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Marine Ecology Progress Series

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MEPS 291:103-113 (2005)  -  doi:10.3354/meps291103

Denaturing gradient gel electrophoresis (DGGE) as a tool for identification of marine nematodes

A. A. Cook1,2,6, P. Bhadury3, N. J. Debenham1, B. H. M. Meldal1,4, M. L. Blaxter5, G. R. Smerdon3, M. C. Austen3, P. J. D. Lambshead1, A. D. Rogers2,*

1Nematode Research Group, Department of Zoology, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
2Natural Environment Research Council, British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
3Plymouth Marine Laboratory, Prospect Place, West Hoe, Plymouth PL1 3DH, UK
4School of Ocean and Earth Science, Southampton Oceanography Centre, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
5Institute of Cell, Animal and Population Biology, Ashworth Laboratories, University of Edinburgh, King’s Buildings, West Mains Road, Edinburgh EH9 3JT, UK
6Present address: The International Seabed Authority, 14–20 Port Royal Street, Kingston, Jamaica
*Corresponding author. Email:

ABSTRACT: Many phyla of marine invertebrates are difficult to identify using conventional morphological taxonomy. Larvae of a wider set of phyla are also difficult to identify as a result of conservation of morphology between species or because morphological characters are destroyed during sampling and preservation. DNA sequence analysis has the potential for identification of marine organisms to the species level. However, sequence analysis of specimens is time-consuming and impractical when species diversity is very high and densities of individuals huge, as they are in many marine habitats. The effectiveness of the 18S rRNA gene sequences for identification of one species-rich marine group, the Nematoda, is analysed. Following identification of variable regions of the 18S rRNA gene, primers were designed to amplify a small segment of sequences suitable for denaturing gradient gel electrophoresis (DGGE). The effectiveness of DGGE for identifying individual species is analysed. DGGE analysis of natural communities of nematodes detected less than 2/3 of the species present. This fraction of the community probably represents the abundant species in the original samples. It is concluded that DGGE is not a useful tool for analysis of species richness in marine communities as it fails to detect rare species of which there are usually many in the marine benthic environment. However, DGGE may be a useful method for detecting changes in communities that influence the abundance of the most common taxa.

KEY WORDS: Marine nematodes · 18S ribosomal DNA · Denaturing gradient gel electrophoresis

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