Abstract
DNA-sequence-based approaches such as single nematode PCR and sequencing have been successfully used in nematode species diagnostics. Here, we use SSU rDNA sequences generated from an artificially-assembled community of nematodes of known identity and relative abundance to assess a relationship between nematode species and operationally clustered taxonomic units (OCTUs). OCTUs that formed at 95% similarity underestimated species richness by ca 30%, and all expected species were recovered only at 99% OCTU similarity. Although the number of OCTUs formed at 99% similarity was considerably higher than the actual number of nematode species, a pattern of the distribution of OCTUs within each species allowed an assignment of OCTUs to specific species. The pattern was highly predictable and helped to discern rather than obscure species recognition. The patterns and parameters that emerged from the control nematode dataset were then used to test our approach on environmental samples of nematodes obtained from a tropical rainforest in Costa Rica.References
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402.
Blaxter, M. (2003) Molecular systematics: counting angels with DNA. Nature, 421, 122–124.
Blaxter, M.L. (2004) The promise of a DNA taxonomy. Journal of the Philosophical Transactions of the Royal Society, B, 359, 669–679.
Blaxter, M., Maan, J., Chapman, T., Thomas, F., Whitton, C., Floyd, R. & Abebe, E. (2005) Defining operational taxonomic units using DNA barcode data. Journal of the Philosophical Transactions of the Royal Society, B, 360, 1935–1943.
Boag, B. & Yeates, G.W. (1998) Soil nematode biodiversity in terrestrial ecosystems. Biodiversity and Conservation, 7, 617–630.
Coomans, A. (2000) Nematode systematics: past, present and future. Nematology, 2, 3–7.
Chou, H. & Holmes, M. (2001) DNA sequence quality trimming and vector removal. Bioinformatics, 12, 1092–1104.
De Ley, P., Tandingam De Ley, I., Morris, K., Abebe, E., Mundo-Ocampo, M., Yoder, M., Heras, J., Waumann, D., Rocha-Olivares, A., Burr, A.H.J., Baldwin, J.G. & Thomas, W.K. (2005) An integrated approach to fast and informative morphological vouchering of nematodes for applications in molecular barcoding. Philosophical Transactions of the Royal Society, Biology, 360, 1945–1958.
Dover, G.A. (1982) Molecular drive: A cohesive mode of species evolution. Nature, 299, 111–117.
Floyd, R., Abebe, E., Papert, A. & Blaxter, M.L. (2002) Molecular barcodes for soil nematode identification. Molecular Ecology, 11, 839–850.
Goldstein, P.Z., DeSalle, R., Amato, G. & Vogler, A. (2000) Conservation genetics at the species boundary. Conservation Biology, 14, 120–131.
Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W. & Hebert, P.D.N. (2006) DNA barcodes distinquish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, 103, 968–971.
Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, B, 270, 313–321.
Holterman, M., van der Wurff, A., van den Elsen, S., van Megen, H., Bongers, T., Holovachov, O., Bakker, J. & Helder, J. (2006) Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades. Molecular Biology and Evolution, 23, 1792–1800.
Hugot, J.P., Baujard, P. & Morand, S. (2001) Biodiversity in helminths and nematodes as a field of study: an overview. Nematology, 3, 199–208.
James, S.A., O’Kelly, M.J.T., Carter, D.M., Davey, R.P., van Oudenaarden, A. & Roberts, I.N. (2009) Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Research, 19, 626–635.
Jenkins, W.R. (1964) A rapid centrifugal-flotation technique for separating nematodes from soil. Plant Disease Reporter, 48, 692.
Kanzaki, N., Giblin-Davis, R.M., Wcislo, W.T., Zeng, Y., Ye, W., Center, B.J., Esquivel, A. & Thomas, W.K. (2010) Acrostichus megaloptae n. sp. (Nematoda: Diplogastridae), a phoretic associate of Megalopta spp. (Hymenoptera: Helictidae) in Central America. Nematology, 12, In Press.
Lawton, J.H., Bignell, D.E., Bolton, B., Bloemers, G.F., Eggleton, P., Hammond, P.M., Hodda, M., Holt, R.D., Larsen, T.B., Mawdsley, N.A., Stork, N.E., Srivarstava, D.S. & Watt, AD. (1998) Biodiversity inventories, indicator taxa and effects of habitat modification in tropical forest. Nature, 391, 72–76.
Porazinska, D.L., Giblin-Davis, R.M., Farmerie, W., Powers, T.O., Kanzaki, N., Faller, L., Morris, K., Sung, W. & Thomas, WK (2009a) Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Molecular Ecology Resources, 9, 1439–1450.
Porazinska, D.L., Sung, W., Giblin-Davis, R.M. & Thomas, W.K. (2009b) Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure. Molecular Ecology Resources doi, 10.1111/j.1755-0998.2009.02819.x
Powers, T.O. (2004) Nematode molecular diagnostics: from bands to barcodes. Annual Review of Phytopathology, 42, 367–83.
Powers, T.O., Todd, T.C., Burnell, A.M., Murray, P.C.B., Fleming, C.C., Szalanski, A.L., Adams, B.J. & Harris, T.S. (1997) The internal transcribed spacer region as a taxonomic marker for nematodes. Journal of Nematology, 29, 441–450.
Powers, T.O., Neher, D.A., Mullin, P., Esquivel, A. Giblin-Davis, R.M., Kanzaki, N., Stock, S.P., Mora, M.M. & Uribe-Lorio, L. (2009) Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest. Molecular Ecology, 18, 985–996.
Skantar, A.M. & Carta, L.K. (2004) Molecular characterization and phylogenetic evaluation of the HSP90 gene from selected nematodes. Journal of Nematology, 36, 466–480.
Smith, M.A., Fisher, B.L. & Hebert, P.D.N. (2005) DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of the Madagascar. Journal of the Philosophical Transactions of the Royal Society, B, 360, 1825–1834.
Shaw, A.K., Halpern, A.L., Beeson, K., Tran, B., Venter, J.C. & Martiny, J.B.H. (2008) It’s all relative: ranking the diversity of aquatic bacterial communities. Environmental Microbiology, 10, 2200–2210.
Sogin, M.L., Morrison, H.G., Huber, J.A., Welch, D.M., Huse, S.M., Neal, P.R., Arrleta, J.M. & Herndl, G.J. (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proceedings of the National Academy of Sciences of the United States of America, 103, 12115–12120.
Stage, D.E. & Eickbush, T.H. (2009) Sequence variation within the rRNA gene loci of 12 Drosophila species. Genome Research, 17, 1888–1897.
Thomas, W.K., Vida, J.T., Frisse, L.M., Mundo, M. & Baldwin, J.G. (1997) DNA sequences from formalin-fixed nematodes, integrating molecular and morphological approaches to taxonomy. Journal of Nematology, 29, 250–254.
Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. (1996) Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiological Reviews, 60, 407–438.
Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., Starr, M.P. & Truper, H.G. (1987) Report of the Ad Hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology, 37, 463–464
Ye, W., Giblin-Davis, R.M., Braasch, H., Morris, K. & Thomas, W.K. (2007) Phylogenetic relationships among Bursaphelenchus species (Nematoda: Parasitaphelenchidae) inferred from nuclear ribosomal and mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution, 43, 1185–1197.
Zhang, Z., Schwartz, S., Wagner, L. & Miller, W. (2000) A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, 7, 203–214.