Fluxes of trace gases, water and energy - the 'breathing of the biosphere' - are controlled by a large number of interacting physical, chemical, biological and ecological processes. In this interdisciplinary book, the authors provide the tools to understand and quantitatively analyse fluxes of energy, organic compounds such as terpenes, and trace gases including carbon dioxide, water vapour and methane. It first introduces the fundamental principles affecting the supply and demand for trace gas exchange at the leaf and soil 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 of commonly used relations in biosphere-atmosphere interactions are provided for reference in appendices. An accessible introduction for graduate students and a key resource for researchers in related fields, such as atmospheric science, hydrology, meteorology, climate science, biogeochemistry and ecosystem ecology.
Preface xi
List of symbols xiv
1 The general nature of biosphere-atmosphere 1 (14)
fluxes
1.1 Biosphere-atmosphere exchange as a 2 (1)
biogeochemical process
1.2 Flux - a unifying concept in 3 (2)
biosphere-atmosphere interactions
1.3 Non-linear tendencies in 5 (5)
biosphere-atmosphere exchange
1.4 Modeling - a tool for prognosis and 10 (2)
diagnosis in ecosystem-atmosphere interactions
1.5 A hierarchy of processes in 12 (3)
surface-atmosphere exchange
2 Thermodynamics, work, and energy 15 (23)
2.1 Thermodynamic systems and fluxes as 16 (1)
thermodynamic processes
2.2 Energy and work 17 (3)
2.3 Free energy and chemical potential 20 (3)
2.4 Heat and temperature 23 (3)
2.5 Pressure, volume, and the ideal gas law 26 (2)
2.6 Adiabatic and diabatic processes 28 (1)
2.7 The Navier-Stokes equations 29 (2)
2.8 Electromagnetic radiation 31 (3)
2.9 Beer's Law and photon transfer through a 34 (4)
medium
3 Chemical reactions, enzyme catalysts, and 38 (26)
stable isotopes
3.1 Reaction kinetics, equilibrium, and 39 (2)
steady state
3.2 The energetics of chemical reactions 41 (5)
3.3 Reduction-oxidation coupling 46 (4)
3.4 Enzyme catalysis 50 (5)
3.5 Stable isotopes and isotope effects 55 (5)
Appendix 3.1 Formal derivations of the 60 (2)
Arrhenius equation and the Q10 model
Appendix 3.2 Derivation of the 62 (2)
Michaelis-Menten model of enzyme kinetics
4 Control over metabolic fluxes 64 (25)
4.1 The principle of shared metabolic control 65 (3)
4.2 Control over photosynthetic metabolism 68 (12)
4.3 Photorespiratory metabolism 80 (2)
4.4 Tricarboxylic acid cycle respiration 82 (3)
("dark respiration") in plants
4.5 C4 photosynthesis 85 (4)
5 Modeling the metabolic CO2 flux 89 (22)
5.1 Modeling the gross rate of CO2 90 (6)
assimilation and photorespiration
5.2 Modeling dark respiration (Rd) 96 (4)
5.3 Net versus gross CO2 assimilation rate 100(9)
5.4 The scaled connections among 109(2)
photosynthetic processes
6 Diffusion and continuity 111(25)
6.1 Molecular diffusion 112(9)
6.2 Diffusion through pores and in 121(10)
multi-constituent gas mixtures
6.3 Flux divergence, continuity, and mass 131(2)
balance
Appendix 6.1 A thermodynamic derivation of 133(3)
Fick's First Law
7 Boundary layer and stomata) control over leaf 136(37)
fluxes
7.1 Diffusive driving forces and resistances 137(1)
in leaves
7.2 Fluid-surface interactions and boundary 138(6)
layer resistance
7.3 Stomatal resistance and conductance 144(22)
7.4 The leaf internal resistance and 166(2)
conductance to CO2 flux
7.5 Evolutionary constraint on leaf diffusive 168(1)
potential
Appendix 7.1 A thermodynamic derivation of 169(1)
diffusive conductances
Appendix 7.2 Derivation of the ternary 169(2)
stomatal conductance to CO2, H2O, and dry air
Appendix 7.3 Derivation of the Leuning and 171(2)
Monteith forms of the Ball-Woodrow-Berry model
8 Leaf structure and function 173(30)
8.1 Leaf structure 174(3)
8.2 Convergent evolution as a source of 177(4)
common patterns in leaf structure and function
8.3 Photon transport in leaves 181(8)
8.4 CO2 transport in leaves 189(2)
8.5 Water transport in leaves 191(2)
8.6 The error caused by averaging 193(5)
non-linearities in the flux relations of
leaves
8.7 Models with explicit descriptions of leaf 198(2)
gradients
Appendix 8.1 Derivation of the Terashima et 200(3)
al. (2001) model describing leaf structure
and its relation to net CO2 assimilation rate
9 Water transport within the 203(19)
soil-plant-atmosphere continuum
9.1 Water transport through soil 204(5)
9.2 Water flow through roots 209(2)
9.3 Water transport through stems 211(6)
9.4 The hydraulic conductance of leaves and 217(1)
aquaporins
9.5 Modeling the hydraulic conductance and 218(2)
associated effects of embolism
9.6 Hydraulic redistribution 220(2)
10 Leaf and canopy energy budgets 222(22)
10.1 Net radiation 223(4)
10.2 Sensible heat exchange between leaves 227(2)
and their environment
10.3 Latent heat exchange, atmospheric 229(3)
humidity, and temperature
10.4 Surface latent heat exchange and the 232(5)
combination equation
Appendix 10.1 Derivation of the 237(2)
Clausius-Clapeyron relation
Appendix 10.2 A thermodynamic approach to 239(3)
derivation of the Penman-Monteith equation
Appendix 10.3 Derivation of the isothermal 242(2)
form of the Penman-Monteith equation
11 Canopy structure and radiative transfer 244(36)
11.1 The structure of canopies 245(5)
11.2 The solar radiation regime of canopies 250(23)
11.3 Remote sensing of vegetation structure 273(2)
and function
Appendix 11.1 Reconciling the concepts of 275(3)
statistical probability and canopy photon
interception
Appendix 11.2 The theoretical linkage between 278(2)
the probability of photon flux penetration
(P0) and the probability of a sunfleck (Psf)
at a specific canopy layer
12 Vertical structure and mixing of the 280(16)
atmosphere
12.1 Structure of the atmosphere 281(6)
12.2 Atmospheric buoyancy, potential 287(3)
temperature, and the equation of state
12.3 Atmospheric stability 290(4)
Appendix 12.1 Derivation of potential 294(2)
temperature and conversion from volume to
pressure in the conservation of energy
equation
13 Wind and turbulence 296(31)
13.1 The general nature of wind 297(1)
13.2 Turbulent wind eddies 298(3)
13.3 Shear, momentum flux, and the wind 301(6)
profile near the surface
13.4 Turbulence kinetic energy (TICE) 307(3)
13.5 Turbulence spectra and spectral analysis 310(4)
13.6 Dimensionless relationships: the 314(1)
Reynolds number and drag coefficient
13.7 The aerodynamic canopy resistance 315(1)
13.8 Eulerian and Lagrangian perspectives of 316(3)
turbulent motions
13.9 Waves, nocturnal jets, and katabatic 319(4)
flows
Appendix 13.1 Rules of averaging with 323(1)
extended reference to Reynolds averaging
Appendix 13.2 Derivation of the Reynolds 324(1)
shear stress
Appendix 13.3 Derivation of the logarithmic 325(2)
wind profile
14 Observations of turbulent fluxes 327(25)
14.1 Turbulent fluxes in the atmospheric 328(2)
surface layer
14.2 The effect of a plant canopy on 330(7)
atmospheric turbulence
14.3 Turbulent fluxes above canopies 337(6)
14.4 Mesoscale fluxes 343(4)
Appendix 14.1 Derivation of Monin-Obukhov 347(2)
similarity relationships
Appendix 14.2 Derivation of the conservation 349(3)
equation for canopy flux
15 Modeling of fluxes at the canopy and 352(21)
landscape scales
15.1 Modeling canopy fluxes 353(9)
15.2 Mass balance, dynamic box models, and 362(3)
surface fluxes
15.3 Eulerian perspectives in canopy flux 365(3)
models
15.4 Lagrangian perspectives in canopy flux 368(3)
models
Appendix 15.1 Derivation of the model for 371(2)
planetary boundary layer (PBL) scalar budgets
in the face of entrainment
16 Soil fluxes of CO2, CH4, and NOX 373(22)
16.1 The decomposition of soil organic matter 373(6)
16.2 Control by substrate over soil 379(2)
respiration rate
16.3 Control by climate over soil respiration 381(3)
rate
16.4 Coupling of soil respiration to net 384(2)
primary production and implications for
carbon cycling in the face of global change
16.5 Methane emissions from soils 386(4)
16.6 The fluxes of nitrogen oxides from soils 390(2)
Appendix 16.1 Derivation of first-order 392(3)
litter decomposition kinetics
17 Fluxes of biogenic volatile compounds 395(20)
between plants and the atmosphere
17.1 The chemical diversity of biogenic 396(3)
volatile organic compounds (BVOCs)
17.2 The biochemical production of BVOCs 399(4)
17.3 Emission of metabolic NH3 and NO2 from 403(1)
plants
17.4 Stomatal control over the emission of 404(2)
BVOCs from leaves
17.5 The fate of emitted BVOCs in the 406(2)
atmosphere
17.6 Formation of organic secondary aerosol 408(4)
particles in the atmosphere
Appendix 17.1 Reactions leading to the 412(3)
oxidation of BVOCs to form tropospheric O3
18 Stable isotope variants as tracers for 415(19)
studying biosphere-atmosphere exchange
18.1 Stable isotope discrimination by Rubisco 416(2)
and at other points in plant carbon metabolism
18.2 Fractionation of stable isotopes in 418(2)
leaves during photosynthesis
18.3 Fractionation of the isotopic forms of 420(1)
H2O during leaf transpiration
18.4 Isotopic exchange of 18O and 16O between 421(2)
CO2 and H2O in leaves
18.5 Assessing the isotopic signature of 423(1)
ecosystem respired CO2 - the "Keeling plot"
18.6 The influence of ecosystem CO2 exchange 424(5)
on the isotopic composition of atmospheric CO2
Appendix 18.1 Derivation of the Farquhar et 429(3)
al. (1982) model and augmentations for leaf
carbon isotope discrimination
Appendix 18.2 Derivation of the leaf form of 432(2)
the Craig-Gordon model
References 434(39)
Index 473
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