fundamentals of geobiology (knoll/fundamentals of geobiology) || index

Fundamentals of Geobiology, First Edition. Edited by Andrew H. Knoll, Donald E. Canfield and Kurt O. Konhauser.

© 2012 Blackwell Publishing Ltd. Published 2012 by Blackwell Publishing Ltd.

437

Index

ACC see amorphous calcium carbonateachondritic meteorites 335acid–base reactions 5acidification 39addition profiles 215aerobic Fe(II) oxidation 69–70, 112, 143aerosols 190–1AFM see atomic force microscopyagriculture 428–30alimentation 197–9ambient pressure photoemission

spectroscopy (APPES) 137AMF see arbuscular mycorrhiza fungiammonia/ammonium

carbon cycle 7–8, 15nitrogen cycle 41–5stable isotope geobiology 261

ammonification 41amoABC genes 42amorphous calcium carbonate (ACC) 151,

156, 166–9, 171–3anaerobic ammonium oxidation 43–5, 261anaerobic chemolithoautotrophic Fe(II)

oxidation 70–1anaerobic Fe(III) reduction 72–3, 108, 143–5anaerobic methane-oxidizing Archaea

(ANME) 239–42anaerobic oxidation of methane

(AOM) 55–7, 238–42anammox see anaerobic ammonium

oxidationangiosperms 414animals as geobiological agents 188,

195–200alimentation, bioturbation and

biomineralization 197–9ecosystem engineering 197Ediacaran–Cambrian radiations 199–200evolutionary engineering 199–200Phanerozoic geobiology 414, 417–18Proterozoic geobiology 389–92

ANME see anaerobic methane-oxidizing Archaea

anoxic Archean biosphere 336–40anoxic deep oceans 380, 382, 387, 391anoxygenic photosynthesis

Archean geobiology 355, 358bacterial biomineralization 108–9, 115–16carbon cycle 11iron cycle 75–6, 82oxygen cycle 94sulfur cycle 50–2, 57

Anthropocene geobiology 3, 425–36agriculture and land use 428–30

carbon cycle and climate change 17, 22–3, 26, 426, 428, 430–3

controversy over commencement 426–7future of geobiology 433–4human evolution 425–7human population growth 427–30nitrogen cycle 39

AOM see anaerobic oxidation of methaneAPPES see ambient pressure photoemission

spectroscopyaquatic systems

carbon cycle 6, 13–15, 23, 29–30erosional processes 208–10, 221–3iron cycle 68nitrogen cycle 39, 44–6stable isotope geobiology 258

arbuscular mycorrhiza fungi (AMF) 195Archaeal lipid biomarkers 277–82Archean geobiology 351–67

bioaccretion of sediment 360–5bioalteration 365–6carbon cycle 30–1, 351–4fossil records 304, 308–9iron cycle 74–6, 83, 355–7mineralogical co-evolution 336–40nitrogen cycle 359–60oxygen cycle 101–2, 357–9phosphorus cycle 360sulfur cycle 354–5

Archer, David 431–3aromatic acids 209–10asteroid impacts 412–14astrobiology, definition 3atmospheric systems

carbon cycle 20–32erosional processes 205iron cycle 65–6nitrogen cycle 37–8, 39, 45–7oxygen cycle 95–6, 97–102plants as geobiological agents 190–1,

193–5atomic force microscopy (AFM) 134–6,

138–9Australopithecus 418–19

back-scattered electron micrography (BSEM) 208

bacterial biomineralization 105–30calcium carbonates 116–25chemoheterotrophy 110–11, 113chemolithoautotrophy 109–10, 113–14context 105geological implications 114–16, 121–5hydrothermal deposits 114

ionized cell surface development 106–7iron hydroxides 111–16metabolic processing 107–8microbial interactions in nature 111mineral nucleation and growth 105–6mineralogical co-evolution 337photosynthesis 108–9, 112–13, 115–16roles of bacteria 106–11sedimentary products 118–25see also eukaryotic skeletal formation

bacterial lipid biomarkers 280–3bacterial precipitates 120, 121–3bacterial sulfate reduction (BSR) 376–7,

387–9bacteriohopanepolyols (BHP) 270–2, 283banded iron formations (BIF)

Archean geobiology 356–7bacterial biomineralization 111, 115–16iron cycle 74mineralogical co-evolution 337–9sulfur cycle 60–1

basaltscarbonization 353–4erosional processes 211, 216–17microboring 365–6

BHP see bacteriohopanepolyolsbiases 284, 353bicarbonate 6, 22–5, 27, 29BIF see banded iron formationsbioaccretion of sediment 360–5bioalteration 365–6biocycling 216biodiversity

Anthropocene geobiology 428–30molecular biology 230nitrogen cycle 39see also mass extinction events

biofilms 141biogenic carbonate 22–3biogenic volatile organic compounds

(BVOC) 191–2biogenic whitings 118–19, 125biogenicity

erosional processes 215–16, 217–18fossil records 304mineral–organic–microbe interfacial

chemistry 145–6biogeochemical cycles 69–73biological weathering 206, 217–20biomarkers 269–96

ancient sediments 284–6bias in biomarker records 284classification of lipids 273–7context 269

Knoll_bindex.indd 437Knoll_bindex.indd 437 2/16/2012 2:10:24 AM2/16/2012 2:10:24 AM

438 Index

biomarkers (cont’d)diagenesis 269–70, 272fossil records 309–10future research directions 287–8isotope composition 270–2lipid biosynthetic pathways 273, 275,

282–3lipids diagnostic of Archaea 277–82lipids diagnostic of bacteria 280–3lipids diagnostic of Eukarya 283mass extinctions 287Neoproterozoic radiation of sponges 288origins of biomarkers 269petroleum and bitumens 286physiology and phylogeny 276–7preservable cores 283–7preservation potential 280Proterozoic geobiology 288, 378, 381–3,

391–2stereochemical considerations 272–3,

277–8taxonomic distribution 280

biomineralization see bacterial biomineralization; eukaryotic skeletal formation; mineralization

biomolecule emergence 317–20biosilica see silica mineralizationbiosphere 2

anoxic Archean 336–40carbon cycle 5–6mineralogical co-evolution 333–50nitrogen cycle 37Proterozoic geobiology 371

bioturbation 197–9bitumens 286black kerogenous shales 358Borlaug, Norman 427–8boron isotope composition 29BSEM see back-scattered electron

micrographyBSR see bacterial sulfate reductionBVOC see biogenic volatile organic

compounds

C/N see carbon:nitrogencalcereous tests 152, 158calcification 22–3, 117–20, 123–5calcified cyanobacteria 29calcified sheaths 118, 119calcium carbonates

bacterial biomineralization 116–25eukaryotic skeletal formation 151–8, 164,

166–9, 171–5stable isotope geobiology 251, 261

calcium phosphates 174calcium silicate minerals 194Calvin-Benson cycle 6, 9–10Cambrian mass extinctions 405Canfield ocean hypothesis 78cap carbonates 386carbon cycle 2

acid–base reactions 5Anthropocene geobiology 426, 428, 430–4Archean geobiology 351–4bacterial biomineralization 109–10balancing the geological carbon

cycle 26–7biological processes 5–18biological reactions 5–8

carbon fixation 6–7, 9–10, 259–0carbonate cycling 22–3, 26, 29chemoautotrophy 7–8, 11erosional processes 205–6, 208evolution through Earth’s history 27–32feedback processes 25–6fossil records 306, 309geological processes 20–35interaction with other biogeochemical

cycles 55–7, 93–4, 95–6, 100–2isotope composition 28–32limitations and perspectives 32limitations to net primary

production 14–16mantle degassing 23–4, 26–7, 30metamorphism 24, 26–7mineralogical co-evolution 342–3molecular biology 238–42net primary production 6, 13–15organic carbon cycling 20–2oxygenic photoautotrophy 11–13, 16Phanerozoic geobiology 404–5, 406–7,

409–12, 415–17photoautotrophy 8–13plants as geobiological agents 188–91,

192–5Proterozoic geobiology 372–4, 385–7proxies and models 27–30redox reactions 5, 7respiration and NPP 16–17silicate weathering 24–5stable isotope geobiology 251–5, 259–63see also photosynthesis

carbon dioxideAnthropocene geobiology 426, 430–4bacterial biomineralization 117–18carbon cycle 5–11, 15–17, 20–5, 28–32carbon fixation 259–60erosional processes 205–6, 208eukaryotic skeletal formation 152fossil records 306mineralogical co-evolution 342oxygen cycle 100–1Phanerozoic geobiology 407, 409–12,

415–16plants as geobiological agents 188–91,

192–5Proterozoic geobiology 372–3stable isotope geobiology 251–5, 259–60

carbon dioxide concentrating mechanism (CCM) 117–18, 121–5

carbon fixation 6–7, 9–10, 259–60carbon:nitrogen (C/N) ratio 37–8, 196carbonate chimneys 282carbonate cycling 22–3, 26, 29carbonate saturation state 121–3Carboniferous geobiology 406–7carotenoids 274Carson, Rachel 430, 434cascading evolutionary radiations 416–20CCM see carbon dioxide concentrating

mechanismCCN see cloud condensation nucleicell cycle 159–60chemical weathering 205–9, 217–20, 339chemoautotrophy 7–8, 10, 11, 16chemoheterotrophy 110–11, 113chemolithoautotrophy 70–1, 109–10, 113–14chirality 322–3

chlorophylls 274chondritic meteorites 334–5clay mineral factory hypothesis 342–3climate change

Anthropocene geobiology 426, 428, 430–3climatic drying 408, 416–20erosional processes 223Phanerozoic geobiology 408, 411–14,

416–20plants as geobiological agents 188–90

cloud condensation nuclei (CCN) 191Cohen, Joel 428columnar precipitate structures 305, 307–8comet impacts 419–20community dynamics 230complexation reactions 210–11compound-specific isotope analysis

(CSIA) 271concentration–depth profiles 217confocal scanning laser microscopes

(CSLM) 139–40, 141, 146copper 210–11, 215corals 156, 412core lipids 279–80Cretaceous climates 411–14crustal oxidation 101crustal reworking 335–6CSIA see compound-specific isotope

analysisCSLM see confocal scanning laser

microscopescuspate microbialites 363cyanobacteria

Archean geobiology 356–7bacterial biomineralization 108, 109, 115,

117–19, 123–5carbon cycle 11–12, 15, 29fossil records 298–300, 307mineralogical co-evolution 340–1oxygen cycle 99, 102

cytokinesis 160

deep ocean oxygenation 80–3deep origins approach 319–20denitrification 15, 41–5, 359–60dense molecular clouds 334deoxyribose nucleic acid (DNA) 323–6depletion–enrichment profiles 215depletion profiles 215, 217–18depositional bias 353Devonian mass extinctions 406DGD see diphytanyl glycerol diethersdiagenesis 269–70, 272diatoms

eukaryotic skeletal formation 151, 157, 158–64

Phanerozoic geobiology 411DIC see dissolved inorganic carbondimethylallyl diphosphate (DMAPP) 273dinitrogen gases

nitrogen cycle 36, 37, 42–4, 46–7plants as geobiological agents 190–1

diphytanyl glycerol diethers (DGD) 278–80DIR see dissimilatory Fe(III)-reducingdisproportionation reactions 51, 54–5dissimilatory Fe(III)-reducing (DIR)

bacteria 81–3dissolved inorganic carbon (DIC) 263–5,

281, 387


Index 439

dissolved organic carbon (DOC) 31, 212–13, 387–9

dissolved organic nitrogen (DON) 36–7DMAPP see dimethylallyl diphosphateDNA see deoxyribose nucleic acidDOC see dissolved organic carbondolomitization 121DON see dissolved organic nitrogendrive for fractionation 252drying of climates 408, 416–20

Early Triassic geobiology 409–10ecosystem dynamics 230ecosystem engineering 197ectomycorrhizal fungi (EMF) 195Ediacaran–Cambrian radiations 199–200Ediacaran geobiology 390–1EDS see energy dispersive spectroscopyEELS see electron energy loss spectroscopyEh-pH diagrams 67Ehrlich, Paul 427, 428electron energy loss spectroscopy

(EELS) 132–4electron spectroscopic imaging (ESI) 134electrostatic accumulation 169elemental profiles in regolith 213–18, 221–3embryo development 170emergence

animals 389–92biomolecules 317–20eukaryotes 380macromolecules 320–3natural selection 326–7self-replicating systems 323–7as a unifying research concept 315–17

EMF see ectomycorrhizal fungienergy dispersive spectroscopy (EDS)

132, 136environmental genes 237–8environmental scanning electron

microscopy (ESEM) 132, 141–2, 144Eocene–Oligocene climatic shift 415–16equatorial glaciations 407–8equilibrium isotope effects 255erosional processes 2, 205–27

Archean geobiology 355–6biological weathering 206, 217–20biota effects 206, 207–9, 221–2carbon cycle 20–2, 23, 29–30chemical weathering 205–9, 217–20context 205–7elemental profiles in regolith 213–18,

221–3iron cycle 68mineralogical co-evolution 339models 217–20organic molecules and weathering

209–11organomarkers 211–13oxygen cycle 97physical weathering 206, 217–20plants as geobiological agents 193–5Proterozoic geobiology 373–4, 385silicate weathering 24–5, 221–3sulfur cycle 49–50time evolution of profile

development 217–18ESEM see environmental scanning electron

microscopy

ESI see electron spectroscopic imagingeukaryotes

carbon cycle 12–13microfossils 300–2, 310, 383–4Proterozoic geobiology 380

eukaryotic skeletal formation 150–87apparent roles of biomolecules 162–4calcium carbonates 151–8, 164, 166–9,

171–5calcium phosphates 174cell cycle 159–60characterization of matrix

macromolecules 168–9, 172–3context 150–1corals 156diatoms 151, 157, 158–64embryo development 170evolutionary history 151, 173–5Foraminifera 151–6future research directions 175–6intracellular biomineralization 174intracellular transport/storage of

silicon 161–2limitations of classical approaches 156–8matrix proteins 166–9, 171–2, 175–6mineralization by unicellular

organisms 151–64mineralization of calcareous tests

152, 158mineralization from seawater 156modes of regulation 169molluscs 166–7multicellular organisms 151, 164–73non-classical mineralization model

169–73phylogenetic distribution 173primary mesenchyme cells 170–2radiolarians 151, 156–8sea urchins 169–73silica mineralization 151, 158–66, 174–5silicon transport pathway 160–1spiculogenesis 164–6, 170–1sponges 157, 164–6vital effects and true environmental

signatures 154–6eutrophication 39euxinic deep oceans

Archean geobiology 360iron cycle 78, 80Proterozoic geobiology 376, 377–80, 387,

392evolutionary engineering 199–200EXAFS see extended X-ray absorption fine

structureexperimental geobiology 258expressing environmental genes 237–8extended X-ray absorption fine structure

(EXAFS) 137, 139extraterrestrial events 334–5, 412–14,

419–20extremeophiles 2

fatty acids/alcohols/ketones 274feedback processes

carbon cycle 25–6mineralogical co-evolution 333plants as geobiological agents 188–95Proterozoic geobiology 391

feldspar clays 24–5

ferric hydroxides 111–16ferrihydrite 68, 71–2fertilizers 39fluorescence in situ hybridization

(FISH) 233–4, 239–40Foraminifera 151–6fossil fuels

Anthropocene geobiology 430–3carbon cycle 17nitrogen cycle 39

fossil records 297–314Archean geobiology 304, 308–9biogenicity 304biomarkers 309–10context 297cyanobacteria 298–300, 307eukaryotes 300–2, 310, 383–4evolutionary history 308–11microbialites 305, 306–8microfossil chemistry and

ultrastructure 302–6microfossil morphology 299–302nature of Earth’s early microbial

record 297–9new technologies 302–6paleobiological inferences 299–302Paleozoic geobiology 310–11permineralized microfossils 299physiology and phylogeny 304–6preservational history 304prokaryotes 300, 310Proterozoic geobiology 309–10, 383–4

Fourier transform infrared (FTIR) spectroscopy 306

Gaia Hypothesis 1GDGT see glycerol dialkyl glycerol

tetraethersgene discovery 240–1genetically-tractable foreign hosts 237–8genetics origin model 325–6, 328geobiology, definition 1GEOCARB III model 29–30, 205–6geochemical origins of life see origins

of lifegeochemistry, definition 1geological carbon cycle 5, 21geophysics, definition 1geosphere 333–50geranyldiphosphate (GPP) 273GIF see granular iron formationglaciation events

mineralogical co-evolution 341–2Phanerozoic geobiology 407–8, 418Proterozoic geobiology 372–4, 385–9, 392

global redox budget 94, 99–100glycerol dialkyl glycerol tetraethers

(GDGT) 278–80, 281GOE see Great Oxidation EventGPP see geranyldiphosphategranitoids 336, 339–40granular iron formation (GIF) 74, 77grasses 417–18Great Oxidation Event (GOE)

Archean geobiology 357, 366iron cycle 76–7, 83mineralogical co-evolution 334, 340–1Proterozoic geobiology 371–5, 387, 392

Green Revolution 427


440 Index

greenhouse gasesAnthropocene geobiology 426, 428Phanerozoic geobiology 408–10Proterozoic geobiology 372–4

helium fluxes 24historical development 1–2historical geobiology 3, 258Holdren, John 428Homo spp. 418–19

see also Anthropocene geobiologyhopanoids 37, 269, 271, 275, 281–3human evolution 418–19

see also Anthropocene geobiologyhuman population growth 427–30hydrocarbon biomarkers 76, 274, 286,

381–3, 391–2hydrogen cycle

early Earth 98–102interaction with other biogeochemical

cycles 94, 96–102loss of hydrogen to space 97–8, 99–100

hydrogen gas 7–8hydrogen sulfide

carbon cycle 7–8, 11oxygen cycle 96sulfur cycle 49, 59, 60

hydrothermal circulation 49–50, 282hydrothermal deposits 114

IC see inorganic carbonICP-MS see inductively coupled plasma

mass spectrometryigneous rock formation 335–6immobile element profiles 213–17inductively coupled plasma mass

spectrometry (ICP-MS) 250, 271–2infrared (IR) spectroscopy 140inorganic carbon (IC) 16–17, 31inorganic geochemistry 65–9intact polar lipids (IPL) 270, 276, 279integrated spicule matrix proteins 171–2intracellular biomineralization 174ionized cell surface development 106–7IPAT equation 428IPL see intact polar lipidsIPP see isopentyl diphosphateIR see infrarediron cycle 2, 65–92

aerobic Fe(II) oxidation 69–70, 112, 143anaerobic chemolithoautotrophic Fe(II)

oxidation 70–1anaerobic Fe(III) reduction 72–3, 108,

143–5Archean geobiology 74–6, 83, 355–7bacterial biomineralization 108, 109–16biogeochemical cycles 69–83biological processes 65, 69–73, 80–3chemoautotrophs 7–8, 11context 65evidence for major biogeochemical

changes 73–80inorganic geochemistry 65–9interaction with other biogeochemical

cycles 58–9, 74, 93, 96–7isotope composition 74, 81middle Proterozoic oceans 77–9, 83mineral–organic–microbe interfacial

chemistry 142–5

Neoproterozoic oceans 79–80, 83origins of life 324–5oxygenation of deep oceans 80–3Paleoproterozoic Great Oxidation

Event 76–7, 83Phanerozoic oceans 80–4photosynthetic Fe(II) oxidation 71–2,

75–6, 82–3Proterozoic geobiology 372, 375–8, 380–1redox reactions 65–73reservoirs and distribution 65–9siderophore acquisition of iron 73stable isotope geobiology 261–2

iron hydroxides 111–16iron–sulfur world hypothesis 324–5isopentyl diphosphate (IPP) 273isotope composition

Archean geobiology 351–60biomarkers 270–2carbon cycle 28–32fossil records 306, 309iron cycle 74, 81Phanerozoic geobiology 417Proterozoic geobiology 372–3, 381, 387–8sulfur cycle 54, 58, 59–60, 74, 98–9see also stable isotope geobiology

isotope ratio mass spectrometry 251isotope spike case studies 260–1

Jurassic geobiology 411–12

kerogenous shales 358kinetic isotope effects 255

land plants see plants as geobiological agents

land surface energy balances 188–90land use 428–30laser Raman imaging 304LCPA see long chain polyaminesLEED see low energy electron diffractionlife’s origins see origins of lifeligand complexation reactions 210–11lipid biomarkers

biosynthetic pathways 273, 275, 282–3classification 273–7lipids diagnostic of Archaea 277–82lipids diagnostic of bacteria 280–3lipids diagnostic of Eukarya 283origins of life 320–1physiology and phylogeny 276–7preservation potential 280taxonomic distribution 280

Lomagundi event 374–5long chain polyamines (LCPA) 162–4long-term feedback processes 192–5low energy electron diffraction (LEED) 134low-elevation glaciations 407–8Lyell, Charles 425–6

macromolecule emergence 320–3mammals 414, 426–7manganese 109–10mantle degassing 23–4, 26–7, 30mantle oxidation 101mantle reworking 335–6marine sediments 20–2, 28, 50marine systems

animals as geobiological agents 198–9

bacterial biomineralization 110, 114–16biomarkers 281carbon cycle 6, 13–15, 23, 25eukaryotic skeletal formation 151–4, 156fossil records 309–11iron cycle 65–6, 68, 74–83nitrogen cycle 37, 39origins of life 319oxygen cycle 96–7Phanerozoic geobiology 405plants as geobiological agents 192–3Proterozoic geobiology 376–83sulfur cycle 60–1

mass extinction eventsbacterial biomineralization 123biomarkers 287Phanerozoic geobiology 405–6, 408–10,

412–14, 417–20mass spectrometry (MS) 250–1, 271–2mass-independent fractionation (MIF) 74,

77, 372–3, 387matrix proteins 166–9, 171–2, 175–6MCR see methyl coenzyme M reductasemegafaunal extinctions and

co-evolution 426–7Meishan GSSP 287MEP see methylerythritol phosphatemetabolic potential 230metabolic processing 107–8metagenomics 234–6, 241–2metamorphism 24, 26–7metaproteomics 234–6metatranscriptomics 234–6metazoans 389–91meteorite evidence 334–5methane

bacterial biomineralization 110biomarkers 282carbon cycle 22, 31molecular biology 238–42oxygen cycle 100, 101–2plants as geobiological agents 190–1Proterozoic geobiology 374sulfur cycle 55–7

methanogenesisArchean geobiology 353, 358oxygen cycle 101–2Proterozoic geobiology 375

methanotrophic bacteriaArchean geobiology 353bacterial biomineralization 110biomarkers 282

methyl coenzyme M reductase (MCR) 240–1

methylerythritol phosphate (MEP) pathway 273

mevalonic acid (MVA) pathway 273micro-FTIR 306microbial fossil records see fossil recordsmicrobial mats 120, 121–3microbialites 305, 306–8microbially induced sedimentary structures

(MISS) 305, 307–8, 364–5microboring 365–6microfossils see fossil recordsmicronutrients 69middle Proterozoic iron cycle 77–9, 83MIF see mass-independent fractionationMiller–Urey experiment 318–19


Index 441

mineral–organic–microbe interfacial chemistry 131–49

biofilms and interfacial processes 141–2biogenicity 145–6biogeochemical processes 145–6context 131interface analysis 137–40mineral–microbe interactions 141–6mineral–organic interactions 140–1past, present and future 146–7processes 140–7redox reactions 141–6surface composition 136–7surface structure and topography 132–6techniques for studying surfaces and

interfaces 131–40mineral origins approach 321–2mineralization 2

animals as geobiological agents 197–9iron cycle 65–6marine systems 151–4, 156mineralogical co-evolution 334, 342–3nitrogen cycle 41, 44oxygen cycle 97silica mineralization 151, 158–66, 174–5see also bacterial biomineralization;

eukaryotic skeletal formationmineralogical co-evolution 333–50

anoxic Archean biosphere 336–40billion year stasis period 341crust and mantle reworking 335–6Great Oxidation Event 334, 340–1meteorite evidence 334–5prebiotic mineral evolution 334–6skeletal mineralization 334, 342–3snowball Earth 334, 341–2ten stages of mineral evolution 334

MISS see microbially induced sedimentary structures

modern environmental studies 258modern ice age 418–19molecular biology 228–49

anaerobic oxidation of methane 238–42applying 16S rRNA sequencing to

microbial ecology 229–35, 239–40approaches 229–38case study 238–42classical genetics and biochemistry 236context 228–9creating genetic systems in relevant

organisms 236–7culture-dependence of culture

independent work 229expressing environmental genes in

genetically-tractable foreign hosts 237–8

fluorescence in situ hybridization 233–4, 239–40

future research directions 242–3gene discovery 240–1geochemical processes 239going beyond the ‘who is there?’

question 232–4metagenomics, metatranscriptomics and

metaproteomics 234–6, 241–2phylogenetic diversity 231stable isotope signatures 239–40

molecular evolution 326–7molecular phylogenies 53

molecular selection 320–2, 326molluscs 166–7molybdenum 99, 378–80MS see mass spectrometrymulticellular organisms

animals as geobiological agents 188, 195–200

eukaryotic skeletal formation 151, 164–73plants as geobiological agents 188–95

MVA see mevalonic acidmycorrhizal fungi 193–5

nacreous layers 166–8NanoSIMS 137–8, 145, 233natural abundance case studies 260natural organic matter (NOM) 216natural selection 326–7Neoproterozoic geobiology 79–80, 83, 288Nernst equation 10net primary production (NPP)

carbon cycle 6, 13–17oxygen cycle 95plants as geobiological agents 190

nickel:iron ratios 116nifH genes 40–1nir genes 43nitrification 15, 41–2, 45, 359–60nitrogen cycle 2, 36–48

Anthropocene geobiology 429–30Archean geobiology 359–60biological reactions 40–5components of global cycle 38–40fossil records 310future research directions 46–7geological processes 36–8interaction with other biogeochemical

cycles 58, 102major nitrogen reserves and fluxes 37–8molecular biology 235net primary production 15–16nitrogen fixation 38–9, 40–1, 46–7, 359–60oxygenic phototrophs 12, 15redox reactions 40stable isotope geobiology 252, 261

nitrogen fixationArchean geobiology 359–60carbon cycle 12, 15–16nitrogen cycle 38–9, 40–1, 46–7

nitrogen oxides 36, 42–4, 46–7, 190–1nitrogen:phosphorus (N/P) ratio 15–16,

196NMD see non-mass-dependentNOM see natural organic matternon-mass-dependent (NMD)

fractionation 74, 77, 372–3, 387nosZ genes 43NPP see net primary production

oceanic systems see marine systemsOligocene geobiology 416Ordovician mass extinction 405–6organic carbon burial 25–6organic carbon cycling 20–2organomarkers 211–13origins of life 315–32

biomolecule emergence 317–20chirality 322–3context and challenges 315deep origins approach 319–20

emergence as a unifying research concept 315–17

genetics origin model 325–6, 328geochemical complexities 316idiosyncrasies and prebiotic

processes 320–2iron–sulfur world hypothesis 324–5macromolecules emergence 320–3metabolism versus genetic

mechanisms 323, 328Miller–Urey experiment 318–19molecular selection 320–2natural selection 326–7RNA world theory 325–6self-replicating systems 323–7sequential emergent steps 316–17three scenarios 327–8

OSC see oxidosqualene cyclaseosmium 409overhunting hypothesis 426oxic deep oceans 376–81, 387–9oxidosqualene cyclase (OSC) 275, 282oxygen cycle 2, 93–104

Archean geobiology 101–2, 357–9bacterial biomineralization 109, 115biological processes 93–5contemporary context 94–8early Earth 98–102geological processes 95–7interaction with other biogeochemical

cycles 57–8, 93–102loss of hydrogen to space 97–8, 99–100mineralogical co-evolution 340–1oxidation of the mantle and crust 101oxygen production in sulfur cycle 57Phanerozoic geobiology 97, 404–5, 406–7,

409plants as geobiological agents 188, 192–3post-biotic Archean atmosphere 101–2prebiotic oxygen concentrations 100–1Proterozoic geobiology 373–5, 376–81,

385, 391recorders of oxygen levels 58redox balance 94, 99–100redox reactions 93–4sinks for oxygen 95–7sources of oxygen 95submarine processes 96–7surface processes 95–6timing and cause of rise in atmospheric

oxygen 98–9, 102oxygenation of deep oceans 80–3oxygenic photoautotrophs 11–13, 15oxygenic photosynthesis see photosynthesisoxyhydroxides 68, 72, 75–6, 81–2ozone 190

Paleocene–Eocene thermal maximum (PETM) 414–15, 432–3

paleoclimate modeling 189paleoenvironmental indicators 151–6Paleozoic geobiology 310–11PALM see photoactivated localization

microscopyparticulate organic carbon (POC) 21–2,

26–7, 32particulate organic nitrogen (PON) 36–7pattern and process 2–3PCR see polymerase chain reaction


442 Index

peat bogs 216pedogenetic minerals 29Permian mass extinctions 408–9Permian–Triassic Boundary (PTB)

event 287permineralized microfossils 299PETM see Paleocene–Eocene thermal

maximumpetroleum 286Phanerozoic geobiology 403–24

animals as geobiological agents 414, 417–18

Cambrian mass extinctions 405carbon cycle 32Carboniferous time 406–7cascading evolutionary radiations 416–20Cretaceous climates 411–14Devonian mass extinctions 406diatoms and the silica cycle 411drying of climates 408, 416–20early land plants 406early Phanerozoic 403–5early Triassic period 409–10Eocene–Oligocene climatic shift 415–16human evolution 418–19iron cycle 80–4low-elevation glaciation near

equator 407–8mid-Cretaceous anoxia 412mineralization 334, 342–3modern ice age 418–19origin of modern climatic regime 415oxygen cycle 97oxygenation of atmosphere 410Paleocene–Eocene climatic shift 414–15Permian mass extinctions 408–9phytoplankton and planktonic

foraminifera 411plants as geobiological agents 406,

417–18re-expansion of Oligocene reefs 416reef-building corals 412Silurian biotic crises 406terminal Cretaceous extraterrestrial

event 412–14terminal Ordovician mass

extinction 405–6terminal Triassic crisis 409–10Toarcian anoxic event 410Younger Dryas 419–20

phosphate partitioning coefficients 116phosphorus cycle

Anthropocene geobiology 429–30Archean geobiology 360erosional processes 216mineralogical co-evolution 342net primary production 15–16

photoactivated localization microscopy (PALM) 139

photoautotrophyArchean geobiology 355bacterial biomineralization 108–9, 112–13carbon cycle 8–13, 15

photochemical model 100–1photoferrotrophy

Archean geobiology 356bacterial biomineralization 113, 115iron cycle 82–3

photosynthesis

Archean geobiology 356–9bacterial biomineralization 108–9,

112–13, 115–16evolution of 11fossil records 307, 310iron cycle 71–2, 75–6, 82–3mineralogical co-evolution 340–1organic carbon cycling 20–2oxygen cycle 94, 99oxygenic photoautotrophs 11–13, 15sulfur cycle 50–2, 57see also carbon cycle

physical weathering 206, 217–20phytoplankton 22, 29, 411planktonic foraminifera 29, 411, 414plants as geobiological agents 188–95

atmospheric composition and aerosols 190–1

erosional processes 193–5evolving feedback processes 191–2land surface energy balances 188–90long-term feedback processes 192–5Phanerozoic geobiology 406, 417–18short-term feedback processes 188–92

plate techtonics 336, 339–40plumose microbialites 363PMC see primary mesenchyme cellsPOC see particulate organic carbonpolar ice core records 191pollution 429–30polymerase chain reaction (PCR) 324PON see particulate organic nitrogenpopulation dynamics 230population growth 427–30porphyrins 9prebiotic processes

mineral evolution 334–6origins of life 320–2oxygen concentrations 100–1

Precambrian sulfur cycle 260precipitate structures 305, 307–8preservable cores 283–7preservation potential 280preservational bias 353preservational history 304primary mesenchyme cells (PMC) 170–2prismatic layers 167–8prokaryotic microfossils 300, 310Proterozoic geobiology 371–402

animals as geobiological agents 389–92billion year stasis period 341, 376, 383,

392biomarkers 288, 378, 381–3, 391–2carbon cycle 31–2early Proterozoic 372–5fossil records 298–302, 309–10, 383–4Great Oxidation Event 76–7, 83, 334,

340–1, 357, 367, 371–5, 387, 392greenhouse gases, redox and

glaciations 372–4, 379–80iron cycle 76–80, 83, 372, 375–8, 380–1late Proterozoic 384–92Lomagundi event 374–5mid-proterozoic 375–81, 383–4oxygenation of the oceans 376–81, 387–9snowball Earth 334, 341–2, 385–7

protonation–deprotonation reactions 106–7

proxy records 27–30

pseudocolumnar branching coniform stromatolites 362–3

pseudopods 154PTB see Permian–Triassic Boundarypyrites

Archean geobiology 355–6, 366bacterial biomineralization 110iron cycle 68, 74, 82mineral–organic–microbe interfacial

chemistry 143–4Proterozoic geobiology 378stable isotope geobiology 261–2sulfur cycle 50, 57, 60–1

radiolarians 151, 156–8Raman spectroscopy 140, 146, 233rare earth elements (REE) 76, 210, 212Rayleigh fractionation 256–7redox balance 94, 99–100redox reactions

carbon cycle 5, 7iron cycle 65–73mineral–organic–microbe interfacial

chemistry 141–6nitrogen cycle 40oxygen cycle 93–4, 99–100Proterozoic geobiology 372–4, 379–80sulfur cycle 60–1

REE see rare earth elementsreef systems 123, 156, 412, 416re-expansion of Oligocene reefs 416regolith profiles 213–18, 221–3residence time 258rhenium 409ribose nucleic acid (RNA) 325–6, 327ribosomal RNA (rRNA) 229–35, 239–40ribulose 1,5-bisphosphate carboxylase/

oxygenase 6–7, 9–10, 15rivers see aquatic systemsRNA world theory 325–6Rodinia supercontinent 384–5rRNA see ribosomal RNA

SAED see selected area electron diffractionSAR11 235–6saturation state 121–3scanning electron microscopy (SEM) 132,

303scanning transmission X-ray microscopy

(STXM) 136scanning tunneling microscopy (STM)

134–5, 140–1, 145SDV see silica deposition vesiclessea urchins 169–73seawater vacuolization 152secondary ion mass spectrometry

(SIMS) 137–8, 145, 233secondary organic aerosols (SOA) 191–2sediment bioaccretion 360–5sediment microboring 365–6selected area electron diffraction

(SAED) 132–3self-replicating systems 323–7SEM see scanning electron microscopyserpentinization 97, 101shales 20–2SHC see squalene–hopene cyclaseshells 166–8short-term feedback processes 188–92


Index 443

Shuram–Wonoka event 373, 388–9, 392–3siderophores 73silacidins/silaffins 162–4silica cycle

erosional processes 24–5, 221–3eukaryotic skeletal formation 151,

158–66, 174–5Phanerozoic geobiology 411

silica deposition vesicles (SDV) 159–60silicateins/silicases 165silicon transporters (SIT) 160–1Silurian biotic crises 406SIMS see secondary ion mass spectrometrySIP see stable isotope probingSIT see silicon transportersskeletal mineralization 334, 342–3slow carbon cycle 5, 21snowball Earth 334, 341–2, 385–7SOA see secondary organic aerosolssoil nutrients 213–17soil water content 189, 207spiculogenesis 164–6, 170–1sponges 157, 164–6, 288, 389–90squalene–hopene cyclase (SHC) 275, 282stable isotope geobiology 250–68

applications 258–61context 250–3drive for fractionation 252flavors of isotopic fractionations 255fundamentals of fractionation 253future research directions 265–6geobiological questions in deep

time 261–5isotope spike case studies 260–1isotopic notation and shorthand 253–5molecular biology 239–40natural abundance case studies 260non-steady state approaches 256–7Phanerozoic geobiology 404–5Proterozoic geobiology 376, 381Rayleigh fractionation 256–7residence time 258steady state approaches 257–8tracking fractionation in a system 255–8

stable isotope probing (SIP) 260–1STED see stimulated emission depletion

microscopysterane biomarkers 76, 381–3, 391–2stereochemistry

biomarkers 272–3, 277–8

matching of crystal faces 169origins of life 322–3

steroids/sterols 269–70, 272, 274–6, 283stimulated emission depletion microscopy

(STED) 139STM see scanning tunneling microscopystomatal distribution 29stratigraphic distributions 262–5, 286stromatolites

Archean geobiology 358, 360–3bacterial biomineralization 120–3fossil records 305, 306–7, 309mineralogical co-evolution 336–8

strontium isotope composition 28, 30, 32STXM see scanning transmission X-ray

microscopysubduction removal 353sugar molecules 320sulfate reduction 50–1, 55, 259–60sulfide oxidation 51, 57sulfide weathering 57–8sulfur cycle 2, 49–64

Anthropocene geobiology 430Archean geobiology 354–5bacterial biomineralization 110biological processes 50–2contemporary context 52–3evolution of sulfur cycle 59–61evolution of sulfur metabolisms 53–5, 56fossil records 309geological processes 49–50, 54–5interaction with other biogeochemical

cycles 55–9, 74, 96–7, 98–9isotope composition 54, 58, 59–60, 74,

98–9mineralogical co-evolution 338–9molecular phylogenies 53ocean redox chemistry 60–1origins of life 324–5Proterozoic geobiology 374–5, 377–81,

387–8stable isotope geobiology 252, 255,

259–60, 265–6sulfate concentrations 59–60

sulfur dioxide 49–50synchrotron technique 145

tectonic cycles 205–6, 209TEM see transmission electron microscopyterminal Ordovician mass extinction 405–6

terrestrial systemsanimals as geobiological agents 195–8carbon cycle 6, 13–15erosional processes 207–10, 213–15nitrogen cycle 37, 45oxygen cycle 95–6plants as geobiological agents 188–92

thorium 212–13thrombolites 305, 307titanium 211Toarcian anoxic event 410transmission electron microscopy

(TEM) 132–4, 145, 301–6travertine 119–20Triassic geobiology 409–10, 412triterpenoids 274–6trophic cascades 196tufa 119–20

ultrastructure 302–6unicellular organisms 151–64upwelling model 386uranium 358

vacuolization 152volcanic outgassing

oxygen cycle 96–7Phanerozoic geobiology 409–10, 412sulfur cycle 49–50

Wächtershäuser’s iron–sulfur world hypothesis 324–5

weathering see erosional processesweathering engine model 213Wheeler plots 265wrinkle structures 305, 308

X-ray absorption near edge structure (XANES) 137

X-ray absorption spectroscopy (XAS) 137X-ray magnetic circular dichroism

(XMCD) 145X-ray photoelectron spectroscopy

(XPS) 136–7, 144

Younger Dryas geobiology 419–20yttrium 210–12

zero-point energies (ZPE) 253–4zirconium 212


fundamentals of geobiology (knoll/fundamentals of geobiology) || index

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