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Import description
This page documents in some detail the import of each source.
Brotas & Plante-Cuny (2003) provide HPLC measurements for 5 species of different groups taken from a bethinc source. The HPLC method used is the one of Kraay et al. (1992) which is similar to Wright et al. (1991), but resolves Chl c1, Chl c2, Chl c3. Data were provided as mass ratios.
Dijkman et al. (2010) provide HPLC measurements for 8 species of Cyanobacteria, bethinc or planktonic. The HPLC method used is similar to the one of Wright et al. (1991), and data were provided as mass ratios. Although the method does not separate between monovinyl and divinyl forms, "Chl a" attribution followed authors attribution to Chl a, since DVChl a is only documented for Prochlorococcus.
Fagín et al. (2019) provide HPLC measurements of two species of Scrippsiella (Dinophyceae). The HPLC method is that of Zapata et al. (2000) and values were reported as molar ratios.
Latasa et al. (2004) provide HPLC measurements for about 20 species of Prasinophytes. The HPLC method used in this study is a modification from Zapata et al. (2000) and values were reported as mass ratios. Up to date species identification RCC strains were retrieved from the Roscoff Culture Collection number.
Lauridsen et al. (2011) provide HPLC measurements for 15 species of oligo-mesotrophic freshwater lakes. The HPLC system used is that of van Heukelem and Thomas (2001) and data is provided as mass ratios.
For Clorophytes, the values of Chlide b and Chl b were summed for the Chl b entry in the database and the value of β,β-Car attributed to Caro (= β,ε-Car + β,β-Car) since β,ε-Car and β,β-Car co-elude in the HPLC method used and Chlorophytes present both pigments. The taxa Stichococcus sp. was changed to Trebouxiophytes, according to taxonomy in WoRMS.
Liu et al. (2014) provide HPLC measurements of 31 species known to form harmful algal blooms (HABs). The HPLC method used in this study is the one from Zapata et al. (2000). It is not clear from the methods if the pigment ratios concern mass ratios of molar ratios. The authors state that molar extinction coefficients were used to retrieve pigment (molar?) concentration from absorbance, but use mass concentrations in other parts of the study. Data is inferred to be molar ratios since it matches in magnitude species in common in the study of Zapata et al. (2012).
Numerical information from Table 4 is imported, with blanks interpreted as zeros. We note however that although no value of Chl c3 is listed for Pseudo-nitzschia pungens, the study of Zapata et al. (2011) using several strains consistently found Chl c3 for this species. Thefore is is classified as DIATO_3. Absences as per the pigment distribution table (aux directory) as added as zeros.
Lopes dos Santos et al. (2016) provide HPLC measurements of 10 species of Chloropicophyceae (Prasinophyte Clade VII). The HPLC method used in this study is a modification from Zapata et al. (2000) that separate Loro and c-Neo. It is not clear if values are provided as mass of molar ratios. The study presents on the same table the values from Latasa et al. (2004) that were determined as mass ratios, but in a later study, Lopes dos Santos et al. (2017) report the previous values together with determinations, stating molar ratios, with the same magnitudes. The decision was to import as molar ratios. Chlide b was summed to Chl b for the database entry of Chl b. Chlide a is provided as a separate value and is not clear if it was included in the Chl a calculation, and those values are not summed during the import. Species names were retrieved from the Roscoff Culture Collection number.
Schlüter et al. (2000) provide HPLC measurements over 16 species of different taxonomic groups in a thorough cultivation study at different light intensities. The "spectral quality" treatments with blue light or green light were not imported in the current version. Schlüter et al. (2004) provide HPLC measurements for 3 species of cyanobacteria. Schlüter et al. (2006) provide HPLC measurements for 20 species of various groups from freshwater habitats. Measurements in "stationray growth" were added per the corresponding light treatment (medium light). The HPLC method used is that of Wright et al. (1991) which does not separate mono and divinyl forms. The method description of the first two studies does not make clear if molar or mass ratios are used, but mass ratios are specified in Schlüter et al. (2006), which compares numerical values directly with the previous studies, from which we infer that all studies provide mass ratios.
Carotenes were provided as a sum of all carotenes and it is attributed to Car, despite the database definition of Car as only the combination of β,ε-Car and β,β-Car. While the resolution between But-Fuco and Siph is not large, authors provide independent values for those pigments and no adjustment is made. The same is true for the separation between MgDVP and Chl c1,2. For pigments that are not resolved by the HPLC method used, the combined pigment form was added when part of the pigment set of the database (e.g., there is no pigment combination of Hex-Fuco and Hex-kFuco in the database) and also attributed to individual pigments if it was possible to resolve it from the known pigment distribution (e.g., attribution of Chl c1,2 to Chl c1 or Chl c2 depending on taxonomic and pigment group, when possible). For the pigment groups that contain both Hex-Fuco and Hex-kFuco (e.g., HAPTO_6, HAPTO_7 and HAPTO_8), the values provided were attributed to Hex-Fuco.
Zapata et al. (2004) provide HPLC measurements for 37 species of Haptophytes. The authors used HPLC methods of Zapata et al. (2000) and Garrido & Zapata (1997). Data is provided as molar ratios. The Chl named "Chl c2 P. gyr type" and Chl c2-MGDG[14/14] were not imported.
Zapata et al. (2011) provide HPLC measurements for 18 species of the diatom genus Pseudo-nitzschia. The authors used a modified HPLC method from Zapata et al. (2000) and data is provided as molar ratios. The authors only presented quantitative information for Chl c1, Chl c2, Chl c3 and Fuco.
Zapata et al. (2012) provide HPLC measurements for 64 species of dinoflagellates. The authors used a modified HPLC method from Zapata et al. (2000), that has good separation in most pigments, in partiuclar in Chl c forms. It has somewhat poorer resolution between Chl b and DVChl b, however, DVChl b is not known to occur in Dinoflagellates, and measurements can be attributed to Chl b. Data is provided as molar ratios.
Numerical values of Tables 3, 4 and 5 were imported, noting that "Neo" corresponds to c-Neo, as per Table 1. Qualitative information on Table 2 on on the pigment distribution table (aux directory) is used to set pigment ratios to zero were appropriate (absence).
Zapata et al. (2012) provides one additional pigment group than Jeffrey et al (2011), but mainly based on pigments that are not included in this database. Zapata's groups 2 and 3 were merged as DINO_2 in Jeffrey's, since those correspond to Dinoflagellates containing Chl c3. The other groups are easy to assign based on the correspondence between their classifications and on the obvious pigment patterns in the dinoflagellate pigment groups.