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Optical measurements to determine the thickness of calcite crystals and the mass of thin carbonate particles such as coccoliths

Nature Protocols volume 9, pages 633–642 (2014)Cite this article

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Abstract

We describe a procedure for measuring the thickness and mass of calcite particles that works for most calcite particles <4.5-μm thick. The calcite particles are observed in cross-polarized light, which enables the light transmitted through the calcite particles to be correlated with their thickness. Three polarizing planes are used to minimize the darkening of crystals at some orientations (black cross). This allows direct measurement of the thickness without recourse to a transfer function. This procedure has been used recently to determine the degree of calcification of coccoliths, which provides an indicator of ocean acidification. It takes only a few minutes per sample, and it is an improvement over the former protocol, which did not allow measurement of the thickness and mass of particles thicker than 1.5 μm.

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Figure 1: Relationship between the thickness of a calcite crystal and the amount of transmitted light.
Figure 2: Images of a rhabdolith.
Figure 3: Three original images of a placolith from left to right: 0°, 35° and 45°, and its merged image on the right.
Figure 4: Relation between hue angle (H° in 8 bits) and retardation (nm).
Figure 5: Effect of focus on measurements of thickness.
Figure 6: Schematic representation of the potential effect of the inclination of a coccolith.
Figure 7: Width (diameter) of rhabdolith stems measured with a microscopic scale compared with the estimated thickness at the same position on the stems.
Figure 8: Illustration of coccolith thickness.
Figure 9

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References

  1. Beaufort, L. et al. Sensitivity of coccolithophores to carbonate chemistry and ocean acidification. Nature 476, 80–84 (2011).

    Article  CAS  PubMed  Google Scholar 

  2. Beltran, C., de Rafelis, M., Person, A., Stalport, F. & Renard, M. Multiproxy approach for determination of nature and origin of carbonate micro-particles so-called 'micarb' in pelagic sediments. Sediment. Geol. 213, 64–76 (2009).

    Article  Google Scholar 

  3. Minoletti, F., Hermoso, M. & Gresier, V. Separation of sedimentary micron-sized particles for palaeoceanography and calcareous nannoplankton biogeochemistry. Nat. Protoc. 4, 14–24 (2008).

    Article  Google Scholar 

  4. Beaufort, L., Couapel, M.J.J., Buchet, N., Claustre, H. & Goyet, C. Calcite production by coccolithophores in the south east Pacific Ocean. Biogeosciences 5, 1101–1117 (2008).

    Article  Google Scholar 

  5. Beaufort, L. & Heussner, S. Coccolithophorids on the continental slope of the Bay of Biscay, I. Production, transport and contribution to mass fluxes. Deep Sea Res. II 46, 2147–2174 (1999).

    Article  Google Scholar 

  6. Young, J. & Ziveri, P. Calculation of coccolith volume and its use in calibration of carbonate flux estimates. Deep Sea Res. 47, 1679–1700 (2000).

    Article  Google Scholar 

  7. Hassenkam, T., Johnsson, A., Bechgaard, K. & Stipp, S.L.S. Tracking single coccolith dissolution with picogram resolution and implications for CO2 sequestration and ocean acidification. Proc. Natl. Acad. Sci. USA 108, 8571–8576 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Stoll, H.M. & Shimizu, N. Micropicking of nannofossils in preparation for analysis by secondary ion mass spectrometry. Nat. Protoc. 4, 1038–1043 (2009).

    Article  CAS  PubMed  Google Scholar 

  9. Takahashi-Shimase, K. & Nakashima, S. Shape changes of calcareous nannofossils upon aqueous dissolution as revealed by atomic force microscope measurements. Geophys. Res. L. 31, L14313 (2004).

    Article  Google Scholar 

  10. Beaufort, L. Weight estimates of coccoliths using the optical properties (birefringence) of calcite. Micropaleontol. 51, 289–298 (2005).

    Article  Google Scholar 

  11. Grelaud, M., Schimmelmann, A. & Beaufort, L. Coccolithophore response to climate and surface hydrography in Santa Barbara Basin, California, AD 1917-2004. Biogeosciences 6, 2025–2039 (2009).

    Article  CAS  Google Scholar 

  12. Engel, A. et al. Testing the direct effect of CO2 concentration on a bloom of the coccolithophorid Emiliania huxleyi in mesocosm experiments. Limnol. Oceanogr. 50, 493–507 (2005).

    Article  CAS  Google Scholar 

  13. Beaufort, L., Probert, I. & Buchet, N. Effects of acidification and primary production on coccolith weight: implications for carbonate transfer from the surface to the deep ocean. Geochem. Geophys. Geosyst. 8, Q08011 (2007).

    Article  Google Scholar 

  14. Michel-Levy, A. & Lacroix, A. Les Minéraux des Roches. 1: Application des Méthodes Minéralogiques et Chimiques à leur Étude Microscopique. 2: Données Physiques et Optiques (Librairie Polytechnique Baudry, 1888).

  15. Sorensen, B.B. A revised Michel-Lévy interference colour chart based on first-principles calculations. Eur. J. Mineral. 25, 5–10 (2013).

    Article  Google Scholar 

  16. Fuertes, M.A., Flores, J.-A. & Sierro, F.J. A new technique for observing calcareous nannofossils: methodology and application. (Oral presentation at International Nannoplankton Association, 15–19 September 2013, Reston, Virginia, USA). Abstract in J. Nannoplankton Res. 33, 59 (2013).

    Google Scholar 

  17. Bollmann, J. Technical note: weight approximation of single coccoliths inferred from retardation estimates using a light microscope equipped with a circular polariser – (the CPR Method). Biogeosciences Discuss. 10, 11155–11179 (2013).

    Article  Google Scholar 

  18. Cubillos, J.C., Henderiks, J., Beaufort, L., Howard, W.R. & Hallegraeff, G.M. Reconstructing calcification in ancient coccolithophores: individual coccolith weight and morphology of Coccolithus pelagicus (sensu lato). Marine Micropaleontol. 92–93, 29–39 (2012).

    Article  Google Scholar 

  19. Giraudeau, J. & Beaufort, L. Coccolithophores from extant populations to fossil assemblages. in Developments in Marine Geology Vol. 1 (eds. Hilaire-Marcel, C. & de Vernal, A.) 409–439 (Elsevier, 2007).

  20. Beaufort, L. Adaptation of the random settling method for quantitative studies of calcareous nannofossils. Micropaleontol. 37, 415–418 (1992).

    Article  Google Scholar 

  21. Rottenfusser, R., Price, S.P. & Davidson, M.W. Microscope Alignment for Köhler Illumination http://zeiss-campus.magnet.fsu.edu/tutorials/basics/microscopealignment/index.html.

  22. Beaufort, L. & Dollfus, D. Automatic recognition of coccoliths by dynamical neural network. Mar. Micropaleontol. 51, 57–73 (2004).

    Article  Google Scholar 

  23. Henriksen, K., Stipp, S.L.S., Young, J.R. & Bown, P.R. Tailoring calcite: nanoscale AFM of coccolith biocrystals. Am. Mineral. 88, 2040–2044 (2003).

    Article  CAS  Google Scholar 

  24. Saruwatari, K., Ozaki, N., Nagasawa, H. & Kogure, T. Comparison of crystallographic orientations between living (Emiliania huxleyi and Gephyrocapsa oceanica) and fossil (Watznaueria barnesiae) coccoliths using electron microscopes. Am. Mineral. 93, 1670–1677 (2008).

    Article  CAS  Google Scholar 

  25. Young, J., Didymus, J.M., Bown, P.R., Prins, B. & Mann, S. Crystal assembly and phylogenetic evolution in heterococcoliths. Nature 356, 516–518 (1992).

    Article  Google Scholar 

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Acknowledgements

We thank M.-P. Aubry and J. Henderiks for useful discussions. This work has received financial support from the EU Seventh Framework program Past4Future and from the Agence Nationale de la Recherche under project ANR-12-B06-0007 (CALHIS).

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Authors and Affiliations

  1. Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Centre Européen de Recherche et d'Enseignement des Géosciences de l'Environnement (CEREGE) UM34, Aix-en-Provence, France

    Luc Beaufort, Nicolas Barbarin & Yves Gally

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  1. Luc Beaufort
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  2. Nicolas Barbarin
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Contributions

L.B. conceived the different aspects of this protocol and wrote the manuscript. N.B. commented on the manuscript, established the equation for the color camera and wrote codes for the color thickness calculation. Y.G. wrote the codes for microscope automation and wrote most of the codes for image analysis. All authors contributed to the protocol and its writing by frequent discussions as well as manuscript reading and correcting.

Corresponding author

Correspondence to Luc Beaufort.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 The Michel-Lévy Interference Color Chart.

This is Figure 2 of Michel-Levy, A. & Lacroix, A. Les Minéraux des roches. 1 : application des méthodes minéralogiques et chimiques à leur étude microscopique. 2 : données physiques et optiques. (Librairie polytechnique Baudry, 1888). It has been found in http://www.modernmicroscopy.com/main.asp?article=15&page=1, a web page written by John Gustav Delly in 2003.

Supplementary information

The Michel-Lévy Interference Color Chart.

This is Figure 2 of Michel-Levy, A. & Lacroix, A. Les Minéraux des roches. 1 : application des méthodes minéralogiques et chimiques ´ leur étude microscopique. 2 : données physiques et optiques. (Librairie polytechnique Baudry, 1888). It has been found in http://www.modernmicroscopy.com/main.asp?article=15&page=1, a web page written by John Gustav Delly in 2003. (PDF 123 kb)

Supplementary Methods

CalciProbe.exe: a macro using the described protocol. (PDF 47 kb)

Supplementary Data

The CalciProbe.exe macro file. (ZIP 712 kb)

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Beaufort, L., Barbarin, N. & Gally, Y. Optical measurements to determine the thickness of calcite crystals and the mass of thin carbonate particles such as coccoliths. Nat Protoc 9, 633–642 (2014). https://doi.org/10.1038/nprot.2014.028

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