Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography Edited by Suzanne Roy, Carole A

Cambridge University Press 978-1-107-00066-7 - Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography Edited by Suzanne Roy, Carole A. Llewellyn, Einar Skarstad Egeland and Geir Johnsen Index More information

Index

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

abscisic acid (ABA), 138 Acaryochloris marina, 101 formation, 132, 139 Acaryochloris sp., 14 abscisic aldehyde, 139 accessory pigments absorption role in light absorption, 509 by non-fluorescent PSI and PPC, 518 Acidiphilium rubrum,81 by non-phytoplankton particles, 520 Advanced Laser Fluorometer (ALF) by pigments, 547 active fluorescence in situ sensors, 546 airborne sensor, 562 absorption coefficient aerobic anoxygenic phototrophic bacteria, chlorophyll a, 367 183, 610 chlorophyll b, 367 HPLC pigment method, 181 in vivo airborne remote sensing measurement problems, 504 advantages, 561 of cellular matter for phytoplankton (acm), 500 Airborne Visible/Infrared Imaging Spectrometer optical properties, 497 (AVIRIS), 561 peak value, with no package effect, 509 Akashiwo sanguinea (¼ Gymnodinium sanguineum) pigment calibration, 212 red tide absorption cross-section mycosporine-like amino acids, 418 PSII reaction centres, 519 ALA-synthase, 88 absorption fingerprints, 555 induction, 88 absorption properties of algal cells Alexandrium excavatum (= A. tamarense) interference from other particles, 505 mycosporine-like amino acids, 418 absorption spectrum Alexandrium sp. analysis by multivariate techniques, 343, 344 mycosporine-like amino acids, 417 decomposition into Gaussian bands, 506 pigment signature, 565 decomposition into Gaussian–Lorentzian Alexandrium tamarense curves, 507 induction of mycosporine-like amino acids, 424 deconvolution of the spectrum, 508 mycosporine-like amino acids, 425 fourth-derivative analysis, 506 nitrogen starvation in vivo phytoplankton, 496 mycosporine-glycine, 426 neural network methods, 507 toxic and non-toxic strains, 618 pigment information retrieval, 506 algae principal component analysis classification, 4, 9, 11 partial least-squares regression, 507 pigment perspective, 5 ratio of photoprotective carotenoids to protistan perspective, 4 light-harvesting pigments, 507 freshwater, 6, 16, 17, 22, 24, 30, 34, 40 reconstruction using pigments, 508 heterokont, 9, 18 stepwise discriminant analysis, 506 Algae Online Analyser (AOA), 556

823

© in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-00066-7 - Phytoplankton Pigments: Characterization, Chemotaxonomy and Applications in Oceanography Edited by Suzanne Roy, Carole A. Llewellyn, Einar Skarstad Egeland and Geir Johnsen Index More information

824 Index

algal bloom, 32, 33, 37 apoprotein, 375, 383 optical monitoring, 538 apparent optical properties (AOP), 546 spatial scale applied phycology, 618 airborne remote sensing, 561 Archaeplastida, 4, 5 algal classes Arctic Ocean, 22 pigment characteristics, 45 ARGO floats algal cultures bio-optical instruments, 558 as authentic sources of pigments, 653 Arthrospira maxima reference for new algal classes and pigments, ketocarotenoids, 135 654 astaxanthin, 42, 44, 129, 136, 138, 732 algal ketolase gene (bkt), 135 commercial interest, 135, 619 algal resting stages formation, 130 secondary carotenoids, 129 LC-MS/MS Algal_2 product loss of toluene, 331 remote sensing for Case II waters, 549 Nannochloropsis sp., 136 allophycocyanin, 14, 15, 16, 17, 525 synthesis from zeaxanthin, 135 absorption spectrum, 384 synthesis from b,b-carotene, 135 spectroscopy, 384 astaxanthin esters allophycocyanin (APC), 378 in dinoflagellates and krill alloxanthin, 34, 35, 37, 144, 258, 261, 565, 728 LC-MS/MS, 334 all-trans-lycopene, 124, 125 in lipid globules in snow algae, 525 5-aminolevulinic acid (ALA), 81 atmospheric correction C4þ1 pathway, 88 for remote sensing of ocean colour data, C5 pathway, 88 559 formation, 83 ATP production ammonium acetate buffer in photosynthesis, 523 allomerization problem, 175 attenuation coefficient, 546 Amphidinium carterae, 37, 134 apparent optical properties, 546 peridinin optical properties, 497 PCP and ACP, 525 Aurearenophyceae, 23 xanthophyll formation, 135 Aureococcus sp., 25 Amphidinium klebsii Aureoumbra sp., 25 pigment ratios, 296 auroxanthin, 734 Anabaena sp. autonomous underwater vehicles (AUVs), 559, myxol-rhamnoside, 138 567, 617 Anabaena variabilis, 129 anomalous diffraction approximation, 500 Bacillariophyceae, 18, 20, See also diatom anoxygenic phototrophic bacteria, 102 Chl c-containing phytoplankton, 497 aromatic carotenoids, 128 xanthophyll cycle, 450 antheraxanthin, 20, 23, 24, 40, 42, 44, 131, 134, backscattering, 505 524, 663, 730 backscattering coefficient, 548 relationship with fluorescence quenching, 453 bacteriochlorin, 79 xanthophyll cycle, 450 bacteriochlorophyll, 79, 609 antioxidant bchE gene, 94 carotenoids, 619 BChl-synthase antioxidant enzyme bchG gene, 99, 100 promoted by abscisic acid, 139 biosynthesis, 611 Apedinella sp., 24 chlorin reductase aphanizophyll, 13 bchX, bchY, bchZ genes, 99 apocarotenoid HPLC method, 183 enzymatic cleavage of carotenoids, 138 HPLC pigment analysis, 182 b-8-apocarotenal, 144 LC-MS, 314 b-apo-100-carotenal LC-MS/MS, 322, 324 formation, 143 APCI, 328 b-apo-100-carotenol, 143 multivariate spectrofluorometric b-apo-13-carotenone, 143 methods, 353 formation, 143 structure, 81

Index 825

bacteriochlorophyll a, 81, 259, 675 blue light, 425 formation, 99 Bolidomonas mediterranea,22 HPLC method, 179 Bolidomonas pacifica,22 mass spectrometry, 94 Bolidophyceae, 18, 22, See also bolidophyte oligotrophic oceans, 610 bolidophyte, 18, 20, 22 bacteriochlorophyll c, 81, 101 pigment markers, 259 pigment analysis problems, 183 xanthophyll cycle, 131 bacteriochlorophyll d, 81, 101 Botrydium sp., 30 bacteriochlorophyll e, 81, 101 Botryococcus braunii LC-MS/MS, 323 harmful algae bacteriochlorophyll g,81 freshwater systems, 566 bacteriochlorophyll g0, 101 Brevebuster, 566 bacteriochlorophyll oxidation products brown algae LC-MS/MS, 328 abscisic acid, 139 bacteriopheophytin a, 102 xanthophyll cycle, 131 bacteriopheophytin b, 102 buoys bacteriophytochlorin for in situ optical instruments, 555 absorption bands, 81 190-butanoyloxyfucoxanthin, 20, 24, 34, 37, 259, 736 Baltic Sea cyanobacteria C:chlorophyll a ratio, 480 CHEMTAX, 299 satellite-derived estimate, 484 phytoplankton pigments C:N ratio spectral in vivo fluorescence 344 using HR-MAS-NMR, 615 benthic diatom C5-pathway UV-damaged xanthophyll cycle, 458 aminolevulinic acid formation, 83 benthic microalgae (microphytobenthos) caloxanthin, 137, 138, 738 extraction efficiency Camptothecium sp., 89 sediment-to-solvent volume, 630 canthaxanthin, 13, 24, 37, 129, 130, 144, 740 extraction of pigments, 631 formation, 136 bilins, 375 Nannochloropsis sp., 136 dimethylesters CaroteNature, 659 hydrolysis conditions, 397 carotene preparation conditions, 397 biosynthesis, 114 biliprotein, 13, 375, 376, 378, 392 formation of aromatic types, 128 absorption compared between native and LC-MS/MS, 331 denatured, 387 a-carotene. See b,ε-carotene conformation, 382 b,b-carotene, 13, 15, 16, 17, 20, 22, 23, 24, 25, cryptophyte 26, 28, 29, 30, 32, 34, 37, 39, 40, 42, 44, variety of chromophores, 383 113, 718 b-subunits, 378 formation, 114, 127 denaturation, 388 LC-MS/MS, 331 diagnostic characteristics, 399 ESI, 329 phytochromes, 378 outside thylakoid membranes, 524 regulation of tetrapyrrole, 390 slow-responding photoprotective carotenoid, subunits isolation, 393 524 used as labelling tool, 613 xanthophyll formation, 134 biliverdin (BV) b,ε-carotene, 15, 17, 35, 37, 39, 42, 126, 127, isolation procedure, 396 134, 720 biliverdin IXa, 382 formation, 114 biofuel b,c-carotene, 37, 42, 44, 126, 137, microalgae, 618 144, 722 biomass normalization, 449 b-carotene ketolase (BKT), 136 bio-optical algorithm, 546 g-carotene. See b,c-carotene regionally-specific, 567 ε,ε-carotene, 25, 724 bio-optical characteristics of phytoplankton, 496 c, c-carotene, See also lycopene bloom dynamics carotenogenesis, 113, 114 changes in bio-optical properties, 558 in cyanobacteria, 144

826 Index

carotenoid Chaetoceros sp. biosynthesis, 113 number of chloroplasts, 446 formation of cyclic carotenes, 126 chemometric methods degradation, 138 full spectrum techniques, 343 in algal resting spores, 611 multi-component analysis, 343 in eyespot, 611 chemotaxonomic marker, 56 in light-harvesting complexes of algae compared chemotaxonomic method, 262 to higher plants, 524 Bayesian compositional estimator (BCE), 264 LC-MS CHEMTAX, 262 APCI and ESI, 329 cluster analysis, 289 FAB ionisation, 329 environmental data, 289 ionisation methods, 329 excel solver, 262 LC-MS/MS, 330 flow cytometry and flowCAM, 289 photodegradation fluorometry, 289 in cyanobacteria, 144 interpretation of pigment data, 289 photoprotective, 247, 294, 445, 497 inverse simultaneous equation, 262 fast responding, 524 microscopy, 289 light-harvesting function, 524 multiple linear regression, 262, 290 quantum yield of photosynthesis, 509 productivity data, 289 slow responding, 524 remote-sensing data, 289 photosynthetic, 247 chemotaxonomy sediment samples, 334 comparison with microscopy, 297 synthesis, 119 problem with symbiotic associations, 298 carotenoid cleavage oxygenases (CCO), 139 quantitative analysis, 257 CCD1 subfamily, 143 CHEMTAX, 56, 259, 262, 264, 618 NSC1 or NosCCD, 144 assumptions and constraints, 265 NSC3, 144 comparison with microscopy, 299 carotenol chlorin esters, 328 comparison with other techniques, 301 Carteria sp., 39 comprehensive analysis, 291 Case I waters, 547 depth strata, 290 Case II waters, 547, 555, 556, 567 Dictyochophyte, 293 CDOM Emiliania huxleyi, 294 determination using absorption gyroxanthin diester, 563 spectroscopy, 519 minimum number of samples, 290 determination using liquid waveguide nutrient responses, 296 spectrophotometers, 519 optimum solution, 288 exponential slope (S), 519 pigment ratios, 265, 291 map of global distribution, 521 in field and algal cultures, 293 Sargasso Sea, 520 variability, 292 solar bleaching, 520 preliminary run, 291 terrestrial origin, 520 ratio limit matrices, 291 cell wall, 13, 14, 17, 20, 22, 26, 28 sub-grouping, 290 dithiothreitol weakening effect, 370 Chlamydomonas reinhardtii, 119, 121, 124, 125 murein, 13 bkt gene, 136 peptidoglycan, 16 CCO genes, 140 silica, 20 genome, 130 cellulose plate, 17, 23, 30, 37 zeaxanthin epoxidase, 132 cellulose wall, 42 Chlamydomonas sp., 39 Ceratium sp., 565 lutein-based xanthophyll cycle, 450 Chaetoceros brevis chlorarachniophyte, 9, 38, 40 xanthophyll cycle cyst, 40 UV effect, 457 Chlorella fusca, 119 UV inhibition, 457 Chlorella protothecoides, 616 Chaetoceros muelleri, 616 Chlorella sp., 39 pigment ratio Chlorella vulgaris,43 nutrient limitation, 295 chlorin, 79

Index 827

chlorin steryl ester chlorophyll a-chlorophyll b protein complexes, 523 HPLC pigment analysis, 182 chlorophyll a-chlorophyll c protein complexes, 523 Chlorobium phaeobacteroides chlorophyll a-chlorophyll c-peridinin protein HPLC pigment analysis, 183 (ACP), 447 LC-MS/MS, 326 chlorophyll allomers Chlorobium sp., 89 influence on spectrofluorometric methods, 361 Chlorobium tepidum chlorophyll a-specific LC-MS/MS of chlorophyll and absorption, 448 bacteriochlorophyll, 329 absorption coefficient, 508 Chloroflexus sp., 89 chlorophyll b, 38, 39, 80, 259, 540, 682 chloromonad, 26, 28 formation, 98 Chlorophyceae, 38, 42 HPLC separation, 171 Chl b-containing phytoplankton, 497 LC-MS/MS, 322 chlorophyll separation from divinyl chlorophyll b, 170 allomerization, 629 spectrofluorometric methods biodegradation, 78 NNLS, 358 biosynthesis, 78, 92, 611 spectrofluorometry compared with HPLC, 359 degradation, 99, 612 chlorophyll, b0, 684 extraction method chlorophyll b-containing algae DMF or DMSO, 368 energy regulation mechanisms, 448 formation, 89 chlorophyll c, 6, 15, 20, 28, 32, 35, 37, 56, 79, 80, LC-MS/MS, 322 101, 174, 259, 540 monomeric solutions absorption spectrum, 79 labile character, 366 algal groups containing, 497 partial least squares analysis, 352 degradation in autosampler, 631 phytochlorin-type function, 79 absorption bands, 81 LC-MS, 314 ring E ESI, 321, 323 hydratase pathway, 94 spectral overlap with phycobiliproteins, 399 spectrophotometric data, 81 structure, 79 structure, 78, 81 chlorophyll c1, 259, 686 transmetalation HPLC separation, 174 pollution, 612 chlorophyll c1-like K. foliaceum-type, 20 transmetallated, 81 chlorophyll c1-MGDG, 259 chlorophyll a, 80, 676 chlorophyll c2, 259, 688 alkyl sulphide derivative non polar, 80 Antarctic lake sediment, 328 chlorophyll c2-like Pavlova gyrans-type, 20, 260 concentration retrieval algorithm, 549 chlorophyll c2-MGDG [14:0/14:0], 34, 37, 95, 259 epimers, 101 chlorophyll c2-MGDG [18:4/14:0], 34, 95, 259, 690 extraction problems, 631 chlorophyll c3, 20, 22, 34, 95, 96, 100, 259, 290, 565, 692 fluorescence harmful algae classes, 566 quantum yield, 512 HPLC separation, 171, 174 quenching processes, 513 in HAB classes involved in fish mortality, 565 in vitro fluorescence, 512 LC-MS/MS, 324 auto-fluorescence, 512 multivariate spectrofluorometric method, 353 in vivo fluorescence, 497, 512 Pseudochattonella verruculosa, 545 excitation spectra, 514 satellite monitoring of Emiliania huxleyi, 564 rapid changes in picoeukaryotes spectrofluorometric methods, 356 photoprotection, 455 spectrofluorometry compared with HPLC, 359 separation from divinyl chlorophyll a, 170 wavelength targeting, 557 solar-stimulated fluorescence, 555 chlorophyll c3 (CS-170), 95, 100, 259 specific absorption coefficient, 518 chlorophyll c-containing algae chlorophyll a oxidase, 612 energy regulation mechanisms, 448 chlorophyll a:C ratio, 449 chlorophyll c-containing phytoplankton functional chlorophyll a0 types C-132 epimer of Chl a, 101, 680 optical discrimination, 569

828 Index

chlorophyll c-MGDG esters, 170 Chrysocystis sp., 25 chlorophyll concentration from ocean colour chrysolaminarin, 20, 23, 25, 29, 33 semi-analytical technique, 521 Chrysophyceae, 5, 22, 23, 24, 26, 28, 29, 30, chlorophyll cycle, 98, 99 See also chrysophyte chlorophyll d, 14, 15, 81, 101, 102, 609, 610, 694 Chl c-containing phytoplankton, 497 chlorophyll f, 102, 610 xanthophyll cycle, 450 chlorophyll oxidation products chrysophyte, 9, 22, 23, 26, 29, 260, 540 LC-MS/MS, 328 conversion of xanthophyll-cycle chlorophyll synthase, 99 pigments, 134 chlorophyllase phytoplankton functional types, 543 HPLC method, 179 pigment markers, 259 chlorophyllide, 80, 88, 356 qE and xanthophyll cycle, 453 LC-MS xanthophyll cycle, 131 MALDI, 317 Cladophora rupestris chlorophyllide a, 696 chlorophyll extraction, 370 esterification, 99 climate and environmental change, 619 influence on spectrofluorometric methods, 361 cobalamine, 90 chlorophyllide a oxygenase (CAO), 97 coccolith, 32, 33 chlorophyllide b, 698 backscattering, 521 esterification, 99 free during post-bloom phase, 564 formation, 97, 98 from MODIS satellite monitoring, 561 chlorophyllide reductase, 611 light scattering, 519 Chlorophyta, 5, 38, 42, 43, See also satellite monitoring of Emiliania huxleyi, 564 chlorophyte scattering, 508 bio-optical discrimination, 540 coccolithophore, 617 state transitions, 447 high scattering chromophytes, 569 chlorophyte, 9, 42, 119, 259, 260, 540 Coccolithophyceae, 33, See also coccolithophyte, genome See also Prymnesiophyceae MEP and MVA pathways, 119 Chl c-containing phytoplankton, 497 pigment markers, 258, 259 coccolithophyte qE and xanthophyll cycle, 453 harmful algae, 566 qE mechanism model, 453 phytoplankton functional types, 543 state transition, 515 coenzyme-F430,90 xanthophyll cycle coloured or chromophoric dissolved organic matter UV effect, 457 (CDOM), 427, 497, 519, 546, 547, 555, zeaxanthin, 262 See also CDOM chloroplast from MODIS, 561 changes associated with photo-acclimation, 446 influence on pigment ratios, 296 chlororespiration commercial suppliers of pigments, 658 xanthophyll cycle, 452 comparative genomics, 119, 140, 144, 615 Chl-synthase continuous flow-FAB, 315 chlG gene, 99 coproporphyrin I, 90 Chondrus crispus coproporphyrinogen I and III, 90 mycosporine-like amino acids, 425 coproporphyrinogen III Chromadex, 659 formation, 91 Chromalveolata, 5, See also chromalveolate algae core-membrane linker, 376 chromalveolate algae, 126, 127, 144, 611 cosmetic sector conversion of xanthophyll-cycle pigments, 134 microalgae, 618 violaxanthin, 132 crocoxanthin, 35, 742 xanthophylls, 128 LC-MS/MS Chromatium sp., 89 APCI, 331 Chromophyta. See also chromophyte cross-sectional area of PSII and PSI, 448 bio-optical discrimination, 540 Cryptophyceae chromophyte, 5, 6, 45, 79, 259, 569 Chl c-containing phytoplankton, 497 evolution, 9 Cryptophyta, 5, 34, 40, See also Chrysochromulina sp. cryptophyte pigment markers, 259 characteristics, 34

Index 829

cryptophyte, 9, 16, 35, 260, 540, 562 variable absorption spectra of endosymbionts, 37 phycobiliproteins, 399 mycosporine-like amino acids, 418 with chlorophyll d, 610 phycobiliprotein-containing phytoplankton, xanthophyll cycle, 455 497 xanthophyll formation, 137 phycobiliproteins, 375, 378 xanthophylls, 128, 129 light-harvesting, 391 zeaxanthin, 262 radiative excitation energy transfer, 525 b,ε-carotene, 126 pigment markers, 258 cyanobacteria bloom cryptoxanthin, 15, 16, 744 remote-sensing, 567 Cyanidioschyzon merolae, 121, 124, 130 cyanobacteriochrome, 613 Cyanidium caldarium, 130 Cyanophora sp., 16 Cyanidium sp., 18, 89 Cyanophyta. See cyanobacteria cyanobacteria, 13, 14, 20, 38, 114, 119, 127, 138, cyclic carotenoid 260, 540, 562, 569, 617 formation, 126 4-keto-myxoxanthophyll, 299 cyclic electron flow abscisic acid, 139 ATP formation, 523 aromatic carotenoids, 128 b-cyclocitral, 143 biosynthesis of carotenoids, 114 Cyclotella meneghiniana carotenoid biosynthesis, 137 xanthophyll formation, 134 characteristics, 12, 13 cyst formation CrtR-enzymes, 129 induced by abscisic acid, 139 detection using hyperspectral imagers, 561 cytochrome P450 formation of lycopene, 124, 125 Synechocystis sp., 142 free phycobilin chromophores, 383 cytochrome P450 enzyme, 143 Gauss-peak spectra method, 350 genes involved in carotenoid biosynthesis, 127, D1 protein, 514 128, 136 Danish Hydraulic Institute (DHI), 658 genomes, 138 dark protochlorophyllide oxidoreductase harmful algae, 566 photosynthetic bacteria, 97 isopentenyl diphosphate isomerases, 120 bchB, bchL and bchB genes, 97 LPOR, 96 de-epoxidation state index, 459 lycopene cyclases, 126 dehydroxylusujirene, 417 MEP pathway, 124 1-deoxy-D-xylulose 5-phosphate, 120 mycosporine-like amino acids, 417, 425 1-deoxy-D-xylulose 5-phosphate reductoisomerase novel pigments, 609 (DXR), 120 phycobiliprotein-containing phytoplankton, 497 1-deoxy-D-xylulose 5-phosphate synthase (DXS), phycobiliproteins, 375 119, 120 light-harvesting, 389 Diacronema sp., 33 radiative excitation energy transfer, 525 diacylglycerol, 100 phycobilisome pigmentation, 385 diadinochrome, 746 phycochromes, 613 diadinoxanthin, 20, 22, 24, 25, 26, 30, 32, 34, 37, 39, phycoerythrin, 378 132, 135, 144, 260, 290, 447, 524, 748 phycourobilin, 384 changes with irradiance, 294 phytoene desaturase genes, 125 formation, 134 phytoplankton functional types, 543 influence on PSII fluorescence, 518 pigment markers, 258, 259 slow-responding photoprotective carotenoid, 524 pigment ratios, 299 xanthophyll cycle, 450 PS I diadinoxanthin de-epoxidase (DDE) chlorophyll a epimers, 101 xanthophyll cycle, 451 qE and xanthophyll cycle, 453 diadinoxanthin xanthophyll cycle, 131 state transition, 515 diatom, 9, 18, 19, 20, 22, 38, 133, 260, 458, symbiotic, 13 540, 617 symbiotic in dinoflagellates, 9 abscisic acid, 139 terrestrial Antarctic mycosporine-like amino acids, 417 mycosporine-like amino acids, 425 UV-B photoreceptor, 425 biomass, 299

830 Index

diatom, (cont.) compared with carbon labelling, 481 centric, 20 drawbacks, 483 endosymbionts, 37 nonlinear model, 479 within foraminifera and dinoflagellates, 20 dimethyl sulphide, 33, 617 freshwater algae, 20 dimethyl sulphide producers genome, 611 phytoplankton functional types, 543 harmful algae, 565 dimethylallyl diphosphate, 119 low scattering chromophytes, 569 dinoflagellate, 9, 35, 260, 540, 617 MEP pathway, 124 chlorophyll-specific absorption coefficient, 509 PDS genes, 125 conversion of xanthophyll-cycle pigments, 134 pennate, 20 cyst, 37 phytoene desaturase genes, 125, 126 grazing impact on algal blooms, 482 phytoplankton functional types, 543 green plastids, 9 pigment markers, 259 ketocarotenoids, 137 pigment ratio mycosporine-like amino acids, 418 irradiance, 294 phytoplankton functional type, 543 qE and xanthophyll cycle, 453, 454 pigment markers, 258, 259, 260 sea ice, 20 pigment types, 35 seasonal succession plastid replacements, 9 xanthophyll cycle, 455 pyrrhoxanthin and peridinin, 133 transcriptomic and metabolomic qE and xanthophyll cycle, 453 approaches, 614 symbiotic, 35 tropical, 20 toxic algae violaxanthin, 132 gyroxanthin esters, 56 xanthophyll cycle, 131 pigment markers, 259 de novo synthesis of diatoxanthin, 453 toxic/harmful algae no UV effect, 457 mycosporine-like amino acids, 428 UV inhibition, 457 xanthophyll cycle, 131, 450 UV-B stimulation, 456 UV effect, 457 zeaxanthin epoxidase, 132 dinoflagellate diatoxanthin, 20, 22, 24, 25, 26, 30, 32, 34, 37, 39, pigment markers, 259 132, 260, 290, 448, 524, 750 Dinophyceae. See also dinoflagellate changes with irradiance, 294 Chl c-containing phytoplankton, 497 co-elution problem, 202 Dinophysis norvegica, 37, 565 daytime increase, 459 Dinophyta, 35, 37 influence on PSII fluorescence, 518 characteristics, 37 potential antioxidant, 456 dinoxanthin, 37, 135, 260, 754 relationship with fluorescence quenching, 453 diode array detection (DAD) UV effects, 458 analysis of mycosporine-like amino xanthophyll cycle, 450 acids, 431 diatoxanthin accumulation dithiothreitol xanthophyll cycle chlorophyll extraction high light exposure, 452 weakens cell walls, 370 diatoxanthin epoxidase Ditylum brightwellii UV-B stimulation, 457 pigment ratios, 296 xanthophyll cycle, 452 divinyl chlorophyll (DVChl), 101 Dictyocha sp., 24 HPLC separation, 173 Dictyochophyceae, 5, 22, 23, divinyl chlorophyll a, 15, 170, 540, 700 See also dictyochophyte co-elution problem, 202 Chl c-containing phytoplankton, 497 spectrofluorometric methods, 356 dictyochophyte, 540 divinyl chlorophyll aþb-containing phytoplankton harmful algae, 566 functional types dihydrolutein, 134, 752 optical discrimination, 569 dihydroxysterol, 32 divinyl chlorophyll b, 170, 540, 702 dilution method Dixoniella sp., 18 assumptions, 477 dry ice combined with HPLC pigment analysis, 479 sample freezing and storage, 628

Index 831

Dunaliella salina Eustigmatos sp., 25 b,b-carotene accumulation, 524 eutreptiellanone, 39, 259, 758 Dunaliella sp., 39, 42 Exanthemachrysis gayraliae Dunaliella tertiolecta chlorophyll c1-like, 170 xanthophyll cycle Exanthemachrysis sp., 33 UV inhibition, 457 Excavata, 5 extinction coefficient. See absorption coefficient echinenone, 13, 15, 127, 130, 136, 144, 756 chlorophyll a and b, 366 Ectocarpus siliculosus, 124 extraction solvent, 628 effective absorption cross section of PSII, 448 acetone/water, 629 efficiency factor dimethyl formamide (DMF), 629 for absorption (Qa), 500 for periphyton, 629 for attenuation (Qc), 500 methanol/acetone/DMF/water, 629 for scattering (Qb), 500 water dilution prior to injection, 629 eicosapentaenoic acid, 26, 28 eyespot, 24, 29, 32, 39, 42, 43, 44, 142 Emiliania huxleyi, 121, 124, 569 carotenoids accumulation, 524 190-hexanoyloxy-4-ketofucoxanthin, 170 diatoxanthin farnesol, 78, 99, 101, 325 UV-B-induced loss, 457 fast repetition rate fluorometry (FRRF), 484, 485, fucoxanthin esters 518, 566 LC-MS/MS, 332 comparison with 14C-uptake, 485 pigment markers, 259 fatty acids, 28, 80, 100 satellite monitoring, 564 Fibrocapsa japonica,28 strains from Southern Ocean, 618 filter xanthophyll formation, 134 comparison between different types, 627 empirical algorithm size categories, 628 for chlorophyll determination from filter extraction remote-sensing, 552 grinding, 630 endosymbiosis, 4, 9, 114, 124, 126 soaking, 630 plastid evolution, 11 sonication, 630 Euglena gracilis, 88, 120, 125 filtration photosynthesis inhibition by metals, 613 clogging, 627 Euglena sp. maximum time, 627 Gauss-peak spectra method, 350 positive pressure, 628 Euglenophyceae. See also euglenophyte recommendations, 627 Chl b-containing phytoplankton, 497 flash-freezing, 628 euglenophyte, 9, 38, 39, 40, 540 Flintiella sp., 18 ketocarotenoid, 136 Florenciella parvula,24 pigment markers, 259 flow cytometry, 508 qE and xanthophyll cycle, 453 FlowCAM, 300 Euhalothece sp. Fluka, 659 mycosporine-like amino acids, 417 fluorescence euhalothece-362, 417 excitation-emission matrices (EEM), 344 Euphausia superba pigment analysis, 344 mycosporine-like amino acids in situ trophic transfer, 426 detection with active sensors, 555 euphotic zone spectral signatures, 556 apparent optical properties, 546 three-dimensional spectroscopy, 344 European Ferrybox sensor system, 561 fluorescence excitation spectrum Eustigmatophyceae, 18, 23, 24, 28, chlorophyll a-specific PSII-scaled, 518 See also eustigmatophyte in situ detection eustigmatophyte, 24, 26, 29 best for Case II waters, 555 conversion of xanthophyll-cycle distinct signatures from different pigment pigments, 134 groups, 566 pigment markers, 259 in vivo detection xanthophyll cycle, 131 general set-up, 515 UV-B stimulation, 456 quantum correction, 516

832 Index

fluorescence excitation spectrum (cont.) gilvin, 519, See coloured or chromophoric dissolved PSII-specific, 517 organic matter (CDOM) quantum correction, 515 Glaucocystis sp., 16 fluorescence line height, 555 Glaucocystophyta, 11, 16, 45, in turbid waters, 556 See also glaucocystophyte limitations of the method, 555 glaucocystophyte, 9, 16 Fluoroprobe, 300 phycobiliproteins, 375 fouling problems phycobilisome pigmentation, 385 in moorings, 558 Glaucophyta, 4 freeze-drying. See lyophilization Glaucosphaera sp., 18 freshwater algae, 23 gliders, 559, 567, 617 chlorophytes, 42 bio-optical instruments, 558 cryptophytes, 34 global ocean observation systems, 617 cyanobacteria, 13, 14 Gloeobacter violaceus, 121, 125, 159 diatoms, 20 Gloeochaete sp., 16 dinoflagellates, 37 glucans euglenophytes, 39 in Chaetoceros muelleri extraction problems, 369 using HR-MAS-NMR, 616 Glaucocystophyta, 16 glutamyl-tRNAGlu-reductase, 88 glaucocystophytes, 11, 16 glycoside carotenoids harmful, 566 myxoxanthophyll, 56, 129 mesostigmatophytes, 11, 44 oscillaxanthin, 56 mycosporine-like amino acids, 417 golden-brown algae, 5, 32, 33 Pavlovophyceae, 32 grazing rate phaeothamniophytes, 11, 26 coupling with growth, 482 prasinophytes, 43 pigment-based method, 472 prochlorophytes, 14 green algae, 4, 38, 114, 127, 130 raphidophytes, 28 abscisic acid, 139 silicoflagellates, 23 genes involved in biosynthesis, 127 synurophytes, 29 phytoene desaturase genes, 126 Trebouxiophyceae, 43 symbiosis, 38 xanthophytes, 30 xanthophyll cycle, 131 fucoxanthin, 6, 20, 22, 23, 24, 25, 26, 28, 29, 32, 34, xanthophylls, 128 37, 56, 133, 144, 259, 290, 448, 760 b,ε-carotene, 126 biosynthesis, 611 green fluorescent protein (GFP), 613 co-elution problem, 202 green photosynthetic bacteria, 79, 81, 101 formation, 134, 135 Gymnodinium breve (=Karenia brevis), 37, 259, 507 LC-MS/MS Gymnodinium chlorophorum,38 APCI and ESI, 332 Gyrodinium dorsum ESI, 330 induction of mycosporine-like amino acids, 425 fucoxanthin esters, 314, 614 mycosporine-like amino acids fucoxanthin-containing dinoflagellates, 563 motility, 417 fucoxanthinol gyroxanthin diester, 25, 37, 259, 762 LC-MS/MS, 332 HPLC and CHEMTAX, 563 in haptophytes, 618 gabaculine, 87 in pelagophytes and haptophytes, 563 Galdieria sulphuraria, 121, 124, 130 in situ detection of Karenia brevis, 562 phycobilisome pigmentation, 385 LC-MS/MS, 332 gelbstoff, 519, See coloured (chromophoric) mean cellular concentration in Karenia brevis, 563 dissolved organic matter (CDOM) toxic dinoflagellate, 299 genomics, 614 gyroxanthin-containing K. brevis geranial, 143 in vivo absorption characteristics, 563 geranylgeraniol, 78, 99, 101, 119 geranylgeranyl diphosphate synthase (GGPS), Hacrobia, 35 124 haem, 81, 88, 89, 92, 396 GF/F filters Haematococcus pluvialis, 130, 135 limitations, 627 Haematococcus sp., 39, 42

Index 833

haptonema, 31, 33, 34 HPLC analysis Haptophyta, 5, 6, 22, 30, 32, 33, 56, performance metrics, 197 See also haptophyte pigments pigment groups, 449 update on methods, 165 xanthophyll cycle, 450 HPLC autosampler, 640 haptophyte, 9, 31, 32, 35, 260, 540, 617 needle blockage, 642 conversion of xanthophyll-cycle needle height, 642 pigments, 134 needle rinse option, 643 endosymbionts, 37 needle-in-loop design, 641 gyroxanthin diester, 259 pull-to-fill design, 641 gyroxanthin esters, 56 push-to-fill design, 641 ketocarotenoids, 136 syringe size, 641 mycosporine-like amino acids, 418, 425 temperature controlled sample tray, 643 pigment markers, 259 HPLC calibration xanthophyll cycle, 131 detector UV-B stimulation, 456 linear response, 645 zeaxanthin epoxidase, 132 HPLC column compartment Haramonas dimorpha,29 temperature-controlled, 647 harmful algae HPLC detectors, 644 pigment signature and toxin information, 565 fluorescence, 644 harmful algal blooms, 25, 26, 28, 582 temperature-controlled flow cell, 647 detection using hyperspectral imagers, 561 UV/visible, 644 in vivo absorption spectra HPLC hardware, 636 specific pigments, 563 HPLC injector, 640 optical monitoring, 538 filled-loop mode, 640 phytoplankton species, pigments and toxins, 583 partial-loop mode, 640 UV absorption, 428 HPLC method harmful coccolithophytes accuracy, 199, 220 wavelength targeting accuracy assessment, 214 chlorophyll c3, 557 ammonium acetate buffer, 174 harmful dinoflagellates bacteriochlorophyll analysis, 182 wavelength targeting C18 column, 170, 182, 222 chlorophyll c3, 557 combined monomeric and polymeric, 181 heliobacteria, 81 polymeric, 175, 180 Heliospirillum sp., 89 C30 column, 170 0 19 -heptanoyloxyfucoxanthin, 170 C8 column, 170, 173, 180, 222 LC-MS/MS, 333 divinyl chlorophylls, 180 190-hexanoyloxy-4-ketofucoxanthin, 170, 260, 618, 766 calibration, 211, 249 LC-MS/MS, 332 multipoint method, 249 190-hexanoyloxyfucoxanthin, 32, 34, 37, response factor, 249 259, 764 single point method, 249 co-elution problem, 202 calibration accuracy, 231 formation, 134 carryover between injections, 202, 203, 229, 640 LC-MS/MS, 332 autosampler, 642 Heterocapsa sp. choice of method, 176 pigment ratios, 296 choice of stationary phase, 170 Heterokontophyta, 18, 20, 22, 23, 24, 25, 26, 28, 29, column polarity, 173 30, 35 column strength, 173 xanthophyll cycle, 450 column temperature, 170, 175 heteroxanthin, 26, 30, 259 control limits (CL), 226 high light stress coupling to mass spectrometry (MS), 182 bkt genes, 135 detector noise, 204, 233 high resolution magic angle spinning nuclear filter water content, 234 magnetic resonance spectroscopy (HR- injection contamination, 203 MAS-NMR), 614 injection precision, 229 whole cell characterisation, 615 intercalibration, 196 HPLC. See also liquid chromatography (LC) internal standard, 215, 227, 231, 233, 234

834 Index

HPLC method (cont.) hyperspectral ion-pairing, 174 imagers, 616, 617 limit of detection, 201 optical sensors, 616 limit of quantitation, 201 remote-sensing reflectance microphytobenthos, 181 best wavelengths, 568 peak resolution, 202 hyperspectral absorption data peak retention time, 202 regional algorithms, 557 performance metrics, 197, 224 performance parameter, 201 ice algae pigment resolution, 202, 227 PSII absorption, 512 polymeric phases, 170 xanthophyll cycle precision, 218 UV effect, 457 pyridine additive, 175 in situ optical sensors, 554 quality assessment (QA), 195, 226 Algae Online Analyser, 556 quality assurance plan (QAP), 195, 226 incubation artifacts, 476 quality control (QC), 195, 226 Indian Ocean quaternary ammonium buffer, 174 mixing velocities repeatability precision, 216 xanthophyll cycle, 460 reproducibility precision, 216 inherent optical properties (IOP), 545, 549 retention time precision, 227 integrating cavity absorption meter (ICAM), 505 reversed-phase, 165 internal standard, 250, 251 role of particle pore size, 171 intracellular self-shading, 446 ruggedness, 216 ionone specificity, 201 formation, 126 stationary phase b-ionone, 126, 130, 143 monomeric, 170 formation, 143 polymeric, 170 ε-ionone, 126, 127, 130 summary, 170 iron limited environments, 614 symbology, 243 irradiance reflectance, 549 tetrabutylammonium acetate buffer, 175 Isochrysis sp. validated method, 197 ketocarotenoids, 136 validation, 198 isopentenyl diphosphate, 119 vial and cap combination, 217 isoprene warning limits (WL), 226 formation, 113, 114 water retained on filters, 251 formation pathways, 119 working and linear ranges, 206 isoprenoid biosynthesis HPLC pump, 643 MEP pathway, 119 binary system, 643 compensation for solvent compression, 644 Joint Global Ocean Flux Study (JGOFS) dwell time, 644 program, 218 dwell volume, 644 protocols, 196 gradient elution, 643 high-pressure mixer, 643 Karenia brevis low-pressure mixer, 643 gyroxanthin diester, 299 quaternary system, 643 nitrogen starvation solvent mixer, 643 mycosporine-glycine, 426 HPLC training resources, 648 similarity index, 507 1H HR-MAS-NMR Karenia cristata, 565 to sort algal species, 616 Karenia sp., 565 2-hydroxymyxoxanthophyll, 138 Karlodinium sp., 565 30-hydroxyechinenone, 135, 136 fucoxanthin-containing, 618 Hydrolight software, 552 ketocarotenoid hydroxymethylbilane (HMB), 90 formation, 135 10-hydroxy-b,c-carotene, 137 in cyanobacteria, 135 81-hydroxy-chlorophyll a, 101 in dinoflagellates, 137 Hyperion in euglenophytes, 136 hyperspectral imager, 561 in green algae, 135

Index 835

in haptophytes, 136 linear-tetrapyrrolic bile pigments Isochrysis sp., 136 phycobilins, 81 Nannochloropsis sp., 136 Lingulodinium polyedra protection from oxidative damage, 135 excretion of mycosporine-like amino ketolase acids, 427 in chlorophytes, 137 harmful algal bloom in chromalveolate algae, 137 UV absorption, 428 in cyanobacteria, 137 lipids 4-keto-190-hexanoyloxyfucoxanthin, 137 using time-domain NMR, 616 4-keto-190-hexanoyloxyfucoxanthin. liquid chromatography-mass spectrometry. See 190-hexanoyloxy-4-ketofucoxanthin See LC-MS 4-ketofucoxanthin, 34, 137, 260 liquid chromatography-nuclear magnetic 4-ketolutein, 136 resonance. See LC-NMR 4-keto-myxoxanthophyll, 13, 259, 299 liquid nitrogen, 628 4-keto-a-carotene, 130 liquid waveguide capillary cell (LWCC), 505 loroxanthin, 40, 42, 43, 56, 134, 768 LC-MS dodecenoate, 40, 770 aquatic environment lower limit of linearity (LLOL) carotenoids, 334 pigment calibration, 206 chlorophylls, 328 lutein, 40, 42, 44, 127, 128, 130, 133, 134, 171, atmospheric pressure chemical ionisation 259, 290, 772 (APCI), 315 co-elution problem, 202 collision induced dissociation (CID), 330 eye-related health care, 619 electrospray ionisation (ESI), 316 HPLC separation, 173 fast atom bombardment (FAB), 315 LC-MS/MS, 330 mass analyser, 318 slow-responding photoprotective carotenoid, ion trap, 319 524 quadrupole, 318 lutein-epoxide, 134 time of flight (TOF), 319 xanthophyll cycle, 450 triple quadrupole, 318 lutein-epoxide cycle matrix-assisted laser desorption ionisation xanthophyll cycle, 131 (MALDI), 317 lycopene, 44, 125, 126, 127, 137, 726 methods for analysis of chlorophylls, 320 accumulation, 126 modes of ionisation, 315 formation, 114, 124 sodiated molecule, 330, 332 trans-lycopene, 126 LC-NMR, 615 lycopene cyclase, 127 analysis of carotenoids, 614 lyophilization (freeze-drying), 630 LC-tandem mass spectrometry, 315 advantages, 630 light absorbed by PSII sediment samples, 631 variation with photoacclimation, 515 light energy transfer efficiency, 448 magic angle spinning (MAS), 614, 615 light history Mallomonas sp., 29, 30 photoresponse dynamics, 455 Mamiellophyceae, 39, 43 light-harvesting antenna, 101 Mantoniella squamata, 134 light-harvesting complexes, 446 mariculture, 25 apoproteins, 522 marker pigments in algae, 522 to distinguish algal classes, 540 in chromophytes, 447 mass spectrometry variable composition, 523 compatibility with HPLC methods, 320 water-soluble, 525 in situ methods, 545 light-harvesting pigments (LHP), 445, 497 instrument, 315 light-harvesting xanthophyll Mastigocladus laminosus formation, 133 phycobilisome pigmentation limit of detection (LOD), 201 absorption spectrum, 385 determination, 204 Matrix-Assisted Laser Desorption Ionisation – limit of quantitation (LOQ), 201 Time of Flight (MALDI-TOF), 614 determination, 204 whole cell characterisation, 615

836 Index

maximum quantum yield of PSII-fluorescence, mooring 513 platform for bio-optical measurements, 558 Mediterranean Sea, 22, 286 profiling for bio-optical constituents, 558 mixing velocities mucocyst, 28 xanthophyll cycle, 460 multivariate spectral method, 348 MEP pathway classical least squares (CLS), 344 genes, 120, 124 non negative least squares (NNLS), 344 MERIS parallel factor analysis (PARAFAC), 344 satellite sensor, 549 partial least squares regression (PLS), 344 mesobiliverdin (MBV) principal component regression (PCR), 344 cryptophyte chromophore, 382 spectral reconstruction method (SRC), 348 Mesodinium rubrum, 35, 258 Muriella (Chlorella) zofingiensis, 136 Mesostigmatophyceae, 38, 44, 45, mutatoxanthin, 780 See also mesostigmatophyte mycosporine-2-glycine, 430 mesostigmatophyte, 44, 45 mycosporine-glycine, 412, 417, 424 metabolomics, 614, 619 antioxidant, 418 methanol mycosporine-like amino acids (MAAs), 412 degradation effects, 629 bacterial degradation, 429 methylerythritol phosphate (MEP) pathway, 119 bio-optical studies, 428 6-methyl-5-hepten-2-one, 143 biosynthesis, 424 mevalonic acid (MVA) detection, 430 pathway, 119 distribution, 418, 424 Mg2þ electrospray ionization (ESI), 431 enzymic insertion into proto IX, 92 extra-cellular release, 427 MGDG extraction from filters, 429 formation, 100 extraction from freshwater algae, 429 MgDVP, 13, 15, 20, 24, 32, 33, 35, 37, 39, 42, 43, 95, filtration problems, 428 96, 259, 704 HPLC methods, 430 formation of chlorophylls c,95 induction, 425 light harvesting, 95 interference with in vivo absorption, 504 Mg-protoporphyrin IX, 88 LC-MS, 431 formation, 92, 93 nitrogen limitation, 426 Mg-rhodochlorins osmotic stress, 426 formation from chlorophyll, 369 packaging, 418 micromonal, 43, 134, 258, 259, 774 photodegradation, 427 Micromonas pusilla, 56, 259 photoprotection, 417 Micromonas sp., 39, 119 primary, 424 micromonol, 134, 144, 259, 776 roles, 417 microphytobenthos secondary, 424, 427 HPLC method, 181 stability of extracts, 429 microplankton standards, 432 pigment fraction, 248 storage of filters, 428 microscopy symbiotic acquisition, 426 for cell identification, 618 trophic transfer, 426 microzooplankton UV-absorbing intereferences, 430 grazing rate mycosporine-taurine, 417 dilution method, 477, 478 antioxidant, 418 role during algal blooms, 482 Myrionecta rubrum,35 Mie–Lorentz theory, 500 myxol, 13, 127, 129 mobile underwater platforms, 559 myxoxanthophyll, 13, 56, 127, 129, 136, 137, moderate resolution imaging spectroradiometer 144, 782 (MODIS), 200, 484 formation, 126, 137 optically-based products, 561 heat dissipation in cyanobacteria, 454 satellite sensor, 549 monadoxanthin, 35, 778 Nannochloropsis oculata,25 monogalactosyldiacylglyceride (MGDG), 80 Nannochloropsis sp. monovinyl chlorophyll c3, 170, 260, 706 ketocarotenoids, 136

Index 837

Nannochloris atomis optical properties extraction problems, 369 absorption, 547 nanoplankton, 25, 30, 33 of particles, 497 chemotaxonomic method, 297 of seawater, 545 pigment based size class, 261 phytoplankton functional types, 540 pigment fraction, 248 scattering, 547 NASA Sensor Intercomparison and Merger optically significant constituents (OSC), 545 for Biological and Interdisciplinary Orange Carotenoid Protein (OCP), 135, 136 Oceanic Studies (SIMBIOS), 196 oscillaxanthin, 13, 56, 137, 792 natural colourant formation, 137 carotenoids and phycobilins, 618 Ostreococcus lucimarinus, 121, 124, 125 90-cis-neochrome, 784 genome, 130 formation, 132 Ostreococcus sp., 119 in chlorarachniophytes, 133 Ostreococcus tauri, 121, 124, 125 in euglenophytes, 133 genome, 130 neoxanthin, 38, 39, 40, 42, 44, 135 oxygen action spectrum, 515 co-elution problem, 202 oxygenic gross photosynthetic rate (PChl a), 485 genes encoding neoxanthin synthase, 133 ozone layer, 412 trans-neoxanthin, 44, 663, 788 formation, 134 P-457, 37 90-cis-neoxanthin, 128, 133, 139, 786 Pacific Ocean, 22, 28 neoxanthin synthase, 133 phosphorus limitation, 295 neurosporene, 134 package effect, 446, 503, 547 nine-cis-epoxy carotenoid dioxygenase (NCED), 139 cell size, 503 nitrogen fixation photoacclimation state, 503 phytoplankton functional types, 543 palythene, 430 nitrogen limitation palythenic acid, 427, 430 bkt genes, 135 palythine-serine, 430 Nodularia spumigena PARAFAC, 344, 355, 362 pigment markers, 259 EEM fluorescence of pigment extracts, 355 non-photochemical fluorescence quenching Paralytic Shellfish Poisoning (PSP), 565 (NPQ), 446, 450, 456, 513 Parmales, 19, 22 energy-dependent (qE), 453, 513 pathlength amplification effect (‘b factor’), 504 photoinhibition (qI), 453, 513 Pavlova gyrans role, 453 chlorophyll c2-like, 170 state transitions (qT), 453, 513 Pavlova sp., 33 xanthophyll cycle, 453 xanthophyll cycle non-photochemical fluorescence quenching (qN), 513 UV inhibition, 457 non-polar chlorophyll c, 259 Pavlovale, 33 Nostoc (Anabaena) sp., 129 Pavlovophyceae, 5, 31, 32, 33 Nostoc flagelliforme characteristics, 32 UV-sensitivity, 418 Chl c-containing phytoplankton, 497 Nostoc sp., 129 Pelagococcus subviridis,25 apocarotenoid cleavage oxygenase, 140 Pelagomonas calceolata volatile isoprenoids formation, 144 18S RNA, 300 nostoxanthin, 13, 137, 138, 790 Pelagomonas sp., 6, 25 nuclear magnetic resonance (NMR), 615, 616 Pelagophyceae, 5, 22, 24, 25, See also pelagophyte nutrients pelagophyte, 18, 25 pigment ratios, 295 gyroxanthin diester, 259 nylon membrane gyroxanthin esters, 56 for sample filtration, 627 harmful algae, 566 pigment markers, 259 okenone, 128 xanthophyll cycle, 131 optical coefficients 190-pentanoyloxyfucoxanthin, 170 of algal suspensions, 502 LC-MS/MS, 332 optical detection of IOP and AOP performance metrics in situ sensors, 554 HPLC analysis, 197

838 Index

peridinin, 9, 35, 37, 38, 56, 133, 144, 258, 260, 448, photoprotective state 565, 794 pigment indicators, 459 Alexandrium sp., 565 photoreceptor co-elution problem, 202 phototaxis regulation, 390 formation, 134 phytochrome, 378 neoxanthin as intermediate, 135 synthesis of mycosporine-like amino acids, 425 peridinin-chlorophyll a-protein complexes (PCPs) photoreversible biliprotein, 613 in dinoflagellates photosynthetic electron transfer rates (ETR), 485 water soluble, 525 photosystem I (PSI) peridininol, 37 chlorophyll a epimers, 101 Phaeocystis phycobilin chromophore chlorophyll c3, 299 absorption maxima, 393 Phaeocystis antarctica attachment modes, 383 mycosporine-like amino acids biosynthesis, 382 trophic transfer, 426 extinction coefficients, 393 Phaeodactylum tricornutum, 20, 121, 124, 125, 611 extraction from biliproteins genes encoding for violaxanthin de-epoxidase, procedure, 397 452 HPLC conditions following tryptic genome, 131 digestion, 395 lycopene cyclase, 127 identification xanthophyll formation, 134 acidic urea denaturation, 393 Phaeogloea sp., 26 gel electrophoresis, 394 Phaeomonas sp., 28 LC isolation and MS, 394 Phaeothamnion sp., 26 isolation procedure, 395 Phaeothamniophyceae, 5, 22, 26, 28 mass spectrometry, 395 pharmaceutical sector quantitative analysis, 400 microalgae, 618 phycobilin chromophore attachment pheophorbide lyases, 383 cyclic form, 182 phycobiliprotein, 35, 375 formation, 99 absorption spectrum, 384 pyro derivatives, 182 variation with solvent conditions, 388 pheophorbide a, 708 algal groups containing, 497 co-elution problem, 202 chromophore identification, 388 pheophorbide oxygenase, 99 complementary chromatic adaptation, 390 pheophytin, 101 conditions for dissociation, 392 partial least squares analysis, 352 core-membrane linker, 383 pheophytin a, 710 fluorescence spectroscopy, 399 pheophytin b, 712 fluorescence spectrum photoacclimation, 445 self-absorption, 392 bio-optical characteristics, 496 future studies, 613 light history, 449 hexamers, 376 long-term, 446 influence of light quality in marine species, 381 pigment ratios, 295 interference by fluorescence, 391 photoacclimation index, 449 interference with phytoplankton photoadaptive strategies absorption, 505 dinoflagellates light-harvesting function, 389 PCP, 525 low phototoxicity, 390 photochemical activity of PSII, 485 monomers, 376 photochemical efficiency (Fv/Fm) nitrogen source, 390 relation with xanthophyll cycle, 456 radiative excitation energy transfer, 525 photochemical fluorescence quenching (qP), 513 reconstitution from chromophores and photo-damaged photosystem II apoproteins, 398 repair promoted by abscisic acid, 139 spectral fluorescence signature method, 556 photodiode array HPLC detector (PDA), 644 spectrophotometric analysis, 399 photoprotection spectral overlap with carotenoids, 399 xanthophyll cycle, 131 spectroscopy tips, 391 photoprotection pigments, 445 structure, 376

Index 839

phycobiliprotein-containing algae phytol chain, 99, 119 bio-optical discrimination, 540 phytoplankton energy regulation mechanisms, 448 absorption spectra imbalance between PSII and PSI, 515 retrieval approach, 521 optical discrimination of functional backscattering coefficient, 505 types, 569 community structure state transitions, 515 from patterns of optical properties, 521 phycobilisome, 13, 16, 17, 35, 376 dynamics, 461 assembly, 376 food quality, 483 dissociation conditions, 392 in situ detection methods, 545 isolation conditions, 392 in vivo absorption fingerprints, 555 stabilized with phosphate buffer, 392 scattering properties, 505, 547 phycobilisomes-containing algae size spectra qE and zeaxanthin accumulation, 454 from semi-analytical optical approach, 522 phycochrome, 613 phytoplankton blooms phycocyanin, 14, 15, 16, 17, 35, 37, 525 in situ monitoring and remote-sensing absorption spectrum, 384, 399 techniques, 553 complementary chromatic adaptation, 390 phytoplankton functional types (PFT), 261, 301, spectroscopy, 384 540, 617 phycocyanin (PC), 378 relationship with pigment-specific algal phycocyanobilin (PCB), 381 groups, 543 isolation procedure, 395 phytoporphyrin, 79 phycoerythrin, 14, 15, 17, 35, 37, 377, 383, 525 picoeukaryote, 261 absorption spectrum, 384, 400 phytoplankton functional types, 543 complementary chromatic adaptation, 390 pico-haptophytes cyanobacteria, 378 DNA sequences, 300 for algal group discrimination picoplankton, 12, 13, 14, 15, 19, 22, 24, 25, 32, 39, advanced laser fluorometer, 562 40, 45 in situ chemotaxonomic method, 297 detection with active sensors, 555 molecular approaches, 300 red algae, 378 pathlength amplification factor, 504 spectroscopy, 384 pigment based size class, 261 phycoerythrin (PE), 378 pigment fraction, 248 phycoerythrin reflectance qE and xanthophyll cycle, 453 used to detect Trichodesmium sp., 564 tropical, 15 phycoerythrobilin (PEB), 378 UV absorption, 427 isolation procedure, 395 xanthophyll cycle, 455 phycoerythrocyanin pigment photochemistry, 390 ancillary, 200, 244 phycoerythrocyanin (PEC), 378 associated with harmful algal blooms, 582 a-phycoerythrocyanin (PEC) breakdown products in cyanobacteria, 378 in sediments, 182 phycourobilin (PUB), 378 changes with irradiance, 294 isolation procedure, 396 degradation products, 181 phycoviolobilin (PVB), 381 degradation rate, 479 isolation procedure, 396 diagnostic, 247, 260 phytochlorin, 79, 80, 100, 101, 102 diversity, 448 phytochrome, 378, 613 environmental factors affecting composition, 257 chromophore binding, 383 Fp index, 260 phytochromobilin (PFB) HPLC analysis isolation procedure, 396 update on methods, 165 phytoene, 124 identification criteria, 179 formation, 114, 124 in situ detection, 553 15-cis-phytoene, 124 light harvesting (LHP), 294 phytoene dehydrogenase, 136 microphytobenthos, 181 phytoene desaturase (PDS), 124, 125 overlap in HPLC chromatogram, 652 phytoene synthase (PSY), 124 precipitation, 629

840 Index

pigment (cont.) plastoquinone, 523 primary, 200, 244 Pleurochloridella sp., 26 secondary, 200, 244 point source integrating cavity absorption meter size classes, 260 (PSICAM), 505 standards, 653 polar chlorophyll c, 170 tertiary, 200, 244 polar region, 23, 29, 33, 37 unambiguous markers for particular algal polyunsaturated fatty acids, 26 groups, 258 porphobilinogen, 87, 89 pigment calibration formation, 89 accuracy and precision, 211 porphyra-334, 418, 424 linear regression Porphyridiophyceae, 18 residuals, 207 Porphyridium sp., 17, 18 lower limit of linearity (LLOL), 206 porphyrin single-point, 212 cancer treatment, 619 upper limit of linearity (ULOL), 206 porphyrin oxidation products working range, 206 fluorescence and absorption, 91 pigment extract potential efficiency of PSII in acetone fluorescence measurements, 514 degradation in autosampler, 631 Prasinophyceae, 38, 43, 45, 56, in methanol See also prasinophyte degradation in autosampler, 631 Chl b-containing phytoplankton, 497 stability in acetone, 630 genome, 132 stability in methanol, 631 pigment groups, 449 pigment identification prasinophyte, 9, 32, 40, 43, 144, 258, 259, 540 co-chromatography, 651 endosymbionts, 37 minimum criteria, 650 phytoene desaturase genes, 125 molecular mass, 651 pigment markers, 258, 259 retention time matching with standard, 651 preprasinoxanthin, 133 pigment labelling method, 472, 473 uriolide, 133 application conditions, 475 xanthophylls, 128 carbon concentration, 473 zeaxanthin, 262 carbon-specific growth rate, 473 prasinoxanthin, 38, 43, 144, 290, 448, 796 carotenoids, 475 co-elution problem, 202 compared with dilution method, 481 formation, 134 in-line flow scintillation counting, 475 preprasinoxanthin, 133 labelling kinetics of pigments, 475 primary productivity, 472 pigment ratios algorithms fluctuating light, 294 major limitations, 484 freshwater algae, 296 spectral models, 522 high nutrient, low chlorophyll (HNLC), 295 Prochlorococcus marinus, 96, 121, 127 irradiance, 294 Prochlorococcus sp., 14, 101, 127 nutrients, 295 biliproteins, 377, 390 photoacclimation, 295 chlorophyll-specific absorption coefficient, 509 Southern Ocean, 295 genes involved in biosynthesis, 127 Western Equatorial Pacific, 296 LC-MS pigment reconstruction ESI, 321 compared with filter pad method, 509 qE and zeaxanthin accumulation, 454 pigment-based growth rate Prochloron sp., 14, 15 combined with CHEMTAX, 480 Prochlorophyta, 13, See also prochlorophyte pigment-based production rate prochlorophyte, 13, 14, 15, 260, 540, 569 photoacclimation problems, 476 bio-optical discrimination, 540 pigment-protein complexes, 446, 522 bio-optical properties, 566 in chlorophyll c-containing chromophytes, 522 characteristics, 13 Pinguiochrysis sp., 28 phycobiliprotein-containing phytoplankton, Pinguiophyceae, 6, 26, 28, See also pinguiophyte 497 pinguiophyte, 28 pigment markers, 258 characteristics, 26 Prochlorothrix sp., 14, 15, 89

Index 841

Procholorococcus marinus quantum yield for oxygenic photosynthesis HPLC pigment separation, 180 theoretical maximum value, 523 production rate quantum yield of photosystem II (PSII) pigment-based method, 472 fluorescence, 485 productivity variation over the day, 555 role of pigments, 619 prokaryote, 11, 18, 79, 81, 95 Raphidophyceae, 26, 28, 30, See also raphidophyte Prorocentrum minimum Chl c-containing phytoplankton, 497 peridinin raphidophyte, 26, 28, 540 PCP and ACP, 525 characteristics, 26 protein chromophore interactions conversion of xanthophyll-cycle pigments, 134 non-covalent mechanisms, 385 cyst, 29 proteorhodopsin, 609, 610 mycosporine-like amino acids, 418 protist, 4 pigment markers, 259 protochlorophyll, 80 xanthophyll cycle, 131 protochlorophyllide, 80, 88 rapid photoprotective mechanisms, 450 protochlorophyllide a reaction centers (RC) formation, 96 photosynthesis, 445 protochlorophyllide a oxidoreductase (POR), 96 reactive oxygen species (ROS), 92, 450, 456 dark form (DPOR), 97 effect on xanthophyll cycle pigments, 457 light-dependent (LPOR), 96 influence on mycosporine-like amino acids, 425 protochlorophyllide b, 100 protection by mycosporine-like amino protochlorophyllide reductase, 611 acids, 418 protoheme, 382 Rebecca sp., 33 protoporphyrin IX, 78 red algae, 4, 16, 81, 101, 130, See also Rhodophyta biosynthesis, 81 and rhodophyte formation, 91 free phycobilin chromophores, 383 protoporphyrinogen IX genome formation, 91 lycopene cyclase, 127 provitamin A, 113 MEP pathway, 124 Prymnesiophyceae, 5, 31, 32, 33, 34, phycobiliproteins, 375 See also prymnesiophyte radiative excitation energy transfer, 525 characteristics, 33 phycobilisome pigmentation, 385 prymnesiophyte, 260 phycourobilin, 384 Pseudochattonella farcimen. See Verrucophora phytoene desaturase genes, 126 farcimen xanthophyll, 128 Pseudochattonella verruculosa xanthophyll cycle, 454 aka Verrucophora farcimen, 545 b,ε-carotene, 126 Pseudo-nitzschia sp. remote sensing, 619 toxin information, 565 influence of UV absorption, 428 Pseudopedinella sp., 24 ocean colour data, 559 PSII photosynthetic unit size, 519 recent improvements, 616 pulse amplitude modulated (PAM) fluorometry, reflectance (Rrs), 521, 546, 548 518, 566 remotely operated vehicles (ROVs), 617 purple photosynthetic bacteria, 81, 88 renierapurpurin, 128, 138 pyrenoid, 17, 20, 22, 24, 25, 26, 28, 29, 30, 32, 33, retinal, 138 35, 39, 40, 42, 44 formation, 140 pyridoxol, 120 reverse genetics, 615 pyropheophorbide a, 714 Rhodella sp., 18 pyropheophytin a, 716 Rhodellophyceae, 18 pyrrhoxanthin, 37, 133 Rhodobacter sphaeroides,88 Rhodomonas marina quality assurance plan, 636 pigment ratios, 296 for pigment determination, 618 Rhodophyta, 16, 17, 18, 35, 89, See also red algae, quantitative filter technique (QFT), 504 rhodophyte quantum correction genes involved in biosynthesis, 127 verification, 516 state transitions, 447

842 Index

rhodophyte, 11, 127, 130, 132, 418, 454, extraction volume precision, 234 See also Rhodophyta and red algae field sampling precision, 230 qE and xanthophyll cycle, 453 HPLC method accuracy, 220 rhodopsin HPLC method precision, 218 eyespot HPLC methods comparison, 218 Chlamydomonas reinhardtii, 142 injection precision, 217 photoreceptor injection solvent, 217 Nostoc sp., 142 limits of detection and quantitation, 204 type I or archaeal, 140 method performance comparison, 225 type II method validation, 221 green algae, 140 overall method precision, 216 rhodopsin type I performance metrics, 197, 224 in cryptophytes, 142 technical reports, 196 in dinoflagellates, 142 SeaWiFS, 200 in euglenophytes, 142 satellite sensor, 549 Rhodospirillum rubrum,88 SeaWiFS HPLC analysis round-robin experiment. Rhodospora sp., 18 See SeaHARRE round robin, 244 SeaWiFS Ocean Optics Protocols, 196 Sentinel-3 Ocean and Land Colour imager S-320 (mycosporine-like amino acid), 412 (OLC), 568 safranal, 143 shikimate pathway, 424 salt stress shinorine, 418, 424, 430 bkt genes, 135 shinorine methyl ester (M-333), 430 sample storage, 628 shoot multiplication signal (SMS) Sarcinochryis sp., 25 strigolactones, 142 Sargasso Sea Sigma, 659 chlorophyll-specific absorption coefficient, silica frustule, 18 509 silica scale, 23, 29 phosphorus limitation, 295 siliceous skeleton, 24 satellite imagery silicoflagellate. See Dictyochophyceae chlorophyll, 484 silicon uptake satellite-based estimates of primary Thalassiosira pseudonana productivity HR-MAS-NMR, 615 advantages and problems, 484 SIMBIOS round robin, 214 scattering coefficient accuracies for the three SeaHARRE activities, influence of absorption properties, 503 224 optical properties, 497 chlorophyll a accuracy, 220 scattering properties comparison between fluorometry and used to extract pigment information, 508 HPLC, 196 Scenedesmus obliquus, 88, 119 field sampling precision, 230 Scientific Committee on Oceanic Research fluorometric and HPLC method comparison, (SCOR), 3 215 Scrippsiella sp. HPLC extraction procedures, 215 pigment ratios, 296 pigment accuracy, 200 scytonemin, 418 quality control, 217 SeaHARRE, 196 validated method, 197, 199 accuracy threshold for analysis of similarity index, 261 chlorophyll, 200 for determination of Karenia brevis, 563 calibration accuracy for chlorophyll a, 211 singlet-state excitation, 449 carryover between injections, 203 siphonaxanthin, 42, 43, 44, 56, 798 comparison between fluorometric, formation, 134 spectrophotometric and HPLC analyses, siphonaxanthin dodecenoate, 800 216 siphonaxanthin esters, 290, 614 data collection error, 219 LC-MS/MS, 332 detectability problem, 204 sirohaem, 81, 90 detector noise, 233 Skeletonema costatum extraction solvent, 215 genome, 131

Index 843

sodium dithionite Streptophyta, 38, 44, 45 to prevent oxidation, 369 strigolactone, 138 Solieria chordalis, 615 formation, 142 sonication stromatolite sediment samples, 631 chlorophyll f, 102 Southern California Bight Stylomatophyceae, 18 chlorophyll-specific absorption sun-induced fluorescence coefficient, 509 satellite sensor specific extinction coefficient MODIS, 485 chlorophyll a, 367 Symbiodinium sp. chlorophyll b, 367 mycosporine-like amino acids, 427 mycosporine-like amino acids, 431 Synchromophyceae, 23 spectral bands in satellite ocean-colour Synechococcus elongatus, 121 sensors, 568 Synechococcus sp., 14, 89, 121, 126, 127 spectral decomposition, 343 biliproteins spectral fluorescence trichromatic R-type PC, 382 artificial light-stimulated, 556 CHEMTAX, 299 spectral fluorescence signatures (SFS) lycopene cyclase genes, 126 advantages and problems, 556 phycobiliproteins spectral reconstruction, 343 absorption maximum, 399 spectrofluorometry, 343, 352 phycobilisome pigmentation analysis of chlorophylls and absorption spectrum, 385 pheopigments, 353 pigment ratios, 296 comparison between CLS and NNLS, 356 renierapurpurin, 138 comparison with HPLC, 355 w-ring formation, 128 NNLS methods Synechocystis sp., 89, 121, 129 comparison with HPLC, 359 apocarotenoid cleavage oxygenase, 140 spectrometric multivariate methods genes comparison with traditional methods, 355 chlorophyll biosynthesis, 95 spectrophotometer retinal-binding opsins, 142 integrating sphere, 504 ketocarotenoids, 135 spectrophotometry, 343 mycosporine-like amino acids, 417 absorption coefficient, 252 myxoxanthophyll, 137 multivariate methods phycobilisome-associated carotenoid-protein, Gauss-peak spectra method (GPS), 350 390 non negative least squares approximation w-ring formation, 128 (NNLS), 350 synechoxanthin, 128, 137 partial least squares regression formation, 138 (PLS), 351 Synura mammillosa,29 pigment concentration calculation, 252 Synurophyceae, 28, 29, 30, See also simultaneous equations, 366 synurophyte chlorophylls a and b, 367 synurophyte, 29 historical aspects, 366 xanthophyll cycle, 131 trichromatic equations, 343 state transition, 447, 448 Takayama tasmanica, 565 in chlorophyte, 515 terrestrial habitat, 13, 37 in chromophytes, 515 xanthophytes, 30 in cyanobacteria, 515 tetrapyrrole pigments redistribution of light-harvesting complexes, biosynthesis, 81, 92 524 Thalassiosira pseudonana, 20, 121, 124, 125, sterol, 119 611, 615 synthesis, 119 genome, 130, 131 steryl chlorin esters lycopene cyclase, 127 LC-MS/MS Thalassiosira sp. zooplankton grazing, 328 photoprotection Stichogloea sp., 26 iron adaptation, 455 stramenopile, 6, 18 Thalassiosira weissflogii, 134

844 Index

Thermosynechococcus elongatus BP-1, 138 Vaucheria sp., 30 thiamine, 120 vaucheriaxanthin, 24, 30, 44, 56, 144, 804 thylakoids, 447 vaucheriaxanthin diester, 259 Tolypothrix tenuis, 390 vaucheriaxanthin ethanoate octanoate, 806 total chlorophyll a (TChl a), 196 Verrucophora farcimen, 24, 545 toxic dinoflagellates toxic algal bloom pigment diversity, 565 pigment signature not specific, 526 toxin, 13, 37 violaxanthin, 20, 23, 24, 28, 29, 38, 40, 42, 44, 128, associated with harmful algal blooms, 582 133, 134, 448, 524, 808 chemotaxonomical markers, 565 co-elution problem, 202 ELISA assays, 545 formation, 132 harmful algae, 565 xanthophyll cycle, 131, 450 transcriptomics, 614, 619 9-cis-violaxanthin, 139 Trebouxia sp., 43 violaxanthin de-epoxidase (VDE), 131 Trebouxiophyceae, 38, 43 genes in prasinophytes, 132 Tribonema sp., 30 UV-B inhibition, 457 Trichodesmium sp., 12, 13 xanthophyll cycle, 451 blooms, 564 Vischeria sp., 25 CHEMTAX, 299 vitamin B12, 81, 94 extra-cellular release of mycosporine-like amino volume scattering function, 506 acids, 427 Volvox carteri, 121, 124 gas vacuoles genome, 130 scattering, 508 mycosporine-like amino acids, 418 wavelength targeting, 567 satellite detection using phycobiliproteins, remote-sensing algorithms, 557 564 spectrofluorometric methods, 356 Xanthophyceae, 5, 26, 28, 30, See also stirring releases UV compounds, 428 xanthophyte triplet-state excitation, 449 xanthophyll cycle, 450 tropical region, 29, 37 xanthophyll tunichlorin, 102 biosynthesis, 128 turnover of standing stock, 482 in cyanobacteria, 129 in prasinophytes and chromalveolates, ultra performance liquid chromatography (UPLC), 129 57, 614, 644 formation, 114 Ulva lactuca LC-MS/MS zeaxanthin ESI, 329 UV-B induced loss, 457 light-harvesting, 128 Ulvophyceae, 6, 38 photoprotection, 128 upper limit of linearity (ULOL) xanthophyll cycle, 131, 446, 448 pigment calibration, 206 algae compared to terrestrial plants, 454 uriolide, 43, 133, 134, 144, 258, 802 description, 450 urogen III. See uroporphyrinogen III diadinoxanthin/diatoxanthin cycle, 131 uroporphyrinogen co-synthase, 88 dynamics of water masses, 459 uroporphyrinogen III, 91 endosymbiotic gene transfer, 133 formation, 89 environmental modulation, 454 tetrapyrrole biosynthesis, 81 estuarine strains compared to oceanic, 455 usujirene, 430 fluctuating light, 455 UV absorbing compounds, 412 fluorescence quenching, 513 UV absorption, 427 lumen pH, 451 UV radiation lutein-based, 450 xanthophyll cycle lutein-epoxide/lutein cycle, 131 ecological relevance, 458 orthologous genes, 132 UV-A, 425 photoprotection, 131 xanthophyll cycle, 457 physiological condition, 456 UV-B, 412, 425 regulation, 451 xanthophyll cycle, 457 role and regulation, 449

Index 845

siphonaxanthin-based, 450 zeaxanthin, 13, 15, 16, 17, 20, 23, 24, 28, 29, 37, 40, size effect, 455 42, 127, 128, 129, 130, 131, 133, 134, 136, stimulation by UV-B exposure, 456 138, 144, 171, 259, 262, 290, 524, 810 types of, 131 accumulation under high light, 450 UV inhibition, 457 changes with irradiance, 294 UV response, 456 co-elution problem, 202 violaxanthin/antheraxanthin/zeaxanthin eye-related health care, 619 cycle, 131 formation, 130 violaxanthin-based HPLC separation, 173 in heterokonts, 450 LC-MS/MS water mixing rate, 459 loss of toluene, 330 xanthophyll de-epoxidation relationship with fluorescence quenching, 453 UV radiation slow-responding photoprotective carotenoid, biological weighting function, 456 524 xanthophyte, 30 xanthophyll cycle, 450 conversion of xanthophyll-cycle pigments, zeaxanthin epoxidase (ZEP), 131, 132 134 mutants, 133 pigment markers, 259 xanthophyll cycle, 451 xanthophyll cycle, 131 Zn-bacteriochlorophyll a, 102 xanthoxin, 139 zooxanthellae, 426