SUBJECT INDEX

Note: Page numbers followed by f and t indicate figures and tables, respectively.

AAcetate pathway

enzyme fatty acid synthase, 186fatty acid derivatives

de novo biosynthesis, 186, 187fenvironmental stress, 188functionalization, alkyl chain,186–187

Jaspis stellifera, 186, 187fLyso-PAF (platelet activatingfactor), 188, 188f

lysophospholipids, 187, 188fphysiological factors, 188primary metabolism, 188–189terrestrial environment, 186

natural products, 185–186polyacetylenes

biosynthetic hypothesis, 189–190,190f

carboxylative process, 190iterative process, 190structures, acetylenic fatty acidderivatives, 189–190, 189f

polyketidesClaisen-type condensation,190–191

endoperoxides, 191–193eribulin mesylate, 190–191macrolides, 191

Adherens junctionscomponents, 24description, 24molecules, 24–25

Alkaloids3-alkylpiperidin

actinomycetes, 212–213biosynthetic pathway, 212–213,213f

halitoxin polymers, 213–214Haplosclerida sponges, 211–212,

212fmollusks, 211–212sarains and manzamines,

212, 213fguanidine

chemical ecological study,214–215

polycyclic, 214, 214fPIA, 211pyrrole-imidazole

biosynthesis, 215, 216fbromopyrroles, 217–218discovery, dibromophakelin,

215–216oroidin, 215–216, 217f

Amplified fragment lengthpolymorphism (AFLP), 298

Aplysina red band syndrome (ARBS),85

Aquiferous systemporocytes and canals

excurrent, 30osculum, 30ostia, 29pinacoderms, 29–30

Wnt role (see Wnt role, canaldifferentiation and polarity)

BBiomedical/biotechnological

application, silicatein andsilintaphin-1

biomedical approach:teeth, 262biotechnological approach

biomimetic, 259–261, 260fdiscovery, silintaphin-1, 259

339

340 Subject Index

Biomedical/biotechnologicalapplication, silicatein andsilintaphin-1 (cont.)

Fourier transform spectroscopy,259

FT-IR ATR, 261immunoblot analyses, 261spiculogenesis, 259–261transmission, light, 261

bone-osteoporosisbiosilica, osteoblasts, osteoclastsand progenitors, 264, 265f

cell mineralization, 264molecular interactions andpathway, 262–264

osteoprotegerin [OPG], 264RANKL, 264

conventional technical procedures,258–259

enzymatic silicatein reaction,258–259

recombinant silica enzymes, 259tissue engineering, 258–259

Biosilica, tissue engineeringmolecular cloning, genes, 233nanobiotechnological applications,

264–265phases, spiculogenesis, 264–265silicatein and silintaphin-1

biomedical approach, teeth, 262biotechnological approach,259–261

bone-osteoporosis, 262–264conventional technicalprocedures, 258–259

enzymatic silicatein reaction,258–259

recombinant silica enzymes, 259tissue engineering, 258–259

sponge skeletoncatabolic enzyme, silicase, 242enzymatic biosilica formation,245–247

metazoan evolution, 236–238morphogenesis and axis formation,235

morphology, spicules, 257–258

phases, silica deposition, 255–257polycondensation, syneresis,

249–251reaction mechanism of silicatein,

238–242silicatein-mediated synthesis, 245,

246fsilintaphin-1, 242–244silintaphin-2, 244–245spicules, S. domuncula, 251–255structure formation, silintaphin-1

in vitro, 247–249sponge species, 233, 234fZoophyta, 233

Bovine spongiform encephalopathy(BSE), 275

CCarbon balance, HMA and LMA

spongesclearance efficiency, 132–133differences

balance equation, tropical andtemperature sponges, 133–135,134t

H. caerulea, 135net growth rates measures, 135

DOC and DOM consumption,131–132

imbalances, ingestion and respiration,131–132

Ipoc/R index, 132–133labelling, 132metabolic rates differences, 132–133restriction, DOM uptake, 132

Carbon metabolism, spongesassimilation, respiration and

production

basal metabolic maintenance and

costs, 127–128biomass, 128–129cyanosponges, 129–130differences, HMA and LMA,

129–130growth measures and physiological

responses, 130growth rates, 128–129

Subject Index 341

inorganic carbon fixation, 130oxygen consumption, 127phototrophic andchemoautotrophic, 129–130

pumping activity, 127–128respiration rates, HMA and LMA,127

balance equationdescribed, 123oxidation, 123–124in situ measurements, 123waste organic carbon, 123–124

compiling, 122–123DOM uptake, 123excretion and egestion

amoebocytes disintegration, 130description, 130faecal pellets, 130–131feeding experiments, 130–131rate estimation, 130–131

improvements, marine sponges,122–123

ingestioncapturing rate and depends, 124description, 124DOC and DOM fraction,125–127

growth, respiration and wastedisposal, 123

harbouring, 127heterotrophic feeding, 127LPOC, nano-and picoplankton,124–125

metabolic rate, in situenvironmental conditions,125, 126t

particle uptake, 124POCdet and re-filtration, 125

Choanoderm epitheliumaquiferous system, 9, 10fcontrol over flow, 16–18differentiation and turnover

cost of production, 16description, 14feeding behaviour, 15–16pinacocytes, 16sponges, 14–15

Tetilla serica, 14–15function-feeding

apopyles and apopylar cells, 13–14,13f

food capture, 14prosopyles, 12–13

organization, 12–13structure

collar microvilli, 10description, 10gasket matrix and cells

surrounding, 12, 12fglycocalyx, 10–12, 11f

Cytomegalovirus (CMV) promoter,321

DDenitrification and anammox

activity, 144–145G. barretti and D. avara, 144–145Ircinia strobilina and M. laxissima,

144–145measurement, dissolved organic

nitrogen, 145net DON uptake, 145

Diels–Alder reaction, 192

EEcological nature symbioses

abundance, microbial symbionts

bacteriosponges, 81divisions, 81FISH techniques, 82HMA and LMA, 81–82nitrification and denitrification,

LMA, 82accentuates mechanisms, 80–81balancing mutualism and parasitism

analyses, T-RELP and DGGE, 86environmental stresses, cyclic and

fatal bleaching, 86–87local environmental conditions,

85–86manipulations, symbiotic

microbial community, 86net positive and negative

interactions, 85–86

342 Subject Index

Ecological nature symbioses (cont.)

stability, 87trade off, conflict and cooperation,85–86

cost and benefits, 80–81mutualisms

benefits, cynobacterial symbionts,82

cost interaction, 82filtrations, 83–84measurements, P:R ratio, 83shading experiments, 83–84

parasitism, costs, host sponges anddiseases

ARBS, 85, 85fcausative agent identification,84–85

coral reef organisms, 84description, 84prevalence, 84quantitative modelling, 84

theory, 80–81Ecological significance, carbon use

bacterioplankton, 136–137benthic community and producers,

135–137food source and diet, 135–136ingest, 135–136schematic outline, organic carbon

net fluxes, 136–137, 136fEndoperoxides

antimicrobial activities, 192–193bacterial cells, 192coral bleaching, 192–193Diels–Alder reaction, 192Plakortis, 191–192, 192fpolyketides, 191–192putative biosynthesis, plakortin and

plakortolide derivatives, 192,193f

reduction process, 192

FFluorescent in situ hybridization

(FISH), 298Fourier transform infra-red

spectroscopy with attenuated

total reflectance (FT-IR ATR),261

HHigh-microbial abundance (HMA),

121

IIn vitro sponge culture

monodispersed cell

primary sponge cell cultures

(1993–2010), 289–291, 292tsponge cell culture medium,

291–294sponge cell dissociation, 291sponge cell enumeration and

viability, 294–298sponge cell-type verification, 298

primmorphscell proliferation, 304–305effect of antibiotics, 304effect of silica and iron, 303formation, 299–303inoculum cell density, 303method, 299, 300fmorphogenesis and spiculogenesis

of primmorphs, 303, 304ftelomerase activity, 298–299

tissue fragments2003–2009, 305, 305tBrdU incorporation, 305–306dissolved oxygen (DO), 306Octopus extract, 306RPMI, 306

LLow-microbial abundance (LMA), 121

MMetazoan evolution

2-D gel electrophoretic analysis,236–238

hexactinellids, 236hydrofluoric acid (HF), 236phylogenetic analysis, 236phylogeny, biosilica skeleton, 236,

237f

Subject Index 343

spicule formation, 236Mevalonate pathway

isocyanide and terpenes

chemical taxonomic marker, 194metabolite transfer, 194–196putative biosynthetic pathways,194, 195f

sponge sesquiterpenes, 196, 196fsymbiotic/host production, 194

oxygenated terpenesoxidized di-and sester-terpenes,199–201

sesquiterpene hydroquinones,197–199

triterpenes and steroids, 201–204terpenoids, 193–194triterpenes and steroids, 201–204

Monodispersed cellAFLP, 298FISH, 298primary sponge cultures

(1993–2010), 289–291, 292tsponge cell dissociation

dissociation method, 291, 293fmechanical and chemicaldissociation, 291

sponge cell enumeration and viabilitybromodeoxyuridine (BrdU), 298flow cytometric cell cycle analysis,294–297, 297f

fluorescein diacetate (FDA), 294haemocytometer, 294MTT assay, 294

sponge cell-type verification, 298sponge culture medium

development, 291–293use, antibiotics and antimycotics,293–294

Morphology, spiculesbiosilicification mechanism, 258physico-chemical laws, 257–258siliceous sponges, 257

NNitrogen fluxes, sponges

denitrification and anammox (seeDenitrification and anammox)

fixationambient dinitrogen (N2)

conversion, 144detection, 144rates, 144sponge-associated

microorganisms, 144nitrification

ammonia and nitrite oxidizingbacteria, 139–143

NOx production, LMA and HMAspecies, 143–144

sponge-mediation, 139–143, 140tremieralization, POM

abundance, symbiotic bacteria,138–139, 138f

conversion, particulate organicnitrogen filter, 138–139

dissolved components, 138–139Nutrient fluxes, sponges

carbon uses

balance, HMA and LMA

(see Carbon balance, HMA andLMA sponges)

ecological significance, 135–137metabolism (see Carbon

metabolism, sponges)C flux, 165chemical elements, 114–115differences, metabolic

pathways, 164direct techniques

advantages, 116–117avoid vessel stagnation/flux,

116–117differences, 117discriminate retention efficiency

and pumping rate, 116–117dissolved nutrients and

sponge-associated microbesacquisition, environmental

transmission, 120–121diversity and metabolic pathways,

121–122HMA and LMA, 121hypothesis, microbial symbionts,

121–122

344 Subject Index

Nutrient fluxes, sponges (cont.)

microorganisms population,120–121, 120f

remove/release organic andinorganic compounds, 118

ecological significance, 146–147emergence, dissolved nutrients,

114–115estimation, uptake rates and efflux

rates, 115functional role, ecosystems, 114–115impact, populations, 165indirect techniques

avoid filter-feeder andre-filtration, 116

closed system and suspensionfeeders, 116

compound concentration changes,surrounding water, 115–116

filter feeders, 115–116use ‘clearance rate’, 115–116

Michaelis-Menten kinetic process,Si, 166

nitrogen and phosphorous usesanaerobic and aerobic process,137–138

consortium, 137–138detection and quantification, 137fluxes (see Nitrogen fluxes,sponges)

N cycle performance and control,137

phosphorous fluxes (seePhosphorous fluxes, sponges)

relation and steps, N cycle,137–138

N role, 166opportunistic suspension feeders, 164P fluxes, 166POM (see Particulate organic matter

(POM))Si consumption, 166silicon (see Silicon metabolism,

sponges)Si-sequestering process, 166ubiquitous marine organisms,

114–115

OOccluding junctions

A. queenslandica, 25–26description, 25septate, 25

Oscillatoria spongeliae, 73–74Oxygenated terpenes

oxidized di-and sester-terpenes

Californian sponges, 200, 201ffuranosesterterpenes, 201, 202ffurans moieties, 200intraspecific variability, 200, 200fintraspecimen variation, 200secondary metabolisms, 201sponge diterpenoids, 199–200

sesquiterpene hydroquinonesantimicrobial activity, 199bacterial symbionts, 197chemical ecology, 198–199, 198fdictyoceratida, 197putative biosynthetic pathway,

197–198, 198ftriterpenes and steroids

bacteriohopanoids, 201–202biosynthetic pathway, 202–203,

204fsaponins, 201–203sponge sterols, 201sponge sterol side-chains, 202,

203fsterol endoperoxides, 203sterol metabolism, 203

PParticulate organic matter (POM)

detritus functions, 117large, smaller and smallest particles,

117–118retention efficiency, picoplankton

cells, 118, 119tPhosphorous fluxes, sponges

biological synthesis and energytransfer process, 145

compounds, 145cycling, 145Dendrilla nigra, 145–146

Pinacoderm epithelium

Subject Index 345

basement membrane, 26–27biomineralization, 27–28cell adhesion and junctions

adherens junctions, 24–25carbohydrates, 23molecules, 23–24occluding, 25–26

cilia and flagellademosponges, 21differentiation, 20–21exopinacocytes, 21–22

description and function, 18–20development, 28–29role, sealing and osmoregulation,

22–23terminology, 20

Polycondensation, syneresisaquaporins, 250–251bio-sintering process, 251gel network, biological system, 250silicateins, 249–250spicule formation, 251, 252f

RReceptor activator for NF-kB ligand

(RANKL), 264

SSaponins

chemodiversity, 203, 205fchemotaxonomic marker, 203–204nitrogenated secondary metabolites,

204triterpene and steroid glycosides, 203

Shikimate pathwaybromotyrosine derivatives

biosynthesis hypothesis, 204–206,206f

chemical transformation, 209sponge chemical diversity,204–206

wound induced bioconversion,207, 208f

discorhabdin derivativeschemical weapons, 210formation and cleavage, 209–210,211f

intraspecific environmentalvariability, 209

putative biosynthetic, 209, 210f

Silica deposition phases, spicule

formationappositional growth, 256–257extracellular phase (shaping), 257intracellular phase, sclerocytes,

255–256Silicatein

reaction mechanism

cyclization reactions, 240–242nucleophilic attack, 240–242, 241fpolycondensation reaction,

238–240tetraethyl orthosilicate (TEOS),

238–240, 239fstructure formation, silintaphin-1

in vitrobiosilica synthesis, 249silica gel, 247–249, 248fsol–gel process, 247–249

Silicatein-associated proteinssilintaphin-1

analogy, 243axial filament formation, 243–244modelling studies, 242–243molecular biological technique,

242–243silintaphin-2

identification, 244polycondensation reaction,

244–245Silicon metabolism, sponges

ecology

diatoms use, DSi, 151dissolution and burial, 159–161DSi demands, 154–157investigation and contribution,

151–152notion, Si cycle, 151–152silica standing stocks, 157–159Si uptake rates, 152–154

intra vs. intercellular modesBSi deposition and simplification,

149–15020th century, 148

346 Subject Index

Silicon metabolism, sponges (cont.)

dissolved (DSi) and biogenic silica(SiO2), 148

fluxes, 148Hexactinellida, 149homosclerophorid spongesinvestigation, 148–149

primmorphs, Suberites domuncula,149–150

production, 149sclerocyte pockets, 149–150silicification, 149–150spiculogenesis, 148

molecular aspectsDSi polymerization, 151extracellular aggregation, Mueller-Schroder, 150–151

reaction mechanism, 150realization, axial filaments, 150silicatein, 150

role, ocean Si cycleaffects, Si partial budgetsestimation, 164

assumptions, 163continental shelves, 164description, 161–163diatom uptake and contribution,161–163

DSi-sequestering process, 164global biogeochemical cycle,161–163, 162f

Si fluxes, 164standing stock, 163–164

structuresgeneric functions, 147–148siliceous skeleton, 147spicules shape and size, 147–148

Specific growth rate (SGR), 285Spicules, S. domuncula

developmental stages, axial filament,251–252, 253f

extracellular deposition, biosilica,255

extracellular growth, sponge spicules,254–255, 254f

immunogold electron microscopy,255, 256f

transition phase, 253–254types, megascleres, 251–252

Sponge aquaculturedesign principles

commercial scale, 283–284culture cycle, 284–285design model, 284SGR, 285

ex situ cultureaquarium systems, 288design feeding regimes, 287–288effects, temperature, 287fragile exhalant structures,

285–287growth and survival, 285, 286tvolumetric productivity, 288

in situ culturebroodstock selection, 281–283growth rates and survival

percentages, 278–281, 279tmariculture, 278natural bacterial composition, 283predation and fouling, 278production method, avarol, 281sausage formation, 283sea-based culture, 278

metabolite productionqualitative assay, 289squeezing, tissue, 289

Sponge chemical diversityacetate pathway

enzyme fatty acid synthase, 186fatty acid derivatives, 186–189natural products, 185–186polyacetylenes, 189–190polyketides, 190–193

alkaloids3-alkylpiperidin, 211–214guanidine, 214–215pyrrole-imidazole, 215–218

biochemical pathways, 185marine environment, 184–185metazoan tree, 184–185mevalonate pathway

isocyanide and terpenes, 194–197oxygenated terpenes, 197–201terpenoids, 193–194

Subject Index 347

triterpenes and steroids, 201–204shikimate pathway

bromotyrosine derivatives,204–209

discorhabdin derivatives, 209–210Sponge-microbe associations diversity

common community, bacterialsymbionts

clone library analyses, 68–69divisions, 67–68exception, 67generation and transmission, 68hypothesis, 67interpretation, 68–69microbial taxa classification, 68patchy distributions, 68–69unique bacterial lineages, 68

host perspectivesdistribution, 66documentation, phototrophicsponges, 66

gross production measurements,66

phothosynthesis and respiration,65

prevalence, 65sponges abundance, 65–66survey, Caribbean sponges, 65–66temperate reefs, 66

measures“clone libraries,” 16S rRNA, 63community profiling, 63–64derived culture, 62development, profiling methods,62

fingerprinting, 63–64microbial taxa, 62microscopic methods, 62next-generation sequencingtechnologies, 63–64

16S rRNA and caveats, 62–63surveys, microbial perspective, 62

perspectives, 64–65Sponge-microbe associations specificity

costs and benefits, 69ecological interactions and dispersal

ability, 74–75

degree of host specificity, 74evolution, mutualism, 74–75observations, 74

host and symboint phylogeniesO. spongeliae, 73–74S. spongiarum, 72–73symbiont clades, 71–72

metazoan-gut symbioses, 69sequence clusters

lack of statistical rigour, SSSCs, 70living microbes, water column, 70phylogenetic trees construction,

69–70, 71fSponge-microbe symbioses

body-plan development, 97compounds identifying, symbionts

and hosts

carbon fixation, 91–9314C radioisotope, 91–93fingerprint co-chromatography,

91–93GC-IRMS, 93pulse-chase experiments, 91–93

cynobacteria, 59diversity (see Sponge-microbe

associations diversity)ecological nature (see Ecological

nature symbioses)ecology and evolution, ancient

symbioses, 58–59enrichment, stable isotope tracers

carbon transfer, 91coral and sponge-zooxanthellae

interactions, 90pulse-chase, 91“pulse-chase” performance, 90reciprocal transplant experiments,

90–91evolution, 98–99goal, ecological and evolutionary

perspectives, 60identifying microbial players, 93–94influence, host sponges, 98interactions models

anoxic niches, 95benefits, host sponges, 95cheating, 96

348 Subject Index

Sponge-microbe symbioses (cont.)

conceptual model, 94–95, 95ffeatures, 96FISH techniques, 96–97leaky vertical transmission, 96Lotka-Volterra, 96qualitative models, 96sponge host, beneficial andharmful symbionts, 94–95

T-RFLP and clone library-basedmethods, 96–97

"leaky vertical transmission, 97–98metazoans, 58–59parallels and integrate knowledge, 98parasitic relationship, 59–60photosynthesis, 59publications and citations, 60, 61fquantitative hypothesis testing, 97recent development, 60reviews, 59–60role, 59specificity (see Sponge-microbe

associations specificity)stable isotope analyses

13C and 15N, 8813C sponge and bacterial cellfractions, 91, 92f

food web, 88nutrition sources, 88–89coral-zooxanthellae symbiosisliterature, 88–89

values d13C and d15N, HMA andLMA, 89–90

Symbiodinium clades, 98symbionts, 59transmission (see Symbiont

transmission)vertical and horizontal transmission,

97–98Sponges, sponge cells and symbionts,

cultivationantiviral properties, 274–275aquaculture

design principles, 283–285ex situ culture, 285–288in situ culture, 278–283metabolite production, 289

biotechnological applications, 274BSE, 275co-cultivation

lichens, 325primary and secondary

metabolism, 324–325cultivation methods, 2773D culture systems, 322drug discovery, 274–275, 276tgrowth media

biomass, 321–322genomics, 322nutritional requirements,

321–322in vitro cell cultures, 277in vitro sponge culture

monodispersed cell, 289–298primmorphs, 278–281tissue fragments, 305–306

immortalizationcell types, 320cytomegalovirus (CMV), 321gemmules/larvae, 320–321genes, 319f, 320–321

metabolites, 275microbial infection, 275pharmaceutical products, 275sponge aquaculture

change, microbiology, 319–320sea-based, 318types, pathogens, 319

stem cellsiPS cells, 320proliferative capacities, 320

symbiont culturegenomic information, 324metagenomics revolution,

322–323poribacterium, 323sequencing technology, 323–324

symbiontsculturable archaea, 316culturable bacteria, 308–316culturable fungi, 317–318microbial diversity, 307–308revolution, DNA sequencing,

306–307

Subject Index 349

Sponge tissuesaquiferous system (see Aquiferous

system)body wall overview

regionalization, 7, 8fsubatrial tissues, 8surface layers nature, 7–8

carnivorous, 4cells, tissues and regionalization, 9choanoderm epithelium (see

Choanoderm epithelium)description, 3environment, 4epithelia

gene expression, 35–36molecules, coordination andtransduction, 33–35

sensory and coordinating tissues,32–33

gross morphologybody structure, 5, 6fCalcarea, 5–7, 6f

immune system function, 43–44pinacoderm epithelium (see

Pinacoderm epithelium)Simpson’s scope, 4–5tissue formation (see Tissue

formation)Symbionts, cultivation

bioactive metabolites, 308culturable archaea, sponges

ammonia oxidation, 316Thaumarchaeota, 316

culturable bacteria, spongesagar plates, 315bacterial profiles, 309, 310fbayesian phylogram, 16SRNA,309–315, 311f

bioactive compound, 308–309environmental extracts, 315–316taxonomic level, 309

culturable fungi, spongesbioactive compounds, 317filtration system, 317–318PCR primers, 317–318

microbial diversity, 307–308molecular techniques, 308

revolution, DNA sequencing,306–307

Symbiont transmissionadvantages and disadvantages, 75description, 75genetic variability and physiological

capabilities, 75–77horizontal

environmental acquisition, 77–78molecular-based surveys,

microbial communities, 77–78squid-Vibrio and legume-

rhizobium symbioses, 78–79leaky vertical

alphaproteobacterium, 79analyses, 16S rRNA gene

sequences, 80common evolutionary outcome, 79documentation, 80Pseudovibrio denitrificans, 79

modes, hypothetical sponge, 75, 76ftypes, 75vertical

confocal micrograph, Tedaniaignis, 77, 79f

life stages, Xestospongia bocatorensis,77, 78f

molecular tools, 77observations, 77

Synechococcus spongiarum, 72–73

TTissue formation

embryogenesis and larvalmorphogenesis

amphiblastula, 37cellular material, 37sexual reproduction, 36types, 36–37

gene expressiondevelopmental, larval, 41–42early embryogenesis, 38–39gastrulation and larval layers,

39–41juvenile and adult sponge tissues

and cells, 42–43regulatory genes, development, 37–38

350 Subject Index

WWnt role, canal differentiation and

polaritydescription, 31

Hydra and Nematostella,31–32

iroquois and NK class, 32and ligand expression, 31