Terrestrial Biosphere-Atmosphere Fluxes

519 Pages·2014·13.848 MB·English

by  Monson R., Baldocchi D.

B M
Fluxes of trace gases, water, and energy between the terrestrial Russell Monson
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biosphere and the atmosphere govern the state and fate of these l
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two coupled systems. This “breathing of the biosphere” is controlled o s Dennis Baldocchi
by a large number of interacting physical, chemical, biological and c o
c n
ecological processes. In this integrated and interdisciplinary book, the h

authors provide the tools to understand and quantitatively analyze i &

fl uxes of energy, organic compounds such as terpenes, and trace
gases including carbon dioxide, water vapor, and methane.
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The book fi rst introduces the fundamental principles that affect the
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supply and demand for trace gas exchange at the leaf and soil scales: r
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thermodynamics, diffusion, turbulence, and physiology. It then builds
s
on these principles to model the exchange of water, carbon dioxide,
t
terpenes, and stable isotopes at the ecosystem scale. Detailed r
i
mathematical derivations of commonly used relations in biosphere– a
l
atmosphere interactions, are provided for reference in Appendices.
B
i
An accessible introduction to this essential component of Earth o
system science for graduate students, this book is also a key resource s
p
for researchers in many related fi elds such as atmospheric science,
h Terrestrial
hydrology, meteorology, climate science, biogeochemistry, and
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ecosystem ecology.
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A Biosphere-Atmosphere
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o Fluxes
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monson
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Short online mathematical supplement guides u
monson
students through basic mathematical principles, x
e
from calculus rules of derivation and integration,
s
to statistical moments and coordinate rotation.
Cover illustration: connectivity among the geosphere, biosphere, and
atmosphere occurs through multiple fl uxes and associated resistances
arranged in series and in parallel. Image designed by Thomas
Zukowski, Lost Nomad Media.
Cover designed by Zoe Naylor
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Terrestrial Biosphere-Atmosphere Fluxes
Fluxes of trace gases, water, and energy between the terrestrial biosphere and the
atmospheregovernthestateandfateofthesetwocoupledsystems.This“breathingofthe
biosphere”iscontrolledbyalargenumberofinteractingphysical,chemical,biological,and
ecologicalprocesses.Inthisintegratedandinterdisciplinarybook,theauthorsprovidethe
toolstounderstandandquantitativelyanalysefluxesofenergy,tracegasessuchascarbon
dioxide,watervapour,methane,andorganiccompounds,suchasterpenes.
Thebookfirstintroducesthefundamentalprinciplesthataffectthesupplyanddemandfor
trace gasexchange attheleafandsoil scales: thermodynamics,diffusion,turbulence,and
physiology. It then builds on these principles to model the exchange of water, carbon
dioxide, terpenes, and stable isotopes at the ecosystem scale. Detailed mathematical
derivations,ofcommonlyusedrelationsinbiosphere-atmosphereinteractions,areprovided
forreferenceinAppendices.
An accessible introduction for graduate students to this essential component of earth
systemscience,thisbookisalsoakeyresourceforresearchersinmanyrelatedfieldssuchas
atmospheric science, hydrology, meteorology, climate science, biogeochemistry, and
ecosystemecology.
Onlineresourcesatwww.cambridge.org/monson
* Short online mathematical supplement guides students through basic mathematical
principles, from calculus rules ofderivation and integration, tostatistical moments and
coordinaterotation.
Russell Monson is Louise Foucar Marshall Professor at the University of Arizona, Tucson
and Professor Emeritus at the University of Colorado, Boulder. His research focuses on
photosynthetic metabolism, the production of biogenic volatile organic compounds and
plantwaterrelationsfromthescaleofchloroplaststotheglobe.Hehasreceivednumerous
awards,includingtheAlexandervonHumboldtFellowship,theJohnSimonGuggenheim
Fellowship and the Fulbright Senior Fellowship, and was also appointed Professor of
Distinction in the Department of Ecology and Evolutionary Biology at the University of
Colorado.ProfessorMonsonisafellowoftheAmericanGeophysicalUnionandhasserved
onadvisoryboardsfornumerousnationalandinternationalorganizationsandprojects.Heis
Editor-in-ChiefofthejournalOecologiaandhasover200peer-reviewedpublications.
DennisBaldocchiisaprofessorofBiometeorologyattheUniversityofCalifornia,Berkeley.
Hisresearchfocusesonphysical,biological,andchemicalprocessesthatcontroltracegas
and energy exchange between vegetation and the atmosphere and the micrometeorology
ii
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of plant canopies. Awards received include the Award for Outstanding Achievement in
BiometeorologyfromtheAmericanMeteorologicalSociety(2009),andtheFacultyAward
for Excellence in Postdoctoral Mentoring (2011) amongst others from the University of
California. Professor Baldocchi is a Fellow of the American Geophysical Union and is a
memberofadvisoryboardsfornationalandinternationalorganizationsandprojects.Heis
Editor-in-ChiefoftheJournalofGeophysicalResearch:Biogeosciencesandhasover200
peer-reviewedpublications.
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Terrestrial Biosphere-Atmosphere
Fluxes
RUSSELL MONSON
UniversityofArizona
DENNIS BALDOCCHI
UniversityofCalifornia,Berkeley
iv
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UniversityPrintingHouse,CambridgeCB28BS,UnitedKingdom
PublishedintheUnitedStatesofAmericabyCambridgeUniversityPress,NewYork
CambridgeUniversityPressispartoftheUniversityofCambridge.
ItfurtherstheUniversity’smissionbydisseminatingknowledgeinthepursuitof
education,learning,andresearchatthehighestinternationallevelsofexcellence.
www.cambridge.org
Informationonthistitle:www.cambridge.org/9781107040656
©RussellMonsonandDennisBaldocchi2014
Thispublicationisincopyright.Subjecttostatutoryexception
andtotheprovisionsofrelevantcollectivelicensingagreements,
noreproductionofanypartmaytakeplacewithoutthewritten
permissionofCambridgeUniversityPress.
Firstpublished2014
PrintedandboundintheUnitedKingdombytheMPGBooksGroup
AcataloguerecordforthispublicationisavailablefromtheBritishLibrary
LibraryofCongressCataloguinginPublicationdata
ISBN978-1-107-04065-6Hardback
Additionalresourcesforthispublicationatwww.cambridge.org/monson
CambridgeUniversityPresshasnoresponsibilityforthepersistenceoraccuracyof
URLsforexternalorthird-partyinternetwebsitesreferredtointhispublication,
anddoesnotguaranteethatanycontentonsuchwebsitesis,orwillremain,
accurateorappropriate.
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Contents
Preface pagexi
Listofsymbols xiv
1 Thegeneralnatureofbiosphere-atmospherefluxes 1
1.1 Biosphere-atmosphereexchangeasabiogeochemicalprocess 2
1.2 Flux–aunifyingconceptinbiosphere-atmosphereinteractions 3
1.3 Non-lineartendenciesinbiosphere-atmosphereexchange 5
1.4 Modeling–atoolforprognosisinecosystem-atmosphereinteractions 10
1.5 Ahierarchyofprocessesinsurface-atmosphereexchange 12
2 Thermodynamics,work,andenergy 15
2.1 Thermodynamicsystemsandfluxesasthermodynamicprocesses 16
2.2 Energyandwork 17
2.3 Freeenergyandchemicalpotential 20
2.4 Heatandtemperature 23
2.5 Pressure,volume,andtheidealgaslaw 26
2.6 Adiabaticanddiabaticprocesses 28
2.7 TheNavier–Stokesequations 30
2.8 Electromagneticradiation 31
2.9 Beer’sLawandphotontransferthroughamedium 35
3 Chemicalreactions,enzymecatalysts,andstableisotopes 38
3.1 Reactionkinetics,equilibrium,andsteadystate 39
3.2 Theenergeticsofchemicalreactions 41
3.3 Reduction-oxidationcoupling 46
3.4 Enzymecatalysis 50
3.5 Stableisotopesandisotopeeffects 55
Appendix3.1 FormalderivationsoftheArrheniusequationandtheQ model 60
10
Appendix3.2 DerivationoftheMichaelis–Mentenmodelofenzymekinetics 62
4 Controlovermetabolicfluxes 64
4.1 Theprincipleofsharedmetaboliccontrol 65
4.2 Controloverphotosyntheticmetabolism 68
4.3 Photorespiratorymetabolism 80
4.4 Tricarboxylicacidcyclerespiration(“darkrespiration”)inplants 82
4.5 C photosynthesis 85
4
v
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vi Contents
5 ModelingthemetabolicCO flux 89
2
5.1 ModelingthegrossrateofCO assimilationandphotorespiration 90
2
5.2 Modelingdarkrespiration(R ) 96
d
5.3 NetversusgrossCO assimilationrate 100
2
5.4 Thescaledconnectionsamongphotosyntheticprocesses 109
6 Diffusionandcontinuity 111
6.1 Moleculardiffusion 112
6.2 Diffusionthroughporesandinmulti-constituentgasmixtures 121
6.3 Fluxdivergence,continuity,andmassbalance 131
Appendix6.1 AthermodynamicderivationofFick’sFirstLaw 133
7 Boundarylayerandstomatalcontroloverleaffluxes 136
7.1 Diffusivedrivingforcesandresistancesinleaves 137
7.2 Fluid-surfaceinteractionsandboundarylayerresistance 139
7.3 Stomatalconductance 144
7.4 TheleafinternalconductancetoCO flux 166
2
7.5 Evolutionaryconstraintonleafdiffusivepotential 168
Appendix7.1 Athermodynamicderivationofdiffusiveconductances 169
Appendix7.2 DerivationoftheternarystomatalconductancetoCO ,H O,
2 2
anddryair 169
Appendix7.3 DerivationoftheLeuningandMonteithformsoftheBWBmodel 171
8 Leafstructureandfunction 173
8.1 Leafstructure 174
8.2 Convergentevolutionasasourceofcommonpatternsin
leafstructureandfunction 177
8.3 Photontransportinleaves 181
8.4 CO transportinleaves 189
2
8.5 Watertransportinleaves 191
8.6 Theerrorcausedbyaveragingnon-linearitesinthefluxrelationsofleaves 193
8.7 Modelswithexplicitdescriptionsofleafgradients 198
Appendix8.1 Derivationofamodeldescribingleafstructureandits
relationtonetCO assimilationrate 200
2
9 Watertransportwithinthesoil-plant-atmospherecontinuum 203
9.1 Watertransportthroughsoil 204
9.2 Waterflowthroughroots 209
9.3 Watertransportthroughstems 211
9.4 Thehydraulicconductanceofleavesandaquaporins 217
9.5 Modelingthehydraulicconductanceandassociatedeffectsofembolism 218
9.6 Hydraulicredistribution 220
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vii Contents
10 Leafandcanopyenergybudgets 222
10.1 Netradiation 223
10.2 Sensibleheatexchangebetweenleavesandtheirenvironment 227
10.3 Latentheatexchange,atmospherichumidity,andtemperature 229
10.4 Surfacelatentheatexchangeandthecombinationequation 232
Appendix10.1 DerivationoftheClausius–Clapeyronrelation 237
Appendix10.2 Athermodynamicapproachtoderivationofthe
Penman–Monteithequation 239
Appendix10.3 DerivationoftheisothermalformofthePenman–Monteith
equation 242
11 Canopystructureandradiativetransfer 244
11.1 Thestructureofcanopies 245
11.2 Thesolarradiationregimeofcanopies 250
11.3 Remotesensingofvegetationstructureandfunction 272
Appendix11.1 Reconcilingtheconceptsofstatisticalprobabilityand
canopyphotoninterception 277
Appendix11.2 Thetheoreticallinkagebetweentheprobabilityofphotonflux
penetration(P0)andtheprobabilityofasunfleck(P )ataspecific
sf
canopylayer 278
12 Verticalstructureandmixingoftheatmosphere 280
12.1 Structureoftheatmosphere 281
12.2 Atmosphericbuoyancy,potentialtemperature,andtheequationofstate 287
12.3 Atmosphericstability 290
Appendix12.1 Derivationofpotentialtemperatureandconversionfrom
volumetopressureintheconservationofenergyequation 294
13 Windandturbulence 296
13.1 Thegeneralnatureofwind 297
13.2 Turbulentwindeddies 298
13.3 Shear,momentumflux,andthewindprofilenearthesurface 301
13.4 Turbulencekineticenergy(TKE) 307
13.5 Turbulencespectraandspectralanalysis 310
13.6 Dimensionlessrelationships:theReynoldsnumberanddragcoefficient 314
13.7 Theaerodynamiccanopyresistance 315
13.8 EulerianandLagrangianperspectivesofturbulentmotions 316
13.9 Waves,nocturnaljets,andkatabaticflows 319
Appendix13.1 RulesofaveragingwithextendedreferencetoReynolds
averaging 323
Appendix13.2 DerivationoftheReynoldsshearstress 324
Appendix13.3 Derivationofthelogarithmicwindprofile 325
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viii Contents
14 Observationsofturbulentfluxes 327
14.1 Turbulentfluxesintheatmosphericsurfacelayer 328
14.2 Theeffectofaplantcanopyonatmosphericturbulence 330
14.3 Turbulentfluxesabovecanopies 337
14.4 Mesoscalefluxes 343
Appendix14.1 DerivationofMonin–Obukhovsimilarityrelationships 347
Appendix14.2 Derivationoftheconservationequationforcanopyflux 349
15 Modelingoffluxesatthecanopyandlandscapescales 352
15.1 Modelingcanopyfluxes 353
15.2 Massbalance,dynamicboxmodels,andsurfacefluxes 362
15.3 Eulerianperspectivesincanopyfluxmodels 365
15.4 Lagrangianperspectivesincanopyfluxmodels 368
Appendix15.1 Derivationofthemodelforplanetaryboundarylayer
(PBL)scalarbudgetsinthefaceofentrainment 371
16 SoilfluxesofCO ,CH ,andNO 373
2 4 x
16.1 Thedecompositionofsoilorganicmatter 373
16.2 Controlbysubstrateoversoilrespirationrate 379
16.3 Controlbyclimateoversoilrespirationrate 381
16.4 Couplingofsoilrespirationtonetprimaryproductionandimplications
forcarboncyclinginthefaceofglobalchange 384
16.5 Methaneemissionsfromsoils 385
16.6 Thefluxesofnitrogenoxidesfromsoils 390
17 Fluxesofbiogenicvolatilecompoundsbetweenplantsandtheatmosphere 395
17.1 ThechemicaldiversityofBVOCs 396
17.2 ThebiochemicalproductionofBVOCs 399
17.3 EmissionofmetabolicNH andNO fromplants 403
3 2
17.4 StomatalcontrolovertheemissionofBVOCsfromleaves 404
17.5 ThefateofemittedBVOCsintheatmosphere 406
17.6 Formationofsecondaryaerosolparticlesintheatmosphere 408
Appendix17.1 ReactionsleadingtotheoxidationofBVOCstoform
troposphericO 412
3
18 Stableisotopevariantsastracersforstudyingbiosphere-atmosphereexchange 415
18.1 StableisotopediscriminationbyRubiscoandatotherpointsinplantcarbon
metabolism 416
18.2 Fractionationofstableisotopesinleavesduringphotosynthesis 418
18.3 FractionationoftheisotopicformsofH2Oduringleaftranspiration 420
18.4 Isotopicexchangeof18Oand16ObetweenCO andH Oinleaves 421
2 2
18.5 AssessingtheisotopicsignatureofecosystemrespiredCO –the“Keeling
2
Plot” 423
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ix Contents
18.6 TheinfluenceofecosystemCO exchangeontheisotopiccompositionof
2
atmosphericCO2 424
Appendix18.1 DerivationoftheFarquharetal.(1982)modeland
augmentationsforleafcarbonisotopediscrimination 429
Appendix18.2 DerivationoftheleafformoftheCraig–Gordonmodel 432
References 434
Index 473
Supplementavailableatwww.cambridge.org/monson
Supplement1:Mathematicalconcepts