PCR-DHPLC assay for the identification of predator-prey interactions

Journal of Plankton Research

Volumn 34, Issue 4, 2012, Pages 277-285

  Olsen, Bernt Rydland ^a   Dahlgren, Kristin ^b   Schander, Christoffer ^a,c   Bmstedt, Ulf ^b   Rapp, Hans Tore ^a,c   Troedsson, Christofer ^c  

^a UNIVERSITY OF BERGEN   (Norway)

^b UMEÅ UNIVERSITY   (Sweden)

^c Uni Research AS   (Norway)

Author keywords

18S rDNA; biodiversity; feeding; trophic interaction; zooplankton

Indexed keywords

BIOASSAY; CRAB; HYBRIDIZATION; IDENTIFICATION METHOD; LIQUID CHROMATOGRAPHY; PARASITE; POLYMERASE CHAIN REACTION; PREDATOR-PREY INTERACTION; SPECIES DIVERSITY; ZOOPLANKTON;

CALANOIDA; CALLINECTES SAPIDUS; COPEPODA; LIMNOCALANUS MACRURUS;

EID: 84858263860     PISSN: 01427873     EISSN: 14643774     Source Type: Journal    
DOI: 10.1093/plankt/fbr110     Document Type: Article

References (28)

1. Barlaan, E. A., Sugimori, M., Furukawa, S. et al. (2005) Profiling and monitoring of microbial populations by denaturing highperformance liquid chromatography. J. Microbiol. Methods., 61, 399-412.
2. Barofsky, A., Simonelli, P., Vidoudez, C. et al. (2010) Growth phase of the diatom Skeletonema marinoi influences the metabolic profile of the cells and the selective feeding of the copepod Calanus spp. J. Plankton Res., 32, 263-272.
3. Begon, M., Harper, J. L. and Townsend, C. R. (1996) Ecology: Individuals, Populations and Communities. 3rd edn. Blackwell, Oxford, pp. 1-1068.
4. Carreon-Martinez, L. and Heath, D. D. (2010) Revolution in food web analysis and trophic ecology: Diet analysis by DNA and stable isotope analysis. Mol. Ecol., 19, 25-27.
5. Dahlgren, K., Olsen, B. R., Troedsson, C., Båmstedt, U. et al. (2012) Seasonal variation in wax ester concentration and gut content in a Baltic Sea copepod (Limnocalanus macrurus (Sars 1863)). J. Plankton Res., 34, 286-297.
6. Deagle, B. E., Eveson, J. P. and Jarman, S. N. (2006) Quantification of damage in DNA recovered from highly degraded samples-a case study on DNA in faeces. Front. Zool., 3, 11.
7. Durbin, E. G., Casas, M. C., Rynearson, T. A. et al. (2008) Measurement of copepod predation on nauplii using qPCR of the cytochrome oxidase I gene. Mar. Biol., 153, 699-707.
8. Farrelly, V., Rainey, F. A. and Stackebrandt, E. (1995) Effect of genome size and RRN gene copy number on PCR amplification of 16s ribosomal-RNA genes from a mixture of bacterial species. Appl. Environ. Microbiol., 61, 2798-2801.
9. Frischer, M. E., Danforth, J. M., Tyner, L. C. et al. (2000) Development of an Argopecten: Specific 18S rRNA targeted genetic probe. Mar. Biotechnol., 2, 11-20.
10. Kanagawa, T. (2003) Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng., 96, 317-323.
11. King, R. A., Read, D. S., Traugott, M. et al. (2008) Molecular analysis of predation: A review of best practice for DNA-based approaches. Mol. Ecol., 17, 947-963.
12. Nejstgaard, J. C., Frischer, M. E., Simonelli, P. et al. (2008) Quantitative PCR to estimate copepod feeding. Mar. Biol., 153, 565-577.
13. Polz, M. F. and Cavanaugh, C. M. (1998) Bias in template-to-product ratios in multitemplate PCR. Appl. Env. Microbiol., 64, 3724-3730.
14. Qiu, X. Y., Wu, L. Y., Huang, H. S. et al. (2001) Evaluation of PCR-generated chimeras: Mutations, and heteroduplexes with 16S rRNA gene-based cloning. Appl. Env. Microbiol., 67, 880-887.
15. Rathbun, M. J. (1896) The genus Callinectes. Proceedings of the United States National Museum, 18, 349-375.
16. Rouge, C., Goldenberg, O., Ferraris, L. et al. (2010) Investigation of the intestinal microbiota in preterm infants using different methods. Anaerobe., 16, 362-370.
17. Sars, G. O. (1863) Oversigt af de indenlandske Ferskvandcopepoder. Forhandlinger i Videnskabs-Selskabet i Christiana Aar., 1862, 212-262.
18. Simonelli, P., Troedsson, C., Nejstgaard, J. C. et al. (2009) Evaluation of DNA extraction and handling procedures for PCR-based copepod feeding studies. J. Plankton Res., 31, 1465-1474.
19. Swofford, D. L. (2001) PAUP. Phylogenetic Analysis Using Parsimony. Version 4.08b. Sinauer Associates, Sunderland, MA.
20. Symondson, W. O. C. (2002) Molecular identification of prey in predator diets. Mol. Ecol., 11, 627-641.
21. Troedsson, C., Frischer, M. E., Nejstgaard, J. C. et al. (2007) Molecular quantification of differential ingestion and particle trapping rates by the Appendicularian Oikopleura dioica as a function of prey size and shape. Limnol. Oceangr., 52, 416-427.
22. Troedsson, C., Lee, R. F., Stokes, V. et al. (2008a) Development of a denaturing high-performance liquid chromatography method for detection of protist parasites of metazoans. Appl. Env. Microbiol., 74, 4336-4345.
23. Troedsson, C., Lee, R. F., Walters, T. et al. (2008b) Detection and discovery of crustacean parasites in blue crabs (Callinectes sapidus) by using 18S rRNA gene-targeted denaturing high-performance liquid chromatography. Appl. Env. Microbiol., 74, 4346-4353.
24. Troedsson, C., Simonelli, P., Naegele, V. et al. (2009). Quantification of copepod gut content by differential length amplification quantitative PCR (dla-qPCR). Mar. Biol., 156, 253-259.
25. Valentini, A., Pompanon, F. and Taberlet, P. (2009) DNA barcoding for ecologists Trends. Ecol. Evol., 24, 110-117.
26. Verity, P. G. and Smetacek, V. (1996) Organism life cycles, predation, and the structure of marine pelagic ecosystems. Mar. Ecol. Prog. Ser., 130, 277-293.
27. Vestheim, H. and Jarman, S. N. (2008) Blocking primers to enhance PCR amplification of rare sequences in mixed samples: A case study on prey DNA in Antarctic krill stomachs. Front. Zool., 5, 1-11.
28. Xiao, W. Z. and Oefner, P. J. (2001) Denaturing highperformance liquid chromatography: A review. Hum. Mutat., 17, 439-474.