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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
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
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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
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
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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
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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
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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
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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
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
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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
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
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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
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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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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