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Index

bold = tables; italics = figures; underline = data sheet

abscisic acid (ABA), 138formation, 132, 139

abscisic aldehyde, 139absorptionby non-fluorescent PSI and PPC, 518by non-phytoplankton particles, 520by pigments, 547in situ sensors, 546

absorption coefficientchlorophyll a, 367chlorophyll b, 367in vivo

measurement problems, 504of cellular matter for phytoplankton (acm), 500optical properties, 497peak value, with no package effect, 509pigment calibration, 212

absorption cross-sectionPSII reaction centres, 519

absorption fingerprints, 555absorption properties of algal cellsinterference from other particles, 505

absorption spectrumanalysis by multivariate techniques, 343, 344decomposition into Gaussian bands, 506decomposition into Gaussian–Lorentzian

curves, 507deconvolution of the spectrum, 508fourth-derivative analysis, 506in vivo phytoplankton, 496neural network methods, 507pigment information retrieval, 506principal component analysis

partial least-squares regression, 507ratio of photoprotective carotenoids to

light-harvesting pigments, 507reconstruction using pigments, 508stepwise discriminant analysis, 506

Acaryochloris marina, 101Acaryochloris sp., 14accessory pigments

role in light absorption, 509Acidiphilium rubrum, 81Advanced Laser Fluorometer (ALF)

active fluorescenceairborne sensor, 562

aerobic anoxygenic phototrophic bacteria,183, 610

HPLC pigment method, 181airborne remote sensing

advantages, 561Airborne Visible/Infrared Imaging Spectrometer

(AVIRIS), 561Akashiwo sanguinea (¼ Gymnodinium sanguineum)

red tidemycosporine-like amino acids, 418

ALA-synthase, 88induction, 88

Alexandrium excavatum (= A. tamarense)mycosporine-like amino acids, 418

Alexandrium sp.mycosporine-like amino acids, 417pigment signature, 565

Alexandrium tamarenseinduction of mycosporine-like amino acids, 424mycosporine-like amino acids, 425nitrogen starvation

mycosporine-glycine, 426toxic and non-toxic strains, 618

algae

classification, 4, 9, 11pigment perspective, 5protistan perspective, 4

freshwater, 6, 16, 17, 22, 24, 30, 34, 40heterokont, 9, 18

Algae Online Analyser (AOA), 556

823

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Cambridge University Press978-1-107-00066-7 - Phytoplankton Pigments: Characterization, Chemotaxonomy andApplications in OceanographyEdited by Suzanne Roy, Carole A. Llewellyn, Einar Skarstad Egeland and Geir JohnsenIndexMore information

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algal bloom, 32, 33, 37optical monitoring, 538spatial scale

airborne remote sensing, 561algal classespigment characteristics, 45

algal culturesas authentic sources of pigments, 653reference for new algal classes and pigments,

654algal ketolase gene (bkt), 135algal resting stagessecondary carotenoids, 129

Algal_2 productremote sensing for Case II waters, 549

allophycocyanin, 14, 15, 16, 17, 525absorption spectrum, 384spectroscopy, 384

allophycocyanin (APC), 378alloxanthin, 34, 35, 37, 144, 258, 261, 565, 728all-trans-lycopene, 124, 1255-aminolevulinic acid (ALA), 81C4þ1 pathway, 88C5 pathway, 88formation, 83

ammonium acetate bufferallomerization problem, 175

Amphidinium carterae, 37, 134peridinin

PCP and ACP, 525xanthophyll formation, 135

Amphidinium klebsiipigment ratios, 296

Anabaena sp.myxol-rhamnoside, 138

Anabaena variabilis, 129anomalous diffraction approximation, 500anoxygenic phototrophic bacteria, 102aromatic carotenoids, 128

antheraxanthin, 20, 23, 24, 40, 42, 44, 131, 134,524, 663, 730

relationship with fluorescence quenching, 453xanthophyll cycle, 450

antioxidantcarotenoids, 619

antioxidant enzymepromoted by abscisic acid, 139

Apedinella sp., 24aphanizophyll, 13apocarotenoidenzymatic cleavage of carotenoids, 138

b-8-apocarotenal, 144b-apo-100-carotenalformation, 143

b-apo-100-carotenol, 143b-apo-13-carotenone, 143formation, 143

apoprotein, 375, 383apparent optical properties (AOP), 546applied phycology, 618Archaeplastida, 4, 5Arctic Ocean, 22ARGO floats

bio-optical instruments, 558Arthrospira maxima

ketocarotenoids, 135astaxanthin, 42, 44, 129, 136, 138, 732

commercial interest, 135, 619formation, 130LC-MS/MS

loss of toluene, 331Nannochloropsis sp., 136synthesis from zeaxanthin, 135synthesis from b,b-carotene, 135

astaxanthin estersin dinoflagellates and krill

LC-MS/MS, 334in lipid globules in snow algae, 525

atmospheric correctionfor remote sensing of ocean colour data,

559ATP production

in photosynthesis, 523attenuation coefficient, 546

apparent optical properties, 546optical properties, 497

Aurearenophyceae, 23Aureococcus sp., 25Aureoumbra sp., 25auroxanthin, 734autonomous underwater vehicles (AUVs), 559,

567, 617

Bacillariophyceae, 18, 20, See also diatomChl c-containing phytoplankton, 497xanthophyll cycle, 450

backscattering, 505backscattering coefficient, 548bacteriochlorin, 79bacteriochlorophyll, 79, 609

bchE gene, 94BChl-synthase

bchG gene, 99, 100biosynthesis, 611chlorin reductase

bchX, bchY, bchZ genes, 99HPLC method, 183HPLC pigment analysis, 182LC-MS, 314LC-MS/MS, 322, 324

APCI, 328multivariate spectrofluorometric

methods, 353structure, 81

824 Index






bacteriochlorophyll a, 81, 259, 675formation, 99HPLC method, 179mass spectrometry, 94oligotrophic oceans, 610

bacteriochlorophyll c, 81, 101pigment analysis problems, 183

bacteriochlorophyll d, 81, 101bacteriochlorophyll e, 81, 101LC-MS/MS, 323

bacteriochlorophyll g, 81bacteriochlorophyll g0, 101bacteriochlorophyll oxidation productsLC-MS/MS, 328

bacteriopheophytin a, 102bacteriopheophytin b, 102bacteriophytochlorinabsorption bands, 81

Baltic Seacyanobacteria

CHEMTAX, 299phytoplankton pigments

spectral in vivo fluorescence 344benthic diatomUV-damaged xanthophyll cycle, 458

benthic microalgae (microphytobenthos)extraction efficiency

sediment-to-solvent volume, 630extraction of pigments, 631

bilins, 375dimethylesters

hydrolysis conditions, 397preparation conditions, 397

biliprotein, 13, 375, 376, 378, 392absorption compared between native and

denatured, 387conformation, 382cryptophyte

variety of chromophores, 383b-subunits, 378

denaturation, 388diagnostic characteristics, 399phytochromes, 378regulation of tetrapyrrole, 390subunits isolation, 393used as labelling tool, 613

biliverdin (BV)isolation procedure, 396

biliverdin IXa, 382biofuelmicroalgae, 618

biomass normalization, 449bio-optical algorithm, 546regionally-specific, 567

bio-optical characteristics of phytoplankton, 496bloom dynamicschanges in bio-optical properties, 558

blue light, 425Bolidomonas mediterranea, 22Bolidomonas pacifica, 22Bolidophyceae, 18, 22, See also bolidophytebolidophyte, 18, 20, 22

pigment markers, 259xanthophyll cycle, 131

Botrydium sp., 30Botryococcus braunii

harmful algaefreshwater systems, 566

Brevebuster, 566brown algae

abscisic acid, 139xanthophyll cycle, 131

buoysfor in situ optical instruments, 555

190-butanoyloxyfucoxanthin, 20, 24, 34, 37, 259, 736

C:chlorophyll a ratio, 480satellite-derived estimate, 484

C:N ratiousing HR-MAS-NMR, 615

C5-pathwayaminolevulinic acid formation, 83

caloxanthin, 137, 138, 738Camptothecium sp., 89canthaxanthin, 13, 24, 37, 129, 130, 144, 740

formation, 136Nannochloropsis sp., 136

CaroteNature, 659carotene

biosynthesis, 114formation of aromatic types, 128LC-MS/MS, 331

a-carotene. See b,ε-caroteneb,b-carotene, 13, 15, 16, 17, 20, 22, 23, 24, 25,

26, 28, 29, 30, 32, 34, 37, 39, 40, 42, 44,113, 718

formation, 114, 127LC-MS/MS, 331

ESI, 329outside thylakoid membranes, 524slow-responding photoprotective carotenoid,

524xanthophyll formation, 134

b,ε-carotene, 15, 17, 35, 37, 39, 42, 126, 127,134, 720

formation, 114b,c-carotene, 37, 42, 44, 126, 137,

144, 722b-carotene ketolase (BKT), 136g-carotene. See b,c-caroteneε,ε-carotene, 25, 724c, c-carotene, See also lycopenecarotenogenesis, 113, 114

in cyanobacteria, 144

Index 825






carotenoidbiosynthesis, 113

formation of cyclic carotenes, 126degradation, 138in algal resting spores, 611in eyespot, 611in light-harvesting complexes of algae compared

to higher plants, 524LC-MS

APCI and ESI, 329FAB ionisation, 329ionisation methods, 329

LC-MS/MS, 330photodegradation

in cyanobacteria, 144photoprotective, 247, 294, 445, 497

fast responding, 524light-harvesting function, 524quantum yield of photosynthesis, 509slow responding, 524

photosynthetic, 247sediment samples, 334synthesis, 119

carotenoid cleavage oxygenases (CCO), 139CCD1 subfamily, 143NSC1 or NosCCD, 144NSC3, 144

carotenol chlorin esters, 328Carteria sp., 39Case I waters, 547Case II waters, 547, 555, 556, 567CDOMdetermination using absorption

spectroscopy, 519determination using liquid waveguide

spectrophotometers, 519exponential slope (S), 519map of global distribution, 521Sargasso Sea, 520solar bleaching, 520terrestrial origin, 520

cell wall, 13, 14, 17, 20, 22, 26, 28dithiothreitol weakening effect, 370murein, 13peptidoglycan, 16silica, 20

cellulose plate, 17, 23, 30, 37cellulose wall, 42Ceratium sp., 565Chaetoceros brevisxanthophyll cycle

UV effect, 457UV inhibition, 457

Chaetoceros muelleri, 616pigment ratio

nutrient limitation, 295

Chaetoceros sp.number of chloroplasts, 446

chemometric methodsfull spectrum techniques, 343multi-component analysis, 343

chemotaxonomic marker, 56chemotaxonomic method, 262

Bayesian compositional estimator (BCE), 264CHEMTAX, 262cluster analysis, 289environmental data, 289excel solver, 262flow cytometry and flowCAM, 289fluorometry, 289interpretation of pigment data, 289inverse simultaneous equation, 262microscopy, 289multiple linear regression, 262, 290productivity data, 289remote-sensing data, 289

chemotaxonomycomparison with microscopy, 297problem with symbiotic associations, 298quantitative analysis, 257

CHEMTAX, 56, 259, 262, 264, 618assumptions and constraints, 265comparison with microscopy, 299comparison with other techniques, 301comprehensive analysis, 291depth strata, 290Dictyochophyte, 293Emiliania huxleyi, 294gyroxanthin diester, 563minimum number of samples, 290nutrient responses, 296optimum solution, 288pigment ratios, 265, 291

in field and algal cultures, 293variability, 292

preliminary run, 291ratio limit matrices, 291sub-grouping, 290

Chlamydomonas reinhardtii, 119, 121, 124, 125bkt gene, 136CCO genes, 140genome, 130zeaxanthin epoxidase, 132

Chlamydomonas sp., 39lutein-based xanthophyll cycle, 450

chlorarachniophyte, 9, 38, 40cyst, 40

Chlorella fusca, 119Chlorella protothecoides, 616Chlorella sp., 39Chlorella vulgaris, 43chlorin, 79

826 Index






chlorin steryl esterHPLC pigment analysis, 182

Chlorobium phaeobacteroidesHPLC pigment analysis, 183LC-MS/MS, 326

Chlorobium sp., 89Chlorobium tepidumLC-MS/MS of chlorophyll and

bacteriochlorophyll, 329Chloroflexus sp., 89chloromonad, 26, 28Chlorophyceae, 38, 42Chl b-containing phytoplankton, 497

chlorophyllallomerization, 629biodegradation, 78biosynthesis, 78, 92, 611degradation, 99, 612extraction method

DMF or DMSO, 368formation, 89LC-MS/MS, 322monomeric solutions

labile character, 366partial least squares analysis, 352phytochlorin-type

absorption bands, 81ring E

hydratase pathway, 94spectrophotometric data, 81structure, 78, 81transmetalation

pollution, 612transmetallated, 81

chlorophyll a, 80, 676alkyl sulphide derivative

Antarctic lake sediment, 328concentration retrieval algorithm, 549epimers, 101extraction problems, 631fluorescence

quantum yield, 512quenching processes, 513

in vitro fluorescence, 512auto-fluorescence, 512

in vivo fluorescence, 497, 512excitation spectra, 514

rapid changes in picoeukaryotesphotoprotection, 455

separation from divinyl chlorophyll a, 170solar-stimulated fluorescence, 555specific absorption coefficient, 518

chlorophyll a oxidase, 612chlorophyll a:C ratio, 449chlorophyll a0

C-132 epimer of Chl a, 101, 680

chlorophyll a-chlorophyll b protein complexes, 523chlorophyll a-chlorophyll c protein complexes, 523chlorophyll a-chlorophyll c-peridinin protein

(ACP), 447chlorophyll allomers

influence on spectrofluorometric methods, 361chlorophyll a-specific

absorption, 448absorption coefficient, 508

chlorophyll b, 38, 39, 80, 259, 540, 682formation, 98HPLC separation, 171LC-MS/MS, 322separation from divinyl chlorophyll b, 170spectrofluorometric methods

NNLS, 358spectrofluorometry compared with HPLC, 359chlorophyll, b0, 684

chlorophyll b-containing algaeenergy regulation mechanisms, 448

chlorophyll c, 6, 15, 20, 28, 32, 35, 37, 56, 79, 80,101, 174, 259, 540

absorption spectrum, 79algal groups containing, 497degradation in autosampler, 631function, 79LC-MS, 314

ESI, 321, 323spectral overlap with phycobiliproteins, 399structure, 79

chlorophyll c1, 259, 686HPLC separation, 174

chlorophyll c1-like K. foliaceum-type, 20chlorophyll c1-MGDG, 259chlorophyll c2, 259, 688

non polar, 80chlorophyll c2-like Pavlova gyrans-type, 20, 260chlorophyll c2-MGDG [14:0/14:0], 34, 37, 95, 259chlorophyll c2-MGDG [18:4/14:0], 34, 95, 259, 690chlorophyll c3, 20, 22, 34, 95, 96, 100, 259, 290, 565, 692

harmful algae classes, 566HPLC separation, 171, 174in HAB classes involved in fish mortality, 565LC-MS/MS, 324multivariate spectrofluorometric method, 353Pseudochattonella verruculosa, 545satellite monitoring of Emiliania huxleyi, 564spectrofluorometric methods, 356spectrofluorometry compared with HPLC, 359wavelength targeting, 557

chlorophyll c3 (CS-170), 95, 100, 259chlorophyll c-containing algae

energy regulation mechanisms, 448chlorophyll c-containing phytoplankton functional

typesoptical discrimination, 569

Index 827






chlorophyll c-MGDG esters, 170chlorophyll concentration from ocean coloursemi-analytical technique, 521

chlorophyll cycle, 98, 99chlorophyll d, 14, 15, 81, 101, 102, 609, 610, 694chlorophyll f, 102, 610chlorophyll oxidation productsLC-MS/MS, 328

chlorophyll synthase, 99chlorophyllaseHPLC method, 179

chlorophyllide, 80, 88, 356LC-MS

MALDI, 317chlorophyllide a, 696esterification, 99influence on spectrofluorometric methods, 361

chlorophyllide a oxygenase (CAO), 97chlorophyllide b, 698esterification, 99formation, 97, 98

chlorophyllide reductase, 611Chlorophyta, 5, 38, 42, 43, See also

chlorophytebio-optical discrimination, 540state transitions, 447

chlorophyte, 9, 42, 119, 259, 260, 540genome

MEP and MVA pathways, 119pigment markers, 258, 259qE and xanthophyll cycle, 453qE mechanism model, 453state transition, 515xanthophyll cycle

UV effect, 457zeaxanthin, 262

chloroplastchanges associated with photo-acclimation, 446

chlororespirationxanthophyll cycle, 452

Chl-synthasechlG gene, 99

Chondrus crispusmycosporine-like amino acids, 425

Chromadex, 659Chromalveolata, 5, See also chromalveolate algaechromalveolate algae, 126, 127, 144, 611conversion of xanthophyll-cycle pigments, 134violaxanthin, 132xanthophylls, 128

Chromatium sp., 89Chromophyta. See also chromophytebio-optical discrimination, 540

chromophyte, 5, 6, 45, 79, 259, 569evolution, 9

Chrysochromulina sp.pigment markers, 259

Chrysocystis sp., 25chrysolaminarin, 20, 23, 25, 29, 33Chrysophyceae, 5, 22, 23, 24, 26, 28, 29, 30,

See also chrysophyteChl c-containing phytoplankton, 497xanthophyll cycle, 450

chrysophyte, 9, 22, 23, 26, 29, 260, 540conversion of xanthophyll-cycle

pigments, 134phytoplankton functional types, 543pigment markers, 259qE and xanthophyll cycle, 453xanthophyll cycle, 131

Cladophora rupestrischlorophyll extraction, 370

climate and environmental change, 619cobalamine, 90coccolith, 32, 33

backscattering, 521free during post-bloom phase, 564from MODIS satellite monitoring, 561light scattering, 519satellite monitoring of Emiliania huxleyi, 564scattering, 508

coccolithophore, 617high scattering chromophytes, 569

Coccolithophyceae, 33, See also coccolithophyte,See also Prymnesiophyceae

Chl c-containing phytoplankton, 497coccolithophyte

harmful algae, 566phytoplankton functional types, 543

coenzyme-F430, 90coloured or chromophoric dissolved organic matter

(CDOM), 427, 497, 519, 546, 547, 555,See also CDOM

from MODIS, 561influence on pigment ratios, 296

commercial suppliers of pigments, 658comparative genomics, 119, 140, 144, 615continuous flow-FAB, 315coproporphyrin I, 90coproporphyrinogen I and III, 90coproporphyrinogen III

formation, 91core-membrane linker, 376cosmetic sector

microalgae, 618crocoxanthin, 35, 742

LC-MS/MSAPCI, 331

cross-sectional area of PSII and PSI, 448Cryptophyceae

Chl c-containing phytoplankton, 497Cryptophyta, 5, 34, 40, See also

cryptophytecharacteristics, 34

828 Index






cryptophyte, 9, 16, 35, 260, 540, 562endosymbionts, 37mycosporine-like amino acids, 418phycobiliprotein-containing phytoplankton,

497phycobiliproteins, 375, 378

light-harvesting, 391radiative excitation energy transfer, 525

pigment markers, 258cryptoxanthin, 15, 16, 744Cyanidioschyzon merolae, 121, 124, 130Cyanidium caldarium, 130Cyanidium sp., 18, 89cyanobacteria, 13, 14, 20, 38, 114, 119, 127, 138,

260, 540, 562, 569, 6174-keto-myxoxanthophyll, 299abscisic acid, 139aromatic carotenoids, 128biosynthesis of carotenoids, 114carotenoid biosynthesis, 137characteristics, 12, 13CrtR-enzymes, 129detection using hyperspectral imagers, 561formation of lycopene, 124, 125free phycobilin chromophores, 383Gauss-peak spectra method, 350genes involved in carotenoid biosynthesis, 127,

128, 136genomes, 138harmful algae, 566isopentenyl diphosphate isomerases, 120LPOR, 96lycopene cyclases, 126MEP pathway, 124mycosporine-like amino acids, 417, 425novel pigments, 609phycobiliprotein-containing phytoplankton, 497phycobiliproteins, 375

light-harvesting, 389radiative excitation energy transfer, 525

phycobilisome pigmentation, 385phycochromes, 613phycoerythrin, 378phycourobilin, 384phytoene desaturase genes, 125phytoplankton functional types, 543pigment markers, 258, 259pigment ratios, 299PS I

chlorophyll a epimers, 101qE and xanthophyll cycle, 453state transition, 515symbiotic, 13symbiotic in dinoflagellates, 9terrestrial

mycosporine-like amino acids, 417UV-B photoreceptor, 425

variable absorption spectra ofphycobiliproteins, 399

with chlorophyll d, 610xanthophyll cycle, 455xanthophyll formation, 137xanthophylls, 128, 129zeaxanthin, 262b,ε-carotene, 126

cyanobacteria bloomremote-sensing, 567

cyanobacteriochrome, 613Cyanophora sp., 16Cyanophyta. See cyanobacteriacyclic carotenoid

formation, 126cyclic electron flow

ATP formation, 523b-cyclocitral, 143Cyclotella meneghiniana

xanthophyll formation, 134cyst formation

induced by abscisic acid, 139cytochrome P450

Synechocystis sp., 142cytochrome P450 enzyme, 143

D1 protein, 514Danish Hydraulic Institute (DHI), 658dark protochlorophyllide oxidoreductase

photosynthetic bacteria, 97bchB, bchL and bchB genes, 97

de-epoxidation state index, 459dehydroxylusujirene, 4171-deoxy-D-xylulose 5-phosphate, 1201-deoxy-D-xylulose 5-phosphate reductoisomerase

(DXR), 1201-deoxy-D-xylulose 5-phosphate synthase (DXS),

119, 120Diacronema sp., 33diacylglycerol, 100diadinochrome, 746diadinoxanthin, 20, 22, 24, 25, 26, 30, 32, 34, 37, 39,

132, 135, 144, 260, 290, 447, 524, 748changes with irradiance, 294formation, 134influence on PSII fluorescence, 518slow-responding photoprotective carotenoid, 524xanthophyll cycle, 450

diadinoxanthin de-epoxidase (DDE)xanthophyll cycle, 451

diadinoxanthin xanthophyll cycle, 131diatom, 9, 18, 19, 20, 22, 38, 133, 260, 458,

540, 617abscisic acid, 139Antarctic

mycosporine-like amino acids, 425biomass, 299

Index 829






diatom, (cont.)centric, 20endosymbionts, 37

within foraminifera and dinoflagellates, 20freshwater algae, 20genome, 611harmful algae, 565low scattering chromophytes, 569MEP pathway, 124PDS genes, 125pennate, 20phytoene desaturase genes, 125, 126phytoplankton functional types, 543pigment markers, 259pigment ratio

irradiance, 294qE and xanthophyll cycle, 453, 454sea ice, 20seasonal succession

xanthophyll cycle, 455transcriptomic and metabolomic

approaches, 614tropical, 20violaxanthin, 132xanthophyll cycle, 131

de novo synthesis of diatoxanthin, 453no UV effect, 457UV inhibition, 457UV-B stimulation, 456

zeaxanthin epoxidase, 132diatoxanthin, 20, 22, 24, 25, 26, 30, 32, 34, 37, 39,

132, 260, 290, 448, 524, 750changes with irradiance, 294co-elution problem, 202daytime increase, 459influence on PSII fluorescence, 518potential antioxidant, 456relationship with fluorescence quenching, 453UV effects, 458xanthophyll cycle, 450

diatoxanthin accumulationxanthophyll cycle

high light exposure, 452diatoxanthin epoxidaseUV-B stimulation, 457xanthophyll cycle, 452

Dictyocha sp., 24Dictyochophyceae, 5, 22, 23,

See also dictyochophyteChl c-containing phytoplankton, 497

dictyochophyte, 540harmful algae, 566

dihydrolutein, 134, 752dihydroxysterol, 32dilution methodassumptions, 477combined with HPLC pigment analysis, 479

compared with carbon labelling, 481drawbacks, 483nonlinear model, 479

dimethyl sulphide, 33, 617dimethyl sulphide producers

phytoplankton functional types, 543dimethylallyl diphosphate, 119dinoflagellate, 9, 35, 260, 540, 617

chlorophyll-specific absorption coefficient, 509conversion of xanthophyll-cycle pigments, 134cyst, 37grazing impact on algal blooms, 482green plastids, 9ketocarotenoids, 137mycosporine-like amino acids, 418phytoplankton functional type, 543pigment markers, 258, 259, 260pigment types, 35plastid replacements, 9pyrrhoxanthin and peridinin, 133qE and xanthophyll cycle, 453symbiotic, 35toxic algae

gyroxanthin esters, 56pigment markers, 259

toxic/harmful algaemycosporine-like amino acids, 428

xanthophyll cycle, 131, 450UV effect, 457

dinoflagellatepigment markers, 259

Dinophyceae. See also dinoflagellateChl c-containing phytoplankton, 497

Dinophysis norvegica, 37, 565Dinophyta, 35, 37

characteristics, 37dinoxanthin, 37, 135, 260, 754diode array detection (DAD)

analysis of mycosporine-like aminoacids, 431

dithiothreitolchlorophyll extraction

weakens cell walls, 370Ditylum brightwellii

pigment ratios, 296divinyl chlorophyll (DVChl), 101

HPLC separation, 173divinyl chlorophyll a, 15, 170, 540, 700

co-elution problem, 202spectrofluorometric methods, 356

divinyl chlorophyll aþb-containing phytoplanktonfunctional types

optical discrimination, 569divinyl chlorophyll b, 170, 540, 702Dixoniella sp., 18dry ice

sample freezing and storage, 628

830 Index






Dunaliella salinab,b-carotene accumulation, 524

Dunaliella sp., 39, 42Dunaliella tertiolectaxanthophyll cycle

UV inhibition, 457

echinenone, 13, 15, 127, 130, 136, 144, 756Ectocarpus siliculosus, 124effective absorption cross section of PSII, 448efficiency factorfor absorption (Qa), 500for attenuation (Qc), 500for scattering (Qb), 500

eicosapentaenoic acid, 26, 28Emiliania huxleyi, 121, 124, 569190-hexanoyloxy-4-ketofucoxanthin, 170diatoxanthin

UV-B-induced loss, 457fucoxanthin esters

LC-MS/MS, 332pigment markers, 259satellite monitoring, 564strains from Southern Ocean, 618xanthophyll formation, 134

empirical algorithmfor chlorophyll determination from

remote-sensing, 552endosymbiosis, 4, 9, 114, 124, 126plastid evolution, 11

Euglena gracilis, 88, 120, 125photosynthesis inhibition by metals, 613

Euglena sp.Gauss-peak spectra method, 350

Euglenophyceae. See also euglenophyteChl b-containing phytoplankton, 497

euglenophyte, 9, 38, 39, 40, 540ketocarotenoid, 136pigment markers, 259qE and xanthophyll cycle, 453

Euhalothece sp.mycosporine-like amino acids, 417

euhalothece-362, 417Euphausia superbamycosporine-like amino acids

trophic transfer, 426euphotic zoneapparent optical properties, 546

European Ferrybox sensor system, 561Eustigmatophyceae, 18, 23, 24, 28,

See also eustigmatophyteeustigmatophyte, 24, 26, 29conversion of xanthophyll-cycle

pigments, 134pigment markers, 259xanthophyll cycle, 131

UV-B stimulation, 456

Eustigmatos sp., 25eutreptiellanone, 39, 259, 758Exanthemachrysis gayraliae

chlorophyll c1-like, 170Exanthemachrysis sp., 33Excavata, 5extinction coefficient. See absorption coefficient

chlorophyll a and b, 366extraction solvent, 628

acetone/water, 629dimethyl formamide (DMF), 629for periphyton, 629methanol/acetone/DMF/water, 629water dilution prior to injection, 629

eyespot, 24, 29, 32, 39, 42, 43, 44, 142carotenoids accumulation, 524

farnesol, 78, 99, 101, 325fast repetition rate fluorometry (FRRF), 484, 485,

518, 566comparison with 14C-uptake, 485

fatty acids, 28, 80, 100Fibrocapsa japonica, 28filter

comparison between different types, 627size categories, 628

filter extractiongrinding, 630soaking, 630sonication, 630

filtrationclogging, 627maximum time, 627positive pressure, 628recommendations, 627

flash-freezing, 628Flintiella sp., 18Florenciella parvula, 24flow cytometry, 508FlowCAM, 300Fluka, 659fluorescence

excitation-emission matrices (EEM), 344pigment analysis, 344

in situdetection with active sensors, 555

spectral signatures, 556three-dimensional spectroscopy, 344

fluorescence excitation spectrumchlorophyll a-specific PSII-scaled, 518in situ detection

best for Case II waters, 555distinct signatures from different pigmentgroups, 566

in vivo detectiongeneral set-up, 515quantum correction, 516

Index 831






fluorescence excitation spectrum (cont.)PSII-specific, 517quantum correction, 515

fluorescence line height, 555in turbid waters, 556limitations of the method, 555

Fluoroprobe, 300fouling problemsin moorings, 558

freeze-drying. See lyophilizationfreshwater algae, 23chlorophytes, 42cryptophytes, 34cyanobacteria, 13, 14diatoms, 20dinoflagellates, 37euglenophytes, 39extraction problems, 369Glaucocystophyta, 16glaucocystophytes, 11, 16harmful, 566mesostigmatophytes, 11, 44mycosporine-like amino acids, 417Pavlovophyceae, 32phaeothamniophytes, 11, 26prasinophytes, 43prochlorophytes, 14raphidophytes, 28silicoflagellates, 23synurophytes, 29Trebouxiophyceae, 43xanthophytes, 30

fucoxanthin, 6, 20, 22, 23, 24, 25, 26, 28, 29, 32, 34,37, 56, 133, 144, 259, 290, 448, 760

biosynthesis, 611co-elution problem, 202formation, 134, 135LC-MS/MS

APCI and ESI, 332ESI, 330

fucoxanthin esters, 314, 614fucoxanthin-containing dinoflagellates, 563fucoxanthinolLC-MS/MS, 332

gabaculine, 87Galdieria sulphuraria, 121, 124, 130phycobilisome pigmentation, 385

gelbstoff, 519, See coloured (chromophoric)dissolved organic matter (CDOM)

genomics, 614geranial, 143geranylgeraniol, 78, 99, 101, 119geranylgeranyl diphosphate synthase (GGPS),

124GF/F filterslimitations, 627

gilvin, 519, See coloured or chromophoric dissolvedorganic matter (CDOM)

Glaucocystis sp., 16Glaucocystophyta, 11, 16, 45,

See also glaucocystophyteglaucocystophyte, 9, 16

phycobiliproteins, 375phycobilisome pigmentation, 385

Glaucophyta, 4Glaucosphaera sp., 18gliders, 559, 567, 617

bio-optical instruments, 558global ocean observation systems, 617Gloeobacter violaceus, 121, 125, 159Gloeochaete sp., 16glucans

in Chaetoceros muelleriusing HR-MAS-NMR, 616

glutamyl-tRNAGlu-reductase, 88glycoside carotenoids

myxoxanthophyll, 56, 129oscillaxanthin, 56

golden-brown algae, 5, 32, 33grazing rate

coupling with growth, 482pigment-based method, 472

green algae, 4, 38, 114, 127, 130abscisic acid, 139genes involved in biosynthesis, 127phytoene desaturase genes, 126symbiosis, 38xanthophyll cycle, 131xanthophylls, 128b,ε-carotene, 126

green fluorescent protein (GFP), 613green photosynthetic bacteria, 79, 81, 101Gymnodinium breve (=Karenia brevis), 37, 259, 507Gymnodinium chlorophorum, 38Gyrodinium dorsum

induction of mycosporine-like amino acids, 425mycosporine-like amino acids

motility, 417gyroxanthin diester, 25, 37, 259, 762

HPLC and CHEMTAX, 563in haptophytes, 618in pelagophytes and haptophytes, 563in situ detection of Karenia brevis, 562LC-MS/MS, 332mean cellular concentration inKarenia brevis, 563toxic dinoflagellate, 299

gyroxanthin-containing K. brevisin vivo absorption characteristics, 563

Hacrobia, 35haem, 81, 88, 89, 92, 396Haematococcus pluvialis, 130, 135Haematococcus sp., 39, 42

832 Index






haptonema, 31, 33, 34Haptophyta, 5, 6, 22, 30, 32, 33, 56,

See also haptophytepigment groups, 449xanthophyll cycle, 450

haptophyte, 9, 31, 32, 35, 260, 540, 617conversion of xanthophyll-cycle

pigments, 134endosymbionts, 37gyroxanthin diester, 259gyroxanthin esters, 56ketocarotenoids, 136mycosporine-like amino acids, 418, 425pigment markers, 259xanthophyll cycle, 131

UV-B stimulation, 456zeaxanthin epoxidase, 132

Haramonas dimorpha, 29harmful algaepigment signature and toxin information, 565

harmful algal blooms, 25, 26, 28, 582detection using hyperspectral imagers, 561in vivo absorption spectra

specific pigments, 563optical monitoring, 538phytoplankton species, pigments and toxins, 583UV absorption, 428

harmful coccolithophyteswavelength targeting

chlorophyll c3, 557harmful dinoflagellateswavelength targeting

chlorophyll c3, 557heliobacteria, 81Heliospirillum sp., 89190-heptanoyloxyfucoxanthin, 170LC-MS/MS, 333

190-hexanoyloxy-4-ketofucoxanthin, 170, 260, 618, 766LC-MS/MS, 332

190-hexanoyloxyfucoxanthin, 32, 34, 37,259, 764

co-elution problem, 202formation, 134LC-MS/MS, 332

Heterocapsa sp.pigment ratios, 296

Heterokontophyta, 18, 20, 22, 23, 24, 25, 26, 28, 29,30, 35

xanthophyll cycle, 450heteroxanthin, 26, 30, 259high light stressbkt genes, 135

high resolution magic angle spinning nuclearmagnetic resonance spectroscopy (HR-MAS-NMR), 614

whole cell characterisation, 615HPLC. See also liquid chromatography (LC)

HPLC analysisperformance metrics, 197pigments

update on methods, 165HPLC autosampler, 640

needle blockage, 642needle height, 642needle rinse option, 643needle-in-loop design, 641pull-to-fill design, 641push-to-fill design, 641syringe size, 641temperature controlled sample tray, 643

HPLC calibrationdetector

linear response, 645HPLC column compartment

temperature-controlled, 647HPLC detectors, 644

fluorescence, 644temperature-controlled flow cell, 647UV/visible, 644

HPLC hardware, 636HPLC injector, 640

filled-loop mode, 640partial-loop mode, 640

HPLC methodaccuracy, 199, 220accuracy assessment, 214ammonium acetate buffer, 174bacteriochlorophyll analysis, 182C18 column, 170, 182, 222

combined monomeric and polymeric, 181polymeric, 175, 180

C30 column, 170C8 column, 170, 173, 180, 222

divinyl chlorophylls, 180calibration, 211, 249

multipoint method, 249response factor, 249single point method, 249

calibration accuracy, 231carryover between injections, 202, 203, 229, 640

autosampler, 642choice of method, 176choice of stationary phase, 170column polarity, 173column strength, 173column temperature, 170, 175control limits (CL), 226coupling to mass spectrometry (MS), 182detector noise, 204, 233filter water content, 234injection contamination, 203injection precision, 229intercalibration, 196internal standard, 215, 227, 231, 233, 234

Index 833






HPLC method (cont.)ion-pairing, 174limit of detection, 201limit of quantitation, 201microphytobenthos, 181peak resolution, 202peak retention time, 202performance metrics, 197, 224performance parameter, 201pigment resolution, 202, 227polymeric phases, 170precision, 218pyridine additive, 175quality assessment (QA), 195, 226quality assurance plan (QAP), 195, 226quality control (QC), 195, 226quaternary ammonium buffer, 174repeatability precision, 216reproducibility precision, 216retention time precision, 227reversed-phase, 165role of particle pore size, 171ruggedness, 216specificity, 201stationary phase

monomeric, 170polymeric, 170

summary, 170symbology, 243tetrabutylammonium acetate buffer, 175validated method, 197validation, 198vial and cap combination, 217warning limits (WL), 226water retained on filters, 251working and linear ranges, 206

HPLC pump, 643binary system, 643compensation for solvent compression, 644dwell time, 644dwell volume, 644gradient elution, 643high-pressure mixer, 643low-pressure mixer, 643quaternary system, 643solvent mixer, 643

HPLC training resources, 6481H HR-MAS-NMRto sort algal species, 616

2-hydroxymyxoxanthophyll, 13830-hydroxyechinenone, 135, 136Hydrolight software, 552hydroxymethylbilane (HMB), 9010-hydroxy-b,c-carotene, 13781-hydroxy-chlorophyll a, 101Hyperionhyperspectral imager, 561

hyperspectralimagers, 616, 617optical sensors, 616remote-sensing reflectance

best wavelengths, 568hyperspectral absorption data

regional algorithms, 557

ice algaePSII absorption, 512xanthophyll cycle

UV effect, 457in situ optical sensors, 554

Algae Online Analyser, 556incubation artifacts, 476Indian Ocean

mixing velocitiesxanthophyll cycle, 460

inherent optical properties (IOP), 545, 549integrating cavity absorption meter (ICAM), 505internal standard, 250, 251intracellular self-shading, 446ionone

formation, 126b-ionone, 126, 130, 143

formation, 143ε-ionone, 126, 127, 130iron limited environments, 614irradiance reflectance, 549Isochrysis sp.

ketocarotenoids, 136isopentenyl diphosphate, 119isoprene

formation, 113, 114formation pathways, 119

isoprenoid biosynthesisMEP pathway, 119

Joint Global Ocean Flux Study (JGOFS)program, 218protocols, 196

Karenia brevisgyroxanthin diester, 299nitrogen starvation

mycosporine-glycine, 426similarity index, 507

Karenia cristata, 565Karenia sp., 565Karlodinium sp., 565

fucoxanthin-containing, 618ketocarotenoid

formation, 135in cyanobacteria, 135in dinoflagellates, 137in euglenophytes, 136in green algae, 135

834 Index






in haptophytes, 136Isochrysis sp., 136Nannochloropsis sp., 136protection from oxidative damage, 135

ketolasein chlorophytes, 137in chromalveolate algae, 137in cyanobacteria, 137

4-keto-190-hexanoyloxyfucoxanthin, 1374-keto-190-hexanoyloxyfucoxanthin.

See 190-hexanoyloxy-4-ketofucoxanthin4-ketofucoxanthin, 34, 137, 2604-ketolutein, 1364-keto-myxoxanthophyll, 13, 259, 2994-keto-a-carotene, 130

LC-MSaquatic environment

carotenoids, 334chlorophylls, 328

atmospheric pressure chemical ionisation(APCI), 315

collision induced dissociation (CID), 330electrospray ionisation (ESI), 316fast atom bombardment (FAB), 315mass analyser, 318

ion trap, 319quadrupole, 318time of flight (TOF), 319triple quadrupole, 318

matrix-assisted laser desorption ionisation(MALDI), 317

methods for analysis of chlorophylls, 320modes of ionisation, 315sodiated molecule, 330, 332

LC-NMR, 615analysis of carotenoids, 614

LC-tandem mass spectrometry, 315light absorbed by PSIIvariation with photoacclimation, 515

light energy transfer efficiency, 448light historyphotoresponse dynamics, 455

light-harvesting antenna, 101light-harvesting complexes, 446apoproteins, 522in algae, 522in chromophytes, 447variable composition, 523water-soluble, 525

light-harvesting pigments (LHP), 445, 497light-harvesting xanthophyllformation, 133

limit of detection (LOD), 201determination, 204

limit of quantitation (LOQ), 201determination, 204

linear-tetrapyrrolic bile pigmentsphycobilins, 81

Lingulodinium polyedraexcretion of mycosporine-like amino

acids, 427harmful algal bloom

UV absorption, 428lipids

using time-domain NMR, 616liquid chromatography-mass spectrometry.

See LC-MSliquid chromatography-nuclear magnetic

resonance. See LC-NMRliquid nitrogen, 628liquid waveguide capillary cell (LWCC), 505loroxanthin, 40, 42, 43, 56, 134, 768

dodecenoate, 40, 770lower limit of linearity (LLOL)

pigment calibration, 206lutein, 40, 42, 44, 127, 128, 130, 133, 134, 171,

259, 290, 772co-elution problem, 202eye-related health care, 619HPLC separation, 173LC-MS/MS, 330slow-responding photoprotective carotenoid,

524lutein-epoxide, 134

xanthophyll cycle, 450lutein-epoxide cycle

xanthophyll cycle, 131lycopene, 44, 125, 126, 127, 137, 726

accumulation, 126formation, 114, 124

trans-lycopene, 126lycopene cyclase, 127lyophilization (freeze-drying), 630

advantages, 630sediment samples, 631

magic angle spinning (MAS), 614, 615Mallomonas sp., 29, 30Mamiellophyceae, 39, 43Mantoniella squamata, 134mariculture, 25marker pigments

to distinguish algal classes, 540mass spectrometry

compatibility with HPLC methods, 320in situ methods, 545instrument, 315

Mastigocladus laminosusphycobilisome pigmentation

absorption spectrum, 385Matrix-Assisted Laser Desorption Ionisation –

Time of Flight (MALDI-TOF), 614whole cell characterisation, 615

Index 835






maximum quantum yield of PSII-fluorescence,513

Mediterranean Sea, 22, 286mixing velocities

xanthophyll cycle, 460MEP pathwaygenes, 120, 124

MERISsatellite sensor, 549

mesobiliverdin (MBV)cryptophyte chromophore, 382

Mesodinium rubrum, 35, 258Mesostigmatophyceae, 38, 44, 45,

See also mesostigmatophytemesostigmatophyte, 44, 45metabolomics, 614, 619methanoldegradation effects, 629

methylerythritol phosphate (MEP) pathway, 1196-methyl-5-hepten-2-one, 143mevalonic acid (MVA)pathway, 119

Mg2þ

enzymic insertion into proto IX, 92MGDGformation, 100

MgDVP, 13, 15, 20, 24, 32, 33, 35, 37, 39, 42, 43, 95,96, 259, 704

formation of chlorophylls c, 95light harvesting, 95

Mg-protoporphyrin IX, 88formation, 92, 93

Mg-rhodochlorinsformation from chlorophyll, 369

micromonal, 43, 134, 258, 259, 774Micromonas pusilla, 56, 259Micromonas sp., 39, 119micromonol, 134, 144, 259, 776microphytobenthosHPLC method, 181

microplanktonpigment fraction, 248

microscopyfor cell identification, 618

microzooplanktongrazing rate

dilution method, 477, 478role during algal blooms, 482

Mie–Lorentz theory, 500mobile underwater platforms, 559moderate resolution imaging spectroradiometer

(MODIS), 200, 484optically-based products, 561satellite sensor, 549

monadoxanthin, 35, 778monogalactosyldiacylglyceride (MGDG), 80monovinyl chlorophyll c3, 170, 260, 706

mooringplatform for bio-optical measurements, 558profiling for bio-optical constituents, 558

mucocyst, 28multivariate spectral method, 348

classical least squares (CLS), 344non negative least squares (NNLS), 344parallel factor analysis (PARAFAC), 344partial least squares regression (PLS), 344principal component regression (PCR), 344spectral reconstruction method (SRC), 348

Muriella (Chlorella) zofingiensis, 136mutatoxanthin, 780mycosporine-2-glycine, 430mycosporine-glycine, 412, 417, 424

antioxidant, 418mycosporine-like amino acids (MAAs), 412

bacterial degradation, 429bio-optical studies, 428biosynthesis, 424detection, 430distribution, 418, 424electrospray ionization (ESI), 431extra-cellular release, 427extraction from filters, 429extraction from freshwater algae, 429filtration problems, 428HPLC methods, 430induction, 425interference with in vivo absorption, 504LC-MS, 431nitrogen limitation, 426osmotic stress, 426packaging, 418photodegradation, 427photoprotection, 417primary, 424roles, 417secondary, 424, 427stability of extracts, 429standards, 432storage of filters, 428symbiotic acquisition, 426trophic transfer, 426UV-absorbing intereferences, 430

mycosporine-taurine, 417antioxidant, 418

Myrionecta rubrum, 35myxol, 13, 127, 129myxoxanthophyll, 13, 56, 127, 129, 136, 137,

144, 782formation, 126, 137heat dissipation in cyanobacteria, 454

Nannochloropsis oculata, 25Nannochloropsis sp.

ketocarotenoids, 136

836 Index






Nannochloris atomisextraction problems, 369

nanoplankton, 25, 30, 33chemotaxonomic method, 297pigment based size class, 261pigment fraction, 248

NASA Sensor Intercomparison and Mergerfor Biological and InterdisciplinaryOceanic Studies (SIMBIOS), 196

natural colourantcarotenoids and phycobilins, 618

90-cis-neochrome, 784formation, 132in chlorarachniophytes, 133in euglenophytes, 133

neoxanthin, 38, 39, 40, 42, 44, 135co-elution problem, 202genes encoding neoxanthin synthase, 133

trans-neoxanthin, 44, 663, 788formation, 134

90-cis-neoxanthin, 128, 133, 139, 786neoxanthin synthase, 133neurosporene, 134nine-cis-epoxy carotenoid dioxygenase (NCED), 139nitrogen fixationphytoplankton functional types, 543

nitrogen limitationbkt genes, 135

Nodularia spumigenapigment markers, 259

non-photochemical fluorescence quenching(NPQ), 446, 450, 456, 513

energy-dependent (qE), 453, 513photoinhibition (qI), 453, 513role, 453state transitions (qT), 453, 513xanthophyll cycle, 453

non-photochemical fluorescence quenching (qN), 513non-polar chlorophyll c, 259Nostoc (Anabaena) sp., 129Nostoc flagelliformeUV-sensitivity, 418

Nostoc sp., 129apocarotenoid cleavage oxygenase, 140volatile isoprenoids formation, 144

nostoxanthin, 13, 137, 138, 790nuclear magnetic resonance (NMR), 615, 616nutrientspigment ratios, 295

nylon membranefor sample filtration, 627

okenone, 128optical coefficientsof algal suspensions, 502

optical detection of IOP and AOPin situ sensors, 554

optical propertiesabsorption, 547of particles, 497of seawater, 545phytoplankton functional types, 540scattering, 547

optically significant constituents (OSC), 545Orange Carotenoid Protein (OCP), 135, 136oscillaxanthin, 13, 56, 137, 792

formation, 137Ostreococcus lucimarinus, 121, 124, 125

genome, 130Ostreococcus sp., 119Ostreococcus tauri, 121, 124, 125

genome, 130oxygen action spectrum, 515oxygenic gross photosynthetic rate (PChl a), 485ozone layer, 412

P-457, 37Pacific Ocean, 22, 28

phosphorus limitation, 295package effect, 446, 503, 547

cell size, 503photoacclimation state, 503

palythene, 430palythenic acid, 427, 430palythine-serine, 430PARAFAC, 344, 355, 362

EEM fluorescence of pigment extracts, 355Paralytic Shellfish Poisoning (PSP), 565Parmales, 19, 22pathlength amplification effect (‘b factor’), 504Pavlova gyrans

chlorophyll c2-like, 170Pavlova sp., 33

xanthophyll cycleUV inhibition, 457

Pavlovale, 33Pavlovophyceae, 5, 31, 32, 33

characteristics, 32Chl c-containing phytoplankton, 497

Pelagococcus subviridis, 25Pelagomonas calceolata

18S RNA, 300Pelagomonas sp., 6, 25Pelagophyceae, 5, 22, 24, 25, See also pelagophytepelagophyte, 18, 25

gyroxanthin diester, 259gyroxanthin esters, 56harmful algae, 566pigment markers, 259xanthophyll cycle, 131

190-pentanoyloxyfucoxanthin, 170LC-MS/MS, 332

performance metricsHPLC analysis, 197

Index 837






peridinin, 9, 35, 37, 38, 56, 133, 144, 258, 260, 448,565, 794

Alexandrium sp., 565co-elution problem, 202formation, 134neoxanthin as intermediate, 135

peridinin-chlorophyll a-protein complexes (PCPs)in dinoflagellates

water soluble, 525peridininol, 37Phaeocystischlorophyll c3, 299

Phaeocystis antarcticamycosporine-like amino acids

trophic transfer, 426Phaeodactylum tricornutum, 20, 121, 124, 125, 611genes encoding for violaxanthin de-epoxidase,

452genome, 131

lycopene cyclase, 127xanthophyll formation, 134

Phaeogloea sp., 26Phaeomonas sp., 28Phaeothamnion sp., 26Phaeothamniophyceae, 5, 22, 26, 28pharmaceutical sectormicroalgae, 618

pheophorbidecyclic form, 182formation, 99pyro derivatives, 182

pheophorbide a, 708co-elution problem, 202

pheophorbide oxygenase, 99pheophytin, 101partial least squares analysis, 352pheophytin a, 710pheophytin b, 712

photoacclimation, 445bio-optical characteristics, 496light history, 449long-term, 446pigment ratios, 295

photoacclimation index, 449photoadaptive strategiesdinoflagellates

PCP, 525photochemical activity of PSII, 485photochemical efficiency (Fv/Fm)relation with xanthophyll cycle, 456

photochemical fluorescence quenching (qP), 513photo-damaged photosystem IIrepair promoted by abscisic acid, 139

photodiode array HPLC detector (PDA), 644photoprotectionxanthophyll cycle, 131

photoprotection pigments, 445

photoprotective statepigment indicators, 459

photoreceptorphototaxis regulation, 390phytochrome, 378synthesis of mycosporine-like amino acids, 425

photoreversible biliprotein, 613photosynthetic electron transfer rates (ETR), 485photosystem I (PSI)

chlorophyll a epimers, 101phycobilin chromophore

absorption maxima, 393attachment modes, 383biosynthesis, 382extinction coefficients, 393extraction from biliproteins

procedure, 397HPLC conditions following tryptic

digestion, 395identification

acidic urea denaturation, 393gel electrophoresis, 394LC isolation and MS, 394

isolation procedure, 395mass spectrometry, 395quantitative analysis, 400

phycobilin chromophore attachmentlyases, 383

phycobiliprotein, 35, 375absorption spectrum, 384

variation with solvent conditions, 388algal groups containing, 497chromophore identification, 388complementary chromatic adaptation, 390conditions for dissociation, 392core-membrane linker, 383fluorescence spectroscopy, 399fluorescence spectrum

self-absorption, 392future studies, 613hexamers, 376influence of light quality in marine species, 381interference by fluorescence, 391interference with phytoplankton

absorption, 505light-harvesting function, 389low phototoxicity, 390monomers, 376nitrogen source, 390radiative excitation energy transfer, 525reconstitution from chromophores and

apoproteins, 398spectral fluorescence signature method, 556spectrophotometric analysis, 399

spectral overlap with carotenoids, 399spectroscopy tips, 391structure, 376

838 Index






phycobiliprotein-containing algaebio-optical discrimination, 540energy regulation mechanisms, 448imbalance between PSII and PSI, 515optical discrimination of functional

types, 569state transitions, 515

phycobilisome, 13, 16, 17, 35, 376assembly, 376dissociation conditions, 392isolation conditions, 392stabilized with phosphate buffer, 392

phycobilisomes-containing algaeqE and zeaxanthin accumulation, 454

phycochrome, 613phycocyanin, 14, 15, 16, 17, 35, 37, 525absorption spectrum, 384, 399complementary chromatic adaptation, 390spectroscopy, 384

phycocyanin (PC), 378phycocyanobilin (PCB), 381isolation procedure, 395

phycoerythrin, 14, 15, 17, 35, 37, 377, 383, 525absorption spectrum, 384, 400complementary chromatic adaptation, 390cyanobacteria, 378for algal group discrimination

advanced laser fluorometer, 562in situ

detection with active sensors, 555red algae, 378spectroscopy, 384

phycoerythrin (PE), 378phycoerythrin reflectanceused to detect Trichodesmium sp., 564

phycoerythrobilin (PEB), 378isolation procedure, 395

phycoerythrocyaninphotochemistry, 390

phycoerythrocyanin (PEC), 378a-phycoerythrocyanin (PEC)in cyanobacteria, 378

phycourobilin (PUB), 378isolation procedure, 396

phycoviolobilin (PVB), 381isolation procedure, 396

phytochlorin, 79, 80, 100, 101, 102phytochrome, 378, 613chromophore binding, 383

phytochromobilin (PFB)isolation procedure, 396

phytoene, 124formation, 114, 124

15-cis-phytoene, 124phytoene dehydrogenase, 136phytoene desaturase (PDS), 124, 125phytoene synthase (PSY), 124

phytol chain, 99, 119phytoplankton

absorption spectraretrieval approach, 521

backscattering coefficient, 505community structure

from patterns of optical properties, 521dynamics, 461food quality, 483in situ detection methods, 545in vivo absorption fingerprints, 555scattering properties, 505, 547size spectra

from semi-analytical optical approach, 522phytoplankton blooms

in situ monitoring and remote-sensingtechniques, 553

phytoplankton functional types (PFT), 261, 301,540, 617

relationship with pigment-specific algalgroups, 543

phytoporphyrin, 79picoeukaryote, 261

phytoplankton functional types, 543pico-haptophytes

DNA sequences, 300picoplankton, 12, 13, 14, 15, 19, 22, 24, 25, 32, 39,

40, 45chemotaxonomic method, 297molecular approaches, 300pathlength amplification factor, 504pigment based size class, 261pigment fraction, 248qE and xanthophyll cycle, 453tropical, 15UV absorption, 427xanthophyll cycle, 455

pigmentancillary, 200, 244associated with harmful algal blooms, 582breakdown products

in sediments, 182changes with irradiance, 294degradation products, 181degradation rate, 479diagnostic, 247, 260diversity, 448environmental factors affecting composition, 257Fp index, 260HPLC analysis

update on methods, 165identification criteria, 179in situ detection, 553light harvesting (LHP), 294microphytobenthos, 181overlap in HPLC chromatogram, 652precipitation, 629

Index 839






pigment (cont.)primary, 200, 244secondary, 200, 244size classes, 260standards, 653tertiary, 200, 244unambiguous markers for particular algal

groups, 258pigment calibrationaccuracy and precision, 211linear regression

residuals, 207lower limit of linearity (LLOL), 206single-point, 212upper limit of linearity (ULOL), 206working range, 206

pigment extractin acetone

degradation in autosampler, 631in methanol

degradation in autosampler, 631stability in acetone, 630stability in methanol, 631

pigment identificationco-chromatography, 651minimum criteria, 650molecular mass, 651retention time matching with standard, 651

pigment labelling method, 472, 473application conditions, 475carbon concentration, 473carbon-specific growth rate, 473carotenoids, 475compared with dilution method, 481in-line flow scintillation counting, 475labelling kinetics of pigments, 475

pigment ratiosfluctuating light, 294freshwater algae, 296high nutrient, low chlorophyll (HNLC), 295irradiance, 294nutrients, 295photoacclimation, 295Southern Ocean, 295Western Equatorial Pacific, 296

pigment reconstructioncompared with filter pad method, 509

pigment-based growth ratecombined with CHEMTAX, 480

pigment-based production ratephotoacclimation problems, 476

pigment-protein complexes, 446, 522in chlorophyll c-containing chromophytes, 522

Pinguiochrysis sp., 28Pinguiophyceae, 6, 26, 28, See also pinguiophytepinguiophyte, 28characteristics, 26

plastoquinone, 523Pleurochloridella sp., 26point source integrating cavity absorption meter

(PSICAM), 505polar chlorophyll c, 170polar region, 23, 29, 33, 37polyunsaturated fatty acids, 26porphobilinogen, 87, 89

formation, 89porphyra-334, 418, 424Porphyridiophyceae, 18Porphyridium sp., 17, 18porphyrin

cancer treatment, 619porphyrin oxidation products

fluorescence and absorption, 91potential efficiency of PSII

fluorescence measurements, 514Prasinophyceae, 38, 43, 45, 56,

See also prasinophyteChl b-containing phytoplankton, 497genome, 132pigment groups, 449

prasinophyte, 9, 32, 40, 43, 144, 258, 259, 540endosymbionts, 37phytoene desaturase genes, 125pigment markers, 258, 259preprasinoxanthin, 133uriolide, 133xanthophylls, 128zeaxanthin, 262

prasinoxanthin, 38, 43, 144, 290, 448, 796co-elution problem, 202formation, 134

preprasinoxanthin, 133primary productivity, 472

algorithmsmajor limitations, 484

spectral models, 522Prochlorococcus marinus, 96, 121, 127Prochlorococcus sp., 14, 101, 127

biliproteins, 377, 390chlorophyll-specific absorption coefficient, 509genes involved in biosynthesis, 127LC-MS

ESI, 321qE and zeaxanthin accumulation, 454

Prochloron sp., 14, 15Prochlorophyta, 13, See also prochlorophyteprochlorophyte, 13, 14, 15, 260, 540, 569

bio-optical discrimination, 540bio-optical properties, 566characteristics, 13phycobiliprotein-containing phytoplankton,

497pigment markers, 258

Prochlorothrix sp., 14, 15, 89

840 Index






Procholorococcus marinusHPLC pigment separation, 180

production ratepigment-based method, 472

productivityrole of pigments, 619

prokaryote, 11, 18, 79, 81, 95Prorocentrum minimumperidinin

PCP and ACP, 525protein chromophore interactionsnon-covalent mechanisms, 385

proteorhodopsin, 609, 610protist, 4protochlorophyll, 80protochlorophyllide, 80, 88protochlorophyllide aformation, 96

protochlorophyllide a oxidoreductase (POR), 96dark form (DPOR), 97light-dependent (LPOR), 96

protochlorophyllide b, 100protochlorophyllide reductase, 611protoheme, 382protoporphyrin IX, 78biosynthesis, 81formation, 91

protoporphyrinogen IXformation, 91

provitamin A, 113Prymnesiophyceae, 5, 31, 32, 33, 34,

See also prymnesiophytecharacteristics, 33

prymnesiophyte, 260Pseudochattonella farcimen. See Verrucophora

farcimenPseudochattonella verruculosaaka Verrucophora farcimen, 545

Pseudo-nitzschia sp.toxin information, 565

Pseudopedinella sp., 24PSII photosynthetic unit size, 519pulse amplitude modulated (PAM) fluorometry,

518, 566purple photosynthetic bacteria, 81, 88pyrenoid, 17, 20, 22, 24, 25, 26, 28, 29, 30, 32, 33,

35, 39, 40, 42, 44pyridoxol, 120pyropheophorbide a, 714pyropheophytin a, 716pyrrhoxanthin, 37, 133

quality assurance plan, 636for pigment determination, 618

quantitative filter technique (QFT), 504quantum correctionverification, 516

quantum yield for oxygenic photosynthesistheoretical maximum value, 523

quantum yield of photosystem II (PSII)fluorescence, 485

variation over the day, 555

Raphidophyceae, 26, 28, 30, See also raphidophyteChl c-containing phytoplankton, 497

raphidophyte, 26, 28, 540characteristics, 26conversion of xanthophyll-cycle pigments, 134cyst, 29mycosporine-like amino acids, 418pigment markers, 259xanthophyll cycle, 131

rapid photoprotective mechanisms, 450reaction centers (RC)

photosynthesis, 445reactive oxygen species (ROS), 92, 450, 456

effect on xanthophyll cycle pigments, 457influence on mycosporine-like amino acids, 425protection by mycosporine-like amino

acids, 418Rebecca sp., 33red algae, 4, 16, 81, 101, 130, See also Rhodophyta

and rhodophytefree phycobilin chromophores, 383genome

lycopene cyclase, 127MEP pathway, 124phycobiliproteins, 375

radiative excitation energy transfer, 525phycobilisome pigmentation, 385phycourobilin, 384phytoene desaturase genes, 126xanthophyll, 128xanthophyll cycle, 454b,ε-carotene, 126

remote sensing, 619influence of UV absorption, 428ocean colour data, 559recent improvements, 616reflectance (Rrs), 521, 546, 548

remotely operated vehicles (ROVs), 617renierapurpurin, 128, 138retinal, 138

formation, 140reverse genetics, 615Rhodella sp., 18Rhodellophyceae, 18Rhodobacter sphaeroides, 88Rhodomonas marina

pigment ratios, 296Rhodophyta, 16, 17, 18, 35, 89, See also red algae,

rhodophytegenes involved in biosynthesis, 127state transitions, 447

Index 841






rhodophyte, 11, 127, 130, 132, 418, 454,See also Rhodophyta and red algae

qE and xanthophyll cycle, 453rhodopsineyespot

Chlamydomonas reinhardtii, 142photoreceptor

Nostoc sp., 142type I or archaeal, 140type II

green algae, 140rhodopsin type Iin cryptophytes, 142in dinoflagellates, 142in euglenophytes, 142

Rhodospirillum rubrum, 88Rhodospora sp., 18round robin, 244

S-320 (mycosporine-like amino acid), 412safranal, 143salt stressbkt genes, 135

sample storage, 628Sarcinochryis sp., 25Sargasso Seachlorophyll-specific absorption coefficient,

509phosphorus limitation, 295

satellite imagerychlorophyll, 484

satellite-based estimates of primaryproductivity

advantages and problems, 484scattering coefficientinfluence of absorption properties, 503optical properties, 497

scattering propertiesused to extract pigment information, 508

Scenedesmus obliquus, 88, 119Scientific Committee on Oceanic Research

(SCOR), 3Scrippsiella sp.pigment ratios, 296

scytonemin, 418SeaHARRE, 196accuracy threshold for analysis of

chlorophyll, 200calibration accuracy for chlorophyll a, 211carryover between injections, 203comparison between fluorometric,

spectrophotometric and HPLC analyses,216

data collection error, 219detectability problem, 204detector noise, 233extraction solvent, 215

extraction volume precision, 234field sampling precision, 230HPLC method accuracy, 220HPLC method precision, 218HPLC methods comparison, 218injection precision, 217injection solvent, 217limits of detection and quantitation, 204method performance comparison, 225method validation, 221overall method precision, 216performance metrics, 197, 224technical reports, 196

SeaWiFS, 200satellite sensor, 549

SeaWiFS HPLC analysis round-robin experiment.See SeaHARRE

SeaWiFS Ocean Optics Protocols, 196Sentinel-3 Ocean and Land Colour imager

(OLC), 568shikimate pathway, 424shinorine, 418, 424, 430shinorine methyl ester (M-333), 430shoot multiplication signal (SMS)

strigolactones, 142Sigma, 659silica frustule, 18silica scale, 23, 29siliceous skeleton, 24silicoflagellate. See Dictyochophyceaesilicon uptake

Thalassiosira pseudonanaHR-MAS-NMR, 615

SIMBIOS round robin, 214accuracies for the three SeaHARRE activities,

224chlorophyll a accuracy, 220comparison between fluorometry and

HPLC, 196field sampling precision, 230fluorometric and HPLC method comparison,

215HPLC extraction procedures, 215pigment accuracy, 200quality control, 217validated method, 197, 199

similarity index, 261for determination of Karenia brevis, 563

singlet-state excitation, 449siphonaxanthin, 42, 43, 44, 56, 798

formation, 134siphonaxanthin dodecenoate, 800siphonaxanthin esters, 290, 614

LC-MS/MS, 332sirohaem, 81, 90Skeletonema costatum

genome, 131

842 Index






sodium dithioniteto prevent oxidation, 369

Solieria chordalis, 615sonicationsediment samples, 631

Southern California Bightchlorophyll-specific absorption

coefficient, 509specific extinction coefficientchlorophyll a, 367chlorophyll b, 367mycosporine-like amino acids, 431

spectral bands in satellite ocean-coloursensors, 568

spectral decomposition, 343spectral fluorescenceartificial light-stimulated, 556

spectral fluorescence signatures (SFS)advantages and problems, 556

spectral reconstruction, 343spectrofluorometry, 343, 352analysis of chlorophylls and

pheopigments, 353comparison between CLS and NNLS, 356comparison with HPLC, 355NNLS methods

comparison with HPLC, 359spectrometric multivariate methodscomparison with traditional methods, 355

spectrophotometerintegrating sphere, 504

spectrophotometry, 343absorption coefficient, 252multivariate methods

Gauss-peak spectra method (GPS), 350non negative least squares approximation

(NNLS), 350partial least squares regression

(PLS), 351pigment concentration calculation, 252simultaneous equations, 366

chlorophylls a and b, 367historical aspects, 366

trichromatic equations, 343state transition, 447, 448in chlorophyte, 515in chromophytes, 515in cyanobacteria, 515redistribution of light-harvesting complexes,

524sterol, 119synthesis, 119

steryl chlorin estersLC-MS/MS

zooplankton grazing, 328Stichogloea sp., 26stramenopile, 6, 18

Streptophyta, 38, 44, 45strigolactone, 138

formation, 142stromatolite

chlorophyll f, 102Stylomatophyceae, 18sun-induced fluorescence

satellite sensorMODIS, 485

Symbiodinium sp.mycosporine-like amino acids, 427

Synchromophyceae, 23Synechococcus elongatus, 121Synechococcus sp., 14, 89, 121, 126, 127

biliproteinstrichromatic R-type PC, 382

CHEMTAX, 299lycopene cyclase genes, 126phycobiliproteins

absorption maximum, 399phycobilisome pigmentation

absorption spectrum, 385pigment ratios, 296renierapurpurin, 138w-ring formation, 128

Synechocystis sp., 89, 121, 129apocarotenoid cleavage oxygenase, 140genes

chlorophyll biosynthesis, 95retinal-binding opsins, 142

ketocarotenoids, 135mycosporine-like amino acids, 417myxoxanthophyll, 137phycobilisome-associated carotenoid-protein,

390w-ring formation, 128

synechoxanthin, 128, 137formation, 138

Synura mammillosa, 29Synurophyceae, 28, 29, 30, See also

synurophytesynurophyte, 29

xanthophyll cycle, 131

Takayama tasmanica, 565terrestrial habitat, 13, 37

xanthophytes, 30tetrapyrrole pigments

biosynthesis, 81, 92Thalassiosira pseudonana, 20, 121, 124, 125,

611, 615genome, 130, 131

lycopene cyclase, 127Thalassiosira sp.

photoprotectioniron adaptation, 455

Thalassiosira weissflogii, 134

Index 843






Thermosynechococcus elongatus BP-1, 138thiamine, 120thylakoids, 447Tolypothrix tenuis, 390total chlorophyll a (TChl a), 196toxic dinoflagellatespigment diversity, 565

toxin, 13, 37associated with harmful algal blooms, 582chemotaxonomical markers, 565ELISA assays, 545harmful algae, 565

transcriptomics, 614, 619Trebouxia sp., 43Trebouxiophyceae, 38, 43Tribonema sp., 30Trichodesmium sp., 12, 13blooms, 564CHEMTAX, 299extra-cellular release of mycosporine-like amino

acids, 427gas vacuoles

scattering, 508mycosporine-like amino acids, 418satellite detection using phycobiliproteins,

564spectrofluorometric methods, 356stirring releases UV compounds, 428

triplet-state excitation, 449tropical region, 29, 37tunichlorin, 102turnover of standing stock, 482

ultra performance liquid chromatography (UPLC),57, 614, 644

Ulva lactucazeaxanthin

UV-B induced loss, 457Ulvophyceae, 6, 38upper limit of linearity (ULOL)pigment calibration, 206

uriolide, 43, 133, 134, 144, 258, 802urogen III. See uroporphyrinogen IIIuroporphyrinogen co-synthase, 88uroporphyrinogen III, 91formation, 89tetrapyrrole biosynthesis, 81

usujirene, 430UV absorbing compounds, 412UV absorption, 427UV radiationxanthophyll cycle

ecological relevance, 458UV-A, 425xanthophyll cycle, 457

UV-B, 412, 425xanthophyll cycle, 457

Vaucheria sp., 30vaucheriaxanthin, 24, 30, 44, 56, 144, 804vaucheriaxanthin diester, 259vaucheriaxanthin ethanoate octanoate, 806Verrucophora farcimen, 24, 545

toxic algal bloompigment signature not specific, 526

violaxanthin, 20, 23, 24, 28, 29, 38, 40, 42, 44, 128,133, 134, 448, 524, 808

co-elution problem, 202formation, 132xanthophyll cycle, 131, 450

9-cis-violaxanthin, 139violaxanthin de-epoxidase (VDE), 131

genes in prasinophytes, 132UV-B inhibition, 457xanthophyll cycle, 451

Vischeria sp., 25vitamin B12, 81, 94volume scattering function, 506Volvox carteri, 121, 124

genome, 130

wavelength targeting, 567remote-sensing algorithms, 557

Xanthophyceae, 5, 26, 28, 30, See alsoxanthophyte

xanthophyll cycle, 450xanthophyll

biosynthesis, 128in cyanobacteria, 129in prasinophytes and chromalveolates,129

formation, 114LC-MS/MS

ESI, 329light-harvesting, 128photoprotection, 128

xanthophyll cycle, 131, 446, 448algae compared to terrestrial plants, 454description, 450diadinoxanthin/diatoxanthin cycle, 131dynamics of water masses, 459endosymbiotic gene transfer, 133environmental modulation, 454estuarine strains compared to oceanic, 455fluctuating light, 455fluorescence quenching, 513lumen pH, 451lutein-based, 450lutein-epoxide/lutein cycle, 131orthologous genes, 132photoprotection, 131physiological condition, 456regulation, 451role and regulation, 449

844 Index






siphonaxanthin-based, 450size effect, 455stimulation by UV-B exposure, 456types of, 131UV inhibition, 457UV response, 456violaxanthin/antheraxanthin/zeaxanthin

cycle, 131violaxanthin-based

in heterokonts, 450water mixing rate, 459

xanthophyll de-epoxidationUV radiation

biological weighting function, 456xanthophyte, 30conversion of xanthophyll-cycle pigments,

134pigment markers, 259xanthophyll cycle, 131

xanthoxin, 139

zeaxanthin, 13, 15, 16, 17, 20, 23, 24, 28, 29, 37, 40,42, 127, 128, 129, 130, 131, 133, 134, 136,138, 144, 171, 259, 262, 290, 524, 810

accumulation under high light, 450changes with irradiance, 294co-elution problem, 202eye-related health care, 619formation, 130HPLC separation, 173LC-MS/MS

loss of toluene, 330relationship with fluorescence quenching, 453slow-responding photoprotective carotenoid,

524xanthophyll cycle, 450

zeaxanthin epoxidase (ZEP), 131, 132mutants, 133xanthophyll cycle, 451

Zn-bacteriochlorophyll a, 102zooxanthellae, 426

Index 845






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