Journal of Paleolimnology

, Volume 33, Issue 1, pp 13–38

Diatom-based models for reconstructing past water quality and productivity in New Zealand lakes



The trophic status of lakes in New Zealand is, on average, low compared to more densely populated areas of the globe. Despite this, trends of eutrophication are currently widespread due to recent intensification in agriculture. In order to better identify baseline productivity and establish long-term trends in lake trophic status, diatom-based transfer functions for productivity-related parameters were developed. Water quality data and surface sediment diatom assemblages from 53 lakes across the North and South Islands of New Zealand were analysed to determine species responses to the principal environmental gradients in the data set. Repeat sampling of water chemistry over a 12-month period enabled examination of species responses to annual means as well as means calculated for stratified and mixed periods. Variables found to be most strongly correlated with diatom species distributions were chlorophyll a (Chl a), total phosphorus (TP), dissolved reactive phosphorus (DRP), ionic concentration (measured as electrical conductivity (EC)) and pH. These variables were used to develop diatom-based transfer functions using weighted averaging regression and calibration (simple, tolerance down-weighted and with partial least squares algorithm applied). Overall, models derived for stratified means were weaker than those using annual or isothermal means. For specific variables, the models derived for the isothermal mean of EC (WA-tol r2jack = 0.79; RMSEP = 0.15 log10 μS cm−1),the annual mean of pH (WA r2jack = 0.72; RMSEP = 0.25 pH units) and the isothermal mean of Chl a (WA r2jack = 0.71; RMSEP = 0.18 log10 mg m−3 Chl a) performed best. The models derived for TP were weak in comparison (for the annual mean of TP: WA r2jack = 0.50; RMSEP = 0.24 log10 mg m−3 TP) and residuals on estimates for this model were correlated with several other water quality variables, suggesting confounding of species responses to TP concentrations. The model derived for the isothermal mean of DRP was relatively strong (WA-tol r2jack = 0.78; RMSEP = 0.17 log10 mg m−3 DRP); however, residual values for this model were also found to be strongly correlated with several other water quality variables. It is concluded that the poor performance of the TP and DRP transfer functions relative to that of the Chl a model reflects the coexistence of nitrogen and phosphorus limitation within the lakes in the data set. In spite of this, the suite of transfer functions developed from the training set is regarded as a valuable addition to palaeolimnological studies in NewZealand.


Chlorophyll a Diatoms New Zealand lakes Nutrients Transfer function Weighted averaging 


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  1. 1.
    Anderson, N.J. 1998Variability of diatom-inferred phosphorus profiles in a small lake basin and its implications for histories of lake eutrophicationJ. Paleolimnol.204755Google Scholar
  2. 2.
    Bennion, H. 1994A diatom-phosphorus transfer function for shallow, eutrophic ponds in southeast EnglandHydrobiologia275–276391410Google Scholar
  3. 3.
    Bennion, H., Appleby, P.G. 1999An assessment of recent environmental change in Llangorse Lake using palaeolimnologyAquat. Conserv: Mar. Freshw. Ecosyst.9361375Google Scholar
  4. 5.
    Bennion, H., Smith, M.A. 2000Variability in the water chemistry of shallow ponds in southeast Englandwith special reference to the seasonality of nutrients and implications for modelling trophic statusHydrobiologia436145158Google Scholar
  5. 4.
    Bennion, H., Appleby, P.G., Phillips, G.L. 2001Reconstructing nutrient histories in the Norfolk Broads, UK: implications for the role of diatom-total phosphorus transfer functions in shallow lake managementJ. Paleolimnol.26181204Google Scholar
  6. 6.
    Birks, H.J.B. 1998Numerical tools in palaeolimnology – progress, potentialities, and problemsJ. Paleolimnol.20307332Google Scholar
  7. 7.
    Birks, H.J.B., Line, J.M, Juggins, S., Stevenson, A.C., ter Braak, C.J.F. 1990Diatoms and pH reconstructionPhil. Trans. R. Soc., Lond. B.327263278Google Scholar
  8. 8.
    Borcard, D., Legendre, P., Drapeau, P. 1992Partialling out the spatial component of ecological variationEcology7310451055Google Scholar
  9. 9.
    Burns, C.W. 1991New Zealand lakes research1967–91New Zeal. J. Mar. Fresh.25359379Google Scholar
  10. 11.
    Burns, N.M., Rutherford, J.C. 1998Results of monitoring New Zealand Lakes, 1992–1996. Volume 1 – General Findings. NIWA Client Report No. MFE80216/1National Institute of Water & Atmospheric Research LtdHamilton30Google Scholar
  11. 10.
    Burns, N.M., Deely, J., Hall, J., Stafi, K. 1997Comparing past and present trophic states of seven Central Volcanic Plateau lakes in New ZealandNew Zeal. J. Mar. Fresh.317187Google Scholar
  12. 12.
    Burns, N.M., Rutherford, J.C., Clayton, J.S. 1999A monitoring and classification system for New Zealand lakes and reservoirsLake Reserv. Manage.15255271Google Scholar
  13. 13.
    Burns, N., Bryers, G., Bowman, E. 2000Protocols for monitoring trophic levels of New Zealand lakes and reservoirsNew Zealand Ministry for the EnvironmentWellington138Google Scholar
  14. 14.
    Chague-Goff, C., Dawson, S., Goff, J.R., Zachariasen, K.R., Berryman, K.R., Garnett, D.L., Waldron, H.M., Mildenhall, D.C. 2002A tsunami (ca. 6300 years BP) and other Holocene environmental changes, northern Hawke’s Bay, New ZealandSed. Geol.15089102Google Scholar
  15. 15.
    Charles, D.F., Whitehead, D.R. 1986The PIRLA project: paleolimnological investigation of recent lake acidificationHydrobiologia1431320Google Scholar
  16. 16.
    Cochran, U. 2002a

    Diatom evidence for a distinct salinity change at Taupo Swamp, Plimmerton, New Zealand

    John, J. eds. Proceedings of the 15th International Diatom SymposiumA.R.G. Gantner VerlagLiechtenstein201207
    Google Scholar
  17. 17.
    Cochran U.A. 2002b. Detection of large Holocene earthquakes in the sedimentary record of Wellington, New Zealandusing diatom analysis. Unpublished Ph.D. Thesis. Victoria University of Wellington, 303pp.Google Scholar
  18. 18.
    Davies, S., Metcalfe, S., Caballero, M., Juggins, S. 2002Developing diatom-based transfer functions for Central Mexican lakesHydrobiologia46713Google Scholar
  19. 19.
    Downes, M.T., Hawes, I. 1994Plant pigment stratigraphy in Lake Okaro. NIWA Consultancy Report No SCJ135National Institute of Water and Atmospheric ResearchChristchurch9Google Scholar
  20. 20.
    Foged, N. 1979Diatoms in New Zealandthe North IslandBiblio. Phycol.471224Google Scholar
  21. 21.
    Fritz, S.C., Juggins, S., Battarbee, R.W., Engstrom, D.R. 1991Reconstruction of past changes in salinity and climate using a diatom-based transfer functionNature352706708Google Scholar
  22. 22.
    Gall, M.P., Downes, M.T. 1997Algal pigment stratigraphy in four Rotorua lakes: OkatainaOkarekaOkaro and Rotorua. NIWA Client Report No. CHC97-78National Institute of Water and Atmospheric ResearchChristchurch20Google Scholar
  23. 23.
    Gasse, F., Juggins, S., Ben Khelifa, L. 1995Diatom-based transfer functions for inferring past hydrochemical characteristics of African lakesPalaeogeogr. Palaeoclim. Palaeoecol.1173154Google Scholar
  24. 24.
    Gell, P.A. 1997The development of a diatom database for inferring lake salinity, Western VictoriaAustralia: towards a quantitative approach for reconstructing past climatesAust. J. Bot.45389423Google Scholar
  25. 25.
    Gell, P.A. 1998Quantitative reconstructions of the Holocene palaeosalinity of paired crater lakes based on a diatom transfer functionPalaeoclimates38396Google Scholar
  26. 26.
    Gibbons-Davies, J. 2001Rotorua Lakes Water Quality. Environment Report 2001/29Environment Bay of Plenty Regional CouncilWhakatane45Google Scholar
  27. 27.
    Goff, J.R., Rouse, H.L., Jones, S.L., Hayward, B.W., Cochran, U., McLea, W., Dickinson, W.W., Morley, M.S. 2000Evidence for an earthquake and tsunami about 3100–3400 year agoand other catastrophic saltwater inundations recorded in a coastal lagoon, New ZealandMar. Geol.17012Google Scholar
  28. 28.
    Green, J.D. 1979Palaeolimnological studies on Lake MaratotoNorth IslandNew ZealandPaleolimnol. Lake Biwa Japanese Pleistocene7416438Google Scholar
  29. 29.
    Green, J.D., Lowe, D.J. 1985Stratigraphy and development of c. 17,000 year old Lake MaratotoNorth IslandNew Zealandwith some inferences about climatic changeNew Zeal. J. Geol. Geop.28675699Google Scholar
  30. 30.
    Green, J.D., Lowe, D.J. 1992Palaeolimnology in New ZealandQuat. Austral. Papers102540Google Scholar
  31. 31.
    Green, J.D., Viner, A.B., Lowe, D.J. 1987

    The effect of climate on lake mixing patterns and temperatures

    Viner, A.B. eds. Inland Waters of New ZealandDSIR Science Information Publishing CentreWellington6596
    Google Scholar
  32. 32.
    Hall, R.I., Smol, J.P. 1992A weighted-averaging regression and calibration model for inferring total phosphorus concentration from diatoms in British Colombia (Canada) lakesFreshwater Biol.27417434Google Scholar
  33. 33.
    Hamilton, D.P., Mitchell, S.F. 1997Wave-induced shear stresses, plant nutrients and chlorophyll in seven shallow lakesFreshwater Biol.38159168Google Scholar
  34. 34.
    Harper, M.A., Howorth, R., McLeod, M. 1986Late Holocene diatoms in Lake Poukawa: effects of airfall tephra and changes in depthNew Zeal. J. Mar. Fresh.20107118Google Scholar
  35. 35.
    Hill, M.O., Gauch, H.G. 1980Detrended Correspondence Analysis: an improved ordination techniqueVegetatio424758Google Scholar
  36. 36.
    James, T.I., Harding, J., Lattimore, S.A. 1999The State of West Coast Surface Water Quality. Volume I: Summary, Methods, Discussion and RecommendationsWest Coast Regional CouncilGreymouth88Google Scholar
  37. 37.
    Jeppesen, E., Lauridsen, T.L., Mitchell, S.F., Christoffersen, K., Burns, C.W. 2000Trophic structure in the pelagial of 25 shallow New Zealand lakes: changes along nutrient and fish gradientsJ. Plankton Res.22951968Google Scholar
  38. 38.
    Jolly, V.H. 1968The comparitive limnology of some New Zealand lakes. 1. Physical and chemicalNew Zeal. J. Mar. Fresh.2214259Google Scholar
  39. 39.
    Jolly, V.H., Irwin, J. 1975

    Thermal conditions

    Jolly, V.H.Brown, J.M.A. eds. New Zealand LakesAuckland University PressAuckland90105
    Google Scholar
  40. 40.
    Jones, V.J., Juggins, S. 1995The construction of a diatom-based chlorophyll a transfer function and its application at three lakes on Signy Island (maritime Antarctic) subject to differing degrees of nutrient enrichmentFreshwater Biol.34433445Google Scholar
  41. 41.
    Juggins, S. 2003C2 Software for Ecological and Palaeoecological Data Analysis and Visualisation. User Guide Version 1.3University of NewcastleNewcastle69Google Scholar
  42. 42.
    Krammer, K., Lange-Bertalot, H. 1986Susswasserflora von MitteleuropaBacillariophyceae i Teil NaviculaceaeGustav Fischer VerlagStuttgart876Google Scholar
  43. 43.
    Krammer, K., Lange-Bertalot, H. 1988Susswasserflora von MitteleuropaBacillariophyceae ii Teil BacillariaceaeEpithemiaceaeSurirellaceaeGustav Fischer VerlagStuttgart610Google Scholar
  44. 44.
    Krammer, K., Lange-Bertalot, H. 1991aSusswasserflora von Mitteleuropa. Bacillariophyceae iii Teil Centrales, FragilariaceaeEunotiaceaeGustav Fischer VerlagStuttgart576Google Scholar
  45. 45.
    Krammer, K., Lange-Bertalot, H. 1991bSusswasserflora von Mitteleuropa. Bacillariophyceae iv Teil AchnanthaceaeGustav Fischer VerlagStuttgart437Google Scholar
  46. 46.
    Lotter, A.F., Birks, H.J.B., Hofmann, W., Marchetto, A. 1998Modern diatomcladocerachironomidand chrysophyte cyst assemblages as quantitative indicators for the reconstruction of past environmental conditions in the Alps. II. NutrientsJ. Paleolimnol.19443463Google Scholar
  47. 47.
    McColl, R.H.S. 1972Chemistry and trophic status of seven New Zealand lakesNew Zeal. J. Mar. Fresh6399447Google Scholar
  48. 48.
    Newnham, R.M., Lowe, D.J., Green, J.D. 1989Palynology, vegetation and climate of the Waikato lowlands, North IslandNew Zealandsince c. 18,000 years agoJ. Roy. Soc. N.Z.19127150Google Scholar
  49. 49.
    Philibert, A, Prairie, Y.T. 2002Is the introduction of benthic species necessary for open-water chemical reconstructions in diatom-based transfer functions?Can. J. Fish. Aquat. Sci.59938951Google Scholar
  50. 50.
    Prebble, M., Schallenberg, M., Carter, J., Shulmeister, J. 2002An analysis of phytolith assemblages for the quantitative reconstruction of Late Quaternary environments of the Lower Taieri Plain, OtagoSouth IslandNew Zealand. I. Modern assemblages and transfer functionsJ. Paleolimnol.27393413Google Scholar
  51. 51.
    Prebble, M., Shulmeister, J. 2002An analysis of phytolith assemblages for the quantitative reconstruction of Late Quaternary environments of the Lower Taieri Plain, OtagoSouth IslandNew Zealand. II. Paleoenvironmental reconstructionJ. Paleolimnnol.27415427Google Scholar
  52. 52.
    Rae, R., Howard Williams, C., Hawes, I., Schwarz, A.-M., Vincent, W.F. 2001Penetration of solar ultraviolet radiation into New Zealand lakes: influence of dissolved organic carbon and catchment vegetationLimnology27989Google Scholar
  53. 53.
    Ramstack, J.M., Fritz, S.C., Engstrom, D.R., Heiskary, S.A. 2003The application of a diatom-based transfer function to evaluate regional water-quality trends in Minnesota since 1970J. Paleolimnol.297994Google Scholar
  54. 54.
    Reed, J.M. 1998A diatom-conductivity transfer function for Spanish salt lakesJ. Paleolimnol.19399416Google Scholar
  55. 55.
    Roberts, D., McMinn, A. 1998A weighted-averaging regression and calibration model for inferring lakewater salinity from fossil diatom assemblages in saline lakes of the Vestfold Hills: A new tool for interpreting Holocene lake histories in AntarcticaJ. Paleolimnol.1999113Google Scholar
  56. 56.
    Roberts, D., McMinn, A. 1999A diatom-based palaeosalinity history of Ace LakeVestfold Hills, AntarcticaHolocene9401408Google Scholar
  57. 57.
    Sabbe, K., Vanhoutte, K., Lowe, R.L., Bergey, E.A., Biggs, B.J.F., Francoeur, S., Hodgson, D., Vyverman, W. 2001Six new Actinella (Bacillariophyceae) species from Papua New GuineaAustralia and New Zealand: futher evidence for widespread diatom endemism in the Australasian regionEur. J. Phycol.36321340Google Scholar
  58. 58.
    Sayer, C.D. 2001Problems with the application of diatom-total phosphorus transfer functions: examples from a shallow English lakeFreshwater Biol.46743757Google Scholar
  59. 59.
    Schonfelder, I., Gelbrecht, J., Schonfelder, J., Steinberg, C.E.W. 2002Relationships between littoral diatoms and their chemical environment in northeastern German lakes and riversJ. Phycol.386682Google Scholar
  60. 60.
    Siver, P.A., Ricard, R., Goodwin, R., Giblin, A.E. 2003Estimating in-lake alkalinity generation from sulfate reduction and its relationship to lake chemistry as inferred from algal mcirofossilsJ. Paleolimnol.29179197Google Scholar
  61. 61.
    Southland Regional Council2000Southland’s State of the Environment Report for WaterSouthland Regional CouncilInvercargill49Google Scholar
  62. 62.
    Sylvestre, F., Servant-Vildary, S., Roux, M. 2001Diatom-based ionic concentration and salinity models from the south Bolivian Altiplano 15–23 degree SJ. Paleolimnol.25279295Google Scholar
  63. 63.
    ter Braak, C.J.F. 1995


    Jongman, R.H.G.ter Braak, C.J.F.van Tongeren, O.F.R. eds. Data Analysis in Community and Landscape EcologyCambridge University PressCambridge91173
    Google Scholar
  64. 64.
    ter Braak, C.J.F., Juggins, S. 1993Weighted averaging partial least squares regression (WA-PLS): an improved method for reconstructing environmental variables from species assemblagesHydrobiologia269/270485502Google Scholar
  65. 65.
    C.J.F. ter Braak and milauer P. (1998) CANOCO Reference Manual and User’s Guide to Canoco for Windows (Version 4) Centre for Biometry WageningenGoogle Scholar
  66. 66.
    Tibby, J. 2004Development of a diatom-based model for inferring total phosphorus in south-eastern Australian water storagesJ. Paleolimnol.312336Google Scholar
  67. 67.
    Tibby, J., Reid, M.A., Fluin, J., Hart, B.T., Kershaw, A.P. 2003Assessing long-term pH change in an Australian river catchment using monitoring and palaeolimnological dataEnviron. Sci. Technol.3732503255Google Scholar
  68. 68.
    Tyler, P.A. 1996Endemism in freshwater algae. With special reference to the Australian regionHydrobiologia336127135Google Scholar
  69. 69.
    Vant, W.N., Pridmore, R.D., Challis, D.A. 1990Changes in the water quality of Lake Pupuke 1966–1990. Technical Publication Number 93Auckland Regional Water BoardAuckland26Google Scholar
  70. 70.
    Verleyen, E., Hodgson, D.A, Vyverman, W., Roberts, , McMinn, R.A., Vanhoutte, K., Sabbe, K. 2003Modelling diatom responses to climate induced fluctuations in themoisture balance in continental Antarctic LakesJ. Paleolimnol.30195215Google Scholar
  71. 71.
    Vincent, W.F., Forsyth, D.J. 1987

    Geothermally influenced waters

    Viner, A.B. eds. Inland Waters of New ZealandDSIR Science Information Publishing CentreWellington349377
    Google Scholar
  72. 72.
    Vincent, W.F., Gibbs, M.M., Dryden, S.J. 1984Accelerated eutrophication in a New Zealand lake: Lake Rotoiticentral North IslandNew Zeal. J. Mar. Fresh.18431440Google Scholar
  73. 73.
    Viner, A.B. 1984Resistance to mixing in New Zealand LakesNew Zeal. J. Mar. Fresh.187382Google Scholar
  74. 74.
    Viner, A.B., White, E. 1987

    Phytoplankton growth

    Viner, A.B. eds. Inland Waters of New ZealandDSIR Science Information Publishing CentreWellington191223
    Google Scholar
  75. 75.
    Vyverman, W., Sabbe, K. 1995Diatom-temperature transfer functions based on the altitudinal zonation of diatom assemblages in Papua New Guinea: A possible tool in the reconstruction of regional palaeoclimatic changesJ. Paleolimnol.136577Google Scholar
  76. 76.
    Vyverman, W., Sabbe, K., Mann, D.G., Kilroy, C., Vyverman, R., Vanhoutte, K., Hodgson, D. 1998Eunophora gen. nov. (Bacillariophyta) from Tasmania and New Zealand: description and comparison with Eunotia and amphoroid diatomsEur. J. Phycol.3395111Google Scholar
  77. 77.
    Vyverman, W., Vyverman, R., Hodgson, D., Tyler, P.A. 1995Diatoms from Tasmanian mountain lakes: a reference data-set (TASDAT) for environmental reconstruction and a systematic and autecological studyBiblio. Diatomol.331193Google Scholar
  78. 78.
    Wetzel, R.G. 1975LimnologySaunders College PublishingPhilidelphia743Google Scholar
  79. 79.
    White, E. 1983Lake eutrophication in New Zealand - a comparison with oter countries of the Organisation for Economic Co-operation and DevelopmentNew Zeal. J. Mar. Fresh.17437444Google Scholar
  80. 80.
    Wilmshurst, J.M., Wiser, S.K., Charman, D.J. 2003Reconstructing Holocene water tables in New Zealand using testate amoebae: differential preservation of tests and implications for the use of transfer functionsHolocene136172Google Scholar
  81. 81.
    Yang, X., Kamenik, C., Schmidt, R., Wang, S. 2003Diatom-based conductivity and water-level inference models from eastern Tibetan (Qinghai-Xizang) Plateau lakesJ. Paleolimnol.30119Google Scholar

Copyright information

© Springer 2005

Authors and Affiliations

  1. 1.National Institute for Water and Atmospheric Research Ltd.ChristchurchNew Zealand
  2. 2.Cooperative Research Centre for Freshwater EcologyUniversity of CanberraAustralia

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