Encyclopedia of Geobiology

955 Pages·2011·45.958 MB·English

by  Kirsten Küsel, Harold L. Drake (auth.), Joachim Reitner, Volker Thiel (eds.)

ENCYCLOPEDIA of
GEOBIOLOGY
Encyclopedia of Earth Sciences Series
ENCYCLOPEDIA OF GEOBIOLOGY
Volume Editors
JoachimReitnerisProfessorofPaleontology,HeadoftheDepartmentofGeobiology,andManagingDirectoroftheMuseum,Collectionsand
Geopark,attheUniversityofGöttingen,Germany.HeisalsoEditor-in-ChiefofLectureNotesinEarthSciences(Springer),Co-EditorofFacies
(Springer),andAssociateEditoroftheGeomicrobiologyJournal(Taylor&Francis).Dr.Reitner’sresearchfocusesontheinterplaybetweenorgan-
ismsandtheirmetabolicprocesseswithvariousabioticparameters.Manygeologicalprocessescanbeunderstoodasgeo-physiologicalprocesses,
allowingchemicalreactionstoproceedthatwouldneveroccurunderstandardthermodynamicconditions.Therefore,amajorthrustofDr.Reitner’s
researchistheinvestigationoftheevolutionoftheseprocesses,whicharevisibleinbiosignaturesandbiomineralizationpatterns,andintheir
interactionwithbiogeochemicalcycles.Amonghismanyhonorsandaccolades,Dr.ReitneristherecipientoftheG.W.LeibnizAwardfromthe
DeutscheForschungsgemeinschaft.
VolkerThielisProfessorofOrganicGeochemistryintheGeoscienceCenterattheUniversityofGöttingen,Germany.Dr.Thielhasbeeninvolved
ingeobiologicalresearchforsome15years,withafocusontheuseoforganicmoleculesaschemicaltracers(biomarkers)forbiogeochemicalpath-
ways.Hisresearchinterestsincludelipidbiomarkersasindicatorsforbiogeochemicalprocesses,molecularfossils,biologicalformation,andturn-
over of methane, and microbial control on mineral formation. The results of his studies have significantly contributed to the characterization
ofmicrobialprocessesassociatedwithmethaneturnoverinmodernandancientenvironments.MuchofDr.Thiel’scurrentworkisdevotedto
newapproachestoenhancethespatialresolutionofbiomarkeranalysisingeobiologicalsystems.HeismemberoftheEditorialBoardofthejournal
Geobiology(Wiley-Blackwell).
Editorial Board
Hans-JoachimFritz PamelaReid
CourantResearchCentreGeobiology RosenstielSchoolofMarineandAtmosphericScience
UniversityofGöttingen UniversityofMiami
Goldschmidtstr.3 4600RickenbackerCswy
37077Göttingen MiamiFL33149
Germany USA
AndreasKappler XingliangZhang
CenterforAppliedGeoscience(ZAG) DepartmentofGeology
Sigwartstraße10 NorthwestUniversity
72076Tübingen Xian710069
Germany China
KurtO.Konhauser
DepartmentofEarthandAtmosphericSciences
UniversityofAlberta,Edmonton
Alberta,T6G2E3
Canada
Aims of the Series
TheEncyclopediaofEarthSciencesSeriesprovidescomprehensiveandauthoritativecoverageofallthemainareasintheEarthSciences.Eachvolume
comprisesafocusedandcarefullychosencollectionofcontributionsfromleadingnamesinthesubject,withcopiousillustrationsandreferencelists.
Thesebooksrepresentoneoftheworld’sleadingresourcesfortheEarthSciencescommunity.Previousvolumesarebeingupdatedandnew
workspublishedsothatthevolumeswillcontinuetobeessentialreadingforallprofessionalearthscientists,geologists,geophysicists,climatolo-
gists,andoceanographersaswellasforteachersandstudents.Seehttp://www.springer.comforacurrentlistoftitlesintheEncyclopediaofEarth
SciencesSeries.Gotohttp://www.springerlink.com/reference-works/tovisitthe“EncyclopediaofEarthSciencesSeries”on-line.
About the Series Editor
ProfessorCharlesW.Finklhaseditedand/orcontributedtomorethan8volumesintheEncyclopediaofEarthSciencesSeries.Forthepast25years
hehasbeentheExecutiveDirectoroftheCoastalEducation&ResearchFoundation(CERF)andEditor-in-ChiefoftheinternationalJournalof
Coastal Research. In addition to these duties, he is Research Professor at Florida Atlantic University in Boca Raton, Florida, USA. He is
agraduateoftheUniversityofWesternAustralia(Perth)andpreviouslyworkedforawhollyownedAustraliansubsidiaryoftheInternationalNickel
CompanyofCanada(INCO).Duringhiscareer,heacquiredfieldexperienceinAustralia;theCaribbean;SouthAmerica;SWPacificislands;south-
ernAfrica;WesternEurope;andthePacificNorthwest,Midwest,andSoutheastUSA.
Founding Series Editor
ProfessorRhodesW.Fairbridge(deceased)haseditedmorethan24EncyclopediasintheEarthSciencesSeries.Duringhiscareerhehasworkedas
apetroleumgeologistintheMiddleEast,beenaWWIIintelligenceofficerintheSWPacificandledexpeditionstotheSahara,ArcticCanada,Arctic
Scandinavia,BrazilandNewGuinea.HewasEmeritusProfessorofGeologyatColumbiaUniversityandwasaffiliatedwiththeGoddardInstitute
forSpaceStudies.
ENCYCLOPEDIA OF EARTH SCIENCES SERIES
ENCYCLOPEDIA of
GEOBIOLOGY
edited by
JOACHIM REITNER
VOLKER THIEL
University of Göttingen
Germany
LibraryofCongressControlNumber:2010936497
ISBN: 978-1-4020-9211-4
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Coverillustration:Iron-andsulfide-oxidizingmicrobialmatsintheÄspöHardRockLaboratory,Oskarshamn,Sweden
(photographbyJoachimReitner)
Everyefforthasbeenmadetocontactthecopyrightholdersofthefiguresandtableswhichhavebeenreproduced
fromothersources.Anyonewhohasnotbeenproperlycreditedisrequestedtocontactthepublishers,sothatdue
acknowledgmentmaybemadeinsubsequenteditions.
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Contents
Contributors xiii AnimalBiocalcification,Evolution 53
GertWörheideandDanielJ.Jackson
Preface xxvii
AnimalSkeletons,Advent 58
Acetogens 1
GuoxiangLi,MaoyanZhuandZheChen
KirstenKüselandHaroldL.Drake
Archaea 64
AcidRockDrainage 5
VolkerThiel
LesleyA.Warren
Arsenic 69
Acidophiles 8
JohnF.StolzandRonaldS.Oremland
Acritarchs 8
AsteroidandCometImpacts 69
CharlesS.Cockell
AerobicMetabolism 8
HeribertCypionka
Astrobiology 73
JackD.Farmer
Algae(Eukaryotic) 10
ThomasFriedl,NicoleBrinkmannand
Bacteria 81
KathrinI.Mohr
MichaelHoppert
Alkalinity 20
AndreasReimerandGernotArp Bacterioplankton 89
ThomasPommier
Amber 24
EugenioRagazziandAlexanderR.Schmidt BandedIronFormations 92
NicoleR.Posth,KurtO.Konhauserand
AnaerobicOxidationofMethanewithSulfate 36 AndreasKappler
KatrinKnittelandAntjeBoetius
Basalt(Glass,Endoliths) 103
AnaerobicTransformationProcesses,Microbiology 48 IngunnH.Thorseth
BernhardSchink
Beggiatoa 111
Anammox 53 HeideN.Schulz-Vogt
Entrieswithoutauthornamesareglossaryterms
vi CONTENTS
Biodeterioration(ofStone) 112 CalcitePrecipitation,MicrobiallyInduced 223
ChristinaBeimforde TanjaBosak
Bioerosion 117 CalciumBiogeochemistry 227
AlineTribollet,GudrunRadtkeand AntonEisenhauer
StjepkoGolubic
CapCarbonates 229
Biofilms 134 JoachimReitner
JoachimReitner
Carbon(Organic,Cycling) 230
BiofilmsandFossilization 136 AmberK.HardisonandElizabethA.Canuel
JoachimReitner
Carbon(Organic,Degradation) 234
BiogeochemicalCycles 137 StevenT.Petsch
BiologicalControlonDiagenesis:Influence CarbonCycle 238
ofBacteriaandRelevancetoOcean
Acidification 137 CarbonIsotopes 238
FredT.MackenzieandAndreasJ.Andersson
CarbonateEnvironments 238
BiologicalVolcanicRockWeathering 143 EberhardGischler
CharlesS.Cockell
Carbonates 261
Biomarkers(MolecularFossils) 147 MartinDietzel
JochenJ.BrocksandKlitiGrice
CathodoluminescenceMicroscopy 266
Biomarkers(Organic,Compound-Specific WalterVortisch
Isotopes) 167
KlitiGriceandJochenJ.Brocks Chemolithotrophy 271
VolkerThiel
Biomining(MineralBioleaching,Mineral
Biooxidation) 182 Cherts 272
DouglasEricRawlings VolkerThiel
Bioprotection 185 Chondrites 273
CarlosRodriguez-Navarro,
MariaT.González-Muñoz,Concepción Chroococcidiopsis 273
Jimenez-LopezandManuelRodriguez-Gallego BurkhardBüdel
BiosignaturesinRocks 189 ClayAuthigenesis,Bacterial 274
FrancesWestallandBarbaraCavalazzi KurtO.Konhauser
Biosilicification 201 Coccolithophores 277
VolkerThiel
BlackShales 201
WolfgangOschmann ColdSeeps 278
RobertG.Jenkins
BreakupofRodinia 206
Zheng-XiangLi Comets 290
CalcareousAlgae 211 Commensalism 290
Calcification 211 Community 290
CalcifiedCyanobacteria 211 Copper 290
RobertRiding StephanM.Kraemer
CONTENTS vii
CosmicMolecularClouds 292 Endoliths 348
JoachimReitner BettinaWeberandBurkhardBüdel
CriticalIntervalsinEarthHistory 293 Endosymbiosis 355
FrankWieseandJoachimReitner
Evaporites 355
Cryobiosphere 306
Exoenzymes 355
Cyanobacteria 306 KathrinRiedelandAlexanderGrunau
KathrinI.Mohr,NicoleBrinkmannand
ThomasFriedl
ExtracellularPolymericSubstances(EPS) 359
AlanW.Decho
DeepBiosphereofSaltDeposits 313
HelgaStan-LotterandSergiuFendrihan
ExtremeEnvironments 362
VolkerThiel
DeepBiosphereofSediments 317
Fe(II)-OxidizingProkaryotes 367
DeepBiosphereoftheOceanicDeepSea 317
KristinaL.Straub
KristinaRathsack,Nadia-ValérieQuéricand
JoachimReitner
Fe(III)-ReducingProkaryotes 370
KristinaL.Straub
DeepFluids 322
Fermentation 373
Degradation(ofOrganicMatter) 322
FluorescenceInSituHybridization(FISH) 373
Denitrification 322
NatuschkaM.Lee,DanielaB.Meisinger,
MichaelSchmid,MichaelRothballerand
DesertVarnish 322
FrankE.Löffler
RandallS.Perry
Foraminifera 393
Detachment 325
AlexanderV.Altenbach
Diatoms 326
Frutexites 396
NicoleBrinkmann,ThomasFriedland
MartaRodríguez-Martínez,ChristineHeim,
KathrinI.Mohr
Nadia-ValérieQuéricand
JoachimReitner
Dinoflagellates 331
FungiandLichens 401
DivalentEarthAlkalineCationsinSeawater 331
BettinaWeberandBurkhardBüdel
AntonEisenhauer
Diversity 336 Gallionella 411
KarstenPedersen
Dolomite,Microbial 336
JenniferA.RobertsandPaulA.Kenward Geobacter 412
KristinaL.Straub
EarlyEarth 341
Geochronology 413
EarlyPrecambrianEukaryotes 341 VolkerLiebetrau
JoachimReitner
Geomycology 416
EcologicalNiche 342 GeoffreyM.Gadd
EdiacaranBiota 342 Geyserite 433
DmitriyGrazhdankin
Entrieswithoutauthornamesareglossaryterms
viii CONTENTS
Glass 433 IsotopeFractionation(Metal) 502
ArielD.AnbarandSilkeSevermann
Glaucophytes 433
Isotopes(Methods) 511
Gold 433
Veit-EnnoHoffmann IsotopesandGeobiology 511
JochenHoefs
Gondwanaland,Formation 434
JosephG.Meert Isotopes,Radiogenic 516
BentT.Hansen
GreatOxygenationEvent(GOE) 436
KarstEcosystems 521
GreenAlgae 436 AnnetteS.Engel
LateralGeneTransfer 533
Guild 436
Hans-JoachimFritz
Habitat 437
Leptothrix 535
DavidEmerson
Halobacteria–Halophiles 437
HelgaStan-Lotter
MagnetotacticBacteria 537
MihályPósfai
Haptophytes 441
Manganese(SedimentaryCarbonatesandSulfides) 541
HeavyMetals 441
MichaelE.Böttcher
Histology 441
MassExtinctions,Phanerozoic 543
MichaelGudo,GertaFleissnerand
JoachimReitner
GuentherFleissner
Mat-RelatedSedimentaryStructures 547
HotSpringsandGeysers 447
HubertusPorada
BrianJonesandRobinW.Renaut
Metagenomics 553
Hydrogen 451
WolfgangLiebl
ToriM.Hoehler
Metalloenzymes 558
HydrothermalEnvironments,Fossil 454
MichaelHoppert
JoachimReitner
Metallogenium 563
HydrothermalEnvironments,Marine 456 JoachimReitner
GilbertoE.FloresandAnna-LouiseReysenbach
Metals,AcquisitionbyMarineBacteria 565
HydrothermalEnvironments,Terrestrial 467 AlisonButlerandVanessaV.Homann
RobinW.RenautandBrianJones
Meteoritics 568
HypersalineEnvironments 479 MarkA.Sephton
Ichnology 481 MethaneOxidation(Aerobic) 575
MurrayGingrasandKurtO.Konhauser HelmutBürgmann
Immunolocalization 482 Methane,Origin 578
MichaelHoppertandChristophWrede CarstenJ.Schubert
IronIsotopes 486 Methanogens 586
IronSulfideFormation 486 MicrobialBiomineralization 586
JürgenSchieber ChristineHeim
CONTENTS ix
MicrobialCommunities,Structure,andFunction 592 Nickel,Biology 684
MichaelW.Friedrich MartinKrüger
MicrobialDegradation 596 Nitrification 685
ErikaKothe
Nitrogen 686
MicrobialEcologyofSubmarineCaves 599 VolkerThiel
FrancescoCanganellaandGiovannaBianconi
NitrogenFixation 690
MicrobialMats 606
JoachimReitner Ores,MicrobialPrecipitationandOxidation 691
BedaA.Hofmann
MicrobialSilicification–Bacteria(orPassive) 608
KurtO.KonhauserandBrianJones OrganicCarbon 697
MicrobialSurfaceReactivity 614 Organomineralization 697
DavidA.FowleandKurtO.Konhauser ChristianDéfarge
Microbialites,Modern 617 OriginofLife 701
ChristopheDupraz,R.PamelaReidand MichaelJ.Russell
PieterT.Visscher
OriginsoftheMetazoa 716
Microbialites,Stromatolites,andThrombolites 635 DanielJ.Jackson
RobertRiding
Parasitism 721
Microbial-MetalBinding 654
KurtO.KonhauserandDavidA.Fowle PedogenicCarbonates 721
EricP.Verrecchia
Microbiocorrosion 657
AlineTribollet,StjepkoGolubic,GudrunRadtke PermafrostMicrobiology 726
andJoachimReitner DavidA.GilichinskyandElizavetaM.Rivkina
MicrosensorsforSediments,MicrobialMats, Phosphorus,Phosphorites 732
andBiofilms 658 KarlB.Föllmi
DirkdeBeer
Photosynthesis 736
Molar-toothStructure 662 KerstinSchmidt
BrianR.Pratt
PiezophilicBacteria 738
Moonmilk 666 JiasongFangandLiZhang
JoachimReitner
PoreWaters 742
MudMounds 667 SabineKasten
MartaRodríguez-Martínez
Protozoa(Heterotroph,Eukaryotic) 746
Mutualism 675 JensBoenigk
Mycorrhizae 675 PyriteOxidation 750
Nan(n)obacteria 677 Radioactivity(Natural) 751
MurielPactonandGeorgesE.Gorin BedaA.Hofmann
Nanocrystals,MicrobiallyInduced 681 Radiolaria 754
SusanGlasauer VolkerThiel
Entrieswithoutauthornamesareglossaryterms
x CONTENTS
RamanMicroscopy(Confocal) 754 SodaLakes 824
JanToporski,ThomasDieingand StephanKempeandJozefKazmierczak
ChristineHeim
SodaOceanHypothesis 829
ReductionSpheroids 761 StephanKempeandJozefKazmierczak
BedaA.Hofmann
Soils 833
Reefs 762 ErikaKothe
Remineralization(ofOrganicMatter) 763 Species(Microbial) 836
Rhodophyta 763 Speleothems 836
RomanAubrecht
RNA-World 763
Sponges(Porifera)andSpongeMicrobes 840
SalineLakes 765 FriederikeHoffmannandMarie-LiseSchläppy
CarolD.Litchfield
Stromatactis 847
SalinityHistoryoftheEarth’sOcean 769 RomanAubrecht
L.PaulKnauth
Stromatolites 850
ScanningProbeMicroscopy(IncludesAtomic
ForceMicroscopy) 772 SubsurfaceFilamentousFabrics 851
MichaelHoppert BedaA.Hofmann
SedimentDiagenesis–BiologicallyControlled 777 Sulfate-ReducingBacteria 853
KurtO.Konhauser,MurrayK.Gingrasand HeribertCypionka
AndreasKappler
SulfideMineralOxidation 856
Selenium 784 D.KirkNordstrom
JohnF.StolzandRonaldS.Oremland
SulfurCycle 859
Shales 785 MichaelE.Böttcher
JürgenSchieber
SulfurIsotopes 864
Shewanella 791 MichaelE.Böttcher
Nadia-ValérieQuéric
Symbiosis 866
Siderite 792 SharmishthaDattaguptaandFrankZielinski
VolkerThiel
Syntrophy 870
Siderophores 793
StephanM.Kraemer TerrestrialDeepBiosphere 871
ChristineHeim
SilicaBiomineralization,Sponges 796
HermannEhrlich ThioesterWorld 876
JoachimReitner
Silicoflagellates 808
Thiomargarita 877
Sinter 808 HeideN.Schulz-Vogt
RobinW.RenautandBrianJones
ThiotrophicBacteria 877
Skeleton 814 HeideN.Schulz-Vogt
SmallShellyFossils 814 Thrombolites 880
SnowballEarth 814 TidalFlats 880
PaulF.Hoffman MeinhardSimon