Note: Cover -- PHYTOPLANKTON PIGMENTS -- CAMBRIDGE ENVIRONMENTAL CHEMISTRY SERIES -- Title -- Copyright -- Dedication -- Contents -- Contributors -- Preface -- Acknowledgements -- Abbreviations and symbols -- Pigment names -- Part I Chlorophylls and carotenoids -- 1 Microalgal classes and their signature pigments -- 1.1 Introduction -- 1.2 Algal classification -- 1.2.1 The 'protistan perspective' -- 1.2.2 The classical 'pigment perspective' -- 1.3 Origins of microalgal plastids -- 1.4 Biological characteristics of currently recognized photosynthetic microalgal classes -- 1.4.1 Prokaryotes: the division Cyanophyta -- 1.4.1.1 Cyanophytes (Cyanophyceae) -- including species previously known as Prochlorophytes (Prochlorophyceae) -- 1.4.2 Eukaryotes: the division Glaucocystophyta -- 1.4.3 Eukaryotes: the red radiation -- 1.4.3.1 The division Rhodophyta -- 1.4.3.2 The division Heterokontophyta -- 1.4.3.2.1 Diatoms (class Bacillariophyceae -- division Heterokontophyta) -- 1.4.3.2.2 Bolidophytes (class Bolidophyceae -- division Heterokontophyta) -- 1.4.3.2.3 Chrysophytes (class Chrysophyceae -- division Heterokontophyta) -- 1.4.3.2.4 Silicoflagellates (class Dictyochophyceae -- division Heterokontophyta) -- 1.4.3.2.5 Eustigmatophytes (class Eustigmatophyceae -- division Heterokontophyta) -- 1.4.3.2.6 Pelagophytes (class Pelagophyceae -- division Heterokontophyta) -- 1.4.3.2.7 Phaeothamniophytes (class Phaeothamniophyceae -- division Heterokontophyta) -- 1.4.3.2.8 Pinguiophytes (class Pinguiophyceae -- division Heterokontophyta) -- 1.4.3.2.9 Raphidophytes (chloromonads) (class Raphidophyceae -- division Heterokontophyta) -- 1.4.3.2.10 Synurophytes (Class Synurophyceae -- Division Heterokontophyta) -- 1.4.3.3 The division Haptophyta -- 1.4.3.3.1 Pavlovophytes (class Pavlovophyceae -- division Haptophyta). , 1.4.3.3.2 Characteristics of golden-brown algae (class Prymnesiophyceae ≡ Coccolithophyceae) -- 1.4.3.4 The division Cryptophyta -- 1.4.3.4.1 Class Cryptophyceae -- division Cryptophyta -- 1.4.3.5 The division Dinophyta -- 1.4.3.5.1 Class Dinophyceae -- division Dinophyta -- 1.4.4 Eukaryotes: the green radiation -- 1.4.4.1 The division Euglenophyta -- 1.4.4.2 The division Chlorarachniophyta -- 1.4.4.3 The division Chlorophyta (Classes Chlorophyceae, Prasinophyceae and Trebouxiophyceae) -- 1.4.4.4 The division Streptophyta -- 1.5 Pigment characteristics of currently recognized photosynthetic microalgal classes -- 1.5.1 Introduction -- 1.5.2 Signature pigments in the cyanobacterial lineage, the Glaucocystophyta and the red and green algal lineages -- 1.5.3 Future developments -- Acknowledgements -- Glossary of important terms used in protistan taxonomy -- Abbreviations -- References -- 2 Recent advances in chlorophyll and bacteriochlorophyll biosynthesis -- 2.1 Introduction -- 2.2 Structures of chlorophylls -- 2.2.1 Phytoporphyrin-type chlorophylls -- 2.2.2 Phytochlorin-type chlorophylls -- 2.2.3 Bacteriophytochlorin-type chlorophylls -- 2.3 Biosynthesis of protoporphyrin IX -- 2.3.1 Formation of 5-aminolevulinic acid and its regulation -- 2.3.2 Distribution of the C4+1 pathway -- 2.3.3 Distribution of the C5 pathway -- 2.3.4 Conversion of 5-aminolevulinate to monopyrrolic porphobilinogen -- 2.3.5 Formation of uroporphyrinogen III from porphobilinogen -- 2.3.6 Decarboxylation of uroporphyrinogen III to coproporphyrinogen III -- 2.3.7 Oxidative decarboxylation of coproporhyrinogen III to protoporphyrinogen IX -- 2.3.8 Oxidation of protoporphyrinogen IX to protoporphyrin IX -- 2.4 Biosynthesis of chlorophylls -- 2.4.1 Formation of Mg-protoporphyrin IX by Mg-chelatase. , 2.4.2 Formation of Mg-protoporphyrin IX-monomethylester by S-adenosylmethionine: Mg-protoporphyrin IX methyltransferase -- 2.4.3 Formation of the isocyclic ring E by Mg-protoporphyrin IX-monomethylester cyclase -- 2.4.3.1 The hydratase pathway -- 2.4.3.2 The oxygenase pathway -- 2.4.4 Protochlorophyllide a formation by 8-vinyl reductase -- 2.4.5 Reduction of ring D by protochlorophyllide a oxidoreductases -- 2.4.5.1 Light-dependent protochlorophyllide oxidoreductases -- 2.4.5.2 Light-independent (dark) protochlorophyllide oxidoreductases -- 2.4.6 Conversion of chlorophyllide a to chlorophyllide b by chlorophyllide a oxygenase -- 2.4.7 Reduction of chlorophyll(ide) b to chlorophyll(ide) a: the chlorophyll cycle -- 2.4.8 Esterification of chlorophyllides a and b to chlorophylls a and b by chlorophyll synthase -- 2.4.9 Formation of bacteriochlorophyll a: reduction of ring B by chlorin-reductase -- 2.4.10 Unusual chlorophylls and unusual side chains -- 2.4.10.1 In the phytoporphyrin family -- 2.4.10.2 In the phytochlorin family -- 2.4.10.3 In the bacteriophytochlorin family -- 2.5 Concluding remarks -- Acknowledgements -- Abbreviations -- References -- 3 Carotenoid metabolism in phytoplankton -- 3.1 Introduction -- 3.2 Biosynthesis of carotenes -- 3.2.1 Formation of the active isoprene -- 3.2.2 Formation of the first carotenoid phytoene -- 3.2.3 Formation of lycopene -- 3.2.4 Formation of cyclic carotenes -- 3.2.5 Formation of aromatic carotenes in cyanobacteria -- 3.3 Biosynthesis of xanthophylls -- 3.3.1 Hydroxylation -- 3.3.2 Epoxidation, de-epoxidation and the xanthophyll cycles -- 3.3.3 Formation of light-harvesting xanthophylls -- 3.3.4 Formation of ketocarotenoids -- 3.3.5 Formation of xanthophylls specific to cyanobacteria -- 3.4 Carotenoid catabolism and carotenoids as precursors of other physiologically important metabolites. , 3.4.1. Abscisic acid -- 3.4.2 Retinal -- 3.4.3 Strigolactones -- 3.4.4 Other products of carotenoid cleavage -- 3.5 Outlook -- Acknowledgements -- Abbreviations -- References -- Part II Methodology guidance -- 4 New HPLC separation techniques -- 4.1 Introduction -- 4.2 HPLC algal pigment methods published since the 1997 UNESCO monograph -- 4.3 Separation principles and applications of new HPLC pigment techniques -- 4.3.1 Polymeric bonded phases -- 4.3.2 Monomeric C8 bonded phases -- 4.3.3 Mobile phase additives -- 4.3.4 Column temperature -- 4.4 Choice of HPLC method -- 4.5 Applications -- 4.5.1 Analysis of pigments from pelagic phytoplankton communities -- 4.5.2 Analysis of pigments from microphytobenthos communities -- 4.5.3 Analysis of degradation products -- 4.5.4 Analysis of bacteriochlorophylls -- References -- 5 The importance of a quality assurance plan for method validation and minimizing uncertainties in the HPLC analysis of phytoplankton pigments -- 5.1 Introduction -- 5.2 Method validation -- 5.2.1 The analytical requirement -- 5.2.2 Performance parameters -- 5.2.2.1 Specificity -- 5.2.2.2 Limits of detection and quantitation -- 5.2.2.3 Working and linear ranges -- 5.2.2.4 Calibration -- 5.2.2.5 Accuracy and precision -- 5.2.2.6 Ruggedness -- 5.3 Results from inter-laboratory comparisons -- 5.3.1 Precision -- 5.3.2 Accuracy -- 5.3.3 Validity of the round-robin approach -- 5.4 Performance metrics -- 5.5 Quality assurance plan -- 5.5.1 QC measurements and QA applications -- 5.5.1.1 Pigment resolution and retention time precision (daily) -- 5.5.1.2 Analysis precision and carryover (daily) -- 5.5.1.3 Chla calibration accuracy (daily) -- 5.5.1.4 Sample extract analysis precision (daily) -- 5.5.1.5 Method precision (each sample batch or at least 5% of samples) -- 5.5.1.6 Repipette accuracy and precision (daily). , 5.5.1.7 Calibration accuracy (spectrophotometric and HPLC analysis) -- 5.5.1.8 Chla linearity (with new column installation) -- 5.5.1.9 Detector noise (variable frequency) -- 5.5.1.10 QC and QA elements from data manipulations -- 5.5.2 Control charts -- 5.6 Future directions -- Acknowledgements -- Abbreviations and symbols -- References -- Appendix 5A A symbology and vocabulary for an HPLC lexicon -- References -- 6 Quantitative interpretation of chemotaxonomic pigment data -- 6.1 Introduction -- 6.2 Qualitative assessment of data -- 6.2.1 Specific markers for algal types -- 6.3 Non-taxonomic interpretation of pigment data sets -- 6.3.1 Pigment based size classes -- 6.3.2 Ecological similarity indices -- 6.4 Mathematical tools for taxonomic interpretation of pigment data sets -- 6.4.1 Assumptions and constraints of inverse simultaneous equations and CHEMTAX -- 6.4.2 Reaching the optimum solution -- 6.4.3 Guide to quantitative chemotaxonomic interpretation of pigment data -- 6.4.3.1 Pigment data exploration -- 6.4.3.2 CHEMTAX analysis -- 6.5 Variability of marker pigment:Chl a from cultures and field studies -- 6.5.1 Pigment:Chl a ratios in culture versus field -- 6.5.2 Irradiance -- 6.5.3 Nutrients -- 6.6 Comparison with results from microscopy and other techniques -- 6.6.1 Relative strengths and weaknesses of chemotaxonomy and microscopy -- 6.6.2 Verification of pigment chemotaxonomy -- 6.6.3 Other techniques -- 6.7 Conclusions -- Acknowledgements -- References -- 7 Liquid chromatography-mass spectrometry for pigment analysis -- 7.1 LC-MS analysis of chlorophylls and carotenoids: introduction -- 7.2 Description of instrumentation -- 7.2.1 Modes of ionisation used in pigment analysis -- Fast atom bombardment (FAB) -- Atmospheric pressure chemical ionisation (APCI) -- Electrospray ionisation (ESI) -- Matrix-assisted laser desorption ionisation (MALDI). , 7.2.2 Mass analysers.