[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, 259, 265

    sediment depth and, 240, 260

    stream sediment, 2478

    substrate availability and, 255

    temperature and, 255, 25960

    time of day for, 260

    trace element deficiency and, 251

    water column nitrate, 258

    Desulfoarculus baarsii, 184

    Desulfobacter

    acetate oxidation by, 20

    evolutionary distance between species

    of genus, 12

    Desulfobotulus sapovarans, 14, 21

    Desulfotignum phosphitoxidans, 331

    Desulfovibrio, 21

    evolutionary distance between species

    of genus, 12

    lactate utilization by, 201

    Desulfovibrio desulfuricans

    growth stages, 28

    nitrite reductase purified from, 252

    oxidation by incomplete, 3313

    Desulfovibrio oxyclinae, 3367

    Desulfuromonas, 343

    Detritus

    anaerobic decomposition degradation

    of, 1478

    composition, 1323

    decomposition, 137, 160

    DOM and, 13744

    fungi as decomposers of, 134

    herbivores supplementing nutrition

    with, 135

    mangrove forest handling of, 4969

  • SUBJECT INDEX 613mangrove forest microbial decomposition

    of, 498

    microorganisms and breakdown of, 134

    nitrogen reservoirs of dead organic, 208

    organisms decomposing, 1347

    prokaryotes as decomposers of, 134

    sediment decomposition of, 228

    Detritus food chain, 13244

    chemical nature of, 1323

    macroalgae as source in, 132

    phytoplankton as source in, 132

    plant/algae chemical composition

    and, 132, 134

    vascular plants as source in, 132

    Detritus pool, 130, 132, 133, 137

    Diatom

    asexual cell division of, 445

    BSi production and aquatic, 445

    carbon pump, 4612

    DSi access and presence of, 4589

    DSi extraction from sea water by, 463

    DSi inhibited growth of, 4601

    DSi uptake by, 449

    evolution, 463

    frustules, 443, 445, 446

    growth, 450

    microbial mat surface population of, 467

    nucleation/growth of, valves, 449

    sediment burial and dissolved frustules

    of, 453

    silica content in, 446

    silica dissolution from, pH and, 452

    silica formed by, 44550

    silica in frustules of marine, 445

    temperature and growth of, 450

    valves, 446, 44950

    Diazotrophs

    aerobic, 215

    energy metabolism of, 209, 210

    microaerophilic, 215

    nitrogen fixation by, 215

    nitrogenase protected from oxygen

    by, 21415

    DIC. see Dissolved inorganic carbon

    DiVusion, 24

    growth limited by, 245

    oxic-anoxic interface and, 259

    oxygen microgradients and, 1967

    solute transport in stagnant water columns

    and, 196

    timescale, 24Dioxygenases, 180, 181

    DIP. see Dissolved inorganic phosphorus

    Disproportionation

    acetate, 390

    isotope fractionation and sulfur, 379, 380

    metabolism and, 371, 372

    physiological adaptations to sulfur, 373

    sulfite, 374, 379

    sulfur, 3714, 379, 380

    sulfur oxidation, 3704

    thermodynamics of, 372

    thiosulfate, 368, 3734

    Dissimilatory sulfite reductase (DSR)

    gene, 3267

    gene transfer and, 327, 328

    rRNA and, 327, 328

    Dissolved inorganic carbon (DIC), 4758,

    479, 480

    Dissolved inorganic phosphorus (DIP), 427

    DOP mineralization to, 435

    ocean surface water, 4334, 435

    phytoplankton assimilation of, 4345

    sediment release of, 439

    Dissolved organic carbon (DOC)

    aquatic environment delivery of, 138

    bacteria energy source, 194

    carbon decomposition and production

    of, 142

    carbon released as, 138

    cellular utilization of, 97

    heterotrophic prokaryote consumption

    of, 140

    purple nonsulfur bacteria, 363

    reactive organic matter rate and

    concentration of, 1423

    sediment, 143

    size, 140

    source, 1434

    turnover time for oceanic, 140

    water-column, 143

    Dissolved organic matter (DOM), 55

    aquatic, 137, 139

    biochemical classes, 137

    carbon flow in aquatic systems and, 137

    chemical composition of, 1378

    concentration, 138, 13940

    definition, 137

    detritus and, 130, 13744

    land entry of, 139

    mangrove forest, 499

    marine, 139

  • 614 SUBJECT INDEXDissolved organic matter (DOM) (cont.)

    microbial loop, 1412

    phytoplankton release of, 138

    plant release of, 138

    refractory, 143

    size, 137

    sources, 138

    Dissolved organic phosphorus

    (DOP), 4334, 435

    DIP mineralization from, 435

    as phosphorus source, 435

    recycled polymeric, 436

    Dissolved silica (DSi), 4423

    accumulation, 453

    aquatic environment and, 4423, 458, 459,

    460, 461

    assimilation, 445

    benthic infauna stimulating release of, 454

    biological uptake depletion of, 443

    Black Sea coastal water concentrations

    of, 460, 461

    BSi dissolution and temporal development

    of, 450, 451

    concentrations of, 460, 461, 462

    decreasing levels of, 458, 459

    depletion, 443, 458, 459, 460, 461

    diatom growth inhibited by, 45960

    diatom presence and access to, 4578

    diatom uptake of, 449

    diatoms and oceanic extraction of, 463

    fluxes, 454

    human influence on depletion of, 460

    macrofauna and fluxes of, 454

    Michaelis-Menten kinetics and, 449

    Michigan, lake and depleted, 459

    Monod kinetics and, 449

    nitrogen and depletion of, 458

    nutrient loading and depletion of, 459

    oceanic reservoir concentration of, 443, 462

    phosphorus and depletion of, 458

    river damming and depletion of, 460, 461

    riverine load of, 443

    silica saturation concentration and

    accumulation of, 453

    DNA, 35

    DAPI binding to, 126

    mutation of, 5

    PCR and amplification of, 13

    phylogenetic analysis, 13

    phylogeny construction from, 8

    polymerase, 13prokaryote uptake of, 60

    protein synthesis and, 4

    structure, 23

    Thermus aquaticus polymerase of, 13

    viral infection transfer of, 61

    DOM. see Dissolved organic matter

    DOP. see Dissolved inorganic phosphorus;

    Dissolved organic phosphorus

    DPOC. see Dead particulate organic carbon

    DSi. see Dissolved silica

    DSR. see Dissimilatory sulfite reductase gene

    E. coli. see Escherichia coli

    Electrode potential

    anoxygenic phototroph electron donor

    and, 104

    electron tower and, 79, 812

    environment and calculation of, 80

    equilibrium constant and, 78

    Gibbs free energy and, 77

    in nature, 78

    non-standard condition, 7880

    oxidation, glucose and, 77

    pH and, 79

    redox reactions and, 76

    SHE and, 76, 79

    Electron acceptors

    anaerobic, 311

    Beggiatoa, 355

    general considerations, 132, 1448,

    1505, 1701

    iron as carbon oxidation, 311

    iron reduction, 298

    manganese reduction, 298

    sulfate as anaerobic, 311

    thermodynamics, 88-90

    vertical distribution of, 1512

    Electron donors, 1945

    AOM, 41314

    competition for, 902

    concentration, 87, 91

    electrode potential and anoxygenic

    phototrophs, 104

    electron shuttles and oxidation of, 297

    electron transfer, 82, 83

    electrons replenished by oxidation

    of reduced, 104, 105

    free energy gain and oxidation of, 89

    hydrogen, 868, 967, 401

    iron reducer consuming of, 307

    iron reduction, 293, 297, 3001

  • SUBJECT INDEX 615manganese reduction, 293, 297, 3001

    methanogenesis, 397, 401

    nitrification, 233

    oxic-anoxic interface oxygen consumption

    and, 197

    oxidation, 297

    oxygen, 2012

    oxygen respiration, 194

    photosynthesis, 105

    positive redox potential utilization of, 98

    redox pairs, 99

    sulfate reduction activity and, 325, 330, 332,

    3334

    Electron flow

    cyclic, 100, 102, 104ATP production and, 104

    noncyclic, 104

    reverse, 99, 104

    Electron shuttles, 2978

    Electron transfers, 75

    electrode potential and, 757

    electron acceptor in, 82, 83

    electron carriers and, 81

    electron donor in, 82, 83

    metal oxide, 297, 298

    proton motive force and, 82

    redox reactions and, 75

    Electron transport

    ATP synthesis and, 299

    chains, 1857

    electron carriers involved in, 99

    intracellular, 2989

    iron and photosystem, 286

    iron reduction and, 299

    manganese reduction and, 299

    metal oxide respiration and system of, 299

    proton translocation and chain of, 186, 187

    reverse system of, 98, 233

    Energy conservation

    chemoautotrophic, 98

    photosynthesis, 102103

    phototrophic, 99105

    Energy metabolisms

    naming, 924

    Enthalpy, 667

    endothermic reaction and, 67

    formation, 67

    Hesss Law of Summation calculation of, 67

    as state function, 66

    STP-relative definition of, 66

    Entropychange component parts in, 678

    Gibbs free energy and, 6770

    Glutamate dehydrogenase (GDH), 21314

    as state function, 67

    EPS. see Extracellular polymeric substrates

    Equilibrium

    ammonification and porewater/particle

    distribution of, 229, 230

    chemical, evaluation of, 71

    chemical species distribution at, 70

    electrode potential and constant, 78

    oxidation and, 77, 78

    thermodynamically favorable chemical

    reactions and, 70

    Escherichia coli (E. coli)

    branched electron transport chains in, 186

    colony development by, 63

    gene diVerences in, 48

    iron requirement for, 276

    oxygen respiration rate of, 183

    peroxidase-catalyzed reduction in, 183

    phosphate transport system of, 423

    proton translocation and, 187

    substrate concentrations for, 29

    Eukarya

    anaerobiosis in, 188

    Archaea and, 11, 18

    deepest-branching members of, 18

    evolutionary distance in, 11, 12

    membrane-bound nucleus of, 17

    metabolic diversity of, 1718

    oxygen respiration, 188

    rRNA sequence and, 9

    SSU rRNA domain, 11

    Tree of Life domain, 1719

    Eukaryotes

    cellular complexity of, 18

    evolution, 18

    genome, 18

    nitrogen and growth of, 206

    prokaryotes symbiotic relationship

    with, 59

    ribosome subunit of, 8

    Euryarchaeota

    members of Archaea as, 167

    methanogens, 390

    nitrogen fixation and, 216

    Evolution

    carbon fixation pathways, 1136

    cyanobacteria, 17980

    iron reduction, 2934

  • 616 SUBJECT INDEXEvolution (cont.)

    later gene transfer and, 1920, 254,

    3278

    oxygen respiration, 188190

    photosynthesis, 102, 17980, 369

    phylogeny microbial and, 1214

    Rubisco, 115, 1189

    silica cycle, 4623

    sulfur reduction elemental, 3445

    Extracellular polymeric substrates (EPS), 470

    Extremophiles, 167

    Fermentation

    acetate, 390

    ATP generation and, 858

    oxidation-reduction reactions and reactions

    of, 86

    Ferroglobus placidus, 284

    FISH. see Fluorescent in situ hybridization

    Fluorescent in situ hybridization (FISH), 49

    aerobic bacterioplankton and, 192

    diYculties with, 4950

    microbial diversity visualized with, 49

    probes, 49

    Free energy gain

    electron donor oxidation and, 89

    hydrogen, acetate oxidation and, 89, 90

    in nature, 92

    methanogenesis and, 8990

    organic material oxidation, 1678

    oxic respiration and, 8990

    pH and, 92, 93

    reaction center, 1012, 104

    respiratory processes and, 87, 8990, 91

    sediment depth and, 155

    Fungi, 1415

    detritus decomposed by, 134

    oxidases, 182

    Gas solubility, 734

    Henrys Law and, 734

    oxygen, 1712

    salt influence on, 73, 74

    temperature and, 73, 74

    thermodynamics and, 734

    GDH. see glutamate dehydrogenase

    Gene expression, 634

    Gene transfer, lateral, 254, 327, 328

    phylogeny influence on, 1920

    Genetics, 35Geobacter metallireducens

    electron-shuttling, 297

    iron reduction and, 284

    Gibbs free energy. see also Free energy gain

    component determination in, 689

    electrode potential and, 77

    entropy and, 6770

    environmental conditions and, 6970

    mineralization reactions, 86, 87

    standard, 90

    as state function, 68

    STP, 68

    thermodynamically favorable reaction

    and, 68

    Glutamate, 2223

    Granick hypothesis, 369

    Green nonsulfur bacteria, 358, 359, 3657

    environments, 366

    genera, 361, 366

    green sulfur bacteria and, 3656

    photosynthesis, anoxygenic, 369

    Green sulfur bacteria, 358, 359, 3645

    anaerobes, obligate and, 364

    consortium partner signaling and, 365

    deep-water, 361, 362, 365

    environments for, 3645

    evolution, 369

    genera of, 364

    green nonsulfur bacteria and, 3656

    light and, 364

    photoautotrophic growth of, 364

    phototrophs, obligate and, 364

    purple sulfur bacteria emergence and, 369

    stratified water body, 489

    Growth rate

    depth and water-column bacteria

    microbial, 345

    energy for, 889, 956

    growth yield and, 32

    measurement methods for, 34

    microbial, 889, 195

    microorganism, and temperature, 3943

    osmotic pressure for, 445

    pH and, 434

    water-column bacteria microbial, 345

    Gulfo Dulce

    ammonium oxidation in, 481

    anammox in, 481

    anoxygenic photosynthesis in, 481

    carbon mineralization, 481, 482

    nitrate sulfide oxidation in, 4812

  • SUBJECT INDEX 617sulfide accumulation in, 481

    water chemistry, 481, 482

    Halophilic organisms, 42, 45

    HDOC. see High-molecular-weight dissolved

    organic carbon

    Heliobacteria, 358, 359, 367

    Henrys Law, 734

    Herbivorous animals

    detritus particles as nutrition supplements

    for, 135

    primary production consumed by, 1345

    substrate feeding of, 135

    Hesss Law of Summation, 67

    Heterotrophs, 51, 93, 235, 242

    High-molecular-weight dissolved organic

    carbon (HDOC), 142

    Hydrogen

    autotrophic metabolisms fueled by, 97

    electron donor of, 868, 967, 401

    interspecies transfer of, 878

    methanogenesis and carbon dioxide

    reduction with, 393, 394, 401

    methanogenesis electron donor, 397, 401

    methanogenesis requirement of, 396

    respiratory reactions consuming, 88

    syntrophic relationship with, 878

    water and solubility of, 73, 86

    Hyperthermophiles, 41, 42

    membrane lipids of, 43

    temperature adaption of, 43

    Informational genes, 1920

    Iron. see also Iron reduction, Iron oxidation

    abiotic reduction mobilization of, 2712

    abundance of, continental crust, 269

    assimilation, 2769

    bacteria obtaining, and proteins

    binding, 277

    carbon oxidation and respiration of, 500

    chelators, 2867

    cycles, 269312

    cycles, global, 2702

    cycles, redox, 26970, 271

    denitrification and, 284

    electron transport to photosystem with, 286

    enzymes dependent on, 276

    ferric, 283, 303, 304, 306

    fluxes, benthic, 272

    geochemistry, environmental, 2725

    hydrogen sulfide reduction with, 275isotopes, 312

    manganese and, 270

    mangrove forests rich in, 500, 501

    mobility, 2712, 283

    MR mobilization of, 2712

    oceanic, 271, 277, 2789

    oceanic transportation of, 271, 272

    oxides, 302

    particulate fluxes, oceanic delivery of, 271

    pH and solubility of, 271, 273, 277

    phosphorus and, 426, 433

    piracy, 277

    proteins bound to, 277

    recycled, ocean, 277, 278

    recycling of, 30810

    redox, 26970, 271, 276

    redox reactions, abiotic and, 2745

    requirement, 276

    river particulate speciation of, 273

    sediment, mobilization, 2712

    solubility, 270, 271, 272, 273, 277

    species interaction of, 271, 2723

    sulfide, phases, 316

    as trace element, 276

    uptake of, microorganism, 277

    weathering release of, 2701

    Iron cycles

    iron isotopes and, 312

    oxic-anoxic interface, 271

    sediment resuspension and stimulation

    of, 309

    Iron oxidation, 270, 274, 275

    abiotic, 275

    acidophilic, 2856

    aerobic, neutrophilic bacteria for, 283

    Archaea, 27686

    Bacteria, 2801, 282, 2856

    chemotrophic, 2801

    denitrification and, 284

    energy yielded from, 274, 27980, 285

    evolution, 287

    Ferroglobus placidus growth and nitrate, 284

    iron, ferric mobility and, 283

    kinetics, 2734, 305

    manganese and, 3412, 3456

    microbial, 27989, 308

    nitrate, 282, 2835

    nitrate and ferrous, 285

    oxygen distribution and, 280, 283

    pH and, 285, 286

    pH and phototrophs for, 286

  • 618 SUBJECT INDEXIron oxidation (cont.)

    phosphorus adsorption and, 425

    photoautotrophic growth and, 287

    phototrophs for, anoxygenic, 2867

    problems with, 280

    prokaryotes for, 285

    quinones reduced, 275

    redox potential and phototrophs for,

    274, 286

    sulfide reaction with manganese and, 3456

    sulfur formation, manganese and, 3412

    thermodynamic stability and, 302

    Iron reduction, 270, 2734, 284

    abiotic, 3078

    acidophilic, 301

    aquatic environment microbial, 299312

    aquatic sediment, 303

    Archaea, 291

    bacteria, phylogeny of dissimilatory, 296

    carbon mineralization, benthic and, 31011

    carbon oxidation and, 31011

    carbon source for microbial, 301

    competition, 273, 302

    dissimilatory, 295, 303, 3067, 310, 311

    diversity of microbial, 2914, 299300

    electricity and, 296

    electron acceptors for, 293, 2956, 298

    electron donors for, 293, 2945, 297, 301

    electron transport in, 299

    environmentally important reducers

    for, 299300

    enzymes, 2989

    freshwater environment microbial, 311

    Geobacter metallireducens and, 284

    growth and, 291, 293

    hydrogen and microbial, 301

    iron, ferric and, 303, 304, 306

    kinetics, 2734

    location, outer membrane and activity

    of, 297

    mechanisms of, 2968

    metabolic diversity in, 2946

    metabolism and, 291, 2946

    methanogenesis suppression and, 302

    Michaelis-Menten-type kinetics, 305

    microbial, 290312

    oxide speciation and, 3013

    oxygen and acidophilic, 301

    oxygen and microbial, 300

    phylogenetic diversity for

    dissimilatory, 2934phylogeny of microbial, 2914

    population size of reducers, 307

    quantification of microbial, 3034

    redox potential and, 2901

    reducer groups in, 2912, 293, 295

    sediment microbial, 304, 309

    substrate competition and, 301

    sulfate reduction and, 304, 306, 307

    in vitro activity of, 2989

    water column, 31112

    Isotope fractionation, 2658

    3-hydroxypropionate cycle, 1213

    AOM and, 417, 418

    carbon fixation pathways, 1203

    denitrification and, 266

    denitrification associated, 2656

    iron, 312

    mechanisms, 41718

    methane cycle, 41418

    methane formation pathways and, 416

    methane in aquatic sediments and, 415

    methanogenesis, 41417

    methanotrophy, 41718

    nitrification and, 267

    nitrite availability and, 266

    nitrogen and, 266, 267

    nitrogen fixation, 2667

    nutrient uptake and, 267

    oxygen, 2024

    phytoplankton expression of, 266, 268

    reductive acetyl-CoA pathway, 1213

    reductive citric acid cycle, 1213

    reductive pentose phosphate cycle, 1213

    sediment denitrification and, 266

    sulfate reduction, 3758

    sulfur compounds, 3748

    sulfur compound disproportionation,

    379381

    sulfur oxidation, 3789

    temperature and, 416, 417

    Kinetics

    decomposition, 15962

    degradability, 15962

    iron oxidation, 2734

    iron reduction, 2734

    manganese oxidation, 2734, 305

    manganese reduction, 2734

    methane oxidation, 407, 408

    methanotrophy, 4079

    oxygen consumption, 193

  • SUBJECT INDEX 619oxygen respiration, 193

    regulation and, 1878

    Kinetics, Michaelis-Menten, 301

    ammonium oxidation and, 23940

    denitrification and, 256

    DSi and, 449

    iron reduction, 305

    methanogenesis, 400

    microbial growth and, 36

    nitrite oxidation and, 2412

    sulfide oxidation, biological and, 347

    Krebs cycle, 109, 114

    LDOC. see Low-molecular-weight dissolved

    organic carbon

    Lithotroph, 93

    Living particulate organic carbon

    (LOPC), 1291

    LOPC. see Living particulate organic carbon

    Low-molecular-weight dissolved organic

    carbon (LDOC), 142

    Mahoney Lake, 4867

    chemolithoautotrophic organisms in, 487

    chemoorganoheterotrophic organisms

    in, 487

    density stratification, 486

    light distribution and density stratification

    of, 486

    salinity gradient of, 486

    sulfate reduction, 486, 487

    sulfide oxidation in, 487, 488

    Manganese

    abiotic reduction mobilization of, 2712

    abundance, continental crust, 270

    assimilation, 2769

    availability, 2767

    cycles, 269312

    cycles, global, 2702

    cycles, redox, 271

    geochemistry, environmental, 2725

    iron and, 270, 280

    isotopes, 312

    mobilization, sediment of, 2712

    MR mobilization of, 2712

    nitrite to nitrate oxidation with, 275

    oceanic transportation of, 271, 272

    oxic-anoxic interface cycles, redox, 271

    particulate fluxes, oceanic delivery of, 271

    pH and solubility of, 271, 273

    redox reactions and, 2745requirement, 2767

    river particulate speciation of, 273

    sediment retention of, 289

    solubility, 270, 271, 272, 273

    solubility of oxidized, 270, 271

    species interaction of, 271, 2723

    as trace element, 276

    uptake of, microorganism, 277

    weathering release of, 2701

    Manganese cycles, 309

    Manganese oxidation, 270, 271, 275, 303

    abiotic, 275

    ammonium reduced, 275

    aquatic environment microbial, 289, 290

    diversity and, 303

    energy yielded from, 27980, 2889

    hydrogen sulfide reduced, 275

    kinetics, 2734, 305

    microbial, 27989, 290

    multi-copper oxidase and microbial, 289

    nitrate, 289

    oxidizers, 288

    problem with, 280

    reduction of, 308

    sediment biogeochemistry and, 289

    sulfide reaction with iron and, 3456

    Manganese reduction, 154, 155, 270, 2734

    ammonium as electron donor for, 2945

    aquatic environment microbial, 299312

    carbon mineralization, benthic and, 31011

    carbon oxidation and microbial, 310, 311

    carbon source for microbial, 301

    controls of microbial, 3003

    dissimilatory, 2934, 303, 310, 311

    diversity of microbial, 2914, 299300

    electron acceptors for, 293, 2956, 298

    electron donors for, 293, 2945, 297,

    300, 301

    electron transport in, 299

    kinetics, 2734

    mechanisms of, 2968

    metabolic diversity in, 2946

    microbial, 290312

    nitrate reduction competition with, 301

    oxide, 297

    oxide speciation and, 3013

    oxygen and microbial, 300

    phylogenetic diversity for

    dissimilatory, 2934

    phylogeny of microbial, 2914

    quantification of microbial, 3034

  • 620 SUBJECT INDEXManganese reduction (cont.)

    recycling, 30810

    reducers, 2912, 293, 299300

    sediment microbial, 304, 309

    substrate competition and, 301

    versatility of reducers in, 295

    water column, 31112

    Mangrove forests, 493506

    algae in, 496

    basin, 493

    carbon mineralization in, 5002

    carbon nitrogen ratio and, 495, 499, 502

    carbon oxidation in sediment of, 500

    creeks, 5056

    definition, 4936

    denitrification rates and sewage discharges

    in, 503

    detritus decomposition by microbes

    and, 498

    detritus handling in, 4969

    DOM, leached and, 499

    food webs, 4969

    iron-rich, 500, 501

    litter, 496, 4989, 502

    litter nutrient content in, 498

    matter/nutrients exported from, 505

    nitrogen demand in, 502, 504

    nitrogen fixation in sediments of, 5045

    nitrogen importation by creeks in, 506

    nitrogen retention/recycling in, 502

    phosphorus importation by creeks in, 506

    primary production rates in waterways

    of, 505

    respiration and sediments in, 500

    riverine, 493

    sediment carbon and nitrogen in, 495,

    499505

    sediment decay of litter in, 4989

    sediments, 4946, 499, 500, 5045

    sewage discharges in, 503

    tidal elevation in, 502, 503, 505

    Marinobacter, 337

    Mehler reaction

    oxygen consumption by, 203

    photosynthesis, terrestrial and, 183

    Mesophiles, 41, 42

    nitrification by, 242

    temperature and nitrification by, 242

    Messenger RNA (mRNA), 4

    Metabolism. see also Anabolic metabolism;

    Carbon metabolism; Catabolic metabolism;Energy metabolisms; Microbial

    metabolism; Oxygen metabolism; Sulfur

    metabolisms

    aerobic, 1878

    amensalism and, 56

    anammox pathway of, 262

    anoxygenic phototroph, 97

    Bacteria and, 1516

    benthic, 1525

    cell size and, 25

    cellular biomass produced by, 1234

    chemolithoheterotrophic, 349

    disproportionation and, 371, 372

    Eukarya, 1718

    free energy, 912

    hydrogen fueled autotrophic, 97

    iron reduction, 291, 2946

    methanotroph, 407

    Michaelis Menten approximation of, 31

    microorganism, and temperature, 3941, 43

    naming an organisms, 934

    nitrifier, 242

    nutrient limitations and, 356

    oxidation-reduction and, 75

    oxidative, 337

    oxygen and aerobic, 1878

    oxygen levels and, 172

    oxygen produced during anoxygenic

    phototroph, 97

    prokaryote, 388

    purple nonsulfur bacteria, 363

    reductive pentose phosphate cycle and

    oxygen, 108, 109

    respiration pathway partitioning

    of benthic, 1525

    sediment, 199

    sediment disruption and measuring, 153

    substrate concentration and, 30, 31

    substrate limitation and increased, 31

    sulfate reducer, 330, 331, 333, 337, 340

    sulfate reducer oxidative, 337

    sulfate reduction, 373, 376, 377

    sulfide oxidation and

    chemolithoheterotrophic, 349, 350

    sulfur, 3434

    sulfur reduction, elemental and, 343

    temperature and, 32, 401, 43, 71, 242

    temperature and nitrifier, 242

    Methane. see also Anaerobic oxidation

    of methane; Methane clathrate hydrate;

    Methanogen

  • SUBJECT INDEX 621atmospheric escape of, 406

    clathrate hydrate formation by, 385, 387

    climate change and release of, 383, 3848

    concentrations, 384, 385

    environmental production of, 400

    formation pathways, 416

    greenhouse gas, 384

    gun hypothesis, 3878

    isotope fractionation and production

    of, 41417

    isotope fractionation between diVerent

    formation pathways of, 416

    marine environment production of, 398, 400

    methanol oxidation, 403

    methanotrophy as microbial oxidation

    of, 402

    methyl carbon reduction to, 393, 395

    microbial oxidation of, 402

    production, 3834, 400

    release, 383, 3848

    sink, 384

    sources, 384, 386, 485

    stratified water body accumulation

    of, 4856

    stratified water body sources for, 485

    sulfate depletion and accumulation

    of, 3967

    sulfate reduction removal of, 410

    Methane clathrate hydrate, 3856, 387

    dissolved, 387

    environment and, 3856

    marine sediment stability of, 3867, 388

    Methane cycle, 383418

    Methane monooxygenase (MMO), 403

    Methane oxidation. see also Anaerobic

    oxidation of methane

    aerobic, 417

    anaerobic, 40914

    initial step of, 403, 404

    intensity, 405, 406

    isotope fractionation and aerobic, 417

    kinetics, 407, 408

    marine sediment, 409

    methanogen, 41112

    methanogenesis and, 412

    sulfate reduction and anaerobic, 411

    Methane oxidation, anaerobic

    sulfate reduction and, 411

    Methanococcus jannaschii, 11617

    Methanogenesis, 383, 388402

    acetate, 393, 395acetate as electron donor for, 397

    acetate required for, 396

    acetoclastic, 390

    acetotrophic, 390

    aquatic environment, 232, 398, 399, 415

    Archaea, 390, 3923

    biochemistry, 3925

    carbon dioxide reduction with

    hydrogen, 393, 394, 401

    carbon mineralization, 3979

    electron donors, 397, 401

    energy conservation and, 393, 404

    energy required for, 394

    environmental significance of, 395402

    fermentation reactions and pathways of, 394

    freshwater environment, 398, 399

    hydrogen as electron donor for, 397, 401

    hydrogen required for, 396

    isotope fractionation, 41417

    methane oxidation and, 412

    methanol and methyl-containing

    compound, 393, 395

    Michaelis-Menten kinetics and, 400

    pathways, 394

    process of, 3923

    substrates for, 38890

    thermodynamics, 400

    Methanogens, 3889

    anoxic environment, 395

    Archaea cluster among, 412, 413

    compounds used by, 389

    energy yield, 395

    Euryarchaeota, 390

    evolution, 3902

    isotope fractionations by diVerent groups

    of, 416, 417

    methane oxidation by, 41112

    methylamine as substrates for, 390

    orders of, 391, 392

    phylogeny, 3902, 412, 413

    sulfate reducing conditions and, 400

    sulfur reducer co-occurance with, 397

    taxonomy, 3902

    Methanol

    ATP formation and, 4045

    formaldehyde conversion from, 403, 404

    Methanotrophs

    activity, 4078

    aerobic, 4029

    animals, invertebrate symbiotic relationship

    with, 4067

  • 622 SUBJECT INDEXMethanotrophs (cont.)

    carbon fixation pathways for aerobic, 4025

    environmental distribution of, 4057

    metabolism, 407

    Methylococcacaea, 402, 403

    Methylocystaceae, 403

    organisms for aerobic, 4025

    oxygen concentrations, 4089

    phylogeny for aerobic, 4025

    significance of, 4057

    Methanotrophy, 15, 40214

    ammonium inhibition of, 406

    anoxic conditions of, 402

    factors limiting, 407

    isotope fractionation and, 41718

    kinetics, 4079

    methanotroph groups for, 402, 403

    microbial biomass production during, 418

    Methylococcacaea, 402, 403

    Methylocystaceae, 403

    Methylotrophs, 402

    MGE. see Microbial growth eYciency

    Microaerophilic organisms, 144

    Microbial diversity, 4650

    extreme environments and, 46

    FISH visualization of, 49

    functional, 49

    molecular studies and, 479

    phenotypic, 46

    species, 47, 49

    stress and, 46

    true, 48

    Microbial ecosystems, 465506

    mangrove forest, 493506

    microbial mat, 46680

    stratified water body, 48093

    Microbial growth, 2836

    basic constituents of, 155, 156

    Microbial growth eYciency (MGE), 157

    anabolic process energy and reduced, 158

    anoxic sediments and low, 1589

    factors regulating, 2836, 1578

    variation in, 59, 157

    Microbial interactions, 5060

    amensalism as, 56

    commensalism as, 50, 56

    competition as, 502, 901

    mutualism as, 57

    neutralism as, 567

    parasitism as, 535

    predation as, 535symbiosis as, 5760

    synergism as, 53

    syntrophy as, 53

    Microbial loop

    DOM in, 1412

    importance of, 1412

    prokaryotes in, 141

    Microbial mats, 46580

    ammonia sequestered by nighttime

    community of, 47880

    anoxygenic phototrophic, 466

    biogeochemistry, 47480

    carbon cycling within, 4758, 479

    carbon source for, 475

    characteristics of, 46970

    chemical constituent measurement with

    microsensors in, 466

    cyanobacteria density and, 467, 468

    depth, 467, 468, 4712

    DIC diVusion from, 478, 480

    DIC sources in, 478

    diversity, 469

    ecology, 4704

    ecosystem structure of, 46770

    elements cycling internally in, 4758

    EPS stabilizing, 470

    light in, 466, 4723

    light measurement with microsensors in, 466

    Microcoleus chthonoplastes

    dominated, 468, 470

    organism migration with light in, 4723

    organisms and depth of, 4712

    oxygen concentration in, 467, 474, 478

    oxygen consumption in, 475, 478

    oxygen cycling in, 478

    oxygen diVusion into, 480

    oxygenic phototrophic, 466

    pH in, 466, 474

    photosaturation, 4701

    photosynthesis, 470, 474

    phototrophic, 466, 469, 470

    population structure of, 467469

    primary production of, 474, 476

    salinity, 475, 476

    sulfate reduction and temperature in, 473

    sulfide accumulation in, 474

    temperature and, 473, 474

    vertical structure, 467, 468

    Microbial populations

    acetate concentration and, 39

    acetate utilization and, 378

  • SUBJECT INDEX 623amensalism and, 56

    carbon content and, 37, 38

    cell diVerentiation in, 614

    cell size and, 356

    commensalism in, 50, 56

    competition between, 66

    controlling processes of, 36

    density, 37, 38

    diversity, 4550

    ecology, 4560

    energy, activation for, 41

    factors influencing, 37

    FISH visualizing structure of, 49

    growth, 2364

    horizontal gene transfer and ecology

    of, 601

    identity prediction in, 47

    Michaelis-Menten-like kinetics and growth

    of, 36

    morphological diVerentiation in, 623

    neutralism in, 567

    nutrient limitations and, 35

    overpopulation, 34

    phenotypic diversity in, 456

    quorum sensing in, 63

    sediment depth and, 39

    social behavior, 614

    stratified water body positioning of, 480

    structure of, 2364

    substrate and colonization by, 137

    substrate limitations and, 51

    synergism, 53

    syntrophy, 53

    thermodynamics and competition

    between, 66

    viral infection control of, 55

    Microbial production (MP), 157

    Microbial respiration (MR), 157

    iron mobilization with, 2712

    manganese mobilization with, 2712

    natural environment, 190203

    Microcoleus chthonoplastes, 468, 470

    Microorganisms

    ammonium assimilation and, 228, 229

    anaerobic respiring of, 150

    aquatic environment particulate/organic

    polymer degradation by, 144, 145

    Arrhenius equation/temperature and, 412

    chemostat and growth physiology of, 33

    classification, 12

    classification, comparative biology of, 2detritus breakdown by, 134

    energy for growth of, 131

    environmental extremes and, 3945

    growth, 32, 131

    growth temperature for, 40

    iron uptake by, 277

    manganese uptake by, 277

    metabolism temperature for, 401, 71

    pH and, 434

    physiological similarities and competition

    between, 501

    salt and, 445

    temperature and, 403, 71

    toxic oxygen protection by, 145

    Mitochondria, 18, 19

    MMO. see Methane monooxygenase

    Monera, 1415

    Monod equation, 2930

    chemostat population growth and, 33

    DSi and, 449

    Monooxygenases, 181

    Most probable number (MPN), 36

    MP. see Microbial production

    MPN. see Most probable number

    MR. see Microbial respiration

    Mutualism, 57

    Nanobacteria, 25, 26

    Neutralism, 567

    Neutrophiles, 434

    nifH gene

    Bacteria containing, 217

    cluster organization and phylogeny of, 216

    copies, 217

    nitrogen fixation pathway and, 216, 217

    phylogeny, 216, 217

    Nitrate, 2067. see also Nitrate reduction

    ammonification, 2513, 259, 260

    ammonium oxidation to, 233

    ammonium reduction of, 251

    chemolithoautotrophic ammonification

    of, 253

    denitrification and, 250, 256, 265

    diVusion, 256, 258

    glucose fermentation by ammonifiers

    of, 2503

    iron oxidation with, 282, 2835

    isotope fractionation and denitrification

    from, 266

    manganese oxidation with, 289

    nitrification production of, 232

  • 624 SUBJECT INDEXNitrate (cont.)

    nitrite respiratory transformation

    to, 252, 263

    nitrogen detrification from, 250

    oxygen dependence by, 2569

    reductase, 249

    sediment, coastal marine ammonifiers

    of, 252

    sediment diVusion of, 256

    sediment production of, 256, 258

    stratified water body forms of, 484, 485

    stratified water body interface between

    ammonium and, 484, 485

    sulfide oxidation, 253, 351

    temperature and ammonification of, 259

    Nitrate reduction

    Beggiatoa, 351

    dissimilatory, 24651

    manganese reduction competition with, 301

    nitrite intermediate in, 246

    pathways, 2467

    prokaryotes for, 2467

    sediment, 247

    Thiomargarita, 351

    Nitrification, 2325, 266

    ammonium availability and, 237

    ammonium oxidation step in, 239

    anammox and oxic, 261

    anoxia tolerance and, 239

    aquatic environment, 2412

    bacteria, 233, 234

    biochemistry, 2335

    chemolithoautotroph, 2357

    determining total, 247

    electron donors for, 233

    environmental factors aVecting rates

    of, 2375

    heterotroph, 235, 236, 242

    inhibitors, 245

    invertebrates, burrowing and, 257

    isotope fractionation and, 266

    light and, 237, 245

    measuring, 245, 2467

    mesophilic, 242

    metabolism and temperature for, 242

    microelectrode measuring of, 2456

    nitrate produced by, 232

    nitrogen fluxes and measuring, 245

    nitrogen isotope pairing technique for

    measuring, 2478

    nitrogen loss and, 232Nitrosomonas, 234

    oxic, 261

    oxygen availability and, 237, 238, 239, 243

    pH and, 237, 2412

    pH, optimal for, 241

    phylogeny of chemolithoautotroph, 2357

    salinity and, 237, 244

    salinity sensitivity of Nitrosomonas, 244

    sediment, 2389, 2412, 243

    sediment depth and, 240

    stream sediment, 2478, 249

    substrate concentrations and, 240

    substrates for, 23840

    sulfide concentration and, 237

    temperature and, 237, 2423

    temperature and oxygen availability for, 243

    temperature and shallow water

    sediment, 243

    thermodynamics, 2335

    Nitrite, 2067

    detoxification, 251

    diVusion, 257, 258

    isotope fractionation and availability of, 265

    light and oxidation of, 245

    Michaelis-Menten kinetics and oxidation

    of, 23940

    nitrate respiratory transformation

    from, 252, 263

    nitrification and oxidation to, 232

    oxidation, 23940, 245

    oxidizers, 2367

    reductase, 249, 252

    Nitrobacter

    ammonium oxidized by, 236

    nitrite oxidized by, 237, 238

    Nitrogen. see also Nitrification; Nitrogen

    isotope pairing technique

    ammonia reduced from, 213

    ammonification, 206, 21920

    ammonium fixed from, 207

    anammox, 2623

    anammox and sediment production

    of, 2623

    assimilation, 21932, 2667

    biological importance and pool size of, 208

    biologically available forms of fixed, 2078

    budgets, 2189, 230, 232

    carbon and, 224

    carbon, ratio, 220, 221, 224, 226, 228

    cell biomass incorporation of dissolved

    inorganic, 224

  • SUBJECT INDEX 625decomposition removal of, 220, 221

    deficiency, 264

    degradation, 224

    denitrification measured by production

    of, 245

    denitrification produced, 263

    DSi depletion and, 459

    eukaryote growth requirement of, 206

    excess, 224, 225

    fixed, 2078, 209

    freshwater lake limitation of, 218

    immobilization, 2235, 226

    incorporation, 223

    inventory, 422

    isotopes, 264

    liberation, 207

    limitation, 218

    loss, 2067, 20910, 211, 232

    mangrove creek importation of, 506

    mangrove forest demand of, 502, 504

    mangrove forest retention/recycling of, 502

    marine budgets for, 2189

    marine, coastal cycling of, 2302

    measuring incorporation of, 223

    new, 2302

    nitrite as oxidized form of, 2067

    nitrogen fixation replacing lost, 210, 219

    nitrogen fixation supplying open water

    ecosystems with, 218

    nitrogenase and ammonia reduced

    from, 213

    non biological sources of fixed, 209

    oceanic, 220, 2302, 422

    organic, 219, 220

    organic, deep sea, 220

    pelagic ecosystem, 2302

    phosphorus, ratio, 422

    phytoplankton demand of, 230

    phytoplankton growth and, 433

    recycling, 207

    redox cycling and, 206

    reductase, 2501

    regenerated, 2302

    reservoirs, atmospheric, 208

    reservoirs, earth, 207

    reservoirs of, dead organic detritus in, 208

    sediment, 499505

    sediment depth and carbon, ratio, 228

    sediment depth and incorporation of, 228

    sediment production of, 2634

    sediment surface deposited, 232sources, 230, 231, 232

    transformations, 224

    water column regeneration of, 230

    Nitrogen cycling, 20568

    denitrification, 249

    human perturbation in global, 2079

    isotope fractionation and, 2637

    nitrification and, 232

    Nitrogen fixation, 206, 209, 2667

    acetylene reduction assay and study

    of, 2112

    ammonium formed during, 2134

    anaerobes, obligate for, 215

    aquatic environment, 2189

    ATP and, 213

    benthic, 219

    biological, 20919

    Bradyrhizobium japonicum, 188

    cellular material incorporation

    of ammonium formed during, 2134

    cyanobacteria and, 174, 175, 176, 2156, 218

    cyanobacteria and planktonic, 218

    diazotroph, 209, 215

    industrial, 209

    industrial v. prokaryote, 210

    isotope fractionation and, 266

    land biological, 209

    mangrove sediment, 5045

    marine environment biological, 209

    measuring, 2112

    nifH gene and pathway of, 2167

    nitrogen replaced by, 210, 219

    nitrogen source for, 266

    nitrogen supplied to open water ecosystems

    through, 218

    organisms for, 2167

    pelagic, 218

    photosynthesis separated from, 215

    phylogeny of organisms for, 2167

    planktonic, 218

    prokaryote, 209, 210

    prokaryote mediation of benthic, 219

    prokaryote v. industrial, 210

    seagrass bed, 219

    sediment, 218, 219

    Trichodesmium, 2156

    wetlands, 219

    Nitrogen isotope pairing technique, 245,

    2478

    denitrification measured with, 245, 2478

    nitrification measured with, 245, 2478

  • 626 SUBJECT INDEXNitrogen mineralization, 219, 220, 2259

    anaerobic, 2259

    anoxic pathways of, 227

    carbon oxidation and, 2278

    microbial, 2234

    nitrogen, excess and, 224, 225

    oxic water column, 220

    sediment, 2257

    Nitrogen mobilization, 2235

    carbon, ratio and, immobilization, 224, 226

    microbial mineralization and nitrogen

    immobilization and, 224

    Nitrogenase, 2123

    components associated with, 212

    cyanobacteria, phototrophic and

    inactivation of, 215

    diazotroph and protection of, 2145

    dinitrogenase and, 212

    forming/maintaining enzyme complex

    of, 212

    genes, 216, 217

    inactivation, 215

    oxygen and, 2146

    trace metals protein for, 2123

    Nitrosococcus oceanus

    ammonium oxidized by, 2356, 237

    nitrite oxidized by, 236

    Nitrosomonas

    nitrification, 244

    nitrification fractionation by, 266

    NO. see Nitric oxide

    OET. see Oxygen exposure time

    Operational taxonomic units (OTU), 47

    Organelle origin, 18

    Organic matter

    composition, 160

    decomposition, 1601, 163

    mineralization, 8992

    respiration energetics and mineralization

    of, 8992

    Organotroph, 93, 201

    Oscillochloris, 1058, 114, 3667

    OTU. see Operation taxonomic units

    Oxaloacetate, 109, 110

    Oxic-anoxic interface, 1978

    aphotic sediments near, 170, 197

    depth, 200

    diVusion and, 259

    electron donors and oxygen consumption

    near, 197iron redox cycling around, 271

    manganese redox cycling around, 271

    metabolic diversity and, 197

    metabolites reoxidized at, 170, 171

    microbial activity in, 171

    oxygen consumption near, 197

    phosphorus and, 431

    Oxidases, 180, 1813

    bacterial manganese oxidation and

    extracellular, 182

    extracellular, 182

    fungal, 182

    heme copper, 188, 189

    nitric oxide reductase evolution into, 18990

    oxygen respiration terminal, 183

    Oxidation-reduction, 7580. see also Redox

    reactions

    electrode potential and glucose, 77

    electron carriers and reactions of, 81

    fermentation reactions and, 86

    free energy data computation and, 78

    metabolism and, 75

    microbial ecology and, 75

    MR reactions and, 75

    reactions, 75, 80, 81

    SHE, 7576

    Oxygen. see also Oxygenic photosynthesis

    aerobic metabolism and, 1878

    aerobic organisms and, 173

    anaerobic metabolism and levels of, 184

    anaerobic organisms and, 173

    anaerobic respiration and, 187

    anammox and, 264

    anoxia and, 1723

    aquatic sediment, 169, 170

    atmospheric, 1689

    atmospheric production of, 168, 190

    Bacteroides fragilis required saturation

    of, 173

    benthic uptake of, 199

    biosphere, 190

    bottom dwellers and transport of, 170,

    1989

    chemical considerations for, 1703

    consumption, 1467

    cycle, 167204

    denitrification and absence of, 255

    diazotroph protection of nitrogenase

    from, 21415

    diVusion and microgradients of, 1967

    dioxygenase catalyzation of, 180

  • SUBJECT INDEX 627electron donors for, 2012

    environmental budgets for, 1978

    flux, 200

    hydrogen peroxide as source of, 190

    iron, ferrous as electron donor for, 2012

    iron oxidation and, 280, 283

    iron reduction and, 300, 301

    isotopes, 2024

    levels, 172

    limitation, 193, 194

    lingolysis and reactions dependent on, 182

    macrophyte release of, 259

    manganese reduction , microbial and, 300

    metabolism and levels of, 172

    methanotroph, 4089

    microbial mat concentrations of, 474, 478

    microbial mat consumption of, 475, 478

    microbial mat cycling of, 478

    microbial mat diVusion of, 480

    nitrate reduction dependence on, 2568

    nitrification and availability of, 237, 238,

    239, 243

    nitrogenase and, 21416

    oceanic, 1689

    oceanic minimum zones of, 169

    organic matter abiotic reaction with, 172

    oxidation state of, 1701

    photosynthesis and supersaturation

    of, 170, 172

    reactive, species, 1834

    reoxidation and diversion of, 201

    sediment, 146, 338

    sediment penetration by, 146, 200, 257

    sediment rates for uptake of, 199200

    solubility, 1712

    sources, 190

    stratified water body interface between

    sulfide and, 4823, 484

    stratified water body minimum zones of, 481

    stratified water body penetration of, 4823

    sulfate reduction and, 3367

    sulfide reaction rate with, 3467, 4823, 484

    superoxide generated from, 190

    supersaturation, 170, 172

    thermodynamics of, 1678

    transport, 170, 1989

    Oxygen consumption

    anaerobe, 185

    ATP increased yield and non-

    respiratory, 182

    benthic, 200, 2012depth and, 196

    enzymatic processes of, 180

    fauna, 201

    Ficks laws, depth and, 196

    kinetics, 193

    Mehler reaction, 2023

    microbial, 1805

    non-respiratory, 182

    oxic-anoxic interface, electron donors

    and, 197

    oxidases and, 180

    oxygenases and, 180

    photorespiration, 2023

    reactions, 201

    sediments, 198202

    solute, 196

    Oxygen exposure time (OET), 164

    Oxygen respiration, 170, 1858, 2023

    aerobic microbe, 201

    aquatic environment control of, 1936

    Bacteria, 188

    electron donor for, 194

    electron transport chains and, 1857

    Eukarya, 188

    evolution, 18890

    kinetics, 1878, 193

    macroorganism, 201

    nutrients and aquatic environment, 195

    organotrophic, 1978, 199, 2001

    origin, 190

    oxidases, terminal and, 183

    oxidation of manganese and, 198

    oxygen concentration for, 188

    oxygen consumption by, 203

    oxygen reduction to water in, 185

    phylogeny of, 18890

    POC and source of substrate for, 195

    regulation and, 1878

    substrate, 195

    temperature and aquatic environment, 195

    Oxygenases, 180, 182

    Oxygenic photosynthesis, 95, 96, 1045, 168,

    170, 17380, 190

    bacterial, 170, 17380

    isotope fractionation during, 2012

    microbial mats, 47480

    prokaryote, 173

    Parasitism, 535, 57

    Particulate organic carbon (POC), 142

    bacteria energy source, 194

  • 628 SUBJECT INDEXParticulate organic carbon (POC) (cont.)

    oxygen respiration substrate source and, 195

    Particulate organic nitrogen (PON), 266, 267

    PCR. see Polymerase chain reaction

    pH, 434

    aerobic respiration, 191

    cytoplasmic regulation of, 434

    denitrification and, 251

    diatom dissolution of silica and, 453

    electrode potential and, 79

    environmental, 92

    free energy reduction and, 92, 93

    iron oxidation and, 285

    iron oxidizing phototrophs and, 286

    iron solubility and, 271, 273

    manganese solubility and, 271, 273

    microbial mat oxygen concentrations

    and, 474

    nitrification and, 237

    oxidation and, 274, 279, 280, 282

    oxide phases, solid and, 295

    phosphate adsorption by iron

    oxyhydroxide and, 231

    phosphorus adsorption and, 425, 426

    respiration and, 92

    silica, 442, 450, 452

    siliceous rock dissolution and, 457

    Phagocytosis, 53

    Phosphate

    aluminum oxide adsorption of, 425

    aquatic sediment fractionation of, 426, 429

    assimilated, 429

    Escherichia coli transport system of, 423

    immobilized, 430, 431

    iron oxyhydroxide adsorption of, 231

    pH and iron oxyhydroxide adsorption

    of, 231

    phosphite oxidation to, 424

    phosphorus as, 420

    prokaryote storage of, 423

    regenerated, 429

    sequential extraction fractionation

    of sediment, 426

    sink, 431

    Phosphorite

    carbonate fluorapatite forming into, 431

    formation, 4312

    phosphate sink, 431

    sediment, 431

    in situ formation of, 432

    Phosphorus. see also Dissolved inorganicphosphorus; Dissolved organic phosphorus

    abundance, 420

    adsorption, 4245

    anoxic sediment carbon, ratio, 438

    aquatic environment, 422, 4245, 433

    aquatic sediment, 426

    assimilated, 424, 434

    ATP formation and assimilation of, 424

    availability, 419

    bound, 4234

    burial/diagnosis of aquatic sediment, 426

    carbon, ratio, 430, 438

    dissolved, 422

    DOP as source of, 435

    DSi depletion and, 458

    eutrophic lake loading of, 43840

    eutrophication and anoxic condition release

    of, 438

    extraction, 426

    geochemistry, 4245

    inventory, 422

    iron and, 426, 433

    iron oxide adsorption of, 425

    iron, ratio, 433

    mangrove creek importation of, 506

    marine water column, 422

    microbial metabolism, 4224

    nitrogen, ratio, 422

    oceanic, 4201, 422

    oceanic transfer of, 422

    oxic-anoxic interface, 431

    oxidation states of, 419

    pH sensitive adsorption of, 425, 427

    phytoplankton and, 433, 438

    reservoirs, 420, 421

    sediment loading of, 438, 439

    sediment regeneration of, 4378

    sediment release of, 438

    sediments, 420, 426, 4367

    sinks, 422

    soluble, 4234

    sources, 420, 421, 435

    terrestrial incorporation, 421

    Phosphorus cycle, 41940

    aquatic environment, 43240

    global, 4202

    marine sediment, 4368

    microbes in, 42731

    phosphorite formation in, 4312

    seasonal marine sediment, 436, 437

    water column, 4336

  • SUBJECT INDEX 629Photoautotroph

    iron oxidation and growth of, 287

    light harvested by, 99101

    purple sulfur bacteria growth through, 362

    Photolithoautrophy, 95

    Photolithoheterotroph, 94

    Photoorganoheterotrophs, 358

    Photorespiration

    oxygen consumption by, 2023

    photosynthesis, terrestrial and, 183

    Photosynthesis. see also Anoxygenic

    photosynthesis; Oxygenic photosynthesis

    Archaea, 97

    carbon fixation by, 492

    carbon produced by, 175

    cyanobacteria, 1789, 474, 476

    cyanobacteria and nitrogen demands of, 179

    electron donors during, 105

    energy conservation during, 1023

    Granick hypothesis and, 369

    light intensity and anoxygenic, 492

    light intensity and rates of, 178

    Mehler reaction and terrestrial, 183

    microbial mat, 470, 474

    nitrogen fixation separation from, 215

    oxygen supersaturation and, 170, 172

    oxygenic, 287, 369, 491

    oxygen-reduction reactions in, 80

    photorespiration and terrestrial, 183

    phototroph, anoxygenic, 100

    phylogenies obtained from diVerent genes

    of, 370

    purple sulfur bacteria, 362

    stratified water bodies and anoxygenic, 481,

    4903

    temperature and, 474

    Phototroph. see also Photosynthesis

    anoxygenic photosynthesis, 96, 99101,

    2867, 357367

    ATP production and energy conserved

    by, 99

    chlorophyll molecules and oxygen-

    producing, 100

    compound/matter recycling and, 97

    electron flow of oxygenic, 103, 104

    energy conservation and, 99105

    green sulfur bacteria obligate, 364

    iron oxidizing, 274, 2867

    microbial mats and, 470

    oxygenic, 100, 1012, 103, 104

    pH and iron oxidizing, 286photosynthetic process in

    oxygenic, 1012, 103

    photosystems of oxygenic, 102

    redox potential and iron oxidizing, 274, 286

    stratified water body competition between

    anoxygenic, 48790

    sulfide oxidizing, 357367

    Phototrophy, 95127

    Phylogeny, 121

    Archaea, 412, 413

    carbon fixation pathways, 1136

    chemoautotrophic organism ecosystems

    nitrification and, 2357

    constructing, 68, 12

    denitrification and diversity of, 254

    denitrification detection by, 2535

    DNA construction of, 8

    DNA for analysis with, 1213

    genetic element construction of, 67

    iron reduction, dissimilatory, 296

    iron reduction, microbial, 2914

    manganese reduction, microbial, 2914

    methanogens, 3902, 412, 413

    methanotrophs, aerobic, 4025

    molecular sequence analysis and

    information about, 8

    nifH gene, 216, 217

    nitrification, chemolithoautotroph, 2357

    nitrogen fixer, 21617

    oxygen respiration, 18890

    photosynthetic organism genes and, 370

    prokaryote, 6

    reconstruction, 7, 8, 10

    rRNA molecule, 810, 1920

    SSU rRNA, 8, 10, 1920

    sulfate reducer spectrum of, 377

    sulfate reduction, dissimilatory, 3257

    sulfide oxidizer, 3524

    sulfur reduction, 3424

    Phytoplankton

    carbon pump, 4612

    chemical composition of, 133, 134

    as detritus source, 132

    DIP assimilation of, 4345

    DOM released by, 138

    nitrogen and, 230, 433

    nitrogen isotope fractionation expression

    by, 265, 267

    phosphorus and, 433, 438

    Planctomycetes, 18

    Plantae, 1415

  • 630 SUBJECT INDEXPOC. see Particulate organic carbon

    Polymerase chain reaction (PCR), 1213

    PON. see Particulate organic nitrogen

    Predation, 535

    Prochlorococcus

    as cyanobacteria, 1767

    nitrate utilization by, 178

    oceanic distribution of, 177

    photosynthesis compensation intensities

    and, 177, 1789

    water column depth and, 177

    Prokaryotes, 1, 80

    aquatic, oxic environment, 191

    ATP production and cell yield of, 156

    benthic nitrogen fixation mediated by, 219

    carbon fixation by, 10511

    chemical composition of, 1323

    community behavior displayed by, 24

    competitive fitness increase and, 51

    consortia formed between, 58

    constituents, basic for growth of, 155, 156

    death phase of, 28, 29

    denitrification and, 254

    detritus decomposed by, 134

    diazotrophs as, 209

    DNA structure and cataloging of, 23

    DNA uptake and, 60

    DOC consumed by heterotrophic, 140

    eukaryote symbiotic relationship with, 59

    evolution of, 48

    growth absence and energy production

    by, 156

    growth of, 28, 29, 32, 346

    heterotrophic, 1401

    high-molecular-weight compounds

    produced/excreted by, 139

    identification, 2

    iron oxidizing, 285

    lag phase growth of, 28

    lineage organisms of, 191

    metabolic rate, 30

    metabolism, 388

    methane oxidation growth of, 402

    methane production and metabolism of, 388

    microbial loop and, 141

    nitrate-reducing, 2468

    nitrogen fixation by, 209

    organismal phylogenies among, 6

    parasites, 54

    parasitic symbiosis in, 57

    pH, 434phosphate storage by, 423

    phylogenetic grouping of, 23

    physical associations between, 57, 58

    population growth, 28

    predatory behavior exhibited by, 54

    protozoan impact on population of, 54

    protozoan predation of, 535

    protozoans mutualistic symbiosis

    with, 5960

    redox-sensitive elements role of, 23

    reproduction, 48

    ribosome, 8

    size, 24, 26

    species, 48

    stationary phase growth of, 289

    substrate concentrations and, 29, 33

    sulfide-oxidizing, 125

    sulfur in, 316, 318

    sulfur reducing, 342

    symbiosis, 57

    transportation modes of, 24

    viral infection, 61

    viral infection and mortality of, 54

    water column, 141

    Proteobacteria

    Delta subdivision of, 14, 20

    divisions within, 12

    fresh water, 1923

    purple sulfur bacteria in, 360

    sea water, 1923

    sulfide oxidation, 3523

    sulfur reducing, 14, 20, 342

    Protista, 1415

    Protozoans

    prokaryote and, 535, 5960

    Strombidium pupureum as housing for, 60

    Psychrophiles, 413

    Purple nonsulfur bacteria, 358, 359, 363

    chemolithoautotrophic growth of, 363

    distribution, 363

    diversity, 363

    DOC, 363

    light and, 363

    metabolism, 363

    oxygen concentrations and, 363

    photolithoautotrophic growth of, 363

    photoorganotrophy as metabolism for, 363

    physiological generalism and, 363

    Purple sulfur bacteria, 358, 359, 3603

    anaerobes, obligate, 362

    anoxic habitat, 362

  • SUBJECT INDEX 631chemolithoautotrophic growth of, 362

    genera of, 360, 361

    green sulfur bacteria emergence and, 369

    light and, 360, 361

    organic compound assimilation and

    photosynthesis of, 362

    photolithoautotrophic growth of, 362

    photosynthesis of, 362

    stratified water body, 489

    synthesis with, 360

    Pyrococcus furiosus, 184

    Quorum sensing, 63

    Redox reactions, 757

    abiotic, 2745

    electrode potential and, 76

    electron tower, 7980

    electron transfers and, 75

    free energy change of, 77

    iron oxidizing phototrophs and potential

    for, 274, 286

    iron properties of, 276

    iron reduction and potential of, 2901

    organism promotion of favorable, 956

    oxidation and, 76, 78, 173

    Ribosomal RNA (rRNA), 4. see also

    SSU rRNA

    Archaea and sequences of, 9

    Bacteria and sequences of, 9

    DSR gene, 327, 328

    DSR gene and, 327, 328

    Eukarya and sequences of, 9

    phylogenies from, 810

    phylogeny, 810, 1920

    Ribosome. see also Ribosomal RNA

    prokaryotic organism, 8

    subunit, 8, 9

    Ribulose monophosphate pathway

    (RuMP), 404

    Riftia pachyptila, 121, 122

    RNA, 35. see also Messenger RNA;

    Ribosomal RNA; Transfer RNA

    molecular structure of, 4

    protein synthesis and, 4

    rRNA. see Ribosomal RNA

    Rubisco, 108, 11620

    adaption to poor performance by, 11718

    algal, 11718

    Archaea, 108, 115, 116, 118

    carbon fixation reductive pentosephosphate cycle and, 116

    carbon isotope fractionation magnitude

    and, 11920

    carbon specificity of, 117

    carboxylase and oxygenase activity

    of, 116, 117

    carboxylase reaction specificity of, 117

    Chlorobium, 108, 116

    competition within, 116

    cyanobacterial, 11718, 11819, 1745

    fractionation, 121

    like genes, 115

    Methanococcus jannaschii, 11617, 118

    oxygen specificity of, 117

    oxygenase activity of, 115, 118, 119, 183

    oxygenic phototroph, 116

    phylogenies, parallel from, 114

    poor performance by, 11718

    proteobacteria, 116

    RuMP. see Ribulose monophosphate

    pathway

    Secondary ion mass spectrometry (SIMS), 413

    Sediments

    ammonium absorption by, 223

    ammonium in, 223, 2259

    anaerobic respiration and depth of,

    150, 151

    anammox and nitrogen production

    by, 2634

    AOM in marine, 410

    aquatic, 1645, 169, 2478, 2545, 260, 303,

    322, 323, 324, 341, 410, 415

    BSi depositing onto, 445

    BSi dissolution in surface, 452

    BSi loss and burial of, 462

    BSi preservation in, 4545

    carbon in, 499505

    carbon mineralization in anoxic, 227

    carbon: nitrogen ratio and depth of, 228

    carbon oxidation in, 153, 500

    carbon preservation in marine, 1645

    decomposition products from marine

    anoxic, 227

    denitrification and population diversity in

    marine, 2545

    denitrification in, 240, 2478, 255, 259,

    260, 265

    detritus decomposition in, 228

    DIP released from, 439

    inhomogeneities of, 151

  • 632 SUBJECT INDEXSediments (cont.)

    iron mobilization in, 2712

    iron reduction in, 303, 304

    isotope fractionation and denitrification

    in, 266

    lake, 324

    macrophyte communities and

    denitrification in, 259

    manganese mobilization in, 2712

    manganese reduction, microbial in, 304

    manganese retention in, 289

    mangrove, 4946, 500

    mangrove forest litter decay in, 4989

    marine, 1645, 253, 2545, 322, 3234, 338,

    341, 409, 4368

    metabolic measuring and disrupting, 153

    methane in aquatic, 415

    methane oxidation in marine, 409

    nitrate ammonifiers in coastal marine, 253

    nitrate diVusion into, 256

    nitrate production in, 257, 258

    nitrate reduction in, 247

    nitrification, 2389, 240, 241, 243

    nitrification in stream, 2478

    nitrogen deposited on surface of, 232

    nitrogen fixation rates in, 218, 219

    nitrogen incorporation and depth of, 228

    nitrogen mineralization in, 2257

    nitrogen production by, 2634

    organic components of, 1656

    organic matter preservation in, 1634

    oxygen consumption in, 198202

    oxygen in aquatic, 146, 169, 170, 338

    oxygen penetration into, 467, 200, 257

    oxygen transported into, 146

    oxygen uptake rates, 200

    pH and nitrification in, 241

    phosphorite, 431

    phosphorus and, 420, 426, 43640

    phosphorus release from, 438

    respiration and mangrove forest, 500

    seasonal phosphorus cycle in

    marine, 436, 437

    sequential extraction fractionation

    of phosphorus, 426

    stream, 2478

    sulfate reduction in, 321, 322, 323

    sulfide oxidation in, 370

    sulfur in marine, 341

    temperature and denitrification in

    aquatic, 260temperature for nitrification in shallow

    water, 243

    SHE. see Standard hydrogen electrode (SHE)

    Silica. see also Biogenic silica; Dissolved silica

    algal production and, 4589

    aquatic environment dissolution of, 4589

    aquatic system primary production and, 441

    biogenic production of, 4467, 448

    biological transformations and, 442

    carbon pump, biological and, 4612

    cell-specific content of, 4456

    chemistry, 442

    depletion, 45760, 462

    diatom formation of, 44550

    dissolution, 4506

    DSi accumulation and saturation

    concentration of, 453

    mineralogy, 442

    pelagic production of, 447

    pH and, 442, 450, 452

    protease activity and dissolution of, 4556

    regeneration, microbe-mediated, 456

    salinity and diatom content of, 446

    weathering, 443

    Silica cycle

    evolution of, 4623

    global, 4425

    oceanic, 443

    terrestrial biogeochemical, 443

    Silicate

    dissolution, 456

    microbes and weathering of, 4567

    organic acids and dissolution of, 457

    weathering, 4567

    Silicon

    abundance of, 441

    biogeochemistry, 4507

    carbon and, 441

    forms, 441

    Silicon cycle, 44163

    aquatic environment, 45862

    oceanic, global, 443, 444

    silica depletion and aquatic

    environment, 45861

    SIMS. see Secondary ion mass spectrometry

    Small subunit (SSU) rRNA, 8, 10, 1214

    biological innovation timing constraint

    and, 1314

    diVerences, 12

    evolution, 1214

    five-kingdom division of life and, 1415

  • SUBJECT INDEX 633phylogenetic reconstruction and, 8, 10

    phylogeny, 1920

    taxonomic organization and, 8, 10, 201

    Tree of Life from comparisons of, 1014

    SSU. see Small subunit

    SSU rRNA. see Small subunit rRNA

    Standard hydrogen electrode (SHE), 756

    Standard state (STP)

    enthalpy defined relative to, 66

    Gibbs free energy, 68

    temperature, 74

    Stokes-Einstein relationship, 24

    STP. see Standard state

    Stratified water bodies, 48093

    Black Sea as, 4826

    chemically, 480

    Chlorobium in, 489

    Chromatium vinosum in, 48990

    Chromatium weissei in, 48990

    green sulfur bacteria in, 489

    Golfo Dulce, 4812

    hyper-sulfidic, 481

    light, spectral quality of and depth of water

    columns in, 488

    Mahoney Lake, 4867

    microbial, and interaction, 4807

    microbial population positioning in, 480

    oxygen minimum zones in, 481

    photosynthesis, anoxygenic and, 4903

    phototrophs, anoxygenic competition

    in, 48790

    purple sulfur bacteria in, 489

    Suboxic environments, 173

    Substrate concentration

    chemostat, 33

    energy and, 334

    Escherichia coli, 29

    expression for, 38

    metabolic rate and, 30, 31

    modeling, 389

    in nature, 369

    population density and input, 33

    prokaryotes and, 29, 32

    Substrates

    competition for, 512, 901, 301

    consumption rate of, 37

    denitrification and availability of, 255

    herbivores feeding on, 135

    iron/manganese reduction competition

    for, 301

    methanogen, 390methanogenesis, 38890

    microbial population and limitations of, 51

    nitrification, 23840

    oxygen respiration, 195

    production, 368

    sulfate reduction and, 32934

    Sulfate. see also Sulfate reduction

    accumulation, 329

    exchange, 376

    isotope fractionation and exchange of, 376

    limitation, organism of, 376

    marine concentration of, 3378

    sulfide isotope diVerence from, 380, 381

    sulfide oxidation to, 351, 352, 368

    sulfide reduction and, 31516, 337

    sulfur compound formed to, 316

    sulfur oxidation to, 358

    Sulfate reduction

    acetate oxidation by, 330, 333

    aerobic, 325

    anaerobic methane oxidation and, 411

    anoxic environment, 337

    anoxic water column, 3212, 324

    AOM and, 411, 412, 41314

    AOM and electron donor for, 41314

    Archaea, 325

    assimilatory, 318, 31920

    Bacteria, 325

    carbon availability and, 338

    carbon fixation and, 334

    carbon mineralization and, 320, 3223,

    3979

    carbon oxidation rates by, 322, 338

    Desulfovibrio desulfuricans oxidation

    and, 3313

    Desulfovibrio oxyclinae, 3367

    dissimilatory, 318, 32040

    electron donor and, 325, 330, 332, 3334,

    4134

    energy for assimilatory, 320

    energy gained during, 327

    environmental significance/distribution

    of dissimilatory, 3205

    factors controlling rates of, 33640

    freshwater environment, 398, 399

    gram-positive reducers for, 3256

    hydrogen as electron donor for, 330, 332,

    3334

    iron oxidation and, 433, 434

    iron reduction and, 304, 306, 307

    isotope fractionation, 3778

  • 634 SUBJECT INDEXSulfate reduction (cont.)

    lake sediment, 324

    mangrove environment suppression of, 323

    marine environment, 320, 3223, 329

    marine sediment, 322, 3234

    Marinobacter, 337

    measuring rates of, 3212

    metabolic adaptations to temperature

    by, 340

    metabolism, 330, 331, 333, 373, 376, 377

    metabolism, oxidative for, 337

    methane oxidation and, 41011

    methane removed by, 410

    methanogens and, 400

    microbial mat temperature and, 473

    molybdate inhibited, 412

    organic matter reactivity in the

    environment and, 338, 339

    oxic zone, 325

    oxidation and, 327, 330, 3334

    oxygen and, 3367

    PAPS pathway of assimilatory, 31920

    phylogenic spectrum of reducers of, 377

    phylogeny of dissimilatory, 3257

    physiology of reducers in, 335

    proteobacteria, 325, 326

    proton gradients in reducers for, 3279

    rates, 3389, 376

    shallow water environment carbon

    mineralization and, 3223

    stratified water body, 486, 487

    substrate oxidation and, 332, 333

    substrate utilization in, 32934

    sulfate and, 337

    sulfide source from, 357

    suppressed, 323

    temperature and population of reducers

    in, 335

    temperatures, 326, 33840

    Sulfide. see also Sulfide oxidation

    formation, 318

    iron, phases, 316

    manganese/iron oxidation reaction

    with, 3456

    microbial mat accumulation of, 474

    oxygen reaction rate with, 3467, 4823,

    484

    reoxidation to sulfur compounds of, 316

    reoxidized, 370, 371

    stratified water body accumulation of, 481

    stratified water body interface betweenoxygen and, 4823, 484

    sulfate isotope diVerence from, 380, 381

    sulfate reduction source of, 357

    sulfate reduction to, 31516

    sulfite reduction to, 374

    sulfur compound formed to, 316, 357

    water column, 345

    Sulfide oxidation

    aerobes, facultative for, 351

    aerobes, obligate for, 351

    Archaea, 3523

    ATP and, 368

    Beggiatoa, 349, 351

    cell density and, 347

    chemolithoheterotrophic metabolism

    and, 349, 350

    environments, 358

    enzymatics, 367

    green nonsulfur bacteria as oxidizers

    for, 358, 359, 3657

    green sulfur bacteria as oxidizers for, 358,

    359, 3645

    heliobacteria as oxidizers for, 358, 359, 367

    incomplete, 370

    inorganic, 3457, 3478

    maximum rate of environmental, 347, 348

    metal oxides, 3547

    Michaelis-Menten kinetics and

    biological, 347

    microoxic conditions for, 351

    nitrate in, 351, 4812

    non-phototrophic biologically

    mediated, 34957

    organisms for, 34952

    oxidizers, 349, 3524, 35867

    pathways, 3678

    phototrophic, 35770

    phylogeny of oxidizers for, 3524

    products, 341, 3701

    proteobacteria, 3523

    purple nonsulfur bacteria as oxidizers

    for, 358, 359, 363

    purple sulfur bacteria as oxidizers for, 358,

    359, 3603

    sediment, 370

    solid phase, 357

    steps in, 357, 36777

    stratified water body, 485, 487, 488

    sulfate from, 351, 352, 368

    sulfite from, 368

    sulfur from, 368, 370

  • SUBJECT INDEX 635temperature and, 3512

    Thioploca, 349, 351

    Sulfolobales

    3-hydroxypropionate cycle, 106, 111, 114

    Sulfur. see also Sulfur disproportionation;

    Sulfur metabolisms; Sulfur oxidation;

    Sulfur reduction

    amino acid, 316, 318

    anoxic water column, elemental, 341, 342

    APS formation pathways for, 318, 319

    Archaea respiration of, 344

    biological transformation, 315

    disproportionation, 3734, 379, 380

    disproportionation organisms of, 3713

    elemental, 3412, 3445, 346, 374

    environment and metabolism of, 315

    isotope fractionation and

    disproportionation of, 379, 380

    isotope fractionation in, 375

    isotopes, 37481

    marine sediment elemental, 341

    methane accumulation and depletion

    of, 3967

    PAPS formation pathways for, 31820

    pathways for formation of, 31820, 341

    physiological adaptations to

    disproportionation of, 373

    prokaryote, 316, 318

    prokaryote cellular metabolism and, 318

    sulfate oxidation from, 358

    sulfate reduction of, 320

    sulfate/sulfide formation from,

    compound, 316

    sulfide oxidation to, 368, 370

    sulfide reoxidation to compounds of, 316

    thermodynamic distributions for isotopes

    of, 374

    Sulfur cycle, 31381

    compound fate in, 316

    discipline and concept of, 314

    global biogeochemical perspective

    of, 31415

    isotope geochemistry, stable in, 37481

    metabolically active compounds of, 316, 317

    microbial ecological perspective of, 315

    Sulfur disproportionation, 316

    Sulfur oxidation, 316

    disproportionation, 3704

    oxidizers in, structural role of, 318

    sulfate esters and, 318

    sulfite from, 368sulfonates and, 318

    Sulfur reduction, 316

    Archaea, 343

    ATP generated in, 343

    biochemistry of, 345

    compounds, 35758

    Desulfuromonas elemental, 343

    distribution of reducers for, 344

    electrons driving, 345

    elemental, 3415, 34951

    environmental distribution

    of elemental, 3445

    metabolism and elemental, 343

    methanogen co-occurance with, 397

    organisms for elemental, 341, 3424

    phylogeny and organisms for

    elemental, 3424

    prokaryotes for elemental, 342

    proteobacteria for elemental, 342

    steps in, 345

    substrates and organisms for

    elemental, 3424

    sulfur, elemental as compound of, 357

    Thermotoga, 343

    thiosulphate as compound of, 357

    Symbiosis, 5760, 64, 4067

    Synechococcus

    as cyanobacteria, 1767

    oceanic distribution of, 177

    Synergism, 53

    Syntrophy, 53

    Systematics, 121

    TCA. see Tricarboxylic acid

    TEM. see Transmission electron microscopy

    Temperature

    ammonification, nitrate and, 260

    bacterial growth and, 195

    BSi solubility and dependence on, 450, 451

    cyanobacteria growth and, 176

    denitrification and, 255, 259, 260

    diatom growth and, 452

    gas solubility and, 73, 74

    growth rate and range of, 413

    hyperthermophiles adaptation to, 43

    isotope fractionation and, 416, 417

    metabolism and, 32, 403, 71, 242, 340

    microbial mats and, 473

    microorganism, 403, 71

    microorganism growth rate and, 403

    microorganism metabolism and, 403, 71

  • 636 SUBJECT INDEXTemperature (cont.)

    microorganisms, Arrhenius equation

    and, 412

    nitrification and, 237, 242

    nitrifier metabolism and, 242

    oxygen respiration and, 195

    STP, 74

    sulfate reducer metabolism adaptation

    to, 340

    sulfate reduction and, 326, 33840, 473

    sulfate reduction in microbial mats and, 473

    sulfide oxidation, 3512

    thermodynamics and, 71

    thermophiles adaption to, 43

    Thermodynamics, 68, 70

    activity coeYcient calculations for, 712

    anaerobic respiration and, 150

    disproportionation, 372

    enthalpy as state function of, 667

    entropy as state function of, 67

    equilibrium and, 701

    fermentation process, 88

    gas solubility and, 734

    Gibbs free energy as state function of, 68

    glucose oxidation/oxygen, 77

    iron oxide, 302

    laws of, 66, 6770

    methanogenesis, 400

    microbial metabolism and, 6594

    microbial population competition and, 66

    nitrification, 2335

    oxygen, 1678

    respiration processes and, 91

    state functions, 6670

    sulfur isotope distributions and, 374

    sulfur-disproportionation organism, 6970

    temperature and, 71

    Thermophiles, 413

    membrane lipids of, 43

    temperature adaption of, 43

    Thermoproteus, 106, 115

    Thermotoga, 343

    Thiobacillus, 3534

    Thiomargarita, 351

    Thioploca, 3567

    distribution, 356

    large size of, 27

    nitrate exposure of, 3567oxygen requirements for, 356

    sulfide oxidizers, 349, 351

    Thiosulphate

    sulfur compound formed to, 357

    Thiovulum

    flow field around cluster attached, 356

    oxygen, phobic response of, 355

    Transduction, 61

    Transfer RNA (tRNA), 45

    Transmission electron microscopy (TEM), 26

    Tree of Life, 10

    anoxygenic photosynthesis in, 369

    Aquifex lineage of, 12

    Archaea domain of, 11, 1617, 18

    Bacteria domain of, 1516

    branch length in, 12

    calibration of, 14

    carbon fixation pathway lineages on

    the, 11314

    comparisons with previous, 1415

    Eukarya domain of, 11, 1719

    evolution and, 1213

    SSU rRNA, 1014, 15, 19

    tour through, 1519

    Tricarboxylic acid (TCA), 144

    Trichodesmium

    as cyanobacteria, 176

    iron demands of, 179

    as nitrogen fixers, 21516

    photosynthesis compensation intensities

    and, 177, 1789

    tRNA. see Transfer RNA

    Vibrio fischeri, 64

    Viral infection

    DNA transfer and, 61

    DOM release due to, 55

    parasitism of, 54

    prokaryote, 61

    Viruses

    host interaction with, 55

    parasitism and, 54

    temperate, 55

    Whole-genome sequences, 6, 20

    Zooplankton, 133, 134

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