Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography (Cambridge Environmental Chemistry Series)

Cover......Page 1
PHYTOPLANKTON PIGMENTS......Page 3
CAMBRIDGE ENVIRONMENTAL CHEMISTRY SERIES......Page 6
Title......Page 7
Copyright......Page 8
Dedication......Page 9
Contents
......Page 11
Contributors......Page 17
Preface......Page 23
Acknowledgements......Page 26
Pigment names......Page 27
Part I Chlorophylls and carotenoids 
......Page 31
1.1 Introduction......Page 33
1.2.1 The 'protistan perspective'
......Page 34
1.2.2 The classical 'pigment perspective'
......Page 35
1.3 Origins of microalgal plastids......Page 39
1.4 Biological characteristics of currently recognized photosynthetic microalgal classes......Page 40
1.4.1.1 Cyanophytes (Cyanophyceae); including species previously known as Prochlorophytes (Prochlorophyceae)......Page 42
1.4.3 Eukaryotes: the red radiation......Page 46
1.4.3.1 The division Rhodophyta......Page 47
1.4.3.2.2 Bolidophytes (class Bolidophyceae; division Heterokontophyta)......Page 48
1.4.3.2.3 Chrysophytes (class Chrysophyceae; division Heterokontophyta)......Page 52
1.4.3.2.4 Silicoflagellates (class Dictyochophyceae; division Heterokontophyta)......Page 53
1.4.3.2.5 Eustigmatophytes (class Eustigmatophyceae; division Heterokontophyta)......Page 54
1.4.3.2.6 Pelagophytes (class Pelagophyceae; division Heterokontophyta)......Page 55
1.4.3.2.9 Raphidophytes (chloromonads) (class Raphidophyceae; division Heterokontophyta)......Page 56
1.4.3.2.10 Synurophytes (Class Synurophyceae; Division Heterokontophyta)......Page 59
1.4.3.3 The division Haptophyta......Page 60
1.4.3.3.1 Pavlovophytes (class Pavlovophyceae; division Haptophyta)......Page 62
1.4.3.3.2 Characteristics of golden-brown algae (class Prymnesiophyceae ≡ Coccolithophyceae)......Page 63
1.4.3.4.1 Class Cryptophyceae; division Cryptophyta......Page 64
1.4.3.5 The division Dinophyta......Page 65
1.4.3.5.1 Class Dinophyceae; division Dinophyta......Page 67
1.4.4 Eukaryotes: the green radiation......Page 68
1.4.4.1 The division Euglenophyta......Page 69
1.4.4.2 The division Chlorarachniophyta......Page 70
1.4.4.3 The division Chlorophyta (Classes Chlorophyceae, Prasinophyceae and Trebouxiophyceae)......Page 72
1.4.4.4 The division Streptophyta......Page 74
1.5.2 Signature pigments in the cyanobacterial lineage, the Glaucocystophyta and the red and green algal lineages......Page 75
1.5.3 Future developments......Page 87
Abbreviations and symbols......Page 615
Glossary of important terms used in protistan taxonomy......Page 88
Abbreviations......Page 89
References......Page 90
2.2 Structures of chlorophylls......Page 108
2.2.1 Phytoporphyrin-type chlorophylls......Page 109
2.2.2 Phytochlorin-type chlorophylls......Page 110
2.3 Biosynthesis of protoporphyrin IX......Page 111
2.3.1 Formation of 5-aminolevulinic acid and its regulation......Page 113
2.3.3 Distribution of the C5 pathway......Page 118
2.3.5 Formation of uroporphyrinogen III from porphobilinogen......Page 119
2.3.8 Oxidation of protoporphyrinogen IX to protoporphyrin IX......Page 121
2.4.1 Formation of Mg-protoporphyrin IX by Mg-chelatase......Page 122
2.4.2 Formation of Mg-protoporphyrin IX-monomethylester by S-adenosylmethionine: Mg-protoporphyrin IX methyltransferase......Page 123
2.4.3.2 The oxygenase pathway......Page 124
2.4.5.1 Light-dependent protochlorophyllide oxidoreductases......Page 126
2.4.6 Conversion of chlorophyllide a to chlorophyllide b by chlorophyllide a oxygenase......Page 127
2.4.7 Reduction of chlorophyll(ide) b to chlorophyll(ide) a: the chlorophyll cycle......Page 128
2.4.9 Formation of bacteriochlorophyll a: reduction of ring B by chlorin-reductase......Page 129
2.4.10.1 In the phytoporphyrin family......Page 130
2.4.10.2 In the phytochlorin family......Page 131
2.5 Concluding remarks......Page 132
Acknowledgements......Page 717
Abbreviations......Page 133
References......Page 134
3.1 Introduction......Page 143
3.2 Biosynthesis of carotenes......Page 144
3.2.1 Formation of the active isoprene......Page 149
3.2.3 Formation of lycopene......Page 154
3.2.4 Formation of cyclic carotenes......Page 156
3.3 Biosynthesis of xanthophylls......Page 158
3.3.1 Hydroxylation......Page 159
3.3.2 Epoxidation, de-epoxidation and the xanthophyll cycles......Page 161
3.3.3 Formation of light-harvesting xanthophylls......Page 163
3.3.4 Formation of ketocarotenoids......Page 165
3.3.5 Formation of xanthophylls specific to cyanobacteria......Page 167
3.4 Carotenoid catabolism and carotenoids as precursors of other physiologically important metabolites......Page 168
3.4.1. Abscisic acid......Page 169
3.4.2 Retinal......Page 170
3.4.3 Strigolactones......Page 172
3.4.4 Other products of carotenoid cleavage......Page 173
Acknowledgements......Page 174
Abbreviations......Page 175
References......Page 176
Part II Methodology guidance
......Page 193
4.2 HPLC algal pigment methods published since the 1997 UNESCO monograph......Page 195
4.3.1 Polymeric bonded phases......Page 200
4.3.2 Monomeric C8 bonded phases......Page 203
4.3.3 Mobile phase additives......Page 204
4.3.4 Column temperature......Page 205
4.4 Choice of HPLC method......Page 206
4.5.1 Analysis of pigments from pelagic phytoplankton communities......Page 209
4.5.3 Analysis of degradation products......Page 211
4.5.4 Analysis of bacteriochlorophylls......Page 212
5.1 Introduction......Page 225
5.2 Method validation......Page 228
5.2.1 The analytical requirement......Page 229
5.2.2.1 Specificity......Page 231
5.2.2.2 Limits of detection and quantitation......Page 234
5.2.2.3 Working and linear ranges......Page 236
5.2.2.4 Calibration......Page 241
5.2.2.5 Accuracy and precision......Page 244
5.2.2.6 Ruggedness......Page 246
5.3 Results from inter-laboratory comparisons......Page 247
5.3.1 Precision......Page 248
5.3.2 Accuracy......Page 250
5.3.3 Validity of the round-robin approach......Page 252
5.4 Performance metrics......Page 254
5.5.1 QC measurements and QA applications......Page 256
5.5.1.2 Analysis precision and carryover (daily)......Page 257
5.5.1.4 Sample extract analysis precision (daily)......Page 259
5.5.1.5 Method precision (each sample batch or at least 5% of samples)......Page 260
5.5.1.7 Calibration accuracy (spectrophotometric and HPLC analysis)......Page 277
5.5.1.8 Chla linearity (with new column installation)......Page 278
5.5.1.10 QC and QA elements from data manipulations......Page 279
5.5.2 Control charts......Page 280
5.6 Future directions......Page 282
References......Page 678
Abbreviations and symbols......Page 284
References......Page 285
Appendix 5A A symbology and vocabulary for an HPLC lexicon......Page 289
References......Page 301
6.1 Introduction......Page 303
6.2.1 Specific markers for algal types......Page 304
6.3.1 Pigment based size classes......Page 306
6.3.2 Ecological similarity indices......Page 307
6.4 Mathematical tools for taxonomic interpretation of pigment data sets......Page 308
6.4.1 Assumptions and constraints of inverse simultaneous equations and CHEMTAX......Page 311
6.4.2 Reaching the optimum solution......Page 334
6.4.3 Guide to quantitative chemotaxonomic interpretation of pigment data......Page 335
6.4.3.2 CHEMTAX analysis......Page 336
6.5 Variability of marker pigment:Chl a from cultures and field studies......Page 338
6.5.1 Pigment:Chl a ratios in culture versus field......Page 339
6.5.2 Irradiance......Page 340
6.5.3 Nutrients......Page 341
6.6.1 Relative strengths and weaknesses of chemotaxonomy and microscopy......Page 343
6.6.2 Verification of pigment chemotaxonomy......Page 344
6.6.3 Other techniques......Page 346
References......Page 347
7.1 LC-MS analysis of chlorophylls and carotenoids: introduction......Page 360
Atmospheric pressure chemical ionisation (APCI)......Page 361
Electrospray ionisation (ESI)......Page 362
Matrix-assisted laser desorption ionisation (MALDI)......Page 363
Quadrupole/triple quadrupole......Page 364
Time of flight (TOF)......Page 365
7.3.2 Ionisation methods for the analysis of chlorophylls: APCI and ESI......Page 366
7.3.3 Fragmentation of chlorophylls and bacteriochlorophylls: MS/MS......Page 368
7.3.4 LC-MS/MS analysis of chlorophylls from aquatic environments......Page 374
7.3.5 Ionisation methods for the analysis of carotenoids......Page 375
7.3.6 Fragmentation of the carotenoids: MS/MS......Page 376
7.3.7 LC-MS analysis of carotenoids from the aquatic environment......Page 380
Abbreviations......Page 381
References......Page 382
8.1 Introduction......Page 389
8.2 Presentation of multi-component analysis methods......Page 390
8.3.1 Spectral reconstruction method (SRC)......Page 394
8.3.2 Gauss-peak spectra method (GPS)......Page 396
8.3.3 Multivariate calibration model with partial least squares regression (PLS)......Page 397
8.4 Multi-component spectrofluorometric methods......Page 398
8.4.1 Spectrofluorometric analysis of chlorophylls and pheopigments using CLS and NNLS......Page 399
8.5 Methods comparison......Page 401
8.5.1 Comparison of CLS and NNLS spectrofluorometric derived data......Page 402
8.5.2 Comparison of spectrofluorometric and HPLC methods......Page 405
8.6 Recommendations and future considerations......Page 407
References......Page 408
8A.2 History of Arnon's simultaneous equation method......Page 412
8A.3 Accurate simultaneous equations for use with aqueous 80% acetone extractant......Page 413
8A.4 Extraction methods......Page 414
8A.6.1 Chlorophyll extraction with aqueous 85% methanol containing 2% KOH and 1.5 mM sodium dithionite......Page 415
References......Page 416
Part III Water-soluble 'pigments'
......Page 419
9.1 Introduction......Page 421
9.2 Structures of phycobiliproteins......Page 422
9.3 Biosynthesis of phycobilin chromophores......Page 428
9.4 Optical spectroscopy of phycobiliproteins......Page 430
9.5 Functions of phycobiliproteins......Page 435
9.6.1 Spectroscopy tips......Page 437
9.6.3 Phycobilisome dissociation and separation of individual biliproteins......Page 438
9.6.6 Extinction coefficients of native chromoproteins......Page 439
9.6.8 Identification of binding sites by tryptic digestion followed by mass spectrometry......Page 440
9.6.9 Isolation of chromophores (OCarra and OhEocha, 1966)......Page 441
9.6.10 Reconstitution of phycobiliproteins from chromophores and apoproteins......Page 444
9.6.11 Analysis of phycobiliproteins......Page 445
Abbreviations......Page 446
References......Page 447
10.1 Description and role of MAAs......Page 458
10.2 Distribution of MAAs in marine phytoplankton......Page 464
10.3 Biosynthesis, trophic transfer and extra-cellular release......Page 470
10.3.1 Induction......Page 471
10.3.2 Trophic transfer......Page 472
10.3.3 Extra-cellular release......Page 473
10.5.2 Storage of filtered samples......Page 474
10.5.4 Stability of the extracts......Page 475
10.5.7 MAA detection, identification and quantification......Page 476
10.5.8 Recommendations for standards......Page 478
Abbreviations and symbols......Page 479
References......Page 616
Part IV Selected pigment applications in oceanography......Page 489
11.1 Introduction......Page 491
11.2.2 Light-harvesting complexes and thylakoid membranes......Page 492
11.2.3 Pigment composition and function......Page 494
11.3.1 Role and regulation of the xanthophyll cycle......Page 495
11.3.2 The xanthophyll cycle and non-photochemical quenching......Page 499
11.4.1 Ecophysiology and environmental modulation of the XC......Page 500
11.4.2 The xanthophyll cycle and UV radiation......Page 502
11.4.3 The XC and the dynamics of water masses......Page 505
References......Page 508
12.1 Pigment labelling method......Page 518
12.2 Serial dilution method......Page 523
12.2.1 From pigment to C in dilution experiments......Page 526
12.3.1 Highly dynamic equilibrium......Page 527
12.3.3 Close coupling between growth and grazing......Page 528
12.4 Other methodologies......Page 529
12.4.1. Satellite imagery......Page 530
12.4.2 FRRF-based primary productivity......Page 531
Abbreviations and symbols......Page 533
References......Page 534
13.1 Introduction......Page 542
13.2.1 Theory......Page 543
Efficiency factors......Page 546
Optical coefficients of algal suspensions......Page 548
Influence of absorption on scattering......Page 549
Absorption properties of phytoplankton......Page 550
Scattering properties of phytoplankton......Page 551
Interpretation of absorption and scattering spectra......Page 552
13.2.3 Relationships between individual pigments and in vivo absorption properties......Page 554
Accessory photosynthetic and photoprotective pigments......Page 555
13.3.1 Theory......Page 558
13.3.2 Experimental methods of in vivo fluorescence excitation spectra......Page 560
In vivo fluorescence excitation spectra......Page 561
13.3.3 Combined information from in vivo
......Page 563
13.4 In vivo absorption properties of CDOM and non-phytoplankton particles......Page 565
13.5 Light-harvesting complexes in Chromophyta, Chlorophyta and Cyanobacteria......Page 568
References......Page 572
References......Page 574
14.1 Introduction......Page 584
14.2.1 Inherent and apparent optical properties......Page 591
14.2.3 In situ classification of optically significant constituents: phytoplankton, CDOM and suspended matter......Page 593
14.2.4 Above water remote-sensing retrieval algorithms of optically significant constituents......Page 594
14.3 Current techniques for in situ monitoring and remote sensing of phytoplankton blooms by optical sensors......Page 599
14.3.1 In situ sensors for optical detection of IOP and AOP......Page 600
14.3.2 Remotely sensed fluorescence line height......Page 601
14.3.4 From global to regional algorithms - wavelength targeting......Page 602
14.4 Platforms addressing the varying scales of blooms......Page 603
14.4.1 Moorings......Page 604
14.4.3 Above-water remote sensing......Page 605
14.5.1 In situ monitoring of gyroxanthin diester in Karenia brevis......Page 608
14.5.3 Satellite monitoring of Chl c3 and coccoliths in Emiliania huxleyi......Page 610
14.6.1 Phytoplankton pigments and toxins......Page 611
14.6.2 In situ detection......Page 612
14.6.3 Remote sensing......Page 613
Appendix 14A Pigments and toxins of harmful algae
......Page 628
References......Page 640
Part V Future perspectives 
......Page 653
15.2 Pigments in marine bacteria and cyanobacteria – recent discoveries......Page 655
15.3 Carotenoid biosynthesis – a perspective......Page 656
15.4 Chlorophyll and bacteriochlorophyll biosynthesis – recent advances......Page 657
15.5 Chlorophyll degradation – a perspective......Page 658
15.6 Phycobiliproteins – a perspective......Page 659
15.8 Underpinning technical advances......Page 660
15.9 Characterising algae using HR-MAS-NMR – recent advances......Page 661
15.10 Recent improvements in remote sensing......Page 662
15.11 The increased use of pigments with a cautionary note – a perspective......Page 663
15.12 Applied phycology......Page 664
References......Page 665
Part VI
 Aids for practical laboratory work......Page 671
A.1 Filtration......Page 673
A.1.3 Extraction......Page 674
A.1.4 Stability of extracted samples......Page 676
A.1.5 Benthic microalgae (microphytobenthos)......Page 677
Appendix B HPLC instrument performance metrics and validation 
......Page 682
B.1 Hardware components overview......Page 683
B.3 Autosamplers......Page 686
Needle-in-loop design......Page 687
B.4 Pumps......Page 689
B.5 Detectors......Page 690
B.6 A note on considerations for applications......Page 693
References......Page 695
C.1 Identical UV-visible absorption spectra......Page 696
C.4 Algal cultures......Page 697
References......Page 698
D.1.  SCOR reference cultures......Page 699
D.2.  Reference microalgal cultures proposed for new algal classes and prochlorophytes......Page 700
Appendix E: Commercial suppliers of phytoplankton pigments
......Page 704
References......Page 705
Introduction......Page 711
Names and molecular structures......Page 712
UV-Vis spectral information......Page 713
Pigments presented in data sheets......Page 715
Other phytoplankton pigments......Page 716
References......Page 718
1 Chlorophylls
......Page 721
2 Carotenes
......Page 764
3 Xanthophylls
......Page 774
Index
......Page 869