SUBJECT INDEX

AAP. see Aerobic anoxygenic

photoheterotrophs

Acetylene reduction assay, 211–12

Acidophiles, 43

Activity coeYcient calculations, 71–2

Davies equation, 72

Debye-Huckel equation, 71–2

Adenosine triphosphate (ATP), 66, 83–5

AAP and production of, 97

ADP formed by, 83, 84, 85

ammonium oxidation and production

of, 233–4

biosynthetic reaction, unfavorable

and, 83–5

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, 85–8

formation, 83, 84, 404–5

generation, 85–8, 104, 343

gradient relaxation and, 82

light energy transfer to, 100, 101

methanol and formation of, 404–5

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, 190–3

Alkaliphiles, 43–4, 191

Amensalism, 56

Ammonia

assimilation of, 213–14

cycle, 209

human impact on, 209

microbial mat sequestering of, 478–80

nitrogen gas reduced to, 213

Ammonification, 206, 219–20

aerobic, 220

anaerobic, 220

aquatic environment, 220, 223

glutamate and formation of, 222–3

heterotrophic carbon mineralization

and, 220

measuring, 223

microbial, 219–32

nitrate, 251–3, 259

nitrification and, 232

nitrogen gas release and, 219–20

porewater/particle equilibrium distribution

and, 229, 230

sediment absorption and, 223

temperature and nitrate, 259

Ammonium

anoxic sediment and concentration of, 228

assimilation, 213–14, 222

cellular material incorporation of nitrogen

fixation formation of, 213–14

concentration, 222

deamination, 220–3

incorporation, 220–3

manganese oxidation reduced by, 275

manganese reduction electron donor, 294–5

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, 213–14

Nitrosococcus oceanus as oxidizers

of, 235–6, 237

oxidizers, 235–6, 237

temporal changes in pool of, 223

water, overlaying fluxes of, 228, 229

sediment, 223, 225–9

stratified water body interface between

nitrate and, 484, 485

608 SUBJECT INDEX

Ammonium oxidation, 211, 220, 233–4, 235,

239–40, 245, 481

anaerobic, 235

ATP production and, 233–4

chemolithoautotrophic, 234–5

light and, 245

Michaelis-Menten kinetics and, 239–40

stratified water bodies and, 481

Anabolic metabolism, 131

biopolymer generation and, 156

MGE, reduced and energy for, 158–9

Anabolism, 81

Anaerobic food chains, 168

Anaerobic oxidation of methane (AOM), 294,

384, 402, 485–6

consortium conducting, 412

electron donor for sulfate reducers

conducting, 413–14

geochemical evidence for, 409–11

isotope fractionation and, 417, 418

marine sediment, 410

microbial evidence for, 411–14

sulfate reduction and, 411, 412, 413–14

Anammox, 261–3

chemolithoautotrophs and, 261–2

competition within, 52

enzymes involved in, 262

metabolic pathway for, 262

nitrogen deficiencies and, 264

nitrogen produced by, 262–4

oxic nitrification and, 261

oxygen and, 262

stratified water body, 481

Animalia, 14–15

Anoxia. see also Oxia; Oxic-anoxic interface

cyanobacteria exposure to, 175

environmental, 172

nitrification and tolerance to, 239

oceanic, 169

oxygen and, 172–3

sulfur reduction in, water columns, 324

Anoxygenic photosynthesis, 100, 104, 287,

357, 369, 481, 487–93

cyanobacteria, 104

iron oxidation by, 286–7

microbial mats, 467, 479

sulfide oxidation by, 357–367

stratified water body, 481

Tree of Life, 369

Anoxygenic phototrophs, 96, 97

bacteriochlorophylls utilized by, 100

distribution, 97

electron donors used by, 104

iron oxidizing, 286–7

light range available to, 101

photosynthetic unit in, 100

sulfide oxidizing, 357–367

AOM. see Anaerobic oxidation of methane

Appendices, 508–15

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, 16–17

heme copper oxidases in, 189

heterotrophic, 43

iron oxidizers in, 282, 285–6

iron reduction, 291

kingdoms, 16

methanogen cluster of, 412, 413

methanogenesis, 390, 392–3

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, 352–3

sulfur, elemental respiration by, 344

sulfur reduction, 343

Tree of Life domain, 16–17

Arenicola marina

detritus pool feeding by, 136–7

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 609

denitrification, 253

diversity, physiological in, 16

heme copper oxidases in, 189

iron oxidizers, acidophilic in, 285–6

iron oxidizers in, 280–1, 282

metabolism and, 15–16

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, 15–16

Bacteriophage, 54–5

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, 452–3, 454, 455–6

DSi temporal development during

dissolution of, 450, 451

microbes and dissolution of, 455–6

oceanic, 449–50

radiolabeled silica measuring dissolution

rates of, 452–3

sediment burial loss of, 462

sediment deposit of, 445

sediment preservation of, 454

sediments, surface dissolution of, 452–3

solubility, 450, 451, 452, 453–4

surface area, 452

temperature and dissolution of, 452–3

temperature dependence and solubility

of, 450–1

Biosynthesis, 110

Black Sea, 482–6

AOM in, 485–6

density stratification, 482

methane accumulation in, 485–6

methane source in, 485

nitrate and ammonium interface in, 484, 485

nitrate forms, 484, 485

oxygen and sulfide interface in, 482–3, 484

oxygen penetration depth in, 482–3

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, 461–2

decomposition, flux, 162

degradation, 224

delivery, 129, 130

DOC and release of, 138–9

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, 165–6

methane reduction from methyl, 393, 395

microbial mat cycling of, 475–8, 479

microbial oxidation processes and

burial, 162–5

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, 429–30, 438

phosphorus regeneration from sediments

and, 437–8

photosynthetic production of organic, 175

phytoplankton and carbon pump, 461–2

phytoplankton, photosynthesis uptake

of, 461–2

610 SUBJECT INDEX

Carbon. (cont.)

preservation, 162–6

pump, 461–2

recycled, 162

reservoir, earth of, 130

sediment, 499–505

sediment depth and nitrogen, ratio, 228

sedimentation rate and preservation of, 164

silica and biological, pump, 461–2

silicon and, 441

sink, 462

sulfate reduction and availability of, 338

surface pool cycling of, 130, 162

transformations, 224

Carbon assimilation, 155–9, 404

Carbon fixation

reductive acetyl-CoA pathway, reductive

of, 109–10, 111, 112, 114

aerobic methanotroph, 402–5

anaerobe energy demand for, 112

ancestral, 114

ATP demand of pathways for, 111, 112

Calvin, 234

Calvin cycle, 80

Calvin-Benson-Bassham cycle, 174–5

Chemotroph, 98, 99

eYciency, 115

energetics, 111–13

energy demand, 112, 113

energy, pathway of, 111

environmental situations supporting, 96

induced, 97

isotope fractionation during, 120–3

organic material, 98, 105

pathways, 105–11, 112, 113–14

reductive pentose phosphate cycle,

reductive of, 105–8, 113, 115–16

photosynthesis, 492

phototrophy and, 95–127

prokaryotic organism isotope fractionation

during, 120, 123

reductive citric acid cycle, 108–9, 112,

114, 122–3

Rubisco and, 108, 116

steps in, 98

sulfate reduction and, 334

3-hydroxypropionate cycle, 111, 112, 113

Tree of Life lineages identified pathways

of, 113–14

Carbon metabolism

carbon assimilation and, 155–9

detritus food chain and, 132–44

heterotrophic, 129–66

respiration pathway partitioning

of, 152–3, 154

Carbon mineralization, 152–5, 306

ammonification and heterotrophic, 220

anaerobic, 306, 399

anoxic sediment, 227

benthic, 310–11

denitrification and, 481, 482

heterotrophic, 220

iron reduction and benthic, 310–11

manganese reduction and benthic, 310–11

manganese reduction pathway for, 154, 155

mangrove forest, 500–2

methanogenesis, 397–9

pathways, 154, 155, 323

shallow water environment sulfate

reduction and, 322–3

sulfate reduction and, 320, 322–3, 397–9

Carbon oxidation, 303–4, 306

aerobic, 144–7

anaerobic, 147–55

aquatic sediments and aerobic, 145

fermentation and anaerobic, 148–50

hydrolysis and anaerobic, 148–50

iron as electron acceptor for, 311

iron reduction and, 310–11

iron respiration and, 500

manganese reduction, microbial

and, 310, 311

mangrove sediment, 500

metal oxide reduction and, 310

microorganism, anaerobic, 500

nitrate respiration and, 152–5

nitrogen mineralization and, 227–8

oxygen respiration and shallow

sediment, 153

oxygen-containing radicals and

aerobic, 144–5

respiration, anaerobic and, 150–2

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 611

fermentation in, 131

oxidative reactions of, 156

respiration and, 131

Cell biochemistry, 80–8

anabolism, 80–1

catabolism, 80–1

electron carriers, mobile in, 81–2

energy gain in, 80–1

membrane-bound electron carriers and, 82

oxidative phosphorylation and, 82

Cell numbers

lake/marine, 30, 36

in nature, 36–9

Cell size, 24–7

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, 36–7

diVerentiation, 61–4

diVusion-limited growth of, 24–5

DOC utilization within, 97

energy derivation by, 80

energy, maintenance for, 29

functional/morphological diVerentiation

of, 61–2

growth, 24–5, 28–39

morphological diVerentiation in, 62–3

MPN enumeration of, 35–6

plasmid functions for, 61

population density of, 33

population growth, 28–39

salinity and adaption of, 45

substrate uptake/growth of, 28–32

Chemoautotrophic organism

ecosystems, 123–7

ammonium oxidation by, 234–5

anammox and, 261–2

chemoautotrophic cave ecosystem as, 125

hydrothermal vent systems as, 123–5

nitrate ammonification by, 253

nitrification, 235–7, 241

pH and nitrification with, 241

phylogeny of nitrification by, 235–7

subsurface biosphere as, 125–7

Chemolithoautotroph, 94, 96

Chemostats, 33

biomass production in, 33

microorganism growth physiology and, 33

population growth in, 33

substrate concentration in, 33

Chemotroph, 92–3, 97

Chlorobium

lower light adaptation of, 489

reductive citric acid cycle for, 109, 110

Rubisco in, 108, 116

Chloroflexus, 111, 113–5, 365–7

Chloroplasts, 18

Chondromyces apiculatus, 62

Chromatium vinosum, 489–90

Chromatium weissei, 489–90

Clausius-Clapeyron equation, 74

Commensalism, 50, 56

Compatible solutes, 45

Competition, 50–2, 90–1

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, 174–5

carbon limitation and, 121–2

cell diameters for, 175–6

characteristics of, 174–6

diazotrophic, 179

diversity, 469

ecological niches of, 173

environmental, 176–80

eukaryote microalgae and, 178

evolution, 179–80

freshwater, 176

geobiology, 179–80

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,

215–16, 218

nitrogenase inactivation and

phototrophic, 215

oxygen respiration growth of, 175

612 SUBJECT INDEX

Cyanobacteria (cont.)

oxygenation of Earth’s surface by,

169, 180

photoheterotrophic growth of, 175

photosynthesis, 178–9, 474, 476

photosynthesis nitrogen demands and, 179

photosystems of, 180

Prochlorococcus as, 176–7

as prochlorophytes, 174

reducing conditions and, 104

representatives, 176–7

Rubisco, 174–5

Synechococcus as, 176–7

temperature and growth of, 176

Trichodesmium as, 176, 215–16

visual identification of, 175–6

water column depth and, 177–8

water-spliting complex of, 180

Davies equation, 72

Dead particle organic carbon (DPOC), 130

Deamination

ammonium, 220–3

non-oxidative amino acid, 222

nucleotide, 222

oxidative, 222

Debye-Huckel equation, 71–2

Denitrification, 32, 251, 252

adaptation, environment of, 255

animal influence on, 257, 258–9

aquatic sediment, 247, 248, 254–6, 259

Bacteria, 254

biochemistry, 249–53

carbon mineralization through, 481, 482

diversity and, 256

environmental factors aVecting, 256–61

enzymes, 254

factors influencing, 256–61

invertebrates, burrowing and, 259

iron oxidation and, 284

iron-based, 284

isotope fractionation associated with, 263–4

macrophyte communities and sediment, 257

mangrove forest, 503

marine sediment population diversity

and, 254–5

measuring, 245, 246–7

Michaelis-Menten kinetics for, 256

microelectrode measuring of, 245–6

nir gene in, 253, 254, 255

nitrate, 247, 248, 258, 265

nitrate concentration and, 256

nitrite, 249

nitrogen cycle, 247

nitrogen, from nitrite, 251

nitrogen isotope pairing technique for

measuring, 245, 247

nitrogen produced by, 245, 263–4

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, 253–5

plant influence on, 259–60

respiratory reduction steps of, 247–51

sediment, 240, 247–8, 254–5, 258, 259, 265

sediment depth and, 240, 260

stream sediment, 247–8

substrate availability and, 255

temperature and, 255, 259–60

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, 20–1

Desulfovibrio desulfuricans

growth stages, 28

nitrite reductase purified from, 252

oxidation by incomplete, 331–3

Desulfovibrio oxyclinae, 336–7

Desulfuromonas, 343

Detritus

anaerobic decomposition degradation

of, 147–8

composition, 132–3

decomposition, 137, 160

DOM and, 137–44

fungi as decomposers of, 134

herbivores supplementing nutrition

with, 135

mangrove forest handling of, 496–9

SUBJECT INDEX 613

mangrove forest microbial decomposition

of, 498

microorganisms and breakdown of, 134

nitrogen reservoirs of dead organic, 208

organisms decomposing, 134–7

prokaryotes as decomposers of, 134

sediment decomposition of, 228

Detritus food chain, 132–44

chemical nature of, 132–3

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, 461–2

DSi access and presence of, 458–9

DSi extraction from sea water by, 463

DSi inhibited growth of, 460–1

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, 445–50

silica in frustules of marine, 445

temperature and growth of, 450

valves, 446, 449–50

Diazotrophs

aerobic, 215

energy metabolism of, 209, 210

microaerophilic, 215

nitrogen fixation by, 215

nitrogenase protected from oxygen

by, 214–15

DIC. see Dissolved inorganic carbon

DiVusion, 24

growth limited by, 24–5

oxic-anoxic interface and, 259

oxygen microgradients and, 196–7

solute transport in stagnant water columns

and, 196

timescale, 24

Dioxygenases, 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, 371–4, 379, 380

sulfur oxidation, 370–4

thermodynamics of, 372

thiosulfate, 368, 373–4

Dissimilatory sulfite reductase (DSR)

gene, 326–7

gene transfer and, 327, 328

rRNA and, 327, 328

Dissolved inorganic carbon (DIC), 475–8,

479, 480

Dissolved inorganic phosphorus (DIP), 427

DOP mineralization to, 435

ocean surface water, 433–4, 435

phytoplankton assimilation of, 434–5

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, 142–3

sediment, 143

size, 140

source, 143–4

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, 137–8

concentration, 138, 139–40

definition, 137

detritus and, 130, 137–44

land entry of, 139

mangrove forest, 499

marine, 139

614 SUBJECT INDEX

Dissolved organic matter (DOM) (cont.)

microbial loop, 141–2

phytoplankton release of, 138

plant release of, 138

refractory, 143

size, 137

sources, 138

Dissolved organic phosphorus

(DOP), 433–4, 435

DIP mineralization from, 435

as phosphorus source, 435

recycled polymeric, 436

Dissolved silica (DSi), 442–3

accumulation, 453

aquatic environment and, 442–3, 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, 459–60

diatom presence and access to, 457–8

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, 3–5

DAPI binding to, 126

mutation of, 5

PCR and amplification of, 13

phylogenetic analysis, 13

phylogeny construction from, 8

polymerase, 13

prokaryote uptake of, 60

protein synthesis and, 4

structure, 2–3

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, 81–2

environment and calculation of, 80

equilibrium constant and, 78

Gibbs free energy and, 77

in nature, 78

non-standard condition, 78–80

oxidation, glucose and, 77

pH and, 79

redox reactions and, 76

SHE and, 76, 79

Electron acceptors

anaerobic, 311

Beggiatoa, 355

general considerations, 132, 144–8,

150–5, 170–1

iron as carbon oxidation, 311

iron reduction, 298

manganese reduction, 298

sulfate as anaerobic, 311

thermodynamics, 88-90

vertical distribution of, 151–2

Electron donors, 194–5

AOM, 413–14

competition for, 90–2

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, 86–8, 96–7, 401

iron reducer consuming of, 307

iron reduction, 293, 297, 300–1

SUBJECT INDEX 615

manganese reduction, 293, 297, 300–1

methanogenesis, 397, 401

nitrification, 233

oxic-anoxic interface oxygen consumption

and, 197

oxidation, 297

oxygen, 201–2

oxygen respiration, 194

photosynthesis, 105

positive redox potential utilization of, 98

redox pairs, 99

sulfate reduction activity and, 325, 330, 332,

333–4

Electron flow

cyclic, 100, 102, 104

ATP production and, 104

noncyclic, 104

reverse, 99, 104

Electron shuttles, 297–8

Electron transfers, 75

electrode potential and, 75–7

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, 185–7

electron carriers involved in, 99

intracellular, 298–9

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, 102–103

phototrophic, 99–105

Energy metabolisms

naming, 92–4

Enthalpy, 66–7

endothermic reaction and, 67

formation, 67

Hess’s Law of Summation calculation of, 67

as state function, 66

STP-relative definition of, 66

Entropy

change component parts in, 67–8

Gibbs free energy and, 67–70

Glutamate dehydrogenase (GDH), 213–14

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, 17–18

oxygen respiration, 188

rRNA sequence and, 9

SSU rRNA domain, 11

Tree of Life domain, 17–19

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, 113–6

cyanobacteria, 179–80

iron reduction, 293–4

616 SUBJECT INDEX

Evolution (cont.)

later gene transfer and, 19–20, 254,

327–8

oxygen respiration, 188–190

photosynthesis, 102, 179–80, 369

phylogeny microbial and, 12–14

Rubisco, 115, 118–9

silica cycle, 462–3

sulfur reduction elemental, 344–5

Extracellular polymeric substrates (EPS), 470

Extremophiles, 167

Fermentation

acetate, 390

ATP generation and, 85–8

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, 49–50

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, 89–90

organic material oxidation, 167–8

oxic respiration and, 89–90

pH and, 92, 93

reaction center, 101–2, 104

respiratory processes and, 87, 89–90, 91

sediment depth and, 155

Fungi, 14–15

detritus decomposed by, 134

oxidases, 182

Gas solubility, 73–4

Henry’s Law and, 73–4

oxygen, 171–2

salt influence on, 73, 74

temperature and, 73, 74

thermodynamics and, 73–4

GDH. see glutamate dehydrogenase

Gene expression, 63–4

Gene transfer, lateral, 254, 327, 328

phylogeny influence on, 19–20

Genetics, 3–5

Geobacter metallireducens

electron-shuttling, 297

iron reduction and, 284

Gibbs free energy. see also Free energy gain

component determination in, 68–9

electrode potential and, 77

entropy and, 67–70

environmental conditions and, 69–70

mineralization reactions, 86, 87

standard, 90

as state function, 68

STP, 68

thermodynamically favorable reaction

and, 68

Glutamate, 222–3

Granick hypothesis, 369

Green nonsulfur bacteria, 358, 359, 365–7

environments, 366

genera, 361, 366

green sulfur bacteria and, 365–6

photosynthesis, anoxygenic, 369

Green sulfur bacteria, 358, 359, 364–5

anaerobes, obligate and, 364

consortium partner signaling and, 365

deep-water, 361, 362, 365

environments for, 364–5

evolution, 369

genera of, 364

green nonsulfur bacteria and, 365–6

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, 34–5

energy for, 88–9, 95–6

growth yield and, 32

measurement methods for, 34

microbial, 88–9, 195

microorganism, and temperature, 39–43

osmotic pressure for, 44–5

pH and, 43–4

water-column bacteria microbial, 34–5

Gulfo Dulce

ammonium oxidation in, 481

anammox in, 481

anoxygenic photosynthesis in, 481

carbon mineralization, 481, 482

nitrate sulfide oxidation in, 481–2

SUBJECT INDEX 617

sulfide accumulation in, 481

water chemistry, 481, 482

Halophilic organisms, 42, 45

HDOC. see High-molecular-weight dissolved

organic carbon

Heliobacteria, 358, 359, 367

Henry’s Law, 73–4

Herbivorous animals

detritus particles as nutrition supplements

for, 135

primary production consumed by, 134–5

substrate feeding of, 135

Hess’s 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, 86–8, 96–7, 401

interspecies transfer of, 87–8

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, 87–8

water and solubility of, 73, 86

Hyperthermophiles, 41, 42

membrane lipids of, 43

temperature adaption of, 43

Informational genes, 19–20

Iron. see also Iron reduction, Iron oxidation

abiotic reduction mobilization of, 271–2

abundance of, continental crust, 269

assimilation, 276–9

bacteria obtaining, and proteins

binding, 277

carbon oxidation and respiration of, 500

chelators, 286–7

cycles, 269–312

cycles, global, 270–2

cycles, redox, 269–70, 271

denitrification and, 284

electron transport to photosystem with, 286

enzymes dependent on, 276

ferric, 283, 303, 304, 306

fluxes, benthic, 272

geochemistry, environmental, 272–5

hydrogen sulfide reduction with, 275

isotopes, 312

manganese and, 270

mangrove forests rich in, 500, 501

mobility, 271–2, 283

MR mobilization of, 271–2

oceanic, 271, 277, 278–9

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, 308–10

redox, 269–70, 271, 276

redox reactions, abiotic and, 274–5

requirement, 276

river particulate speciation of, 273

sediment, mobilization, 271–2

solubility, 270, 271, 272, 273, 277

species interaction of, 271, 272–3

sulfide, phases, 316

as trace element, 276

uptake of, microorganism, 277

weathering release of, 270–1

Iron cycles

iron isotopes and, 312

oxic-anoxic interface, 271

sediment resuspension and stimulation

of, 309

Iron oxidation, 270, 274, 275

abiotic, 275

acidophilic, 285–6

aerobic, neutrophilic bacteria for, 283

Archaea, 276–86

Bacteria, 280–1, 282, 285–6

chemotrophic, 280–1

denitrification and, 284

energy yielded from, 274, 279–80, 285

evolution, 287

Ferroglobus placidus growth and nitrate, 284

iron, ferric mobility and, 283

kinetics, 273–4, 305

manganese and, 341–2, 345–6

microbial, 279–89, 308

nitrate, 282, 283–5

nitrate and ferrous, 285

oxygen distribution and, 280, 283

pH and, 285, 286

pH and phototrophs for, 286

618 SUBJECT INDEX

Iron oxidation (cont.)

phosphorus adsorption and, 425

photoautotrophic growth and, 287

phototrophs for, anoxygenic, 286–7

problems with, 280

prokaryotes for, 285

quinones reduced, 275

redox potential and phototrophs for,

274, 286

sulfide reaction with manganese and, 345–6

sulfur formation, manganese and, 341–2

thermodynamic stability and, 302

Iron reduction, 270, 273–4, 284

abiotic, 307–8

acidophilic, 301

aquatic environment microbial, 299–312

aquatic sediment, 303

Archaea, 291

bacteria, phylogeny of dissimilatory, 296

carbon mineralization, benthic and, 310–11

carbon oxidation and, 310–11

carbon source for microbial, 301

competition, 273, 302

dissimilatory, 295, 303, 306–7, 310, 311

diversity of microbial, 291–4, 299–300

electricity and, 296

electron acceptors for, 293, 295–6, 298

electron donors for, 293, 294–5, 297, 301

electron transport in, 299

environmentally important reducers

for, 299–300

enzymes, 298–9

freshwater environment microbial, 311

Geobacter metallireducens and, 284

growth and, 291, 293

hydrogen and microbial, 301

iron, ferric and, 303, 304, 306

kinetics, 273–4

location, outer membrane and activity

of, 297

mechanisms of, 296–8

metabolic diversity in, 294–6

metabolism and, 291, 294–6

methanogenesis suppression and, 302

Michaelis-Menten-type kinetics, 305

microbial, 290–312

oxide speciation and, 301–3

oxygen and acidophilic, 301

oxygen and microbial, 300

phylogenetic diversity for

dissimilatory, 293–4

phylogeny of microbial, 291–4

population size of reducers, 307

quantification of microbial, 303–4

redox potential and, 290–1

reducer groups in, 291–2, 293, 295

sediment microbial, 304, 309

substrate competition and, 301

sulfate reduction and, 304, 306, 307

in vitro activity of, 298–9

water column, 311–12

Isotope fractionation, 265–8

3-hydroxypropionate cycle, 121–3

AOM and, 417, 418

carbon fixation pathways, 120–3

denitrification and, 266

denitrification associated, 265–6

iron, 312

mechanisms, 417–18

methane cycle, 414–18

methane formation pathways and, 416

methane in aquatic sediments and, 415

methanogenesis, 414–17

methanotrophy, 417–18

nitrification and, 267

nitrite availability and, 266

nitrogen and, 266, 267

nitrogen fixation, 266–7

nutrient uptake and, 267

oxygen, 202–4

phytoplankton expression of, 266, 268

reductive acetyl-CoA pathway, 121–3

reductive citric acid cycle, 121–3

reductive pentose phosphate cycle, 121–3

sediment denitrification and, 266

sulfate reduction, 375–8

sulfur compounds, 374–8

sulfur compound disproportionation,

379–381

sulfur oxidation, 378–9

temperature and, 416, 417

Kinetics

decomposition, 159–62

degradability, 159–62

iron oxidation, 273–4

iron reduction, 273–4

manganese oxidation, 273–4, 305

manganese reduction, 273–4

methane oxidation, 407, 408

methanotrophy, 407–9

oxygen consumption, 193

SUBJECT INDEX 619

oxygen respiration, 193

regulation and, 187–8

Kinetics, Michaelis-Menten, 30–1

ammonium oxidation and, 239–40

denitrification and, 256

DSi and, 449

iron reduction, 305

methanogenesis, 400

microbial growth and, 36

nitrite oxidation and, 241–2

sulfide oxidation, biological and, 347

Krebs cycle, 109, 114

LDOC. see Low-molecular-weight dissolved

organic carbon

Lithotroph, 93

Living particulate organic carbon

(LOPC), 129–1

LOPC. see Living particulate organic carbon

Low-molecular-weight dissolved organic

carbon (LDOC), 142

Mahoney Lake, 486–7

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, 271–2

abundance, continental crust, 270

assimilation, 276–9

availability, 276–7

cycles, 269–312

cycles, global, 270–2

cycles, redox, 271

geochemistry, environmental, 272–5

iron and, 270, 280

isotopes, 312

mobilization, sediment of, 271–2

MR mobilization of, 271–2

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, 274–5

requirement, 276–7

river particulate speciation of, 273

sediment retention of, 289

solubility, 270, 271, 272, 273

solubility of oxidized, 270, 271

species interaction of, 271, 272–3

as trace element, 276

uptake of, microorganism, 277

weathering release of, 270–1

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, 279–80, 288–9

hydrogen sulfide reduced, 275

kinetics, 273–4, 305

microbial, 279–89, 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, 345–6

Manganese reduction, 154, 155, 270, 273–4

ammonium as electron donor for, 294–5

aquatic environment microbial, 299–312

carbon mineralization, benthic and, 310–11

carbon oxidation and microbial, 310, 311

carbon source for microbial, 301

controls of microbial, 300–3

dissimilatory, 293–4, 303, 310, 311

diversity of microbial, 291–4, 299–300

electron acceptors for, 293, 295–6, 298

electron donors for, 293, 294–5, 297,

300, 301

electron transport in, 299

kinetics, 273–4

mechanisms of, 296–8

metabolic diversity in, 294–6

microbial, 290–312

nitrate reduction competition with, 301

oxide, 297

oxide speciation and, 301–3

oxygen and microbial, 300

phylogenetic diversity for

dissimilatory, 293–4

phylogeny of microbial, 291–4

quantification of microbial, 303–4

620 SUBJECT INDEX

Manganese reduction (cont.)

recycling, 308–10

reducers, 291–2, 293, 299–300

sediment microbial, 304, 309

substrate competition and, 301

versatility of reducers in, 295

water column, 311–12

Mangrove forests, 493–506

algae in, 496

basin, 493

carbon mineralization in, 500–2

carbon nitrogen ratio and, 495, 499, 502

carbon oxidation in sediment of, 500

creeks, 505–6

definition, 493–6

denitrification rates and sewage discharges

in, 503

detritus decomposition by microbes

and, 498

detritus handling in, 496–9

DOM, leached and, 499

food webs, 496–9

iron-rich, 500, 501

litter, 496, 498–9, 502

litter nutrient content in, 498

matter/nutrients exported from, 505

nitrogen demand in, 502, 504

nitrogen fixation in sediments of, 504–5

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,

499–505

sediment decay of litter in, 498–9

sediments, 494–6, 499, 500, 504–5

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, 187–8

amensalism and, 56

anammox pathway of, 262

anoxygenic phototroph, 97

Bacteria and, 15–16

benthic, 152–5

cell size and, 25

cellular biomass produced by, 123–4

chemolithoheterotrophic, 349

disproportionation and, 371, 372

Eukarya, 17–18

free energy, 91–2

hydrogen fueled autotrophic, 97

iron reduction, 291, 294–6

methanotroph, 407

Michaelis Menten approximation of, 31

microorganism, and temperature, 39–41, 43

naming an organism’s, 93–4

nitrifier, 242

nutrient limitations and, 35–6

oxidation-reduction and, 75

oxidative, 337

oxygen and aerobic, 187–8

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, 152–5

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, 343–4

sulfur reduction, elemental and, 343

temperature and, 32, 40–1, 43, 71, 242

temperature and nitrifier, 242

Methane. see also Anaerobic oxidation

of methane; Methane clathrate hydrate;

Methanogen

SUBJECT INDEX 621

atmospheric escape of, 406

clathrate hydrate formation by, 385, 387

climate change and release of, 383, 384–8

concentrations, 384, 385

environmental production of, 400

formation pathways, 416

greenhouse gas, 384

‘‘gun hypothesis,’’ 387–8

isotope fractionation and production

of, 414–17

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, 383–4, 400

release, 383, 384–8

sink, 384

sources, 384, 386, 485

stratified water body accumulation

of, 485–6

stratified water body sources for, 485

sulfate depletion and accumulation

of, 396–7

sulfate reduction removal of, 410

Methane clathrate hydrate, 385–6, 387

dissolved, 387

environment and, 385–6

marine sediment stability of, 386–7, 388

Methane cycle, 383–418

Methane monooxygenase (MMO), 403

Methane oxidation. see also Anaerobic

oxidation of methane

aerobic, 417

anaerobic, 409–14

initial step of, 403, 404

intensity, 405, 406

isotope fractionation and aerobic, 417

kinetics, 407, 408

marine sediment, 409

methanogen, 411–12

methanogenesis and, 412

sulfate reduction and anaerobic, 411

Methane oxidation, anaerobic

sulfate reduction and, 411

Methanococcus jannaschii, 116–17

Methanogenesis, 383, 388–402

acetate, 393, 395

acetate as electron donor for, 397

acetate required for, 396

acetoclastic, 390

acetotrophic, 390

aquatic environment, 232, 398, 399, 415

Archaea, 390, 392–3

biochemistry, 392–5

carbon dioxide reduction with

hydrogen, 393, 394, 401

carbon mineralization, 397–9

electron donors, 397, 401

energy conservation and, 393, 404

energy required for, 394

environmental significance of, 395–402

fermentation reactions and pathways of, 394

freshwater environment, 398, 399

hydrogen as electron donor for, 397, 401

hydrogen required for, 396

isotope fractionation, 414–17

methane oxidation and, 412

methanol and methyl-containing

compound, 393, 395

Michaelis-Menten kinetics and, 400

pathways, 394

process of, 392–3

substrates for, 388–90

thermodynamics, 400

Methanogens, 388–9

anoxic environment, 395

Archaea cluster among, 412, 413

compounds used by, 389

energy yield, 395

Euryarchaeota, 390

evolution, 390–2

isotope fractionations by diVerent groups

of, 416, 417

methane oxidation by, 411–12

methylamine as substrates for, 390

orders of, 391, 392

phylogeny, 390–2, 412, 413

sulfate reducing conditions and, 400

sulfur reducer co-occurance with, 397

taxonomy, 390–2

Methanol

ATP formation and, 404–5

formaldehyde conversion from, 403, 404

Methanotrophs

activity, 407–8

aerobic, 402–9

animals, invertebrate symbiotic relationship

with, 406–7

622 SUBJECT INDEX

Methanotrophs (cont.)

carbon fixation pathways for aerobic, 402–5

environmental distribution of, 405–7

metabolism, 407

Methylococcacaea, 402, 403

Methylocystaceae, 403

organisms for aerobic, 402–5

oxygen concentrations, 408–9

phylogeny for aerobic, 402–5

significance of, 405–7

Methanotrophy, 15, 402–14

ammonium inhibition of, 406

anoxic conditions of, 402

factors limiting, 407

isotope fractionation and, 417–18

kinetics, 407–9

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, 46–50

extreme environments and, 46

FISH visualization of, 49

functional, 49

molecular studies and, 47–9

phenotypic, 46

species, 47, 49

stress and, 46

true, 48

Microbial ecosystems, 465–506

mangrove forest, 493–506

microbial mat, 466–80

stratified water body, 480–93

Microbial growth, 28–36

basic constituents of, 155, 156

Microbial growth eYciency (MGE), 157

anabolic process energy and reduced, 158

anoxic sediments and low, 158–9

factors regulating, 28–36, 157–8

variation in, 59, 157

Microbial interactions, 50–60

amensalism as, 56

commensalism as, 50, 56

competition as, 50–2, 90–1

mutualism as, 57

neutralism as, 56–7

parasitism as, 53–5

predation as, 53–5

symbiosis as, 57–60

synergism as, 53

syntrophy as, 53

Microbial loop

DOM in, 141–2

importance of, 141–2

prokaryotes in, 141

Microbial mats, 465–80

ammonia sequestered by nighttime

community of, 478–80

anoxygenic phototrophic, 466

biogeochemistry, 474–80

carbon cycling within, 475–8, 479

carbon source for, 475

characteristics of, 469–70

chemical constituent measurement with

microsensors in, 466

cyanobacteria density and, 467, 468

depth, 467, 468, 471–2

DIC diVusion from, 478, 480

DIC sources in, 478

diversity, 469

ecology, 470–4

ecosystem structure of, 467–70

elements cycling internally in, 475–8

EPS stabilizing, 470

light in, 466, 472–3

light measurement with microsensors in, 466

Microcoleus chthonoplastes

dominated, 468, 470

organism migration with light in, 472–3

organisms and depth of, 471–2

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, 470–1

photosynthesis, 470, 474

phototrophic, 466, 469, 470

population structure of, 467–469

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, 37–8

SUBJECT INDEX 623

amensalism and, 56

carbon content and, 37, 38

cell diVerentiation in, 61–4

cell size and, 35–6

commensalism in, 50, 56

competition between, 66

controlling processes of, 36

density, 37, 38

diversity, 45–50

ecology, 45–60

energy, activation for, 41

factors influencing, 37

FISH visualizing structure of, 49

growth, 23–64

horizontal gene transfer and ecology

of, 60–1

identity prediction in, 47

Michaelis-Menten-like kinetics and growth

of, 36

morphological diVerentiation in, 62–3

neutralism in, 56–7

nutrient limitations and, 35

overpopulation, 34

phenotypic diversity in, 45–6

quorum sensing in, 63

sediment depth and, 39

social behavior, 61–4

stratified water body positioning of, 480

structure of, 23–64

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, 271–2

manganese mobilization with, 271–2

natural environment, 190–203

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, 41–2

chemostat and growth physiology of, 33

classification, 1–2

classification, comparative biology of, 2

detritus breakdown by, 134

energy for growth of, 131

environmental extremes and, 39–45

growth, 32, 131

growth temperature for, 40

iron uptake by, 277

manganese uptake by, 277

metabolism temperature for, 40–1, 71

pH and, 43–4

physiological similarities and competition

between, 50–1

salt and, 44–5

temperature and, 40–3, 71

toxic oxygen protection by, 145

Mitochondria, 18, 19

MMO. see Methane monooxygenase

Monera, 14–15

Monod equation, 29–30

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, 56–7

Neutrophiles, 43–4

nifH gene

Bacteria containing, 217

cluster organization and phylogeny of, 216

copies, 217

nitrogen fixation pathway and, 216, 217

phylogeny, 216, 217

Nitrate, 206–7. see also Nitrate reduction

ammonification, 251–3, 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, 250–3

iron oxidation with, 282, 283–5

isotope fractionation and denitrification

from, 266

manganese oxidation with, 289

nitrification production of, 232

624 SUBJECT INDEX

Nitrate (cont.)

nitrite respiratory transformation

to, 252, 263

nitrogen detrification from, 250

oxygen dependence by, 256–9

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, 246–51

manganese reduction competition with, 301

nitrite intermediate in, 246

pathways, 246–7

prokaryotes for, 246–7

sediment, 247

Thiomargarita, 351

Nitrification, 232–5, 266

ammonium availability and, 237

ammonium oxidation step in, 239

anammox and oxic, 261

anoxia tolerance and, 239

aquatic environment, 241–2

bacteria, 233, 234

biochemistry, 233–5

chemolithoautotroph, 235–7

determining total, 247

electron donors for, 233

environmental factors aVecting rates

of, 237–5

heterotroph, 235, 236, 242

inhibitors, 245

invertebrates, burrowing and, 257

isotope fractionation and, 266

light and, 237, 245

measuring, 245, 246–7

mesophilic, 242

metabolism and temperature for, 242

microelectrode measuring of, 245–6

nitrate produced by, 232

nitrogen fluxes and measuring, 245

nitrogen isotope pairing technique for

measuring, 247–8

nitrogen loss and, 232

Nitrosomonas, 234

oxic, 261

oxygen availability and, 237, 238, 239, 243

pH and, 237, 241–2

pH, optimal for, 241

phylogeny of chemolithoautotroph, 235–7

salinity and, 237, 244

salinity sensitivity of Nitrosomonas, 244

sediment, 238–9, 241–2, 243

sediment depth and, 240

stream sediment, 247–8, 249

substrate concentrations and, 240

substrates for, 238–40

sulfide concentration and, 237

temperature and, 237, 242–3

temperature and oxygen availability for, 243

temperature and shallow water

sediment, 243

thermodynamics, 233–5

Nitrite, 206–7

detoxification, 251

diVusion, 257, 258

isotope fractionation and availability of, 265

light and oxidation of, 245

Michaelis-Menten kinetics and oxidation

of, 239–40

nitrate respiratory transformation

from, 252, 263

nitrification and oxidation to, 232

oxidation, 239–40, 245

oxidizers, 236–7

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, 219–20

ammonium fixed from, 207

anammox, 262–3

anammox and sediment production

of, 262–3

assimilation, 219–32, 266–7

biological importance and pool size of, 208

biologically available forms of fixed, 207–8

budgets, 218–9, 230, 232

carbon and, 224

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

cell biomass incorporation of dissolved

inorganic, 224

SUBJECT INDEX 625

decomposition 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, 207–8, 209

freshwater lake limitation of, 218

immobilization, 223–5, 226

incorporation, 223

inventory, 422

isotopes, 264

liberation, 207

limitation, 218

loss, 206–7, 209–10, 211, 232

mangrove creek importation of, 506

mangrove forest demand of, 502, 504

mangrove forest retention/recycling of, 502

marine budgets for, 218–9

marine, coastal cycling of, 230–2

measuring incorporation of, 223

new, 230–2

nitrite as oxidized form of, 206–7

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, 230–2, 422

organic, 219, 220

organic, deep sea, 220

pelagic ecosystem, 230–2

phosphorus, ratio, 422

phytoplankton demand of, 230

phytoplankton growth and, 433

recycling, 207

redox cycling and, 206

reductase, 250–1

regenerated, 230–2

reservoirs, atmospheric, 208

reservoirs, earth, 207

reservoirs of, dead organic detritus in, 208

sediment, 499–505

sediment depth and carbon, ratio, 228

sediment depth and incorporation of, 228

sediment production of, 263–4

sediment surface deposited, 232

sources, 230, 231, 232

transformations, 224

water column regeneration of, 230

Nitrogen cycling, 205–68

denitrification, 249

human perturbation in global, 207–9

isotope fractionation and, 263–7

nitrification and, 232

Nitrogen fixation, 206, 209, 266–7

acetylene reduction assay and study

of, 211–2

ammonium formed during, 213–4

anaerobes, obligate for, 215

aquatic environment, 218–9

ATP and, 213

benthic, 219

biological, 209–19

Bradyrhizobium japonicum, 188

cellular material incorporation

of ammonium formed during, 213–4

cyanobacteria and, 174, 175, 176, 215–6, 218

cyanobacteria and planktonic, 218

diazotroph, 209, 215

industrial, 209

industrial v. prokaryote, 210

isotope fractionation and, 266

land biological, 209

mangrove sediment, 504–5

marine environment biological, 209

measuring, 211–2

nifH gene and pathway of, 216–7

nitrogen replaced by, 210, 219

nitrogen source for, 266

nitrogen supplied to open water ecosystems

through, 218

organisms for, 216–7

pelagic, 218

photosynthesis separated from, 215

phylogeny of organisms for, 216–7

planktonic, 218

prokaryote, 209, 210

prokaryote mediation of benthic, 219

prokaryote v. industrial, 210

seagrass bed, 219

sediment, 218, 219

Trichodesmium, 215–6

wetlands, 219

Nitrogen isotope pairing technique, 245,

247–8

denitrification measured with, 245, 247–8

nitrification measured with, 245, 247–8

626 SUBJECT INDEX

Nitrogen mineralization, 219, 220, 225–9

anaerobic, 225–9

anoxic pathways of, 227

carbon oxidation and, 227–8

microbial, 223–4

nitrogen, excess and, 224, 225

oxic water column, 220

sediment, 225–7

Nitrogen mobilization, 223–5

carbon, ratio and, immobilization, 224, 226

microbial mineralization and nitrogen

immobilization and, 224

Nitrogenase, 212–3

components associated with, 212

cyanobacteria, phototrophic and

inactivation of, 215

diazotroph and protection of, 214–5

dinitrogenase and, 212

forming/maintaining enzyme complex

of, 212

genes, 216, 217

inactivation, 215

oxygen and, 214–6

trace metals protein for, 212–3

Nitrosococcus oceanus

ammonium oxidized by, 235–6, 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, 160–1, 163

mineralization, 89–92

respiration energetics and mineralization

of, 89–92

Organotroph, 93, 201

Oscillochloris, 105–8, 114, 366–7

OTU. see Operation taxonomic units

Oxaloacetate, 109, 110

Oxic-anoxic interface, 197–8

aphotic sediments near, 170, 197

depth, 200

diVusion and, 259

electron donors and oxygen consumption

near, 197

iron 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, 181–3

bacterial manganese oxidation and

extracellular, 182

extracellular, 182

fungal, 182

heme copper, 188, 189

nitric oxide reductase evolution into, 189–90

oxygen respiration terminal, 183

Oxidation-reduction, 75–80. 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, 75–76

Oxygen. see also Oxygenic photosynthesis

aerobic metabolism and, 187–8

aerobic organisms and, 173

anaerobic metabolism and levels of, 184

anaerobic organisms and, 173

anaerobic respiration and, 187

anammox and, 264

anoxia and, 172–3

aquatic sediment, 169, 170

atmospheric, 168–9

atmospheric production of, 168, 190

Bacteroides fragilis required saturation

of, 173

benthic uptake of, 199

biosphere, 190

bottom dwellers and transport of, 170,

198–9

chemical considerations for, 170–3

consumption, 146–7

cycle, 167–204

denitrification and absence of, 255

diazotroph protection of nitrogenase

from, 214–15

diVusion and microgradients of, 196–7

dioxygenase catalyzation of, 180

SUBJECT INDEX 627

electron donors for, 201–2

environmental budgets for, 197–8

flux, 200

hydrogen peroxide as source of, 190

iron, ferrous as electron donor for, 201–2

iron oxidation and, 280, 283

iron reduction and, 300, 301

isotopes, 202–4

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, 408–9

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, 256–8

nitrification and availability of, 237, 238,

239, 243

nitrogenase and, 214–16

oceanic, 168–9

oceanic minimum zones of, 169

organic matter abiotic reaction with, 172

oxidation state of, 170–1

photosynthesis and supersaturation

of, 170, 172

reactive, species, 183–4

reoxidation and diversion of, 201

sediment, 146, 338

sediment penetration by, 146, 200, 257

sediment rates for uptake of, 199–200

solubility, 171–2

sources, 190

stratified water body interface between

sulfide and, 482–3, 484

stratified water body minimum zones of, 481

stratified water body penetration of, 482–3

sulfate reduction and, 336–7

sulfide reaction rate with, 346–7, 482–3, 484

superoxide generated from, 190

supersaturation, 170, 172

thermodynamics of, 167–8

transport, 170, 198–9

Oxygen consumption

anaerobe, 185

ATP increased yield and non-

respiratory, 182

benthic, 200, 201–2

depth and, 196

enzymatic processes of, 180

fauna, 201

Fick’s laws, depth and, 196

kinetics, 193

Mehler reaction, 202–3

microbial, 180–5

non-respiratory, 182

oxic-anoxic interface, electron donors

and, 197

oxidases and, 180

oxygenases and, 180

photorespiration, 202–3

reactions, 201

sediments, 198–202

solute, 196

Oxygen exposure time (OET), 164

Oxygen respiration, 170, 185–8, 202–3

aerobic microbe, 201

aquatic environment control of, 193–6

Bacteria, 188

electron donor for, 194

electron transport chains and, 185–7

Eukarya, 188

evolution, 188–90

kinetics, 187–8, 193

macroorganism, 201

nutrients and aquatic environment, 195

organotrophic, 197–8, 199, 200–1

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, 188–90

POC and source of substrate for, 195

regulation and, 187–8

substrate, 195

temperature and aquatic environment, 195

Oxygenases, 180, 182

Oxygenic photosynthesis, 95, 96, 104–5, 168,

170, 173–80, 190

bacterial, 170, 173–80

isotope fractionation during, 201–2

microbial mats, 474–80

prokaryote, 173

Parasitism, 53–5, 57

Particulate organic carbon (POC), 142

bacteria energy source, 194

628 SUBJECT INDEX

Particulate organic carbon (POC) (cont.)

oxygen respiration substrate source and, 195

Particulate organic nitrogen (PON), 266, 267

PCR. see Polymerase chain reaction

pH, 43–4

aerobic respiration, 191

cytoplasmic regulation of, 43–4

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, 431–2

phosphate sink, 431

sediment, 431

in situ formation of, 432

Phosphorus. see also Dissolved inorganic

phosphorus; Dissolved organic phosphorus

abundance, 420

adsorption, 424–5

anoxic sediment carbon, ratio, 438

aquatic environment, 422, 424–5, 433

aquatic sediment, 426

assimilated, 424, 434

ATP formation and assimilation of, 424

availability, 419

bound, 423–4

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, 438–40

eutrophication and anoxic condition release

of, 438

extraction, 426

geochemistry, 424–5

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, 422–4

nitrogen, ratio, 422

oceanic, 420–1, 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, 437–8

sediment release of, 438

sediments, 420, 426, 436–7

sinks, 422

soluble, 423–4

sources, 420, 421, 435

terrestrial incorporation, 421

Phosphorus cycle, 419–40

aquatic environment, 432–40

global, 420–2

marine sediment, 436–8

microbes in, 427–31

phosphorite formation in, 431–2

seasonal marine sediment, 436, 437

water column, 433–6

SUBJECT INDEX 629

Photoautotroph

iron oxidation and growth of, 287

light harvested by, 99–101

purple sulfur bacteria growth through, 362

Photolithoautrophy, 95

Photolithoheterotroph, 94

Photoorganoheterotrophs, 358

Photorespiration

oxygen consumption by, 202–3

photosynthesis, terrestrial and, 183

Photosynthesis. see also Anoxygenic

photosynthesis; Oxygenic photosynthesis

Archaea, 97

carbon fixation by, 492

carbon produced by, 175

cyanobacteria, 178–9, 474, 476

cyanobacteria and nitrogen demands of, 179

electron donors during, 105

energy conservation during, 102–3

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,

490–3

temperature and, 474

Phototroph. see also Photosynthesis

anoxygenic photosynthesis, 96, 99–101,

286–7, 357–367

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, 99–105

green sulfur bacteria obligate, 364

iron oxidizing, 274, 286–7

microbial mats and, 470

oxygenic, 100, 101–2, 103, 104

pH and iron oxidizing, 286

photosynthetic process in

oxygenic, 101–2, 103

photosystems of oxygenic, 102

redox potential and iron oxidizing, 274, 286

stratified water body competition between

anoxygenic, 487–90

sulfide oxidizing, 357–367

Phototrophy, 95–127

Phylogeny, 1–21

Archaea, 412, 413

carbon fixation pathways, 113–6

chemoautotrophic organism ecosystems

nitrification and, 235–7

constructing, 6–8, 12

denitrification and diversity of, 254

denitrification detection by, 253–5

DNA construction of, 8

DNA for analysis with, 12–13

genetic element construction of, 6–7

iron reduction, dissimilatory, 296

iron reduction, microbial, 291–4

manganese reduction, microbial, 291–4

methanogens, 390–2, 412, 413

methanotrophs, aerobic, 402–5

molecular sequence analysis and

information about, 8

nifH gene, 216, 217

nitrification, chemolithoautotroph, 235–7

nitrogen fixer, 216–17

oxygen respiration, 188–90

photosynthetic organism genes and, 370

prokaryote, 6

reconstruction, 7, 8, 10

rRNA molecule, 8–10, 19–20

SSU rRNA, 8, 10, 19–20

sulfate reducer spectrum of, 377

sulfate reduction, dissimilatory, 325–7

sulfide oxidizer, 352–4

sulfur reduction, 342–4

Phytoplankton

carbon pump, 461–2

chemical composition of, 133, 134

as detritus source, 132

DIP assimilation of, 434–5

DOM released by, 138

nitrogen and, 230, 433

nitrogen isotope fractionation expression

by, 265, 267

phosphorus and, 433, 438

Planctomycetes, 18

Plantae, 14–15

630 SUBJECT INDEX

POC. see Particulate organic carbon

Polymerase chain reaction (PCR), 12–13

PON. see Particulate organic nitrogen

Predation, 53–5

Prochlorococcus

as cyanobacteria, 176–7

nitrate utilization by, 178

oceanic distribution of, 177

photosynthesis compensation intensities

and, 177, 178–9

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, 105–11

chemical composition of, 132–3

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, 2–3

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, 34–6

heterotrophic, 140–1

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, 246–8

nitrogen fixation by, 209

organismal phylogenies among, 6

parasites, 54

parasitic symbiosis in, 57

pH, 43–4

phosphate storage by, 423

phylogenetic grouping of, 2–3

physical associations between, 57, 58

population growth, 28

predatory behavior exhibited by, 54

protozoan impact on population of, 54

protozoan predation of, 53–5

protozoans mutualistic symbiosis

with, 59–60

redox-sensitive elements role of, 23

reproduction, 48

ribosome, 8

size, 24, 26

species, 48

stationary phase growth of, 28–9

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, 192–3

purple sulfur bacteria in, 360

sea water, 192–3

sulfide oxidation, 352–3

sulfur reducing, 14, 20, 342

Protista, 14–15

Protozoans

prokaryote and, 53–5, 59–60

Strombidium pupureum as housing for, 60

Psychrophiles, 41–3

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, 360–3

anaerobes, obligate, 362

anoxic habitat, 362

SUBJECT INDEX 631

chemolithoautotrophic 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, 75–7

abiotic, 274–5

electrode potential and, 76

electron tower, 79–80

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, 290–1

organism promotion of favorable, 95–6

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, 8–10

phylogeny, 8–10, 19–20

Ribosome. see also Ribosomal RNA

prokaryotic organism, 8

subunit, 8, 9

Ribulose monophosphate pathway

(RuMP), 404

Riftia pachyptila, 121, 122

RNA, 3–5. see also Messenger RNA;

Ribosomal RNA; Transfer RNA

molecular structure of, 4

protein synthesis and, 4

rRNA. see Ribosomal RNA

Rubisco, 108, 116–20

adaption to poor performance by, 117–18

algal, 117–18

Archaea, 108, 115, 116, 118

carbon fixation reductive pentose

phosphate cycle and, 116

carbon isotope fractionation magnitude

and, 119–20

carbon specificity of, 117

carboxylase and oxygenase activity

of, 116, 117

carboxylase reaction specificity of, 117

Chlorobium, 108, 116

competition within, 116

cyanobacterial, 117–18, 118–19, 174–5

fractionation, 121

like genes, 115

Methanococcus jannaschii, 116–17, 118

oxygen specificity of, 117

oxygenase activity of, 115, 118, 119, 183

oxygenic phototroph, 116

phylogenies, parallel from, 114

poor performance by, 117–18

proteobacteria, 116

RuMP. see Ribulose monophosphate

pathway

Secondary ion mass spectrometry (SIMS), 413

Sediments

ammonium absorption by, 223

ammonium in, 223, 225–9

anaerobic respiration and depth of,

150, 151

anammox and nitrogen production

by, 263–4

AOM in marine, 410

aquatic, 164–5, 169, 247–8, 254–5, 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, 454–5

carbon in, 499–505

carbon mineralization in anoxic, 227

carbon: nitrogen ratio and depth of, 228

carbon oxidation in, 153, 500

carbon preservation in marine, 164–5

decomposition products from marine

anoxic, 227

denitrification and population diversity in

marine, 254–5

denitrification in, 240, 247–8, 255, 259,

260, 265

detritus decomposition in, 228

DIP released from, 439

inhomogeneities of, 151

632 SUBJECT INDEX

Sediments (cont.)

iron mobilization in, 271–2

iron reduction in, 303, 304

isotope fractionation and denitrification

in, 266

lake, 324

macrophyte communities and

denitrification in, 259

manganese mobilization in, 271–2

manganese reduction, microbial in, 304

manganese retention in, 289

mangrove, 494–6, 500

mangrove forest litter decay in, 498–9

marine, 164–5, 253, 254–5, 322, 323–4, 338,

341, 409, 436–8

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, 238–9, 240, 241, 243

nitrification in stream, 247–8

nitrogen deposited on surface of, 232

nitrogen fixation rates in, 218, 219

nitrogen incorporation and depth of, 228

nitrogen mineralization in, 225–7

nitrogen production by, 263–4

organic components of, 165–6

organic matter preservation in, 163–4

oxygen consumption in, 198–202

oxygen in aquatic, 146, 169, 170, 338

oxygen penetration into, 46–7, 200, 257

oxygen transported into, 146

oxygen uptake rates, 200

pH and nitrification in, 241

phosphorite, 431

phosphorus and, 420, 426, 436–40

phosphorus release from, 438

respiration and mangrove forest, 500

seasonal phosphorus cycle in

marine, 436, 437

sequential extraction fractionation

of phosphorus, 426

stream, 247–8

sulfate reduction in, 321, 322, 323

sulfide oxidation in, 370

sulfur in marine, 341

temperature and denitrification in

aquatic, 260

temperature for nitrification in shallow

water, 243

SHE. see Standard hydrogen electrode (SHE)

Silica. see also Biogenic silica; Dissolved silica

algal production and, 458–9

aquatic environment dissolution of, 458–9

aquatic system primary production and, 441

biogenic production of, 446–7, 448

biological transformations and, 442

carbon pump, biological and, 461–2

cell-specific content of, 445–6

chemistry, 442

depletion, 457–60, 462

diatom formation of, 445–50

dissolution, 450–6

DSi accumulation and saturation

concentration of, 453

mineralogy, 442

pelagic production of, 447

pH and, 442, 450, 452

protease activity and dissolution of, 455–6

regeneration, microbe-mediated, 456

salinity and diatom content of, 446

weathering, 443

Silica cycle

evolution of, 462–3

global, 442–5

oceanic, 443

terrestrial biogeochemical, 443

Silicate

dissolution, 456

microbes and weathering of, 456–7

organic acids and dissolution of, 457

weathering, 456–7

Silicon

abundance of, 441

biogeochemistry, 450–7

carbon and, 441

forms, 441

Silicon cycle, 441–63

aquatic environment, 458–62

oceanic, global, 443, 444

silica depletion and aquatic

environment, 458–61

SIMS. see Secondary ion mass spectrometry

Small subunit (SSU) rRNA, 8, 10, 12–14

biological innovation timing constraint

and, 13–14

diVerences, 12

evolution, 12–14

five-kingdom division of life and, 14–15

SUBJECT INDEX 633

phylogenetic reconstruction and, 8, 10

phylogeny, 19–20

taxonomic organization and, 8, 10, 20–1

Tree of Life from comparisons of, 10–14

SSU. see Small subunit

SSU rRNA. see Small subunit rRNA

Standard hydrogen electrode (SHE), 75–6

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, 480–93

Black Sea as, 482–6

chemically, 480

Chlorobium in, 489

Chromatium vinosum in, 489–90

Chromatium weissei in, 489–90

green sulfur bacteria in, 489

Golfo Dulce, 481–2

hyper-sulfidic, 481

light, spectral quality of and depth of water

columns in, 488

Mahoney Lake, 486–7

microbial, and interaction, 480–7

microbial population positioning in, 480

oxygen minimum zones in, 481

photosynthesis, anoxygenic and, 490–3

phototrophs, anoxygenic competition

in, 487–90

purple sulfur bacteria in, 489

Suboxic environments, 173

Substrate concentration

chemostat, 33

energy and, 33–4

Escherichia coli, 29

expression for, 38

metabolic rate and, 30, 31

modeling, 38–9

in nature, 36–9

population density and input, 33

prokaryotes and, 29, 32

Substrates

competition for, 51–2, 90–1, 301

consumption rate of, 37

denitrification and availability of, 255

herbivores feeding on, 135

iron/manganese reduction competition

for, 301

methanogen, 390

methanogenesis, 388–90

microbial population and limitations of, 51

nitrification, 238–40

oxygen respiration, 195

production, 36–8

sulfate reduction and, 329–34

Sulfate. see also Sulfate reduction

accumulation, 329

exchange, 376

isotope fractionation and exchange of, 376

limitation, organism of, 376

marine concentration of, 337–8

sulfide isotope diVerence from, 380, 381

sulfide oxidation to, 351, 352, 368

sulfide reduction and, 315–16, 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, 321–2, 324

AOM and, 411, 412, 413–14

AOM and electron donor for, 413–14

Archaea, 325

assimilatory, 318, 319–20

Bacteria, 325

carbon availability and, 338

carbon fixation and, 334

carbon mineralization and, 320, 322–3,

397–9

carbon oxidation rates by, 322, 338

Desulfovibrio desulfuricans oxidation

and, 331–3

Desulfovibrio oxyclinae, 336–7

dissimilatory, 318, 320–40

electron donor and, 325, 330, 332, 333–4,

413–4

energy for assimilatory, 320

energy gained during, 327

environmental significance/distribution

of dissimilatory, 320–5

factors controlling rates of, 336–40

freshwater environment, 398, 399

gram-positive reducers for, 325–6

hydrogen as electron donor for, 330, 332,

333–4

iron oxidation and, 433, 434

iron reduction and, 304, 306, 307

isotope fractionation, 377–8

634 SUBJECT INDEX

Sulfate reduction (cont.)

lake sediment, 324

mangrove environment suppression of, 323

marine environment, 320, 322–3, 329

marine sediment, 322, 323–4

Marinobacter, 337

measuring rates of, 321–2

metabolic adaptations to temperature

by, 340

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

metabolism, oxidative for, 337

methane oxidation and, 410–11

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, 333–4

oxygen and, 336–7

PAPS pathway of assimilatory, 319–20

phylogenic spectrum of reducers of, 377

phylogeny of dissimilatory, 325–7

physiology of reducers in, 335

proteobacteria, 325, 326

proton gradients in reducers for, 327–9

rates, 338–9, 376

shallow water environment carbon

mineralization and, 322–3

stratified water body, 486, 487

substrate oxidation and, 332, 333

substrate utilization in, 329–34

sulfate and, 337

sulfide source from, 357

suppressed, 323

temperature and population of reducers

in, 335

temperatures, 326, 338–40

Sulfide. see also Sulfide oxidation

formation, 318

iron, phases, 316

manganese/iron oxidation reaction

with, 345–6

microbial mat accumulation of, 474

oxygen reaction rate with, 346–7, 482–3,

484

reoxidation to sulfur compounds of, 316

reoxidized, 370, 371

stratified water body accumulation of, 481

stratified water body interface between

oxygen and, 482–3, 484

sulfate isotope diVerence from, 380, 381

sulfate reduction source of, 357

sulfate reduction to, 315–16

sulfite reduction to, 374

sulfur compound formed to, 316, 357

water column, 345

Sulfide oxidation

aerobes, facultative for, 351

aerobes, obligate for, 351

Archaea, 352–3

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, 365–7

green sulfur bacteria as oxidizers for, 358,

359, 364–5

heliobacteria as oxidizers for, 358, 359, 367

incomplete, 370

inorganic, 345–7, 347–8

maximum rate of environmental, 347, 348

metal oxides, 354–7

Michaelis-Menten kinetics and

biological, 347

microoxic conditions for, 351

nitrate in, 351, 481–2

non-phototrophic biologically

mediated, 349–57

organisms for, 349–52

oxidizers, 349, 352–4, 358–67

pathways, 367–8

phototrophic, 357–70

phylogeny of oxidizers for, 352–4

products, 341, 370–1

proteobacteria, 352–3

purple nonsulfur bacteria as oxidizers

for, 358, 359, 363

purple sulfur bacteria as oxidizers for, 358,

359, 360–3

sediment, 370

solid phase, 357

steps in, 357, 367–77

stratified water body, 485, 487, 488

sulfate from, 351, 352, 368

sulfite from, 368

sulfur from, 368, 370

SUBJECT INDEX 635

temperature and, 351–2

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, 373–4, 379, 380

disproportionation organisms of, 371–3

elemental, 341–2, 344–5, 346, 374

environment and metabolism of, 315

isotope fractionation and

disproportionation of, 379, 380

isotope fractionation in, 375

isotopes, 374–81

marine sediment elemental, 341

methane accumulation and depletion

of, 396–7

PAPS formation pathways for, 318–20

pathways for formation of, 318–20, 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, 313–81

compound fate in, 316

discipline and concept of, 314

global biogeochemical perspective

of, 314–15

isotope geochemistry, stable in, 374–81

metabolically active compounds of, 316, 317

microbial ecological perspective of, 315

Sulfur disproportionation, 316

Sulfur oxidation, 316

disproportionation, 370–4

oxidizers in, structural role of, 318

sulfate esters and, 318

sulfite from, 368

sulfonates and, 318

Sulfur reduction, 316

Archaea, 343

ATP generated in, 343

biochemistry of, 345

compounds, 357–58

Desulfuromonas elemental, 343

distribution of reducers for, 344

electrons driving, 345

elemental, 341–5, 349–51

environmental distribution

of elemental, 344–5

metabolism and elemental, 343

methanogen co-occurance with, 397

organisms for elemental, 341, 342–4

phylogeny and organisms for

elemental, 342–4

prokaryotes for elemental, 342

proteobacteria for elemental, 342

steps in, 345

substrates and organisms for

elemental, 342–4

sulfur, elemental as compound of, 357

Thermotoga, 343

thiosulphate as compound of, 357

Symbiosis, 57–60, 64, 406–7

Synechococcus

as cyanobacteria, 176–7

oceanic distribution of, 177

Synergism, 53

Syntrophy, 53

Systematics, 1–21

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, 41–3

hyperthermophiles adaptation to, 43

isotope fractionation and, 416, 417

metabolism and, 32, 40–3, 71, 242, 340

microbial mats and, 473

microorganism, 40–3, 71

microorganism growth rate and, 40–3

microorganism metabolism and, 40–3, 71

636 SUBJECT INDEX

Temperature (cont.)

microorganisms, Arrhenius equation

and, 41–2

nitrification and, 237, 242

nitrifier metabolism and, 242

oxygen respiration and, 195

STP, 74

sulfate reducer metabolism adaptation

to, 340

sulfate reduction and, 326, 338–40, 473

sulfate reduction in microbial mats and, 473

sulfide oxidation, 351–2

thermodynamics and, 71

thermophiles’ adaption to, 43

Thermodynamics, 68, 70

activity coeYcient calculations for, 71–2

anaerobic respiration and, 150

disproportionation, 372

enthalpy as state function of, 66–7

entropy as state function of, 67

equilibrium and, 70–1

fermentation process, 88

gas solubility and, 73–4

Gibbs free energy as state function of, 68

glucose oxidation/oxygen, 77

iron oxide, 302

laws of, 66, 67–70

methanogenesis, 400

microbial metabolism and, 65–94

microbial population competition and, 66

nitrification, 233–5

oxygen, 167–8

respiration processes and, 91

state functions, 66–70

sulfur isotope distributions and, 374

sulfur-disproportionation organism, 69–70

temperature and, 71

Thermophiles, 41–3

membrane lipids of, 43

temperature adaption of, 43

Thermoproteus, 106, 115

Thermotoga, 343

Thiobacillus, 353–4

Thiomargarita, 351

Thioploca, 356–7

distribution, 356

large size of, 27

nitrate exposure of, 356–7

oxygen 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), 4–5

Transmission electron microscopy (TEM), 26

Tree of Life, 10

anoxygenic photosynthesis in, 369

Aquifex lineage of, 12

Archaea domain of, 11, 16–17, 18

Bacteria domain of, 15–16

branch length in, 12

calibration of, 14

carbon fixation pathway lineages on

the, 113–14

comparisons with previous, 14–15

Eukarya domain of, 11, 17–19

evolution and, 12–13

SSU rRNA, 10–14, 15, 19

tour through, 15–19

Tricarboxylic acid (TCA), 144

Trichodesmium

as cyanobacteria, 176

iron demands of, 179

as nitrogen fixers, 215–16

photosynthesis compensation intensities

and, 177, 178–9

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