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Organisms Diversity & Evolution

, Volume 18, Issue 1, pp 51–62 | Cite as

Do we similarly assess diversity with microscopy and high-throughput sequencing? Case of microalgae in lakes

  • Frédéric Rimet
  • Valentin Vasselon
  • Barbara A.-Keszte
  • Agnès Bouchez
Original Article

Abstract

Diatoms are a species-diverse phylum of microalgae often presenting high biomass in aquatic habitats. This makes them excellent ecological indicators in rivers and lakes. They are routinely used to assess ecological quality of rivers and lakes using microscopy, which is time consuming. An alternative is to determine species in samples based on short DNA barcodes and high-throughput sequencing (HTS). Former studies showed that community structure and water quality assessments based on diatoms deliver similar results with both methods. But, none evaluated if diversities were assessed in the same way despite the importance of this ecological metric. Based on littoral benthic samplings carried out in 56 pristine alpine lakes, we compared different diversity indices measured with microscopy and metabarcoding. Each lake was sampled in three different places of its littoral. We showed that α (diversity measured in a single sampling site of a given lake) and ϒ (total diversity in a lake where three independent samples were considered) diversities obtained with HTS were higher than those obtained with microscopy. This may be explained by the capacity of HTS to detect morphologically cryptic species and to better detect rare taxa. On the other hand, β diversity obtained with HTS was smaller, which may be explained by the capacity of HTS to detect very rare species and free-floating extracellular DNA. Nevertheless, diversity indices obtained with both methodologies were well correlated each other. This study validates the possibility to assess diatom diversity with HTS in a comparable way to the classical microscopic analysis.

Keywords

Diatom Diversity Environmental DNA Metabarcoding OTU 

Notes

Acknowledgements

We thank Pr. E. Dambrine for initiating this study with the students of Savoie-Mont-Blanc University, F. Arthaud for following this study and managing the data, Léa Feret and David Pobel for their participation in determining diatom samples under microscope, and Cécile Chardon, Sonia Lacroix, and Louis Jacas for processing the samples in molecular biology.

References

  1. Abarca, N., Jahn, R., Zimmermann, J., & Enke, N. (2014). Does the cosmopolitan diatom Gomphonema parvulum (Kutzing) Kutzing have a biogeography? PLoS One, 9, 1–18.CrossRefGoogle Scholar
  2. Amend, A. S., Seifert, K. A., & Bruns, T. D. (2010). Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Molecular Ecology, 19, 5555–5565.CrossRefPubMedGoogle Scholar
  3. Apothéloz-Perret-Gentil, L., Cordonier, A., Straub, F., Iseli, J., Esling, P., & Pawlowski, J. (2017). Taxonomy-free molecular diatom index for high-throughput eDNA biomonitoring. Molecular Ecology Resources.  https://doi.org/10.1111/1755-0998.12668.
  4. Baird, D. J., & Hajibabaei, M. (2012). Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing. Molecular Ecology, 1–6.Google Scholar
  5. Berthon, V., Marchetto, A., Rimet, F., Dormia, E., Jenny, J. P., Pignol, C., & Perga, M. E. (2013). Trophic history of French sub-alpine lakes over the last ~150 years: phosphorus reconstruction and assessment of taphonomic biases. Journal of Limnology, 72, 417–429.CrossRefGoogle Scholar
  6. Bray, J. R., & Curtis, J. T. (1957). An ordination of upland forest communities of southern Wisconsin. Ecological Monographs, 27, 325–349.CrossRefGoogle Scholar
  7. Cantonati, M., & Lowe, R. L. (2014). Lake benthic algae: toward an understanding of their ecology. Freshwater Science, 33(2), 475–486.CrossRefGoogle Scholar
  8. Chonova, T., Keck, F., Labanowski, J., Montuelle, B., Rimet, F., & Bouchez, A. (2016). Seperate treatment of hospital and urban wastewaters: a real scale comparison of effluents and their effect on microbial communities. Science of the Total Environment, 542, 965–975.CrossRefPubMedGoogle Scholar
  9. Civade, R., Dejean, T., Valentini, A., Roset, N., Raymond, J.-C., Bonin, A., et al. (2016). Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS One, 11(6), e0157366.  https://doi.org/10.1371/journal.pone.0157366.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Copeland, C. (2016). Clean Water Act: A Summary of the Law. Congressional Research Service, CRS report, number 7–5700 RL30030, pp. 1–10.Google Scholar
  11. Debroas, D., Hugoni, M., & Domaizon, I. (2015). Evidence for an active rare biosphere within freshwater protists community - Debroas - 2015 - Molecular Ecology - Wiley Online Library. Molecular Ecology, 24, 1236–1247.  https://doi.org/10.1111/mec.13116.CrossRefPubMedGoogle Scholar
  12. Debroas, D., Domaizon, I., Humbert, J.-F., Jardillier, L., Lepère, C., Oudart, A., & Taïb, N. (2017). Overview of freshwater microbial eukaryotes diversity: a first analysis of publicly available metabarcoding data. FEMS Microbiology Ecology, 93(4).  https://doi.org/10.1093/femsec/fix023.
  13. Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., & Miaud, C. (2011). Persistence of environmental DNA in freshwater ecosystems. PLoS One, 6(8), e23398.  https://doi.org/10.1371/journal.pone.0023398.CrossRefPubMedPubMedCentralGoogle Scholar
  14. European Commission. (2000). Directive 2000/60/EC of the European Parliament and of the Council of 23rd October 2000 establishing a framework for Community action in the field of water policy. Official Journal of the European Communities, 327, 1–72.Google Scholar
  15. European Committee for Standardization (2014a) EN 13946 Water quality—guidance for the routine sampling and preparation of benthic diatoms from rivers and lakes. CEN standard, 1–18.Google Scholar
  16. European Committee for Standardization (2014b). EN 14407 Water quality—guidance for the identification and enumeration of benthic diatom samples from rivers and lakes. CEN standard, 1–13.Google Scholar
  17. Evans, K. M., Wortley, A. H., Simpson, G. E., Chepurnov, V. A., & Mann, D. G. (2008). A molecular systematic approach to explore diversity within the Sellaphora pupula species complex (Bacillariophyta). Journal of Phycology, 44(1), 215–231.CrossRefPubMedGoogle Scholar
  18. Feret, L., Bouchez, A., & Rimet, F. (2017). Benthic diatom communities in high altitude lakes: a large scale study in the French Alps. International Journal of Limnology.  https://doi.org/10.1051/limn/2017026.
  19. Ferreira da Silva, E., Almeida, S. F. P., Nunes, M. L., Luís, A. T., Borg, F., Hedlund, M., et al. (2009). Heavy metal pollution downstream the abandoned Coval da Mó mine (Portugal) and associated effects on epilithic diatom communities. Science of the Total Environment, 407(21), 5620–5636.  https://doi.org/10.1016/j.scitotenv.2009.06.047.CrossRefPubMedGoogle Scholar
  20. Fontana, G., Ugland, K. I., Gray, J. S., Willis, T. J., & Abbiati, M. (2008). Influence of rare species on beta diversity estimates in marine benthic assemblages. Journal of Experimental Marine Biology and Ecology, 366(1), 104–108.  https://doi.org/10.1016/j.jembe.2008.07.014.CrossRefGoogle Scholar
  21. Hammer, O., Harper, D. A. T., & Ryan, P. D. (2001). PAST: paleontological statistics software package for education and data analysis. Palaeontologia Electronica, 4, 1–9.Google Scholar
  22. Hebert, P., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B-Biological Sciences, 270, 313–321.CrossRefPubMedCentralGoogle Scholar
  23. Hoagland, K. D. (1981). Diatom colonization, community structure and succession on artificial substrate in freshwater. phD, University of Nebraska, Lincoln, USA.Google Scholar
  24. Hoffman, G., Werum, M., & Lange-Bertalot, H. (2011). Diatomeen im Susswasser-benthos von Mitteleuropa. Rugell: A.R.G. Gantner Verlag K.G..Google Scholar
  25. Kebschull, J. M., & Zador, A. M. (2015). Sources of PCR-induced distortions in high-throughput sequencing data sets. Nucleic Acids Research, 43, e143.CrossRefPubMedPubMedCentralGoogle Scholar
  26. Keck, F., Vasselon, V., Tapolczai, K., Rimet, F., & Bouchez, A. (2017). Freshwater biomonitoring in the Information Age. Frontiers in Ecology and the Environment, 15(5), 266–274.  https://doi.org/10.1002/fee.1490.
  27. Kermarrec, L., Bouchez, A., Rimet, F., & Humbert, J. F. (2012). First evidence of the existence of semi-cryptic species and of a phylogeographic structure in the Gomphonema parvulum (Kützing) Kützing complex (Bacillariophyta). Protist, 164, 686–705.CrossRefGoogle Scholar
  28. Kermarrec, L., Franc, A., Rimet, F., Chaumeil, P., Humbert, J. F., & Bouchez, A. (2013). Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms. Molecular Ecology Resources, 13(4), 607–619.CrossRefPubMedGoogle Scholar
  29. Kermarrec, L., Franc, A., Rimet, F., Chaumeil, P., Frigerio, J. M., Humbert, J. F., & Bouchez, A. (2014). A next-generation sequencing approach to river biomonitoring using benthic diatoms. Freshwater Science, 33(1), 349–363.CrossRefGoogle Scholar
  30. King, L., Clarke, G., Bennion, H., Kelly, M., & Yallop, M. (2006). Recommendations for sampling littoral diatoms in lakes for ecological status assessments. Journal of Applied Phycology, 18(1), 15–25.  https://doi.org/10.1007/s10811-005-9009-3.CrossRefGoogle Scholar
  31. Kociolek, J. P. (2005). Taxonomy and ecology: further considerations. Proceedings of the California Academy of Sciences, 56, 99–106.Google Scholar
  32. Kociolek, J. P., Sabbe, K., Vandepitte, L., Decock, W., & Vanhoorn, B. (2016). Catalogue of diatom names resurrected: DiatomBase will be the new authority resource for diatom names and more. 24th International Diatom Symposium, 100.Google Scholar
  33. Krammer, K., & Lange-Bertalot, H. (1986). Bacillariophyceae 1. Teil: Naviculaceae. Susswasserflora von Mitteleuropa. Stuttgart: Gustav Fischer Verlag.Google Scholar
  34. Krammer, K., & Lange-Bertalot, H. (1988). Bacillariophyceae 2. Teil: Bacillariaceae, Epithemiaceae, Surirellaceae. Susswasserflora von Mitteleuropa. Stuttgart: Gustav Fischer Verlag.Google Scholar
  35. Krammer, K., & Lange-Bertalot, H. (1991a). Bacillariophyceae 3. Teil: Centrales, Fragilariaceae, Eunotiaceae. Susswasserflora von Mitteleuropa. Stuttgart: Gustav Fischer Verlag.Google Scholar
  36. Krammer, K., & Lange-Bertalot, H. (1991b). Bacillariophyceae 4. Teil: Achnanthaceae. Kritische Erganzungen zu Navicula (Lineolatae) und Gomphonema. Gesamtliteraturverzeichnis Teil 4. Susswasserflora von Mitteleuropa. Stuttgart: Gustav Fischer Verlag.Google Scholar
  37. Lange-Bertalot, H., & Metzeltin, D. (1996). Indicators of oligotrophy. 800 taxa representative of three ecologically distinct lakes. Carbonate buffered - Oligodystrophic - Weakly buffered soft water. Konigstein: Koeltz scientific books.Google Scholar
  38. Lejzerowicz, F., Esling, P., Pillet, L., Wilding, T. A., Black, K. D., & Pawlowski, J. (2015). High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems. Scientific Reports, 5.  https://doi.org/10.1038/srep13932.
  39. Levkov, Z., Krstic, S., Metzeltin, D., & Nakov, T. (2007). Diatoms of Lakes Prespa and Ohrid. about 500 taxa from ancient lake system. Iconographia Diatomologica, volume 16 (p. 613). ARG Gantner Verlag KG.Google Scholar
  40. Loman, N. J., Misra, R. V., Dallman, T. J., Constantinidou, C., Gharbia, S. E., Wain, J., & Pallen, M. J. (2012). Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30, 434–439.CrossRefPubMedGoogle Scholar
  41. Luís, A. T., Teixeira, P., Almeida, S. F. P., Ector, L., Matos, J. X., & Silva, E. A. F. d. (2009). Impact of acid mine drainage (AMD) on water quality, stream sediments and periphytic diatom communities in the surrounding streams of Aljustrel mining area (Portugal). Water, Air, and Soil Pollution, 200(1–4), 147–167.  https://doi.org/10.1007/s11270-008-9900-z.CrossRefGoogle Scholar
  42. Mangot, J. F., Domaizon, I., Taib, N., Marouni, N., Duffaud, E., Bronner, G., & Debroas, D. (2013). Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes. Environmental Microbiology, 15, 1745–1758.CrossRefPubMedGoogle Scholar
  43. Mann, D. G., & Vanormelingen, P. (2013). An inordinate fondness? The number, distributions and origins of diatom species. Journal of Eukaryotic Microbiology, 60, 1–26.CrossRefGoogle Scholar
  44. Mann, D. G., McDonald, S. M., Bayer, M. M., Droop, S. J. M., Chepurnov, V. A., Loke, R. E., et al. (2004). The Sellaphora pupula species complex (Bacillariophyceae): morphometric analysis, ultrastructure and mating data provide evidence for five new species. Phycologia, 43(4), 459–482.CrossRefGoogle Scholar
  45. Mantel, N. (1967). The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209–220.PubMedGoogle Scholar
  46. Morin, S., Bonet, B., Corcoll, N., Guasch, H., Bottin, M., & Coste, M. (2015). Cumulative stressors trigger increased vulnerability of diatom communities to additional disturbances. Microbial Ecology, 70, 585–595.CrossRefPubMedGoogle Scholar
  47. Nolte, V., Pandey, R. V., Jost, S. T., Medinger, R., Ottenwalder, O., Boengik, J., & Schlotterer, C. (2010). Contrasting seasonal niche separation between rare and abundant taxa conceals the extent of protist diversity. Molecular Ecology, 19, 2908–2915.CrossRefPubMedPubMedCentralGoogle Scholar
  48. Pandey, L. K., Bergey, E. A., Lyu, J., Park, J., Choi, S., Lee, H., et al. (2017). The use of diatoms in ecotoxicology and bioassessment: insights, advances and challenges. Water Research, 118, 39–58.CrossRefPubMedGoogle Scholar
  49. Passy, S. I. (2008). Continental diatom biodiversity in stream benthos declines as more nutrients become limiting. Proceedings of the National Academy of Sciences of the United States of America, 105, 9663–9667.CrossRefPubMedPubMedCentralGoogle Scholar
  50. Passy, S. I. (2009). The relationship between local and regional diatom richness is mediated by the local and regional environment. Global Ecology and Biogeography, 18(3), 383–391.CrossRefGoogle Scholar
  51. Pinto, A. J., & Raskin, L. (2012). PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One, 7, e43093.CrossRefPubMedPubMedCentralGoogle Scholar
  52. Pompanon, F., Coissac, E., & Taberlet, P. (2011). Metabarcoding a new way to analyze biodiversity. Biofutur, 319, 30–32.Google Scholar
  53. Potapova, M., & Charles, D. F. (2007). Diatom metrics for monitoring eutrophication in rivers of the United States. Ecological Indicators, 7(1), 48–70.CrossRefGoogle Scholar
  54. Ricciardi, F., Bonnineau, A., Faggiano, L., Geiszinger, A., Guasch, H., Lopez-Doval, J. C., et al. (2009). Is chemical contamination linked to the diversity of biological communities in rivers? Trends in Analytical Chemistry, 28, 592–602.CrossRefGoogle Scholar
  55. Rimet, F. (2012). Recent views on river pollution and diatoms. Hydrobiologia, 683, 1–24.CrossRefGoogle Scholar
  56. Rimet, F., Kermarrec, L., Bouchez, A., Hoffmann, L., Ector, L., & Medlin, L. (2011). Molecular phylogeny of the family Bacillariaceae based on 18S rDNA sequences: focus on freshwater Nitzschia of the Lanceolatae section. Diatom Research, 26, 273–291.CrossRefGoogle Scholar
  57. Rimet, F., Trobajo, R., Mann, D. G., Kermarrec, L., Franc, A., Domaizon, I., & Bouchez, A. (2014). When is sampling complete? The effects of geographical range and marker choice on perceived diversity in Nitzschia palea (Bacillariophyta). Protist, 165(3), 245–259.CrossRefPubMedGoogle Scholar
  58. Rimet, F., Chaumeil, P., Keck, F., Kermarrec, L., Vasselon, V., Kahlert, M., et al. (2016). R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. Database: The Journal of Biological Databases and Curation, 2016(1), 21.  https://doi.org/10.1093/database/baw016.Google Scholar
  59. Rimet, F., Abarca, N., Bouchez, A., Kusber, W. H., Jahn, R., Kahlert, M., et al. (2018). The potential of high throughput sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes. Fottea.  https://doi.org/10.5507/fot.2017.013.
  60. Rivera, S., Vasselon, V., Jacquet, S., Ariztegui, D., Bouchez, A., & Rimet, F. (2018). Metabarcoding of lake benthic diatoms: from structure assemblages to ecological assessment. Hydrobiologia, 1–12  https://doi.org/10.1007/s10750-017-3381-2.
  61. Routledge, R. D. (1977). On Whittaker’s components of diversity. Ecology, 58, 1120–1127.CrossRefGoogle Scholar
  62. Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., et al. (2009). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75, 7537–7541.CrossRefPubMedPubMedCentralGoogle Scholar
  63. Stevenson, R. J. (2014). Ecological assessments with algae: a review and synthesis. Journal of Phycology, 50, 437–461.CrossRefPubMedGoogle Scholar
  64. Stevenson, R. J., Pan, Y., & Van Dam, H. (2010). Assessing environmental conditions in rivers and streams with diatoms. In J. P. Smol & E. F. Stoermer (Eds.), The Diatoms: Applications for the Environmental and Earth Sciences (second ed., pp. 57–85). London: Cambridge University Press.CrossRefGoogle Scholar
  65. Tapolczai, K., Vasselon, V., Bouchez, A., Stenger-Kovacs, C., Padisak, J., & Rimet, F. (2017). Taxonomy-free DNA biomonitoring for rivers: How to choose the sequence similarity threshold? Under revision.Google Scholar
  66. Trobajo, R., Clavero, E., Chepurnov, V., Sabbe, K., Mann, D. G., Ishihara, S., & Cox, E. J. (2009). Morphological, genetic and mating diversity within the widespread bioindicator Nitzschia palea (Bacillariophyceae). Phycologia, 48, 443–459.CrossRefGoogle Scholar
  67. Trobajo, R., Mann, D. G., Clavero, E., Evans, K. M., Vanormelingen, P., & McGregor, R. C. (2010). The use of partial cox1, rbcL and LSU rDNA sequences for phylogenetics and species identification within the Nitzschia palea species complex (Bacillariophyceae). European Journal of Phycology, 45(4), 413–425.CrossRefGoogle Scholar
  68. Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., et al. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25(4), 929–942.  https://doi.org/10.1111/mec.13428.CrossRefPubMedGoogle Scholar
  69. Vasselon, V., Domaizon, I., Rimet, F., Kahlert, M., & Bouchez, A. (2016). Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: do DNA extraction methods matter? Freshwater Science, 36(1), 162–177.CrossRefGoogle Scholar
  70. Vasselon, V., Bouchez, A., Rimet, F., Jacquet, S., Trobajo, R., Corniquel, M., et al. (2017a). A correction factor inferred from cell biovolume improves quantification in diatom metabarcoding. Methods in Ecology and Evolution,  https://doi.org/10.1111/2041-210X.12960.
  71. Vasselon, V., Rimet, F., Tapolczai, K., & Bouchez, A. (2017b). Assessing ecological status with diatoms DNA metabarcoding: scaling-up on a WFD monitoring network (Mayotte island, France). Ecological Indicators, 82, 1–12.  https://doi.org/10.1016/j.ecolind.2017.06.024.CrossRefGoogle Scholar
  72. Visco, J., Apotheloz-Perret-Gentil, L., Cordonier, A., Esling, P., Pillet, L., & Pawlowski, J. (2015). Environmental monitoring: inferring the diatom index from next-generation sequencing data. Environmental Science and Technology, 49, 7597–7605.CrossRefPubMedGoogle Scholar
  73. Weaver, W., & Shannon, C. E. (1949). The mathematical theory of communication.Google Scholar
  74. Werum, M., Lange-Bertalot, H., & Werum, M. (2004). Diatoms in springs from Central Europe ane elsewhere under the influence of hydrogeology and anthropogenic impacts. Iconographia Diatomologica, volume 13. A.R.G. Ruggell: Gantner Verlag K.G..Google Scholar
  75. Whittaker, R. H. (1960). Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 279–338.CrossRefGoogle Scholar
  76. Youssef, N. H., Couger, M. B., & Elshahed, M. S. (2010). Fine-scale bacterial beta diversity within a complex ecosystem (Zodletone Spring, OK, USA): the role of the rare biosphere. PLoS One, 5, e12414.  https://doi.org/10.1371/journal.pone.0012414.CrossRefPubMedPubMedCentralGoogle Scholar
  77. Zimmermann, J., Jahn, R., & Gemeinholzer, B. (2011). Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols. Organisms Diversity and Evolution, 11, 173.  https://doi.org/10.1007/s13127-011-0050-6.CrossRefGoogle Scholar
  78. Zimmermann, J., Glöckner, G., Jahn, R., Enke, N., & Gemeinholzer, B. (2014). Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies. Molecular Ecology Resources, 15, 526–542.CrossRefPubMedGoogle Scholar

Copyright information

© Gesellschaft für Biologische Systematik 2018

Authors and Affiliations

  1. 1.INRA, UMR-CARRTELThonon-les-Bains CedexFrance
  2. 2.Doctoral School of Environmental SciencesEötvös Loránd University (ELTE)BudapestHungary

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