, Matthieu ^a,b   Agudelo, Natalia ^b   Mills, Suzanne C ^a   Meyer, Christopher P ^b  

^a Centre de Biologie et d Ecologie Tropicale et Méditerranéenne   (France)

^b DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PRIMER RNA; RESTRICTION ENDONUCLEASE;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORAL REEF; DIET; DNA BARCODING; DNA LIBRARY; DNA RESTRICTION; DNA TEMPLATE; DYNAMICS; INTESTINE; LAND BIOME; MARINE ENVIRONMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDATOR PREY INTERACTION; PROTEIN SECRETION; TISSUE HOMOGENATE;

ANIMALS; CORAL REEFS; DIET; DNA BARCODING, TAXONOMIC; DNA PRIMERS; DNA RESTRICTION ENZYMES; FISHES; FOOD CHAIN; GASTROINTESTINAL CONTENTS; PHYLOGENY; POLYMERASE CHAIN REACTION; PREDATORY BEHAVIOR;

ANTHOZOA;

EID: 84876003047     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058076     Document Type: Article

References (69)

1. Valentini A, Miquel C, Nawaz MA, Bellemain E, Coissac E, et al. (2009) New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Resources 9: 51-60.
2. Pompanon F, Deagle BE, Symondson WOC, Brown DS, Jarman SN, et al. (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology 21: 1931-1950.
3. Carreon-Martinez L, Heath DD, (2010) Revolution in food web analysis and trophic ecology: diet analysis by DNA and stable isotope analysis. Molecular Ecology 19: 25-27.
4. Sheppard SK, Harwood JD, (2005) Advances in molecular ecology: tracking trophic links through predator-prey food-webs. Functional Ecology 19: 751-762.
5. King RA, Read DS, Traugott M, Symondson WOC, (2008) Molecular analysis of predation: a review of best practice for DNA-based approaches. Molecular Ecology 17: 947-963.
6. Deagle BE, Tollit DJ, Jarman SN, Hindell MA, Trites AW, et al. (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Molecular Ecology 14: 1831-1842.
7. Jarman SN, Deagle BE, Gales NJ, (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Molecular Ecology 13: 1313-1322.
8. Leray M, Boehm JT, Mills SC, Meyer CP, (2012) Moorea BIOCODE barcode library as a tool for understanding predator-prey interactions: insights into the diet of common predatory coral reef fishes. Coral Reefs 31: 383-388.
9. Dunn MR, Szabo A, McVeagh MS, Smith PJ, (2010) The diet of deepwater sharks and the benefits of using DNA identification of prey. Deep-Sea Research Part I-Oceanographic Research Papers 57: 923-930.
10. Braley M, Goldsworthy SD, Page B, Steer M, Austin JJ, (2010) Assessing morphological and DNA-based diet analysis techniques in a generalist predator, the arrow squid Nototodarus gouldi. Molecular Ecology Resources 10: 466-474.
11. Passmore AJ, Jarman SN, Swadling KM, Kawaguchi S, McMinn A, et al. (2006) DNA as a dietary biomarker in antarctic krill, Euphausia superba. Marine Biotechnology 8: 686-696.
12. Deagle BE, Jarman SN, Pemberton D, Gales NJ, (2005) Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). Journal of Heredity 96: 417-423.
13. Admassu B, Juen A, Traugott M, (2006) Earthworm primers for DNA-based gut content analysis and their cross-reactivity in a multi-species system. Soil Biology & Biochemistry 38: 1308-1315.
14. Clare EL, Fraser EE, Braid HE, Fenton MB, Hebert PDN, (2009) Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): using a molecular approach to detect arthropod prey. Molecular Ecology 18: 2532-2542.
15. Harwood JD, Desneux N, Yoo HJS, Rowley DL, Greenstone MH, et al. (2007) Tracking the role of alternative prey in soybean aphid predation by Orius insidiosus: a molecular approach. Molecular Ecology 16: 4390-4400.
16. Harwood JD, Yoo HJS, Greenstone MH, Rowley DL, O'Neil RJ, (2009) Differential impact of adults and nymphs of a generalist predator on an exotic invasive pest demonstrated by molecular gut-content analysis. Biological Invasions 11: 895-903.
17. Corse E, Costedoat C, Chappaz R, Pech N, Martin JF, et al. (2010) A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces. Molecular Ecology Resources 10: 96-108.
18. Blankenship LE, Yayanos AA, (2005) Universal primers and PCR of gut contents to study marine invertebrate diets. Molecular Ecology 14: 891-899.
19. Vestheim H, Deagle BE, Jarman SN, (2011) Application of blocking oligonucleotides to improve signal-to-noise ratio in a PCR. PCR Protocols, Methods in Molecular Biology. 687: 265-274.
20. 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 doi:10.1186/1742-9994-5-12.
21. O'Rorke R, Lavery S, Jeffs A, (2012) PCR enrichment techniques to identify the diet of predators. Molecular Ecology Resources 12: 5-17.
22. Jarman SN, Redd KS, Gales NJ, (2006) Group-specific primers for amplifying DNA sequences that identify Amphipoda, Cephalopoda, Echinodermata, Gastropoda, Isopoda, Ostracoda and Thoracica. Molecular Ecology Notes 6: 268-271.
23. Harper GL, King RA, Dodd CS, Harwood JD, Glen DM, et al. (2005) Rapid screening of invertebrate predators for multiple prey DNA targets. Molecular Ecology 14: 819-827.
24. Bohmann K, Monadjem A, Noer CL, Rasmussen M, Zeale MRK, et al. (2011) Molecular diet analysis of two African free-tailed bats (Molossidae) using high throughput sequencing. Plos One 6(6): e21441 doi:10.1371/journal.pone.0021441.
25. Clare EL, Barber BR, Sweeney BW, Hebert PDN, Fenton MB, (2011) Eating local: influences of habitat on the diet of little brown bats (Myotis lucifugus). Molecular Ecology 20: 1772-1780.
26. Dunshea G, (2009) DNA-based diet analysis for any predator. Plos One 4(4): e5252 doi:10.1371/journal.pone.0005252.
27. Kane C, Brooks A, Holbrook S, Schmitt R, (2009) The role of microhabitat preference and social organization in determining the spatial distribution of a coral reef fish. Environmental Biology of Fishes 84: 1-10.
28. Bachet P, Lefevre Y, Zysman T (2007) Guide des poissons de Tahiti et de ses îles. Au vent des îles.
29. Randall JE (2005) Reef and shore fishes of the South Pacific. University of Hawai'i Press.
30. Check E, (2006) Treasure island: pinning down a model ecosystem. Nature 439: 378-379.
31. Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, (1994) DNA primers for amplification of mitochondrial Cytochrome c. Oxidase Subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294-299.
32. Meyer CP, (2003) Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biological Journal of the Linnean Society 79: 401-459.
33. Hall TA, (1999) BioEdit: a user friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95-98.
34. Wagner A, Blackstone N, Cartwright P, Dick M, Misof B, et al. (1994) Surveys of gene families using polymerase chain reaction - PCR selection and PCR drift. Systematic Biology 43: 250-261.
35. Plaisance L, Brainard RE, Caley MJ, Knowlton N, (2011) Using DNA barcoding and standardized sampling to compare geographic and habitat differentiation of crustaceans: a Hawaiian islands example. Diversity 4: 581-591.
36. Plaisance L, Knowlton N, Paulay G, Meyer C, (2009) Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding. Coral Reefs 28: 977-986.
37. Plaisance L, Caley MJ, Brainard RE, Knowlton N, (2011) The diversity of coral reefs: what are we missing? Plos One 6(10): e25026 doi:10.1371/journal.pone.0025026.
38. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75: 7537-7541.
39. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and clustal X version 2.0. Bioinformatics 23: 2947-2948.
40. Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, et al. (2011) Geneious v5.5. Available: http://www.geneious.com.
41. Huber T, Faulkner G, Hugenholtz P, (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317-2319.
42. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 12: 102.
43. Machida RJ, Hashiguchi Y, Nishida M, Nishida S, (2009) Zooplankton diversity analysis through single-gene sequencing of a community sample. BMC Genomics 10: 438 doi:10.1186/1471-2164-10-438.
44. Munch K, Boomsma W, Huelsenbeck JP, Willerslev E, Nielsen R, (2008) Statistical assignment of DNA sequences using Bayesian phylogenetics. Systematic Biology 57: 750-757.
45. Colwell RK (2006) EstimateS: Statistical estimation of species richness and shared species from samples. Available:purl.oclc.org/estimates.
46. Colwell RK, Mao CX, Chang J, (2004) Interpolating, extrapolating, and comparing incidence-based species accumulation curves. Ecology 85: 2717-2727.
47. Wu DY, Ugozzoli L, Pal BK, Qian J, Wallace RB, (1991) The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction. DNA and Cell Biology 10: 233-238.
48. Hyslop EJ, (1980) Stomach contents analysis - a review of methods and their application. Journal of Fish Biology 17: 411-429.
49. Pierce GJ, Boyle PR, (1991) A review of methods for diet analysis in piscivorous marine mammals. Oceanography and Marine Biology 29: 409-486.
50. Budarf AC, Burfeind DD, Loh WKW, Tibbetts IR, (2011) Identification of seagrasses in the gut of a marine herbivorous fish using DNA barcoding and visual inspection techniques. Journal of Fish Biology 79: 112-121.
51. Deagle BE, Eveson JP, Jarman SN, (2006) Quantification of damage in DNA recovery from highly degraded samples- a case study on DNA in faeces. Frontiers in Zoology 3: 11 doi:10.1186/1742-9994-3-11.
52. Deagle BE, Kirkwood R, Jarman SN, (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology 18: 2022-2038.
53. Nejstgaard JC, Frischer ME, Simonelli P, Troedsson C, Brakel M, et al. (2008) Quantitative PCR to estimate copepod feeding. Marine Biology 153: 565-577.
54. Hoareau TB, Boissin E, (2010) Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata. Molecular Ecology Resources 10: 960-967.
55. Harwood JD, Phillips SW, Sunderland KD, Symondson WOC, (2001) Secondary predation: quantification of food chain errors in an aphid-spider-carabid system using monoclonal antibodies. Molecular Ecology 10: 2049-2057.
56. Sheppard SK, Bell J, Sunderland KD, Fenlon J, Skervin D, et al. (2005) Detection of secondary predation by PCR analyses of the gut contents of invertebrate generalist predators. Molecular Ecology 14: 4461-4468.
57. Odinetz MO (1983) Ecologie et structure des peuplements de crustacés décapodes associés aux coraux du genre Pocillopora en Polynésie Francaise et en Micronésie (Guam). PhD thesis. Paris: Université Pierre et Marie Curie.
58. Glynn PW, (1987) Some ecological consequences of coral crustacean guard mutualisms in the Indian and Pacific Oceans. Symbiosis 4: 301-323.
59. Stewart HL, Holbrook SJ, Schmitt RJ, Brooks AJ, (2006) Symbiotic crabs maintain coral health by clearing sediments. Coral Reefs 25: 609-615.
60. Stier AC, Gil MA, McKeon CS, Lemer S, Leray M, et al. (2012) Housekeeping mutualisms: do more symbionts facilitate host performance? Plos One 7(4): e32079 doi:10.1371/journal.pone.0032079.
61. Stier AC, McKeon CS, Osenberg CW, Shima JS, (2010) Guard crabs alleviate deleterious effects of vermetid snails on a branching coral. Coral Reefs 29: 1019-1022.
62. 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.
63. Hebert PDN, deWaard JR, Landry JF, (2010) DNA barcodes for 1/1000 of the animal kingdom. Biology Letters 6: 359-362.
64. Valentini A, Pompanon F, Taberlet P, (2009) DNA barcoding for ecologists. Trends in Ecology & Evolution 24: 110-117.
65. Zaidi RH, Jaal Z, Hawkes NJ, Hemingway J, Symondson WOC, (1999) Can multiple-copy sequences of prey DNA be detected amongst the gut contents of invertebrate predators? Molecular Ecology 8: 2081-2087.
66. Hoogendoorn M, Heimpel GE, (2001) PCR-based gut content analysis of insect predators: using ribosomal ITS-1 fragments from prey to estimate predation frequency. Molecular Ecology 10: 2059-2067.
67. Meusnier I, Singer GAC, Landry JF, Hickey DA, Hebert PDN, et al. (2008) A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9: 214 doi:10.1186/1471-2164-9-214.
68. Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, et al. (2010) An in silico approach for the evaluation of DNA barcodes. BMC Genomics 11: 434 doi:10.1186/1471-2164-11-434.
69. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.