Fisheries and Aquatic Sciences

The Korean Society of Fisheries and Aquatic Science (한국수산과학회)
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PCR of Gut Contents for a Food Web Study of a Marine Ecosystem

  • Kim, Nack-Keun (Department of Marine Biology, Pukyong National University) ;
  • Kim, Kyoung-Sun (Department of Marine Biology, Pukyong National University) ;
  • Kim, Hyun-Woo (Department of Marine Biology, Pukyong National University)
  • Published : 2007.12.31
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Abstract

Understanding dietary habits is one of the most important factors in studying food webs and other ecological processes. Here we designed universal primers to amplify portions of the 18S and 28S rDNA sequences to examine gut contents using PCR techniques. The gut contents of sailfin sandfish (Arctoscopus japonicus) and pacific squid (Todarodes pacificus) were examined. In total, 11 families of prey were identified with 18S and 28S rDNA using the universal primers. The DNA sequence data indicated that the primer sets successfully amplified a wide spectrum of species and represented gut contents in a relatively convenient way. We found that information in the NCBI database was not yet sufficient to discriminate the species we isolated. In addition, technology for the separation of heterogeneous PCR products and better resolution and quantification protocols would help increase data accuracy.

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References

  1. Adoutte, A., G. Balavoine, N. Lartillot and R. de Rosa. 1999. Animal evolution. The end of the intermediate taxa? Trends Genet., 15, 104-108 https://doi.org/10.1016/S0168-9525(98)01671-0
  2. Aguinaldo, A.M., J.M. Turbeville, L.S. Linford, M.C. Rivera, J.R. Garey, R.A. Raff and J.A. Lake. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature, 387, 489-493 https://doi.org/10.1038/387489a0
  3. Agusti, N., S.P. Shayler, J.D. Harwood, I.P. Vaughan, K.D. Sunderland and W.O. Symondson. 2003. Collembola as alternative prey sustaining spiders in arable ecosystems: prey detection within predators using molecular markers. Mol. Ecol., 12,3467-3475 https://doi.org/10.1046/j.1365-294X.2003.02014.x
  4. Blankenship, L.E. and A.A. Yayanos. 2005. Universal primers and PCR of gut contents to study marine invertebrate diets. Mol. Ecol., 14, 891-899 https://doi.org/10.1111/j.1365-294X.2005.02448.x
  5. Deagle, B.E., S.N. Jarman, D. Pemberton and N.J. Gales. 2005. Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). J. Hered., 96, 417-423 https://doi.org/10.1093/jhered/esi036
  6. Halanych, K.M., J.D. Bacheller, A.M. Aguinaldo, S.M. Liva, D.M. Hillis and J.A. Lake. 1995. Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. Science, 267,1641-1643 https://doi.org/10.1126/science.7886451
  7. Hebert, P.D., A. Cywinska, S.L. Ball and J.R. deWaard. 2003. Biological identifications through DNA barcodes. Proc. Biol. Sci., 270, 313-321
  8. Jarman, S.N., B.E. Deagle and N.J. Gales. 2004. Groupspecific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Mol. Ecol., 13, 1313-1322 https://doi.org/10.1111/j.1365-294X.2004.02109.x
  9. Kim, H.W, E.S. Chang and D.L. Mykles. 2005. Three ca1pains and ecdysone receptor in the land crab Gecarcinus lateralis: sequences, expression and effects of elevated ecdysteroid induced by eyesta1k ablation. J. Exp. Biol., 208, 3177-3197 https://doi.org/10.1242/jeb.01754
  10. Long, E.O. and I.B. Dawid. 1980. Repeated genes in eukaryotes. Annu. Rev. Biochem., 49, 727-764 https://doi.org/10.1146/annurev.bi.49.070180.003455
  11. Mallatt, J. and G. Giribet. 2006. Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch. Mol. Phylogenet. Evol., 40, 772-794 https://doi.org/10.1016/j.ympev.2006.04.021
  12. Mallatt, J.M., J.R. Garey and J.W. Shultz. 2004. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and l8S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol., 31, 178-191 https://doi.org/10.1016/j.ympev.2003.07.013
  13. Markaida, U. 2006. Food and feeding of jumbo squid Dosidicus gigas in the Gulf of California and adjacent waters after the 1997-98 E INino event. Fish. Res., 79, 16-27 https://doi.org/10.1016/j.fishres.2006.02.016
  14. Markmann, M. and D. Tautz. 2005. Reverse taxonomy: an approach towards determining the diversity of meiobenthic organisms based on ribosomal RNA signature sequences. Philos. Trans. Roy. Soc. Lond., B. Biol. Sci., 360, 1917-1924 https://doi.org/10.1098/rstb.2005.1723
  15. Moritz, C. and C. Cicero. 2004. DNA barcoding: promise and pitfalls. Plos. Biol., 2, e354 https://doi.org/10.1371/journal.pbio.0020354
  16. Nubel, U., F. Garcia-Pichel, M. Kuhl and G. Muyzer. 1999. Quantifying microbial diversity: morphotypes, 16S rRNA genes, and carotenoids of oxygenic phototrophs in microbial mats. Appl. Environ. Microbiol., 65, 422-430
  17. O'Dor, R.K. and M.J. Wells. 1987. Energy and nutrient flow in cephalopods. In: Celphalopod Life Cycles. Vol. II. Boyle, P.R. ed., Academic Press, London, UK, 109-133
  18. Passamaneck, Y.J., C. Schander and K.M. Halanych. 2004. Investigation of molluscan phylogeny using largesubunit and small-subunit nuclear rRNA sequences. Mol. Phylogenet. Evol., 32, 25-38 https://doi.org/10.1016/j.ympev.2003.12.016
  19. Pintado, J., J.P. Guyot and F. Ampe. 2003. Multiple competitive PCR-DGGE as a tool for quantifying and profiling defined mixed cultures of lactic acid bacteria during production of probiotics from complex polysaccharides. J. Appl. Microbiol., 95, 921-933 https://doi.org/10.1046/j.1365-2672.2003.02058.x
  20. Prokopowich, C.D., T.R. Gregory and T.J. Crease. 2003. The correlation between rDNA copy number and genome size in eukaryotes. Genome, 46, 48-50 https://doi.org/10.1139/g02-103
  21. Song, H.J., G.W Baeck, S.A. Kim and S.H. Huh. 2006. Feeding habits of Todarodes pacijicus (Cephalopods: Ommnastrephidae) in the coastal waters of Busan, Korea. J. Kor. Fish. Soc., 39,42-48 https://doi.org/10.5657/kfas.2006.39.1.042
  22. Zaidi, R.H., Z. Jaal, N.J. Hawkes, J. Hemingway and W.O. Symondson. 1999. Can multiple-copy sequences of prey DNA be detected amongst the gut contents of invertebrate predators? Mol. Ecol., 8, 2081-2087 https://doi.org/10.1046/j.1365-294x.1999.00823.x