[Advances in Marine Biology] Aquatic Geomicrobiology Volume 48 || Subject Index

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  • SUBJECT INDEXAAP. see Aerobic anoxygenic

    photoheterotrophs

    Acetylene reduction assay, 21112

    Acidophiles, 43

    Activity coeYcient calculations, 712

    Davies equation, 72

    Debye-Huckel equation, 712

    Adenosine triphosphate (ATP), 66, 835

    AAP and production of, 97

    ADP formed by, 83, 84, 85

    ammonium oxidation and production

    of, 2334

    biosynthetic reaction, unfavorable

    and, 835

    carbon fixation pathway demand

    of, 111, 112

    catabolic reactions generating, 131

    cyclic electron flow and, 104

    electron transport and synthesis of, 299

    energy needed to produce, 88

    fermentation and generation of, 858

    formation, 83, 84, 4045

    generation, 858, 104, 343

    gradient relaxation and, 82

    light energy transfer to, 100, 101

    methanol and formation of, 4045

    nitrogen fixation reaction and, 213

    oxidative phosphorylation-generated, 84, 88

    oxygen consumption, non-respiratory and

    increased, 182

    phosphorus assimilation and formation

    of, 426

    phototroph conserved energy and

    production of, 99

    prokaryote cell yield and production of, 156

    proton translocation and formation of, 100,

    103, 185

    protons and generation of, 104

    sulfide oxidation and, 368

    sulfur reduction generating, 343

    Aerobic anoxygenic photoheterotrophs

    (AAP), 97

    Aerobic food chains, 168

    Aerobic organisms, 173, 1903

    Alkaliphiles, 434, 191

    Amensalism, 56Ammonia

    assimilation of, 21314

    cycle, 209

    human impact on, 209

    microbial mat sequestering of, 47880

    nitrogen gas reduced to, 213

    Ammonification, 206, 21920

    aerobic, 220

    anaerobic, 220

    aquatic environment, 220, 223

    glutamate and formation of, 2223

    heterotrophic carbon mineralization

    and, 220

    measuring, 223

    microbial, 21932

    nitrate, 2513, 259

    nitrification and, 232

    nitrogen gas release and, 21920

    porewater/particle equilibrium distribution

    and, 229, 230

    sediment absorption and, 223

    temperature and nitrate, 259

    Ammonium

    anoxic sediment and concentration of, 228

    assimilation, 21314, 222

    cellular material incorporation of nitrogen

    fixation formation of, 21314

    concentration, 222

    deamination, 2203

    incorporation, 2203

    manganese oxidation reduced by, 275

    manganese reduction electron donor, 2945

    methanotrophy inhibited by, 406

    microorganism assimilation of, 228, 229

    nitrates and, 251, 484, 485

    nitrification and availability of, 237

    Nitrobacter as oxidizers of, 236

    nitrogen fixation and, 207, 21314

    Nitrosococcus oceanus as oxidizers

    of, 2356, 237

    oxidizers, 2356, 237

    temporal changes in pool of, 223

    water, overlaying fluxes of, 228, 229

    sediment, 223, 2259

    stratified water body interface between

    nitrate and, 484, 485

  • 608 SUBJECT INDEXAmmonium oxidation, 211, 220, 2334, 235,

    23940, 245, 481

    anaerobic, 235

    ATP production and, 2334

    chemolithoautotrophic, 2345

    light and, 245

    Michaelis-Menten kinetics and, 23940

    stratified water bodies and, 481

    Anabolic metabolism, 131

    biopolymer generation and, 156

    MGE, reduced and energy for, 1589

    Anabolism, 81

    Anaerobic food chains, 168

    Anaerobic oxidation of methane (AOM), 294,

    384, 402, 4856

    consortium conducting, 412

    electron donor for sulfate reducers

    conducting, 41314

    geochemical evidence for, 40911

    isotope fractionation and, 417, 418

    marine sediment, 410

    microbial evidence for, 41114

    sulfate reduction and, 411, 412, 41314

    Anammox, 2613

    chemolithoautotrophs and, 2612

    competition within, 52

    enzymes involved in, 262

    metabolic pathway for, 262

    nitrogen deficiencies and, 264

    nitrogen produced by, 2624

    oxic nitrification and, 261

    oxygen and, 262

    stratified water body, 481

    Animalia, 1415

    Anoxia. see also Oxia; Oxic-anoxic interface

    cyanobacteria exposure to, 175

    environmental, 172

    nitrification and tolerance to, 239

    oceanic, 169

    oxygen and, 1723

    sulfur reduction in, water columns, 324

    Anoxygenic photosynthesis, 100, 104, 287,

    357, 369, 481, 48793

    cyanobacteria, 104

    iron oxidation by, 2867

    microbial mats, 467, 479

    sulfide oxidation by, 357367

    stratified water body, 481

    Tree of Life, 369

    Anoxygenic phototrophs, 96, 97

    bacteriochlorophylls utilized by, 100distribution, 97

    electron donors used by, 104

    iron oxidizing, 2867

    light range available to, 101

    photosynthetic unit in, 100

    sulfide oxidizing, 357367

    AOM. see Anaerobic oxidation of methane

    Appendices, 50815

    Aquifex, 12

    Aquifex-Hydrogenobacter,106, 108

    Archaea

    Bacteria characteristics distinguished

    from, 15

    cell wall features characterizing, 17

    diversity, physiological in, 16

    Eukarya and, 11, 18

    evolutionary distance in, 11, 12

    halophiles in, 1617

    heme copper oxidases in, 189

    heterotrophic, 43

    iron oxidizers in, 282, 2856

    iron reduction, 291

    kingdoms, 16

    methanogen cluster of, 412, 413

    methanogenesis, 390, 3923

    nitrogen fixation and, 216

    organisms in, 17

    photosynthesis within, 7

    phylogeny of methanogens and related,

    412, 413

    rRNA sequence and, 9

    Rubisco in, 108, 116, 118

    SSU rRNA domain, 11

    sulfate reducers in, 325

    sulfide oxidizers in, 3523

    sulfur, elemental respiration by, 344

    sulfur reduction, 343

    Tree of Life domain, 1617

    Arenicola marina

    detritus pool feeding by, 1367

    prokaryote density and, 136

    prokaryote digestion by, 137

    Arrhenius equation, 41, 42

    ATP. see Adenosine triphosphate

    Bacteria, 1

    anoxygenic phototroph distribution as, 97

    Archaea characteristics distinguished

    from, 15

    cell rigidifier peptidoglycan and, 16

    cyanobacteria in, 174

  • SUBJECT INDEX 609denitrification, 253

    diversity, physiological in, 16

    heme copper oxidases in, 189

    iron oxidizers, acidophilic in, 2856

    iron oxidizers in, 2801, 282

    metabolism and, 1516

    nifH gene contained by, 217

    nitrogen fixation and, 216

    organisms in domain of, 16

    oxygen respiration, 188

    rRNA sequence and, 9

    SSU rRNA domain, 11

    sulfate reducers in, 325

    Tree of Life domain of, 1516

    Bacteriophage, 545

    Bacterioplankton

    aerobic, 192

    FISH and aerobic, 192

    growth rate/eYciency of, 158

    Bacteroides fragilis, 173

    Bdellovibrio bacteriovorus, 54, 55

    Beggiatoa

    distribution, 355

    electron acceptor, 355

    microbial mat migration of, 472

    nitrate reduction, 351

    phobic response to light of, 354

    sulfate oxidation, 353, 354

    sulfide oxidation, 349, 351

    Biogenic silica (BSi), 443

    benthic infauna and dissolution of, 454

    diatom and production of, 445

    dissolution, 450, 451, 4523, 454, 4556

    DSi temporal development during

    dissolution of, 450, 451

    microbes and dissolution of, 4556

    oceanic, 44950

    radiolabeled silica measuring dissolution

    rates of, 4523

    sediment burial loss of, 462

    sediment deposit of, 445

    sediment preservation of, 454

    sediments, surface dissolution of, 4523

    solubility, 450, 451, 452, 4534

    surface area, 452

    temperature and dissolution of, 4523

    temperature dependence and solubility

    of, 4501

    Biosynthesis, 110

    Black Sea, 4826

    AOM in, 4856density stratification, 482

    methane accumulation in, 4856

    methane source in, 485

    nitrate and ammonium interface in, 484, 485

    nitrate forms, 484, 485

    oxygen and sulfide interface in, 4823, 484

    oxygen penetration depth in, 4823

    salinity and density stratification in, 482

    sulfide oxidation in, 485

    BSi. see Biogenic silica

    Canon Diablo troilite standard, 375

    Carbon. see also Dead particle organic

    carbon; Living particulate organic carbon

    aerobic mineralization of, 131

    anaerobic mineralization of, 131

    anoxic sediment phosphorus, ratio, 438

    atmospheric release of, 461

    biomass converted to inorganic, 130

    burial, 162, 438

    carbon pump and atmospheric, 4612

    decomposition, flux, 162

    degradation, 224

    delivery, 129, 130

    DOC and release of, 1389

    DOC production during decomposition

    of sedimentary organic, 142

    DOM and aquatic system flow of, 137

    fossil, 130

    incorporation of, 224

    inorganic, 129, 130

    lithosphere transformation of, 130

    marine sediment preservation of, 1656

    methane reduction from methyl, 393, 395

    microbial mat cycling of, 4758, 479

    microbial oxidation processes and

    burial, 1625

    mineralization, 131

    nitrogen and, 224

    nitrogen, ratio, 220, 221, 224, 226, 228

    ocean as sink for, 462

    OET and preservation of, 164

    organic, 132, 142, 175

    oxidation, 131

    phosphorus, ratio, 42930, 438

    phosphorus regeneration from sediments

    and, 4378

    photosynthetic production of organic, 175

    phytoplankton and carbon pump, 4612

    phytoplankton, photosynthesis uptake

    of, 4612

  • 610 SUBJECT INDEXCarbon. (cont.)

    preservation, 1626

    pump, 4612

    recycled, 162

    reservoir, earth of, 130

    sediment, 499505

    sediment depth and nitrogen, ratio, 228

    sedimentation rate and preservation of, 164

    silica and biological, pump, 4612

    silicon and, 441

    sink, 462

    sulfate reduction and availability of, 338

    surface pool cycling of, 130, 162

    transformations, 224

    Carbon assimilation, 1559, 404

    Carbon fixation

    reductive acetyl-CoA pathway, reductive

    of, 10910, 111, 112, 114

    aerobic methanotroph, 4025

    anaerobe energy demand for, 112

    ancestral, 114

    ATP demand of pathways for, 111, 112

    Calvin, 234

    Calvin cycle, 80

    Calvin-Benson-Bassham cycle, 1745

    Chemotroph, 98, 99

    eYciency, 115

    energetics, 11113

    energy demand, 112, 113

    energy, pathway of, 111

    environmental situations supporting, 96

    induced, 97

    isotope fractionation during, 1203

    organic material, 98, 105

    pathways, 10511, 112, 11314

    reductive pentose phosphate cycle,

    reductive of, 1058, 113, 11516

    photosynthesis, 492

    phototrophy and, 95127

    prokaryotic organism isotope fractionation

    during, 120, 123

    reductive citric acid cycle, 1089, 112,

    114, 1223

    Rubisco and, 108, 116

    steps in, 98

    sulfate reduction and, 334

    3-hydroxypropionate cycle, 111, 112, 113

    Tree of Life lineages identified pathways

    of, 11314

    Carbon metabolism

    carbon assimilation and, 1559detritus food chain and, 13244

    heterotrophic, 12966

    respiration pathway partitioning

    of, 1523, 154

    Carbon mineralization, 1525, 306

    ammonification and heterotrophic, 220

    anaerobic, 306, 399

    anoxic sediment, 227

    benthic, 31011

    denitrification and, 481, 482

    heterotrophic, 220

    iron reduction and benthic, 31011

    manganese reduction and benthic, 31011

    manganese reduction pathway for, 154, 155

    mangrove forest, 5002

    methanogenesis, 3979

    pathways, 154, 155, 323

    shallow water environment sulfate

    reduction and, 3223

    sulfate reduction and, 320, 3223, 3979

    Carbon oxidation, 3034, 306

    aerobic, 1447

    anaerobic, 14755

    aquatic sediments and aerobic, 145

    fermentation and anaerobic, 14850

    hydrolysis and anaerobic, 14850

    iron as electron acceptor for, 311

    iron reduction and, 31011

    iron respiration and, 500

    manganese reduction, microbial

    and, 310, 311

    mangrove sediment, 500

    metal oxide reduction and, 310

    microorganism, anaerobic, 500

    nitrate respiration and, 1525

    nitrogen mineralization and, 2278

    oxygen respiration and shallow

    sediment, 153

    oxygen-containing radicals and

    aerobic, 1445

    respiration, anaerobic and, 1502

    sulfate reduction, 322, 338

    sulfate reduction and sediment depth

    of, 154, 155

    water column, 146

    Catabolic metabolism, 131

    aerobic processes and, 144

    ATP generated by, 131

    chemotrophic, 131, 132

    decomposition in, 131

    energy, non-growth requirements for, 158

  • SUBJECT INDEX 611fermentation in, 131

    oxidative reactions of, 156

    respiration and, 131

    Cell biochemistry, 808

    anabolism, 801

    catabolism, 801

    electron carriers, mobile in, 812

    energy gain in, 801

    membrane-bound electron carriers and, 82

    oxidative phosphorylation and, 82

    Cell numbers

    lake/marine, 30, 36

    in nature, 369

    Cell size, 247

    cell contents and, 25

    cytoplasm/vacuole volume in, 27

    large, 27

    metabolism and, 25

    microbe, 35

    minimum, 25

    Cells

    chemostate and growth rates of, 32

    cytoplasm/vacuole volume in, 27

    death, 29, 367

    diVerentiation, 614

    diVusion-limited growth of, 245

    DOC utilization within, 97

    energy derivation by, 80

    energy, maintenance for, 29

    functional/morphological diVerentiation

    of, 612

    growth, 245, 2839

    morphological diVerentiation in, 623

    MPN enumeration of, 356

    plasmid functions for, 61

    population density of, 33

    population growth, 2839

    salinity and adaption of, 45

    substrate uptake/growth of, 2832

    Chemoautotrophic organism

    ecosystems, 1237

    ammonium oxidation by, 2345

    anammox and, 2612

    chemoautotrophic cave ecosystem as, 125

    hydrothermal vent systems as, 1235

    nitrate ammonification by, 253

    nitrification, 2357, 241

    pH and nitrification with, 241

    phylogeny of nitrification by, 2357

    subsurface biosphere as, 1257

    Chemolithoautotroph, 94, 96Chemostats, 33

    biomass production in, 33

    microorganism growth physiology and, 33

    population growth in, 33

    substrate concentration in, 33

    Chemotroph, 923, 97

    Chlorobium

    lower light adaptation of, 489

    reductive citric acid cycle for, 109, 110

    Rubisco in, 108, 116

    Chloroflexus, 111, 1135, 3657

    Chloroplasts, 18

    Chondromyces apiculatus, 62

    Chromatium vinosum, 48990

    Chromatium weissei, 48990

    Clausius-Clapeyron equation, 74

    Commensalism, 50, 56

    Compatible solutes, 45

    Competition, 502, 901

    Conjugation, 61

    Continuous culture, 33

    Cyanobacteria

    anoxia exposure of, 175

    anoxygenic photosynthesis by, 104

    aquatic system, 174

    carbon fixation through the Calvin-

    Benson-Bassham cycle in, 1745

    carbon limitation and, 1212

    cell diameters for, 1756

    characteristics of, 1746

    diazotrophic, 179

    diversity, 469

    ecological niches of, 173

    environmental, 17680

    eukaryote microalgae and, 178

    evolution, 17980

    freshwater, 176

    geobiology, 17980

    growing conditions, extreme for, 176

    growth of, 175, 176

    iron requirements for, 179

    marine, 176

    metabolic traits of, 173

    microbial mat depth and, 467, 468

    microbial mat oxygen concentration

    and, 467

    nitrogen fixation and, 174, 175, 176,

    21516, 218

    nitrogenase inactivation and

    phototrophic, 215

    oxygen respiration growth of, 175

  • 612 SUBJECT INDEXCyanobacteria (cont.)

    oxygenation of Earths surface by,

    169, 180

    photoheterotrophic growth of, 175

    photosynthesis, 1789, 474, 476

    photosynthesis nitrogen demands and, 179

    photosystems of, 180

    Prochlorococcus as, 1767

    as prochlorophytes, 174

    reducing conditions and, 104

    representatives, 1767

    Rubisco, 1745

    Synechococcus as, 1767

    temperature and growth of, 176

    Trichodesmium as, 176, 21516

    visual identification of, 1756

    water column depth and, 1778

    water-spliting complex of, 180

    Davies equation, 72

    Dead particle organic carbon (DPOC), 130

    Deamination

    ammonium, 2203

    non-oxidative amino acid, 222

    nucleotide, 222

    oxidative, 222

    Debye-Huckel equation, 712

    Denitrification, 32, 251, 252

    adaptation, environment of, 255

    animal influence on, 257, 2589

    aquatic sediment, 247, 248, 2546, 259

    Bacteria, 254

    biochemistry, 24953

    carbon mineralization through, 481, 482

    diversity and, 256

    environmental factors aVecting, 25661

    enzymes, 254

    factors influencing, 25661

    invertebrates, burrowing and, 259

    iron oxidation and, 284

    iron-based, 284

    isotope fractionation associated with, 2634

    macrophyte communities and sediment, 257

    mangrove forest, 503

    marine sediment population diversity

    and, 2545

    measuring, 245, 2467

    Michaelis-Menten kinetics for, 256

    microelectrode measuring of, 2456

    nir gene in, 253, 254, 255

    nitrate, 247, 248, 258, 265nitrate concentration and, 256

    nitrite, 249

    nitrogen cycle, 247

    nitrogen, from nitrite, 251

    nitrogen isotope pairing technique for

    measuring, 245, 247

    nitrogen produced by, 245, 2634

    nitrogen reductase and, 249

    oceanic oxygen minimum zone, 259, 481

    oxic zone thickness and, 256

    oxygen absence and, 255

    pH and, 251

    phylogenic diversity and, 254

    phylogeny detection of, 2535

    plant influence on, 25960

    respiratory reduction steps of, 24751

    sediment, 240, 2478, 2545, 258, 25...