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. 2019 Mar 29;24:103875. doi: 10.1016/j.dib.2019.103875

Dataset on the absorption characteristics of extracted phytoplankton pigments

Lesley A Clementson 1, Bozena Wojtasiewicz 1,∗
PMCID: PMC6461595  PMID: 31011597

Abstract

This article presents the raw and analysed data on the absorption features of 30 pigments commonly occurring in phytoplankton. All unprocessed absorption spectra are given between 350 and 800 nm. The presented data also gives information on the wavelength of the main absorption peaks together with associated magnitudes of the concentration-specific absorption coefficient.

Keywords: Pigments, Phytoplankton, Absorption

Specifications table

Subject area Biology
More specific subject area Phytoplankton biology; Marine biology; Marine bio-optics
Type of data Tables, figures, separate .txt files with entire measured spectra
How data was acquired UV-VIS double-beam spectrophotometer (GBC Scientific Equipment Ltd., Cintra 404); software: Cintral ver. 2.2
Data format Analysed
Experimental factors Pigments were dissolved in either 100% ethanol or 90% acetone as received from DHI (Denmark) or Sigma Aldrich prior to the measurements being made.
Experimental features The absorption spectra were measured in a 1-cm quartz-glass cuvette using a dual-beam spectrophotometer against the pure solvent as a blank. The spectra were measured over the 350–800 nm spectral range in 1.3 nm increments.
Data source location Hobart, TAS, Australia
Data accessibility All data are provided in this article
Related research article Baird, M.E., Mongin, M., Rizwi, F., Bay, L.K., Cantin, N.E., Soja-Woźniak, M., Skerratt, J., 2018. A mechanistic model of coral bleaching due to temperature-mediated light-driven reactive oxygen build-up in zooxanthellae. Ecol. Model. 386, 20–37 [1].
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Value of the data
  • •

    This dataset is unique in that it provides the absorption characteristics together with a pigment concentration for 30 different pigments. From this, concentration-specific absorption coefficients are obtained which can be used for both phytoplankton and bio-optical studies.

  • •

    The dataset can be used in models pertaining to phytoplankton behavior or for theoretical experiments.

  • •

    The dataset can be used to both compare to in situ experimental results or to help explain experimental results.

  • •

    The dataset can be base for theoretical experiments in phytoplankton physiology or ecology and marine bio-optics.

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1. Data

The unprocessed measurement data for the absorption spectra of chlorophylls (chlorophyll-a, chlorophyll-b, DV chlorophyll-a, chlorophyllide-a, phaeophorbide-a, phaeophytin-a, chlorophyll-c3, chlorophyll-c2) and carotenoids (peridinin, 19′-butanoyloxyfucoxanthin, fucoxanthin, neoxanthin, prasinoxanthin, 19′-keto-hexanoyloxyfucoxanthin, violaxanthin, 19′- hexanoyloxyfucoxanthin, astaxanthin, diadinoxanthin, dinoxanthin, antheraxanthin, alloxanthin, myxoxanthophyll, diatoxanthin, zeaxanthin, lutein, canthaxanthin, gyroxanthin diester, echinenone, β,ε-carotene, β,β-carotene) are given in separate files (Appendix A; carotenoids_concentration_specific_spectra.txt, chlorophylls_concentration_specific_spectra.txt). Fig. 1, Fig. 2 present pigment-specific absorption spectra for each of the analysed pigments and Table 1, Table 2 list the location of the main absorption peaks and the magnitude of the pigment-specific absorption coefficients at these local maxima for chlorophylls and carotenoids, respectively.

Fig. 1.

Fig. 1

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Concentration-specific absorption spectra of (a) chlorophyll-a, (b) chlorophyll-b, (c) DV chlorophyll-a, (d) chlorophyllide-a, (e) phaeophorbide-a, (f) phaeophytin-a, (g) chlorophyll-c3, (h) chlorophyll-c2.

Fig. 2.

Fig. 2

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Concentration-specific absorption spectra of (a) peridinin, (b) 19′-butanoyloxyfucoxanthin,(c) fucoxanthin, (d) neoxanthin, (e) prasinoxanthin, (f) 19′-keto-hexanoyloxyfucoxanthin, (g) violaxanthin, (h) 19′- hexanoyloxyfucoxanthin, (i) astaxanthin, (j) diadinoxanthin, (k) dinoxanthin, (l) antheraxanthin, (m) alloxanthin, (n) myxoxanthophyll, (o) diatoxanthin, (p) zeaxanthin, (q) lutein, (r) canthaxanthin, (s) gyroxanthin diester, (t) echinenone, (u) β,ε-carotene, (v) β,β-carotene.

Table 1.

Location of the main absorption peaks and the associated magnitude of the concentration specific absorption coefficient for chlorophyll-a, chlorophyll-b, DV chlorophyll-a, chlorophyllide-a, phaeophorbide-a, phaeophytin-a, chlorophyll-c3, and chlorophyll-c2.

Name of pigment Source Lot/Batch number Solvent Main absorption peaks (nm) Concentration specific absorption coefficient (m2 mg−1)
Chlorophyll-a Sigma BCBK2207V 90% acetone 431 0.0233
663 0.0202
412 0.0179
382 0.0122
617 0.0040
Chlorophyll-b Sigma SLBF7339V 90% acetone 458 0.0330
646 0.0118
DV chlorophyll-a DHI 112 90% acetone 439 0.0276
663 0.0203
Chlorophyllide-a DHI 125 90% acetone 411 0.0387
665 0.0272
615 0.0053
535 0.0029
506 0.0028
Phaeophorbide-a DHI 105 90% acetone 410 0.0363
666 0.0166
505 0.0039
535 0.0034
608 0.0031
Phaeophytin-a DHI 107 90% acetone 410 0.0266
665 0.0119
505 0.0027
535 0.0024
607 0.0021
Chlorophyll-c3 DHI 122 90% acetone 452 0.0766
584 0.0085
626 0.0024
Chlorophyll-c2 DHI 129 90% acetone 444 0.0880
630 0.0113
580 0.0083
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Table 2.

Location of the main absorption peaks and the associated magnitude of the concentration-specific absorption coefficient for carotenoids (peridinin, 190-butanoyloxyfucoxanthin, fucoxanthin, neoxanthin, prasinoxanthin, 190-keto-hexanoyloxyfucoxanthin, violaxanthin, 190- hexanoyloxyfucoxanthin, astaxanthin, diadinoxanthin, dinoxanthin, antheraxanthin, alloxanthin, myxoxanthophyll, diatoxanthin, zeaxanthin, lutein, canthaxanthin, gyroxanthin diester, echinenone, b,ε-carotene, b,b-carotene).

Name of pigment Source Lot/Batch number Solvent Main absorption peaks (nm) Concentration specific absorption coefficient (m2 mg−1)
Peridinin DHI 111 100% ethanol 474 0.0293
19'-Butanoyloxyfucoxanthin DHI 122 100% ethanol 447 0.0362
471 0.0335
Fucoxanthin DHI 119 100% ethanol 449 0.0355
Neoxanthin DHI 122 100% ethanol 438 0.0508
466 0.0489
413 0.0333
Prasinoxanthin DHI 110 100% ethanol 453 0.0367
19'-keto-hexanoyloxyfucoxanthin DHI 101 100% ethanol 448 0.0365
471 0.0337
Violaxanthin DHI 138 100% ethanol 441 0.0555
471 0.0552
417 0.0365
19'-hexanoyloxyfucoxanthin DHI 116 100% ethanol 446 0.0367
471 0.0339
Astaxanthin DHI 105 100% acetone 477 0.0486
Diadinoxanthin DHI 117 100% ethanol 447 0.0588
477 0.0535
426 0.0402
Dinoxanthin DHI 103 100% ethanol 442 0.0468
471 0.0458
417 0.0316
Antheraxanthin DHI 127 100% ethanol 446 0.0523
475 0.0464
423 0.0369
Alloxanthin DHI 112 100% ethanol 453 0.0583
482 0.0511
Myxoxanthophyll DHI 106 100% acetone 477 0.0486
508 0.0427
452 0.0333
Diatoxanthin DHI 133 100% ethanol 452 0.0596
481 0.0524
Zeaxanthin DHI 131 100% ethanol 452 0.0524
479 0.0464
Lutein DHI 128 100% ethanol 446 0.0559
474 0.0508
423 0.0381
Canthaxanthin DHI 131 100% ethanol 478 0.0458
Gyroxanthin diester DHI 105 100% ethanol 445 0.0538
472 0.0473
Echinenone DHI 121 100% ethanol 461 0.0488
β,ε-carotene DHI 126 100% acetone 488 0.0600
476 0.0544
β,β-carotene DHI 126 100% acetone 454 0.0559
480 0.0492
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2. Experimental design, materials, and methods

Pigment standards for chlorophyll-a and chlorophyll-b were prepared from extracts purchased from Sigma-Aldrich (www.sigmaaldrich.com), while other pigment standards were obtained from DHI (www.dhigroup.com). The source and the batch/lot number of each pigment are given in Table 1, Table 2. The standards were in either 90% acetone, 100% acetone or 100% ethanol (Table 1, Table 2). The final concentrations of the standards were measured by HPLC (High Performance Liquid Chromatography) with the CSIRO method [2], which is a modified version of the [3] technique, using C8 column and binary gradient system with an elevated column temperature. Pigments were identified by their retention time and their absorption spectra from the photo-diode array detector. Next, the pigment concentrations were determined through peak integration performed in Empower© software.

The absorption spectra of the pigment standards were measured in a 1-cm quartz-glass cuvette using a Cintra 404 (GBC Scientific Equipment Ltd.) UV-VIS dual-beam spectrophotometer against the pure solvent as a blank. The spectra were measured over the 350–800 nm spectral range in 1.3 nm increments. The absorbance (OD) obtained from the measurements was converted to an absorption coefficient (a(λ), m−1) by multiplying the appropriate baseline-corrected optical density values of each standard by 2.3 and dividing by the optical path length/cuvette thickness (0.01 m):

a(λ)=2.3OD(λ)0.01 (1)

Finally, the concentration specific absorption coefficients (a*(λ), m2 g−1) were calculated by dividing each absorption coefficient by the respective pigment concentration.

Data presented in Fig. 1, Fig. 2 and in Table 1, Table 2 were null-point corrected by subtracting the absorption coefficient value at 750 nm assuming no absorption of pigments in the NIR region of the spectrum [4]. The spectra were also interpolated to yield absorption coefficients between 350 and 750 nm with the resolution of 1 nm using linear interpolation method (MATLAB, interp1.m).

Due to differences in the organic solvent and water refractive index (i.e. 1.352 for acetone, 1.361 for ethanol and 1.330 for water), the spectra may be wavelength-adjusted by using the ratio between the refractive index of the solvent and the water as done by [1].

Acknowledgements

CSIRO strategy funding was used to perform all the laboratory work.

Footnotes

Transparency document associated with this article can be found in the online version at https://doi.org/10.1016/j.dib.2019.103875.

Appendix A

Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2019.103875.

Transparency document

The following is the transparency document related to this article:

Multimedia component 1
mmc1.pdf (423.4KB, pdf)

Appendix A. Supplementary data

The following are the Supplementary data to this article:

mmc2.txt (148.4KB, txt)
mmc3.txt (56.6KB, txt)

References

  • 1.Baird M.E., Mongin M., Rizwi F., Bay L.K., Cantin N.E., Soja-Woźniak M., Skerratt J. A mechanistic model of coral bleaching due to temperature-mediated light-driven reactive oxygen build-up in zooxanthellae. Ecol. Model. 2018;386:20–37. [Google Scholar]
  • 2.Hooker S.B., Van Heukelem L., Thomas C.S., Claustre H., Ras J., Schlüter L., Clementson L.A., Van der Linde D., Eker-Develi E., Berthon J.-F., Barlow R., Sessions H., Ismail H., Perl J. NASA Goddard Space Flight Center; Greenbelt: 2009. The Third SeaWiFS HPLC Analysis Round-Robin Experiment (SeaHARRE-3) [Google Scholar]
  • 3.Van Heukelem L., Thomas C.S. Computer-assisted high-performance liquid chromatography method development with applications to the isolation and analysis of phytoplankton pigments. J. Chromatogr. A. 2001;910:31–49. doi: 10.1016/s0378-4347(00)00603-4. [DOI] [PubMed] [Google Scholar]
  • 4.Stramski D., Piskozub J. Estimation of scattering error in spectrophotometric measurements of light absorption by aquatic particles form three-dimensional radiative transfer simulations. Appl. Opt. 2003;42:3634–3646. doi: 10.1364/ao.42.003634. [DOI] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Multimedia component 1
mmc1.pdf (423.4KB, pdf)
mmc2.txt (148.4KB, txt)
mmc3.txt (56.6KB, txt)

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