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Identifying chironomids (Diptera: Chironomidae) for biological monitoring with PCR–RFLP

Published online by Cambridge University Press:  09 March 2007

M.E. Carew*
Affiliation:
Centre for Environmental Stress and Adaptation Research, La Trobe University, Bundoora, Victoria 3084, Australia
V. Pettigrove
Affiliation:
Research and Technology, Melbourne Water Corporation, Melbourne, Victoria 3001, Australia
A.A. Hoffmann
Affiliation:
Centre for Environmental Stress and Adaptation Research, La Trobe University, Bundoora, Victoria 3084, Australia
*
*Fax: +61 3 9479 2361 E-mail: m.carew@latrobe.edu.au

Abstract

Chironomids are excellent biological indicators for the health of aquatic ecosystems, but their use at finer taxonomic levels is hindered by morphological similarity of species at each life stage. Molecular markers have the potential to overcome these problems by facilitating species identification particularly in large-scale surveys. In this study, the potential of the polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) approach was tested to rapidly distinguish among chironomids within a geographic area, by considering chironomid species from Melbourne, Australia. By comparing molecular markers with diagnostic morphological traits, RFLP profiles of the cytochrome oxidase I (COI) region were identified that were specific to genera and some common species. These profiles were used to develop an RFLP–based key, which was validated by testing the markers on samples from several wetlands and streams. As well as allowing for rapid identification of species that are difficult to separate on morphological grounds, this approach also has the potential to resolve current taxonomic ambiguities.

Type
Research Article
Copyright
Copyright © Cambridge University Press 2003

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References

Armitage, P.D., Moss, D., Wright, J.F. & Furse, M.T. (1983) The performance of a new biological water quality score system based on macroinvertebrates over a wide range of unpolluted running waters. Water Research 17, 333347.Google Scholar
Armstrong, K.F., Cameron, C.M. & Frampton, E.R. (1997) Fruit fly (Diptera: Tephritidae) species identification: a rapid molecular diagnostic technique for quarantine application. Bulletin of Entomological Research 87, 111118.Google Scholar
Bailey, R.C., Norris, R.H. & Reynoldson, T.B. (2001) Taxonomic resolution of benthic macroinvertebrate communities in bioassessment. Journal of the North American Benthological Society 20, 280286.Google Scholar
Berg, M.B. (1995) Larval food and feeding behaviour. pp.136168in Armitage, P.D., Cranston, P.S. & Pinder, L.C.V. (Eds) The Chironomidae: the ecology and biology of non-biting midges. London, Chapman and Hall.Google Scholar
Breen, P., Walsh, C., Nichols, S., Norris, R., Metzeling, L. & Gooderham, J. (2000) Urban AUSRIVAS: an evaluation of the use of AUSRIVAS models for urban stream assessment. CRC for Freshwater Ecology, Canberra.Google Scholar
Brown, B., Emberson, R.M. & Paterson, A.M. (1999) Mitochondrial COI and II provide useful markers for Wiseania (Lepidoptera: Hepalidae) species identification. Bulletin of Entomological Research 89, 287293.Google Scholar
Brunner, I., Brodbeck, S., Buchler, U. & Sperisen, C. (2001) Molecular identification of fine roots of trees from the Alps: reliable and fast DNA extraction and PCR-RFLP analyses of plastid DNA. Molecular Ecology 10, 20792087.Google Scholar
Bunn, S. (1995) Biological monitoring of water quality in Australia: workshop summary and future direction. Australian Journal of Ecology 20, 220227.Google Scholar
Chessman, B.C. (1995) Rapid assessment of rivers using macroinvertebrates: a procedure based on habitat-specific sampling, family level identification and a biotic index. Australian Journal of Ecology 20, 122129.Google Scholar
Clark, T.L., Meinke, L.J. & Foster, J.E. (2001) PCR-RFLP of the mitochondrial cytochrome oxidase (subunit I) gene provides diagnostic markers for selected Diabrotica species (Coleoptera: Chrysomelidae). Bulletin of Entomological Research 91, 419427.Google Scholar
Cranston, P.S. (1995a) Introduction. pp.15Armitage, P.D., Cranston, P.S. & Pinder, L.C.V. (Eds) The Chironomidae: the ecology and biology of non-biting midges. London, Chapman and Hall.Google Scholar
Cranston, P.S. (1995b) Systematics. pp.3152in Armitage, P.D., Cranston, P.S. & Pinder, L.C.V. (Eds) The Chironomidae: the ecology and biology of non-biting midges. London, Chapman and Hall.Google Scholar
Cranston, P.S. (2000) Electronic identification guide to the Australian Chironomidae. http://entomology.ucdavis.edu/chiropage/index.htmlGoogle Scholar
Cranston, P.S., Fairweather, P. & Clarke, G. (1996) Biological indicators of water quality. pp.143154in Walker, J. & Rueter, D.J. (Eds) Indicators of catchment health: a technical perspective. Melbourne, CSIRO.Google Scholar
Fenton, B., Malloch, G. & Germa, F. (1998) A study of variation in rDNA ITS regions shows that two haplotypes coexist within a single aphid genome. Genome 41, 337345.Google Scholar
Freeman, P. (1961) The Chironomidae (Diptera) of Australia. Australian Journal of Zoology 9, 612737.Google Scholar
Gandolfi, A., Bonilauri, P., Rossi, V. & Menozzi, P. (2001) Intraindividual and intraspecies variability of ITS1 sequences in the ancient asexual Darwinula stevensoni (Crustacea: Ostracoda). Heredity 87, 449455.Google Scholar
Guryev, V.Mararevitch, I.Blinov, A. & Martin, J. (2001) Phylogeny of the genus Chironomus (Diptera) inferred from DNA sequences of mitochondrial cytochrome b and cytochrome oxidase I. Molecular Phylogenetics and Evolution 19, 921.Google Scholar
Herbert, P.N.D., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003) Biological identification through DNA barcodes. Proceedings of the Royal Society of London B 270, 313321.Google Scholar
Hewlett, R. (2000) Implications of taxonomic resolution and sample habitat for stream classification at a broad geographical scale. Journal of the North American Benthological Society 19, 352361.Google Scholar
Hilsenhoff, W.L. (1988) Rapid field assessment of organic pollution with a family-level index. Journal of the North American Benthological Society 7, 6568.Google Scholar
Humphries, P., Growns, J.E., Serafini, L.G., Hawking, J.H., Chick, A.J. & Lake, P.S. (1998) Macroinvertebrate sampling methods for lowland rivers. Hydrobiologia 364, 209218.Google Scholar
King, R.S. & Richardson, C.J. (2002) Evaluating sub sampling approaches and macroinvertebrate taxonomic resolution for wetland bioassessment. Journal of the North American Benthological Society 21, 150171.Google Scholar
Lenat, D.R. & Resh, V.H. (2001) Taxonomy and stream ecology-the benefits of genus- and species-level identifications. Journal of the North American Benthological Society 20, 287298.Google Scholar
Lindegaad, C. (1995) Classification of water-bodies and pollution. pp.385404in Armitage, P.D., Cranston, P.S. & Pinder, L.C.V. (Eds) The Chironomidae: the ecology and biology of non-biting midges. London, Chapman and Hall.Google Scholar
Martin, J., Hoffman, R.T. & Case, S.T. (1996) Identification of divergent homologs of Chironomus tentans SP185 and ITS Balbiani ring 3 gene in Australasian species of Chironomus and Kiefferulus. Insect Biochemistry and Molecular Biology 26, 465473.Google Scholar
Metzeling, L., Robinson, D., Perriss, S. & Marchant, R. (2002) Temporal persistence of benthic invertebrate communities in south-eastern Australian streams: taxonomic resolution and implications for the use of predictive models. Marine and Freshwater Research 53, 12231234.Google Scholar
Miller, L.J., Alisopp, P.G., Graham, G.C. & Yeates, D.K. (1999) Identification of morphologically similar canegrubs (Coleoptera: Scarabaeidae: Melolonthini) using a molecular diagnostic technique. Australian Journal of Entomology 38, 189196.Google Scholar
Muraji, M. & Nakahara, S. (2002) Discrimination among pest species of Bactrocera (Diptera: Tephritidae) based on PCR-RFLP of the mitochondrial DNA. Applied Entomology and Zoology 37, 437446.Google Scholar
Pettigrove, V. (1998) An assessment of metal contamination in sediments from Melbourne's waterways – implications for stream health and waterway management. pp. 1726 in Proceedings of the International Erosion Control Association (Australasian) 6th Annual Soil and Water Management Conference organized by the International Erosion Control Association, Steamboat Springs20–28 October 1998MelbourneInternational Erosion Control Association.Google Scholar
Rabeni, C.F. & Wang, N. (2001) Bioassessment of streams using macroinvertebrates: are the Chironomidae necessary? Environmental Monitoring and Assessment 71, 177185.Google Scholar
Roback, S.S. (1982) The Tanypodinae (Diptera: Chironomidae) of Australia II. Proceedings of the Academy of Natural Sciences of Philadelphia 134, 80112.Google Scholar
Ruse, L.P. (1996) Multivariate techniques relating macroinvertebrate and environmental data from a river catchment. Water Research 30, 30173024.Google Scholar
Saether, O.A. (1979) Chironomid communities as water quality indicators. Holarctic Ecology 2, 6574.Google Scholar
Salazar, M., Theoduloz, C., Vega, V., Poblete, F., Gonzalez, E., Badilla, R. & Meza-Basso, L. (2002) PCR-RFLP identification of the Chilean species of Rhagoletis (Diptera: Tephritidae) attacking Solanaceae. Bulletin of Entomological Research 92, 337341.Google Scholar
Tiller, D. & Metzeling, L. (1998) Rapid bioassessment of Victorian streams. Environmental Protection Agency, Melbourne.Google Scholar
Van Bortel, W., Trung, H.D., Roelants, P., Harbach, R.E., Backeljau, T., Coosemans, M. (2000) Molecular identification of Anopheles minimus, beyond distinguishing the members of the species complex. Insect Molecular Biology 9, 335340.Google Scholar
Walsh, P.S., Metzgar, D.A. & Higuschi, R. (1991) Chelex-100 as medium for simple extraction for PCR-based typing from forensic material. Biotechniques 10, 506513.Google Scholar
Wells, F., Metzeling, L. & Newall, P. (2002) Macroinvertebrate regionalization for the use in the management of aquatic ecosystems. Environmental Monitoring and Assessment 74, 271294.Google Scholar
Wright, J.D., Armitage, P.D. & Furse, M.T. (1989) Prediction of invertebrate communities using stream measurements. Regulated Rivers 4, 147155.Google Scholar
Zamora, M.C. & Alba, T.J. (1996) Bioassessment of organically polluted Spanish rivers, using a biotic index and multivariable methods. Journal of the North American Benthological Society 15, 332352.Google Scholar