Skip to main content
SpringerLink
Log in

Water Quality Assessment

  • Chapter
  • First Online:
Modern Trends in Diatom Identification

Part of the book series: Developments in Applied Phycology ((DAPH,volume 10))

  • 903 Accesses

Abstract

Diatom metrics methods are becoming important tools for the assessment of environmental conditions in aquatic systems. Diatoms have several advantages as bioindicators: their ubiquitous distribution across world aquatic environments, their ability to integrate multiple water quality features, and the relatively simple and standardized sampling and preparation methods. To date, several diatom indices have been developed, most of which are general pollution indices, especially indicative of eutrophication and organic pollution. This chapter reviews the literature concerning diatom-based analyses for biomonitoring purposes, with a first overview on available methods (microscopy-based, automatic identification, and DNA barcoding), and an account on bioassessment tools using phytobenthos in EU countries, with a special focus on the Spanish experience.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 299.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Venkatachalapathy, R., Karthikeyan, P.: Application of diatom-based indices for monitoring environmental quality of riverine ecosystems: a review. In: Environmental Management of River Basin Ecosystems, pp. 593–619. Springer (2015)

    Google Scholar 

  2. Taylor, J., Prygiel, J., Vosloo, A., Pieter, A., van Rensburg, L.: Can diatom-based pollution indices be used for biomonitoring in South Africa? A case study of the Crocodile West and Marico water management area. Hydrobiologia. 592(1), 455–464 (2007)

    Article  Google Scholar 

  3. Lavoie, I., Campeau, S., Grenier, M., Dillon, P.J.: A diatom-based index for the biological assessment of eastern Canadian rivers: an application of correspondence analysis (CA). Can. J. Fish. Aquat. Sci. 63(8), 1793–1811 (2006)

    Article  Google Scholar 

  4. Rakowska, B., Szczepocka, E.: Demonstration of the Bzura River restoration using diatom indices. Biologia. 66(3), 411–417 (2011)

    Article  Google Scholar 

  5. Blanco, S., Bécares, E., Cauchie, H.-M., Hoffmann, L., Ector, L.: Comparison of biotic indices for water quality diagnosis in the Duero Basin (Spain). Archiv für Hydrobiologie Supplement Large Rivers. 161, 267–286 (2007)

    CAS  Google Scholar 

  6. Taylor, J., van Vuuren, M.J., Pieterse, A.: The application and testing of diatom-based indices in the Vaal and Wilge Rivers, South Africa. Water SA. 33(1), (2007)

    Google Scholar 

  7. Feio, M.J., Almeida, S.F., Craveiro, S.C., Calado, A.J.: A comparison between biotic indices and predictive models in stream water quality assessment based on benthic diatom communities. Ecol. Indic. 9(3), 497–507 (2009)

    Article  CAS  Google Scholar 

  8. Schneider, S.C., Kahlert, M., Kelly, M.G.: Interactions between pH and nutrients on benthic algae in streams and consequences for ecological status assessment and species richness patterns. Sci. Total Environ. 444, 73–84 (2013)

    Article  CAS  PubMed  Google Scholar 

  9. Soininen, J.: Environmental and spatial control of freshwater diatoms—a review. Diatom Res. 22(2), 473–490 (2007)

    Article  Google Scholar 

  10. Bere, T.: Are diatom-based biotic indices developed in eutrophic, organically enriched waters reliable monitoring metrics in clean waters? Ecol. Indic. 62, 312–316 (2016)

    Article  CAS  Google Scholar 

  11. Atazadeh, I., Sharifi, M., Kelly, M.: Evaluation of the Trophic Diatom Index for assessing water quality in River Gharasou, western Iran. Hydrobiologia. 589(1), 165–173 (2007)

    Article  CAS  Google Scholar 

  12. Stenger-Kovács, C., Buczko, K., Hajnal, E., Padisák, J.: Epiphytic, littoral diatoms as bioindicators of shallow lake trophic status: Trophic Diatom Index for Lakes (TDIL) developed in Hungary. Hydrobiologia. 589(1), 141–154 (2007)

    Article  Google Scholar 

  13. Blanco, S.: Environmental factors controlling lake diatom communities: a meta-analysis of published data. Biogeosci. Discuss. 11(11), 15889–15909 (2014)

    Article  Google Scholar 

  14. Bate, G., Smailes, P., Adams, J.: A water quality index for use with diatoms in the assessment of rivers. Water SA. 30(4), 493–498 (2004)

    Article  CAS  Google Scholar 

  15. Stevenson, R., Pan, Y.: Assessing environmental conditions in rivers and streams with diatoms. In: The Diatoms: Applications for the Environmental and Earth Sciences, pp. 57–85 (1999)

    Google Scholar 

  16. Kelly, M.: Use of the trophic diatom index to monitor eutrophication in rivers. Water Res. 32(1), 236–242 (1998)

    Article  CAS  Google Scholar 

  17. Kelly, M.: Use of community-based indices to monitor eutrophication in European rivers. Environ. Conserv. 25(1), 22–29 (1998)

    Article  CAS  Google Scholar 

  18. Kelly, M., et al.: The Trophic Diatom Index: A User’s Manual Revised edition R&D Technical Report E2/TR2. Environment Agency, Bristol (2001)

    Google Scholar 

  19. Fornells, N.P., Solà, C., Munné, A.: QBR: un índice rápido para la evaluación de la calidad de los ecosistemas de ribera. Tecnología del Agua. 175, 20–39 (1998)

    Google Scholar 

  20. Pardo, I., et al.: El hábitat de los ríos mediterráneos. Diseño de un índice de diversidad de hábitat. Limnetica. 21(3–4), 115–133 (2002)

    Google Scholar 

  21. Soeprobowati, T.R., Tandjung, S.D., Sutikno, S., Hadisusanto, S., Gell, P.: The minimum number of valves for diatoms identification in Rawapening Lake, Central Java. BIOTROPIA Southeast Asian J. Trop. Biol. 23(2), 97–100 (2017)

    Google Scholar 

  22. Chessman, B., Growns, I., Currey, J., Plunkett-Cole, N.: Predicting diatom communities at the genus level for the rapid biological assessment of rivers. Freshw. Biol. 41(2), 317–331 (1999)

    Article  Google Scholar 

  23. Rimet, F., Bouchez, A.: Life-forms, cell-sizes and ecological guilds of diatoms in European rivers. Knowl. Manag. Aquat. Ecosyst. 406, 01 (2012)

    Article  Google Scholar 

  24. Rice, A., Baird, E., Eaton, R.: Standard methods for examination of water and wastewater. American Public Health Association, Washington, DC (2017)

    Google Scholar 

  25. Sournia, A.: Phytoplankton Manual. UNESCO, Paris (1978)

    Google Scholar 

  26. Utermöhl, H.: Zur Vervollkommnung der quantitativen Phytoplankton-Methodik: Mit 1 Tabelle und 15 abbildungen im Text und auf 1 Tafel. Internationale Vereinigung für theoretische und angewandte Limnologie: Mitteilungen. 9(1), 1–38 (1958)

    Google Scholar 

  27. Lund, J., Kipling, C., Le Cren, E.: The inverted microscope method of estimating algal numbers and the statistical basis of estimations by counting. Hydrobiologia. 11(2), 143–170 (1958)

    Article  Google Scholar 

  28. CEN: Water quality-Guidance standard for the routine sampling and pretreatment of benthic diatoms from rivers. EN 13946: 2003. Comité Européen de Normalisation, Geneva (2003)

    Google Scholar 

  29. CEN: Water Quality–Guidance Standard for the Identification, Enumeration and Interpretation of Benthic Diatom Samples from Running Waters. EN 14407: 2004. Comité Européen de Normalisation, Geneva (2004)

    Google Scholar 

  30. Kelly, M.: International and European standards for algal-based monitoring. Oceanol. Hydrobiol. Stud. 1, 77–81 (2004)

    Google Scholar 

  31. Kelly, M., et al.: Recommendations for the routine sampling of diatoms for water quality assessments in Europe. J. Appl. Phycol. 10(2), 215 (1998)

    Article  Google Scholar 

  32. CHD: Metodología para el establecimiento del estado ecológico según la Directiva Marco del Agua. Protocolos de muestreo y análisis para fitobentos (microalgas bentónicas), pp. 1–33. CHD, Zaragoza (2005)

    Google Scholar 

  33. Pardo, I., García, L., Delgado, C., Costas, N., Abraín, R.: Protocolos de muestreo de comunidades biológicas acuáticas fluviales en el ámbito de las Confederaciones Hidrográficas del Miño-Sil y Cantábrico. MARM, Madrid (2010)

    Google Scholar 

  34. Stevenson, R., Bahls, L.: Periphyton protocols: revision to rapid bioassessment protocols for use in streams and rivers: periphyton, benthic macroinvertebrates and fish. EPA, Washington, DC (1999)

    Google Scholar 

  35. Blanco, S., Álvarez, I., Cejudo, C.: A test on different aspects of diatom processing techniques. J. Appl. Phycol. 20(4), 445–450 (2008)

    Article  Google Scholar 

  36. Moss, B., et al.: The estimation of numbers and pigment content in epipelic algal populations. Limnol. Oceanogr. 11(4), 584–595 (1966)

    Article  Google Scholar 

  37. Battarbee, R.W.: A new method for the estimation of absolute microfossil numbers, with reference especially to diatoms. Limnol. Oceanogr. 18(4), 647–653 (1973)

    Article  Google Scholar 

  38. McBride, T.P.: Preparing random distributions of diatom valves on microscope slides. Limnol. Oceanogr. 33, 1627–1629 (1988)

    Article  Google Scholar 

  39. Schrader, H.: Proposal for a standardized method of cleaning diatom-bearing deep-sea and land-exposed marine sediments. Nova Hedwig. Beih. 45, 403–409 (1973)

    Google Scholar 

  40. Alverson, A.J., Manoylov, K.M., Stevenson, R.J.: Laboratory sources of error for algal community attributes during sample preparation and counting. J. Appl. Phycol. 15(5), 357–369 (2003)

    Article  Google Scholar 

  41. Van der Werff, A.: A new method of concentrating and cleaning diatoms and other organisms. Internationale Vereinigung für theoretische und angewandte Limnologie: Verhandlungen. 12(1), 276–277 (1953)

    Google Scholar 

  42. Setty, M.A.P.: Preparation and method of study of fossil diatoms. Micropaleontology. 12, 511–514 (1966)

    Article  Google Scholar 

  43. Brown, S.-D., Austin, A.: A method of collecting periphyton in lentic habitats with procedures for subsequent sample preparation and quantitative assessment. Internationale Revue der gesamten Hydrobiologie und Hydrographie. 56(4), 557–580 (1971)

    Article  Google Scholar 

  44. Ma, J.C.W., Jeffrey, L.M.: Description and comparison of a new cleaning method of diatom frustules for light and electron microscope studies. J. Microsc. 112(2), 235–238 (1978)

    Article  Google Scholar 

  45. Carr, J.M., Hergenrader, G.L., Troelstrup Jr., N.H.: A simple, inexpensive method for cleaning diatoms. Trans. Am. Microsc. Soc. 152–157 (1986)

    Article  Google Scholar 

  46. Scherer, R.P.: A new method for the determination of absolute abundance of diatoms and other silt-sized sedimentary particles. J. Paleolimnol. 12(2), 171–179 (1994)

    Article  Google Scholar 

  47. Charles, D.F., Knowles, C., Davis, R.S.: Protocols for the analysis of algal samples collected as part of the US Geological Survey National Water-Quality Assessment Program. Patrick Center for Environmental Research Report, Philadelphia, PA (2002)

    Google Scholar 

  48. Rings, A., Lücke, A., Schleser, G.H.: A new method for the quantitative separation of diatom frustules from lake sediments. Limnol. Oceanogr. Methods. 2(1), 25–34 (2004)

    Article  Google Scholar 

  49. Schaumburg, J., Schranz, C., Stelzer, D., Hofmann, G., Gutowski, A., Foerster, J.: Instruction protocol for the ecological assessment of running waters for implementation of the EC Water Framework Directive: macrophytes and phytobenthos. Bavarian Environment Agency, Augsburg (2006)

    Google Scholar 

  50. Blanco, S., Becares, E.: Metodo de muestreo de diatomeas epífitas en lagunas para la aplicación de la Directiva Marco del Agua. Tecnología del Agua. 261, 48–53 (2006)

    Google Scholar 

  51. Li, J., Chen, J.: An effective cleaning method for producing pure diatom samples from lake sediments. Earth Environ. 35(1), 91–96 (2007)

    CAS  Google Scholar 

  52. Metfies, K., et al.: An optimized protocol for the identification of diatoms, flagellated algae and pathogenic protozoa with phylochips. Mol. Ecol. Notes. 7(6), 925–936 (2007)

    Article  CAS  Google Scholar 

  53. Debenest, T., Silvestre, J., Coste, M., Delmas, F., Pinelli, E.: A new cell primo-culture method for freshwater benthic diatom communities. J. Appl. Phycol. 21(1), 65 (2009)

    Article  CAS  Google Scholar 

  54. Evans, K.M., Mann, D.G.: A proposed protocol for nomenclaturally effective DNA barcoding of microalgae. Phycologia. 48(1), 70–74 (2009)

    Article  CAS  Google Scholar 

  55. Díaz-Palma, P., Alucema, A., Hayashida, G., Maidana, N.: Development and standardization of a microalgae test for determining deaths by drowning. Forensic Sci. Int. 184(1–3), 37–41 (2009)

    Article  PubMed  Google Scholar 

  56. Fetscher, A.E., Busse, L., Ode, P.R.: Standard operating procedures for collecting stream algae samples and associated physical habitat and chemical data for ambient bioassessments in California. California State Water Resources Control Board Surface Water Ambient Monitoring Program (SWAMP) Bioassessment SOP 2 (2009)

    Google Scholar 

  57. Watanabe, T., Kodama, Y., Mayama, S.: Application of a novel cleaning method using low-temperature plasma on tidal flat diatoms with heterovalvy or delicate frustule structure. Proc. Acad. Natl. Sci. Phila. 160(1), 83–87 (2010)

    Article  Google Scholar 

  58. Serieyssol, K., et al.: Diatom fossils in mires: a protocol for extraction, preparation and analysis in palaeoenvironmental studies. Mires Peat. 7(12), 1–11 (2010)

    Google Scholar 

  59. Lang, I., Kaczmarska, I.: A protocol for a single-cell PCR of diatoms from fixed samples: method validation using Ditylum brightwellii (T. West) Grunow. Diatom Res. 26(1), 43–49 (2011)

    Article  Google Scholar 

  60. Zoto, G.A., Dillon, D.O., Schlichting Jr., H.E.: A rapid method for clearing diatoms for taxonomic and ecological studies. Phycologia. 12(1), 69–70 (1973)

    Article  Google Scholar 

  61. Friedrichs, L., Maier, M., Hamm, C.: A new method for exact three-dimensional reconstructions of diatom frustules. J. Microsc. 248(2), 208–217 (2012)

    Article  CAS  PubMed  Google Scholar 

  62. Mendes, T., Almeida, S.F., Feio, M.J.: Assessment of rivers using diatoms: effect of substrate and evaluation method. Arch. Hydrobiol. 179(4), 267–279 (2012)

    Article  CAS  Google Scholar 

  63. MacDonald, L.A., Balasubramaniam, A.M., Hall, R.I., Wolfe, B.B., Sweetman, J.N.: Developing biomonitoring protocols for shallow Arctic lakes using diatoms and artificial substrate samplers. Hydrobiologia. 683(1), 231–248 (2012)

    Article  CAS  Google Scholar 

  64. Vermeulen, S., Lepoint, G., Gobert, S.: Processing samples of benthic marine diatoms from Mediterranean oligotrophic areas. J. Appl. Phycol. 24(5), 1253–1260 (2012)

    Article  Google Scholar 

  65. Gautam, S., Arya, A., Vinayak, V.: Protocol to establish axenic cultures for diatoms of fresh water. Int. J. Sci. Res. 5(11), 410–418 (2016)

    Google Scholar 

  66. Tennant, R.K., et al.: A new flow cytometry method enabling rapid purification of fossil pollen from terrestrial sediments for AMS radiocarbon dating. J. Quat. Sci. 28(3), 229–236 (2013)

    Article  Google Scholar 

  67. Seo, Y., Sato, S., Kuroki, K., Kishida, T.: A simple DNA coprecipitation method for the detection of diatoms in heart blood. Forensic Sci. Int. 232(1–3), 154–159 (2013)

    Article  CAS  PubMed  Google Scholar 

  68. Kimura, K., Tomaru, Y.: A unique method for culturing diatoms on agar plates. Plankton Benthos Res. 8(1), 46–48 (2013)

    Article  Google Scholar 

  69. Zhao, J., et al.: Application of the microwave digestion-vacuum filtration-automated scanning electron microscopy method for diatom detection in the diagnosis of drowning. J. Forensic Legal Med. 33, 125–128 (2015)

    Article  Google Scholar 

  70. Jiang, W., Pan, H., Wang, F., Jiang, M., Deng, X., Li, J.: A rapid sample processing method to observe diatoms via scanning electron microscopy. J. Appl. Phycol. 27(1), 243–248 (2015)

    Article  Google Scholar 

  71. Warnock, J.P., Scherer, R.P.: A revised method for determining the absolute abundance of diatoms. J. Paleolimnol. 53(1), 157–163 (2015)

    Article  Google Scholar 

  72. Wang, H., et al.: A simple digestion method with a Lefort aqua regia solution for diatom extraction. J. Forensic Sci. 60, S227–S230 (2015)

    Article  CAS  PubMed  Google Scholar 

  73. Stancheva, R., Busse, L., Kociolek, J., Sheath, R.: Standard operating procedures for laboratory processing and identification of stream algae. California State Water Resources Control Board Surface Water Ambient Monitoring Program (SWAMP) Bioassessment SOP 0003 (2015)

    Google Scholar 

  74. Morin, S., Gómez, N., Tornés, E., Licursi, M., Rosebery, J.: Benthic diatom monitoring and assessment of freshwater environments: standard methods and future challenges. In: Aquatic Biofilms, Ecology, Water Quality and Wastewater Treatment, pp. 111–124 (2016)

    Google Scholar 

  75. Ferrara, M.A., De Tommasi, E., Coppola, G., De Stefano, L., Rea, I., Dardano, P.: Diatom valve three-dimensional representation: a new imaging method based on combined microscopies. Int. J. Mol. Sci. 17(10), 1645 (2016)

    Article  PubMed Central  Google Scholar 

  76. Mansilla, C., Novais, M.H., Faber, E., Martínez-Martínez, D., De Hosson, J.T.: On the 3D reconstruction of diatom frustules: a novel method, applications and limitations. J. Appl. Phycol. 28(2), 1097–1110 (2016)

    Article  CAS  Google Scholar 

  77. Saba, F., et al.: A rapid and reproducible genomic DNA extraction protocol for sequence-based identification of archaea, bacteria, cyanobacteria, diatoms, fungi and green algae. J. Med. Bacteriol. 5(3–4), 22–28 (2017)

    Google Scholar 

  78. Rojas-Camacho, O., Forero, M.G., Menéndez, J.M.: A tuning method for diatom segmentation techniques. Appl. Sci. 7(8), 762 (2017)

    Article  Google Scholar 

  79. Barragán, C., Wetzel, C.E., Ector, L.: A standard method for the routine sampling of terrestrial diatom communities for soil quality assessment. J. Appl. Phycol. 30(2), 1095–1113 (2018)

    Article  CAS  Google Scholar 

  80. Bayer, M., et al.: ADIAC: Using computer vision technology for automatic diatom identification. In: Proceedings of the 16th International Diatom Symposium, Athens, pp. 537–562 (2000)

    Google Scholar 

  81. Du Buf, H., et al.: Diatom identification: a double challenge called ADIAC. In: International Conference on Image Analysis and Processing, Venice, pp. 734–739 (1999)

    Google Scholar 

  82. Du Buf, H., Bayer, M. (eds.): Automatic diatom identification. World Scientific, Singapore (2002)

    Google Scholar 

  83. Kloster, M., Kauer, G., Beszteri, B.: SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects. BMC Bioinf. 15(1), 218 (2014)

    Article  Google Scholar 

  84. Kloster, M., Esper, O., Kauer, G., Beszteri, B.: Large-scale permanent slide imaging and image analysis for diatom morphometrics. Appl. Sci. 7(4), 330 (2017)

    Article  Google Scholar 

  85. Wishkerman, A., Hamilton, P.B.: Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies. Appl. Plant Sci. 6(12), (2018)

    Article  PubMed  PubMed Central  Google Scholar 

  86. Pappas, J., Kociolek, P., Stoermer, E.: Quantitative morphometric methods in diatom research. Nova Hedwig. Beih. 143, 281–306 (2014)

    Google Scholar 

  87. Delgado, C., Novais, M.H., Blanco, S., Almeida, S.F.: Examination and comparison of Fragilaria candidagilae sp. Nov. with type material of Fragilaria recapitellata, F. capucina, F. perminuta, F. intermedia and F. neointermedia (Fragilariales, Bacillariophyceae). Phytotaxa. 231(1), 1–18 (2015)

    Article  Google Scholar 

  88. Poulíčková, A., Neustupa, J., Hašler, P., Tomanec, O., Cox, E.J.: A new species, Navicula lothargeitleri sp. nov., within the Navicula cryptocephala complex (Bacillariophyceae). Phytotaxa. 273(1), 23–33 (2016)

    Article  Google Scholar 

  89. Wengrat, S., Marquardt, G.C., de Campos Bicudo, D., de Mattos Bicudo, C.E., Wetzel, C.E., Ector, L.: Type analysis of Cymbella schubartii and two new Encyonopsis species (Bacillariophyceae) from southeastern Brazil. Phytotaxa. 221(3), 247–264 (2015)

    Article  Google Scholar 

  90. Bueno, G., Deniz, O., Pedraza, A., et al.: Automated diatom classification (Part A): handcrafted feature approaches. Appl. Sci. 7(8), 753 (2017)

    Article  Google Scholar 

  91. Pedraza, A., Bueno, G., Deniz, O., Cristóbal, G., Blanco, S., Borrego-Ramos, M.: Automated diatom classification (Part B): a deep learning approach. Appl. Sci. 7(5), 460 (2017)

    Article  Google Scholar 

  92. Pedraza, A., et al.: Lights and pitfalls of convolutional neural networks for diatom identification. Optics, Photonics and Digital Technologies for Imaging Applications V, International Society for Optics and Photonics 106790G (2018)

    Google Scholar 

  93. Kelly, M., et al., A DNA based Diatom Metabarcoding Approach for Water Framework Directive Classification of Rivers (2018).

    Google Scholar 

  94. Malviya, S.: Global Diatom Biodiversity: An Assessment Using Metabarcoding Approach. Ph.D. Dissertation, Paris (2015)

    Google Scholar 

  95. Nanjappa, D., Audic, S., Romac, S., Kooistra, W.H., Zingone, A.: Assessment of species diversity and distribution of an ancient diatom lineage using a DNA metabarcoding approach. PLoS One. 9(8), e103810 (2014)

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  96. Moniz, M.B.J., Kaczmarska, I.: Barcoding diatoms: is there a good marker? Mol. Ecol. Resour. 9, 65–74 (2009)

    Article  CAS  PubMed  Google Scholar 

  97. Zimmermann, J., Jahn, R., Gemeinholzer, B.: Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Org. Divers. Evol. 11(3), 173 (2011)

    Article  Google Scholar 

  98. Rivera, S., Vasselon, V., Jacquet, S., Bouchez, A., Ariztegui, D., Rimet, F.: Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment. Hydrobiologia. 807(1), 37–51 (2018)

    Article  Google Scholar 

  99. Zimmermann, J.: DNA barcoding and eDNA barcoding in diatoms. Ph.D. Dissertation, Giessen (2015)

    Google Scholar 

  100. Vasselon, V., Domaizon, I., Rimet, F., Kahlert, M., Bouchez, A.: Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: do DNA extraction methods matter? Freshw. Sci. 36(1), 162–177 (2017)

    Article  Google Scholar 

  101. Vasselon, V., Rimet, F., Tapolczai, K., Bouchez, A.: Assessing ecological status with diatoms DNA metabarcoding: scaling-up on a WFD monitoring network (Mayotte island, France). Ecol. Indic. 82, 1–12 (2017)

    Article  CAS  Google Scholar 

  102. Apothéloz-Perret-Gentil, L., Cordonier, A., Straub, F., Iseli, J., Esling, P., Pawlowski, J.: Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring. Mol. Ecol. Resour. 17(6), 1231–1242 (2017)

    Article  PubMed  CAS  Google Scholar 

  103. Piredda, R., Simeone, M.C., Attimonelli, M., Bellarosa, R., Schirone, B.: Prospects of barcoding the Italian wild dendroflora: oaks reveal severe limitations to tracking species identity. Mol. Ecol. Resour. 11(1), 72–83 (2011)

    Article  CAS  PubMed  Google Scholar 

  104. Hoef-Emden, K.: Pitfalls of establishing DNA barcoding systems in protists: the Cryptophyceae as a test case. PLoS One. 7(8), e43652 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Fittipaldi, M., Codony, F., Adrados, B., Camper, A.K., Morató, J.: Viable real-time PCR in environmental samples: can all data be interpreted directly? Microb. Ecol. 61(1), 7–12 (2011)

    Article  CAS  PubMed  Google Scholar 

  106. Urbánková, P., Veselá, J.: DNA-barcoding: a case study in the diatom genus Frustulia (Bacillariophyceae). Nova Hedwigia. 142, 147–162 (2013)

    Google Scholar 

  107. Khan-Bureau, D., Ector, L., Morales, E.A., Wade, E.J., Lewis, L.A.: Contrasting morphological and DNA barcoding methods for diatom (Bacillariophyta) identification from environmental samples in the Eightmile River in Connecticut. Nova Hedwig. Beih. 146, 279–302 (2018)

    Article  Google Scholar 

  108. Hering, D., Moog, O., Sandin, L., Verdonschot, P.F.: Overview and application of the AQEM assessment system. Hydrobiologia. 516(1–3), 1–20 (2004)

    Article  Google Scholar 

  109. Sandin, L., Verdonschot, P.F.: Stream and river typologies—major results and conclusions from the STAR project. In: The Ecological Status of European Rivers: Evaluation and Intercalibration of Assessment Methods, pp. 33–37. Springer (2006)

    Google Scholar 

  110. CEDEX: Directiva 2000/60/CE. Análisis de las características de las demarcaciones. Caracterización de los tipos de ríos y lagos. MARM, Madrid (2004)

    Google Scholar 

  111. Tison, J., et al.: Typology of diatom communities and the influence of hydro-ecoregions: a study on the French hydrosystem scale. Water Res. 39(14), 3177–3188 (2005)

    Article  CAS  PubMed  Google Scholar 

  112. Grenier, M., Lavoie, I., Rousseau, A.N., Campeau, S.: Defining ecological thresholds to determine class boundaries in a bioassessment tool: the case of the Eastern Canadian Diatom Index (IDEC). Ecol. Indic. 10(5), 980–989 (2010)

    Article  Google Scholar 

  113. Pardo, I., et al.: A predictive diatom-based model to assess the ecological status of streams and rivers of Northern Spain. Ecol. Indic. 90, 519–528 (2018)

    Article  Google Scholar 

  114. Karr, J.R.: Biological integrity: a long-neglected aspect of water resource management. Ecol. Appl. 1(1), 66–84 (1991)

    Article  PubMed  Google Scholar 

  115. Leira, M., Sabater, S.: Diatom assemblages distribution in catalan rivers, NE Spain, in relation to chemical and physiographical factors. Water Res. 39(1), 73–82 (2005)

    Article  CAS  PubMed  Google Scholar 

  116. Dallas, H.F.: Ecological status assessment in Mediterranean rivers: complexities and challenges in developing tools for assessing ecological status and defining reference conditions. Hydrobiologia. 719(1), 483–507 (2013)

    Article  Google Scholar 

  117. Munné, A., Prat, N.: Effects of Mediterranean climate annual variability on stream biological quality assessment using macroinvertebrate communities. Ecol. Indic. 11(2), 651–662 (2011)

    Article  Google Scholar 

  118. Sánchez-Montoya, M., et al.: Defining criteria to select reference sites in Mediterranean streams. Hydrobiologia. 619(1), 39 (2009)

    Article  Google Scholar 

  119. Coste, M., Tison, J., Delmas, F.: Flores diatomiques des cours d’eau: proposition de valeurs limites du «Bon État» pour l’IPS et l’IBD. Document de travail–Unité de Recherche Qualité des Eaux–Cemagref, Bordeaux (2004)

    Google Scholar 

  120. Hawkins, C.P., Olson, J.R., Hill, R.A.: The reference condition: predicting benchmarks for ecological and water-quality assessments. J. N. Am. Benthol. Soc. 29(1), 312–343 (2010)

    Article  Google Scholar 

  121. Kelly, M.: Data rich, information poor? Phytobenthos assessment and the Water Framework Directive. Eur. J. Phycol. 48(4), 437–450 (2013)

    Article  Google Scholar 

  122. Álvarez-Blanco, I., Blanco, S., Cejudo-Figueiras, C., Bécares, E.: The Duero Diatom Index (DDI) for river water quality assessment in NW Spain: design and validation. Environ. Monit. Assess. 185(1), 969–981 (2013)

    Article  PubMed  CAS  Google Scholar 

  123. Lobo, E.A., Schuch, M., Heinrich, C.G., et al.: Development of the Trophic Water Quality Index (TWQI) for subtropical temperate Brazilian lotic systems. Environ. Monit. Assess. 187(6), 354 (2015)

    Article  PubMed  CAS  Google Scholar 

  124. Rimet, F.: Recent views on river pollution and diatoms. Hydrobiologia. 683(1), 1–24 (2012)

    Article  Google Scholar 

  125. Kelly, M., Whitton, B.A.: Biological monitoring of eutrophication in rivers. Hydrobiologia. 384(1–3), 55–67 (1998)

    Article  Google Scholar 

  126. Zelinka, M.: Zur Prazisierung der biologischen klassifikation der Reinheid fliessender Gewasser. Arch. Hydrobiol. 57, 389–407 (1961)

    Google Scholar 

  127. CEMAGREF: Etude des méthodes biologiques quantitatives d’appréciation de la qualité des eaux. Rapport Division Qualité, Lyon (1982)

    Google Scholar 

  128. Blanco, S., et al.: Diatom assemblages and water quality assessment in the Duero Basin (NW Spain). Belg. J. Bot. 39–50 (2008)

    Google Scholar 

  129. Potapova, M., Charles, D.F.: Diatom metrics for monitoring eutrophication in rivers of the United States. Ecol. Indic. 7(1), 48–70 (2007)

    Article  Google Scholar 

  130. Rott, E., Pipp, E., Pfister, P.: Diatom methods developed for river quality assessment in Austria and a cross-check against numerical trophic indication methods used in Europe. Algol. Stud. 110(1), 91–115 (2003)

    Google Scholar 

  131. Delgado, C., Pardo, I., García, L.: A multimetric diatom index to assess the ecological status of coastal Galician rivers (NW Spain). Hydrobiologia. 644(1), 371–384 (2010)

    Article  CAS  Google Scholar 

  132. Barragán, C.: Desarrollo de un nuevo índice de diatomeas para la evaluación del estado ecológico de los ríos de la Demarcación Hidrográfica del Tajo. In: 18th Conference of the Iberian Association of Limnology (AIL 2016), Tortosa (2016)

    Google Scholar 

  133. Besse-Lototskaya, A., Verdonschot, P.F., Coste, M., Van de Vijver, B.: Evaluation of European diatom trophic indices. Ecol. Indic. 11(2), 456–467 (2011)

    Article  Google Scholar 

  134. Descy, J.-P., Coste, M.: A test of methods for assessing water quality based on diatoms. Internationale Vereinigung für theoretische und angewandte Limnologie: Verhandlungen. 24(4), 2112–2116 (1991)

    Google Scholar 

  135. Round, F.: A review and methods for the use of epilithic diatoms for detecting and monitoring changes in river water quality. HMSO Publisher, London (1993)

    Google Scholar 

  136. Taylor, J., de la Rey, P.A., van Rensburg, L.: Recommendations for the collection, preparation and enumeration of diatoms from riverine habitats for water quality monitoring in South Africa. Afr. J. Aquat. Sci. 30(1), 65–75 (2005)

    Article  Google Scholar 

  137. Almeida, et al.: Water quality assessment of rivers using diatom metrics across Mediterranean Europe: a methods intercalibration exercise. Sci. Total Environ. 476, 768–776 (2014)

    Article  PubMed  CAS  Google Scholar 

  138. Prygiel, J., et al.: Determination of the biological diatom index (IBD NF T 90–354): results of an intercomparison exercise. J. Appl. Phycol. 14(1), 27–39 (2002)

    Article  Google Scholar 

  139. Barbour, A.M.T., Gerritsen, J., Snyder, B.D., Stribling, J.B.: Rapid bioassessment protocols for use in streams and wadeable rivers: periphyton, benthic macroinvertebrates and fish. EPA, Washington (1998)

    Google Scholar 

  140. Lavoie, I., Campeau, S., Zugic-Drakulic, N., Winter, J., Fortin, C.: Using diatoms to monitor stream biological integrity in Eastern Canada: an overview of 10 years of index development and ongoing challenges. Sci. Total Environ. 475, 187–200 (2014)

    Article  CAS  PubMed  Google Scholar 

  141. Hoagland, K.D., Roemer, S.C., Rosowski, J.R.: Colonization and community structure of two periphyton assemblages, with emphasis on the diatoms (Bacillariophyceae). Am. J. Bot. 69(2), 188–213 (1982)

    Article  Google Scholar 

  142. Pringle, C.M.: Nutrient spatial heterogeneity: effects on community structure, physiognomy and diversity of stream algae. Ecology. 71(3), 905–920 (1990)

    Article  Google Scholar 

  143. Berthon, V., Bouchez, A., Rimet, F.: Using diatom life-forms and ecological guilds to assess organic pollution and trophic level in rivers: a case study of rivers in south-eastern France. Hydrobiologia. 673(1), 259–271 (2011)

    Article  CAS  Google Scholar 

  144. Passy, S.: Diatom ecological guilds display distinct and predictable behavior along nutrient and disturbance gradients in running waters. Aquat. Bot. 86(2), 171–178 (2007)

    Article  Google Scholar 

  145. Kelly, M., et al., “Common freshwater diatoms of Britain and Ireland: an interactive key”, (2005).

    Google Scholar 

  146. Lavoie, I., et al.: Diatom teratologies as biomarkers of contamination: are all deformities ecologically meaningful? Ecol. Indic. 82, 539–550 (2017)

    Article  CAS  Google Scholar 

  147. Coste, M., Boutry, S., Tison-Rosebery, J., Delmas, F.: Improvements of the Biological Diatom Index (BDI): description and efficiency of the new version (BDI-2006). Ecol. Indic. 9(4), 621–650 (2009)

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Instituto de Hidráulica Ambiental de la Universidad de Cantabria (IH Cantabria), Santander, Spain

    A. Goldenberg-Vilar

  2. Cimera Estudios Aplicados S.L. Science to Business, Madrid, Spain

    A. Goldenberg-Vilar, R. Álvarez-Troncoso & V. Roldán

  3. Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, León, Spain

    Saúl Blanco

  4. Laboratorio de diatomología y calidad de aguas, Instituto de Investigación de Medio Ambiente, Recursos Naturales y Biodiversidad, León, Spain

    Saúl Blanco

Authors
  1. A. Goldenberg-Vilar
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. Álvarez-Troncoso
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. V. Roldán
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Saúl Blanco
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to A. Goldenberg-Vilar .

Editor information

Editors and Affiliations

  1. Instituto de Optica (CSIC), Madrid, Spain

    Gabriel Cristóbal

  2. Facultad de Ciencias Biológicas y Ambientales, Departamento de Biodiversidad y Gestión Ambiental, Universidad de León, Laboratorio de diatomología y calidad de aguas, Instituto de Investigación de Medio Ambiente, Recursos Naturales y Biodiversidad, León, Spain

    Saúl Blanco

  3. VISILAB, Universidad de Castilla-La Mancha, Ciudad Real, Spain

    Gloria Bueno

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Goldenberg-Vilar, A., Álvarez-Troncoso, R., Roldán, V., Blanco, S. (2020). Water Quality Assessment. In: Cristóbal, G., Blanco, S., Bueno, G. (eds) Modern Trends in Diatom Identification. Developments in Applied Phycology, vol 10. Springer, Cham. https://doi.org/10.1007/978-3-030-39212-3_13

Download citation

Publish with us

Policies and ethics

Search

Navigation