Course Syllabus, Brief Version

 

November 30, 2001

 

ESPM 129

Biometeorology: Microclimate of Plants and Their Interaction with the Atmosphere

 

Dennis Baldocchi

Acting Associate Professor

Department of Environmental Science, Policy and Management

Ecosystem Science Division

151 Hilgard Hall

University of California, Berkeley

Berkeley, CA

 

Objective: This course describes the physical environment (light, wind, temperature, humidity) about plants and the soil, how the physical environment affects the physiological status plants and how plants affect their physical environment.  This course accomplishes its goals by examining the physical, biological and chemical processes that affect the transfer of momentum, energy and material (water, CO2, and atmospheric trace gases) between vegetation and the atmosphere.  Instrumentation and measurements, associated with the study of plant biometeorology, are also discussed. 

 

Course Outline

 

 

Lecture

Topic

Unit 1

Introductions

1

Introduction, Overview

 

 

Unit 2

Plant and Atmospheric Characteristics

 

 

2

Characterizing the Vegetation, Part I, Canopy Architecture

3

Characterizing the Vegetation, Part II, Canopy Architecture

4

Characterizing Vegetation, Part II, Biogeography and Phenology

5

Solar Radiation, Part I, Theory and Principles

6

Solar Radiation, Part II, Theory and Principles Earth-Sun Geometry

7

Solar Radiation, Part III, and Observations and Instruments

8

Radiative Transfer through Vegetation, Part 1, Theory and Observation

9

Radiative Transfer through Vegetation, Part 2, Theory and Observations

10

Radiative Transfer through Vegetation, Part 3, Theory and Observations

11

Temperature and Thermodynamics

12

Temperature, spatial and temporal patterns

13

Humidity, Pressure and Trace Gas relations

14

Wind and Turbulence, Part 1: Surface Boundary Layer, Theory

15

Wind and Turbulence, Part 2: Surface Boundary Layer, Theory and Observations

16

Wind and Turbulence, Part 3: Surface Boundary Layer, Observations

17

Wind and Turbulence, Part 1: Canopy Air Space: Theory and Observation

18

Wind and Turbulence, Part 2: Canopy Air Space: Theory and Observation

 

 

Unit 3

Mass and Energy Exchange

 

 

19

Concepts of Flux and Mass Conservation, Part 1

20

Concepts of Flux and Mass Conservation, Part 2

21

Leaf Boundary Layers and their Resistances, Part 1

22

Leaf Boundary Layers and their Resistances, Part 2

23

Leaf Energy Balance, part 1

24

Leaf Energy Balance, Part 2

25

Leaf Energy Balance, Part 3

26

Stomatal Conductance, Concepts and Mathematical Models 

27

Stomatal Conductance, observations

28

Canopy Evaporation and Transpiration, Theory, part 1

29

Canopy Evaporation and Transpiration, Theory, part 2

30

Field studies and Observations of H, LE and Rn

31

Soil Physics, temperature and moisture, observations

32

Soil Physics, temperature and moisture, observations

33

Leaf photosynthesis and respiration, Concepts and Processes

34

Leaf photosynthesis and respiration, Mathematical Models

35

CO2, Canopy photosynthesis and soil respiration, Concepts and Observations

36

CO2, Canopy photosynthesis and soil respiration, Observations

37

Water Use Efficiency, Concepts and Theory

38

Trace Gas Fluxes

39

Plant-Atmosphere Interactions

40

Overview

 

Final

 

 

 

Course Syllabus, Detailed Version

 

November 30, 2001

 

Biometeorology: Microclimate of Plants and Their Interaction with the Atmosphere

 

Dennis Baldocchi

Acting Associate Professor

Department of Environmental Science, Policy and Management

Ecosystem Science Division

151 Hilgard Hall

University of California, Berkeley

Berkeley, CA

 

Objective: This course describes the physical environment (light, wind, temperature, humidity) about plants and the soil, how the physical environment affects the physiological status plants and how plants affect their physical environment.  This course accomplishes its goals by examining the physical, biological and chemical processes that affect the transfer of momentum, energy and material (water, CO2, and atmospheric trace gases) between vegetation and the atmosphere.  Instrumentation and measurements, associated with the study of plant biometeorology, are also discussed. 

 

Topic 1. Introduction

 

1. Delineate Goals of the Course:

2. Define Expectations of the Class:

3. State Course Assignments

4. Assign Text Book

5. Overview the Field of Biometeorology.

6. Describe Status of Research in the Field: Basic Research and Applied Problems

7. Future Directions, Continuing Education, Education Resources and Graduate Programs

 

Topic 2, History, Concepts and Tools

 

A. History of Science, an Overview

 

B. Science Philosophy and Methodology

 

C. A Brief History of Physical and Chemical Principles and Concepts that Relate to Biometeorology

            1. Force, work, energy

            2. Gas Law's

            3. Electromagnetism

            4. Heat and Thermodynamics

            5. Fluid Dynamics

            6. Plant Biology

 

D. 20th Century Advances in Micrometeorology and Biometeorology

 

E. Mathematical Tools

 

Topic 3 Characterizing the Vegetation

           

1. The physical characteristics of vegetation canopies

            a. leaf area index

                        i.observations

                        ii. prediction

                        iii. variation with time, season, decade

                        iii. variation with height, height, horizontal, globe

iv.  measurement methods

            b. canopy height

            c. leaf angle distribution

            d. basal area and woody biomass index

 

2. Physical charateristics of leaves and stems

            a. leaf anatomy          

b. specific leaf area

            c. chemical composition of leaves, stems, roots (C/N ratios)

 

3. Roots

a. Rooting Depth

            b. soil depth and water

 

Topic 4 Plant Biogeography and Phenology

 

A. Plant Biogeography

  1. Plant Distribution and Climate
  2. Climate effects on plants
  3. Plant Functional Types              

B. Phenology

    1. Definition
    2. Links to Temperature
    3. Impacts on Carbon Balance

 

Topic 5  Radiation Balance

 

A. Solar Radiation

1. Solar Constant

2. Spectral Composition of Sunlight

            a. Planck’s Law

b. Wein’s Law

3. Sun-Earth Geometry

            a. Lambert’s Cosine Law

            4. Length of day, sun angle calculations

            5. Radiation Components

                        a. Direct

                        b. Diffuse

                        c. Shortwave, Par, Nir

            6. Radiation Climatology

            7. Diurnal and Seasonal Patterns

 

B. Terrestrial Radiation

1. Long wave radiation: Stefan-Boltzmann Law

2. Kirchoff’s Law

3. Spectral Distribution

4. Emissivity

5. Radiation Climatology

6. Diurnal and Seasonal Patterns

7. Effects of clouds and humidity

8. Empirical Algorithms

 

C. Net Radiation

 

D. Radiation Climatology

 

E. Diurnal and Seasonal Patterns

 

F. Albedo

            1. Diurnal patterns

            2. Effect of stand type

 

G. Radiation on inclined surfaces, mountain slopes, etc

 

Topic 6, Radiative transfer through vegetation.

 

A. Observations

1. Profiles of radiation within canopies, closed and open

                        a. total, direct and diffuse

            2. Statistics of Light, Probability distributions

                        a. umbra, penumbra, sunflecks

            3. Horizontal Transects

 

B. Beer-Bouguer’s Law

            1. Sunlit leaf area

            2. Gap distribution

 

C. Sun-Leaf Geometry, roles of leaf angles and clumping

 

D. Light Scattering

            1. radiative properties of leaves and soil, reflection, transmittance, absorption

            2. Single and multiple scattering

                        a. hot spot

 

E. Two-Stream Models

 

F. Application: Evaluation of Leaf Area Index. Pros and Cons

 

Topic 7, Temperature 

 

A. Why is temperature important?

1. Kinetics of photosynthesis, respiration, isoprene emission.

2. Growth, phenology on temperature summation units.

 

B. Temperature Definitions: Physics textbooks define thermodynamic and kinetic temperatures.

1. Kinetic Temperature

            2. Thermodynamic temperature, T-P relation

3. Radiative temperature

4. Aerodynamic temperature

5. Virtual temperature

6. Potential temperature

 

C. Conservation equation for heat.

D. Temperature Profiles,

1. Above plant canopies

a. Inversions and adiabatic lapse rates,

b. Concepts of stable, neutral and unstable conditions

            2. Within vegetation

 

E. Temperature climatology

            1. Diurnal patterns

2. Seasonal Patterns

 

Topic 8, Humidity and Trace Gas relations.

 

A. Why is humidity important?

            1. Hydrological Cycle

            2. Physical and Chemical Properties of Water

B. Clausis-Claperon Equation:

C. Saturation Vapor Pressure

           D.. Slope of the saturation vapor pressure-temperature relation, des(T)/dT

            E.. Relative Humidity, hr

            F. Vapor Pressure Deficit:

            G. Dew point temperature, the temperature where the saturation vapor pressure equals the actual temperature.

            H. Wet Bulb Temperature and Psychrometric relation.

             I. Absolute humidity or vapor density (g m-3):

            J. Mixing ratio (r) is the mass of water vapor per unit mass of dry air air (g kg-1):

            K. Specific humidity is the mass of water vapor per unit mass of moist air (g kg-1):

            L. Phase change, concept of Latent heat

            M. Conservation equation for humidity

            N. Plant Microclimate

            1. Profiles of humidity over and within plant canopies

            O. Humidity Climatology

            Q. Mole fraction, Partial Pressure

 

Topic 9, Wind and Turbulence

 

A. Wind

            1. Observations

                        a. Wind profiles above short and tall vegetation

b. Wind profiles within canopies: exponential wind profile, secondary wind maximum

c. Wind statistics

d. wind direction and wind roses

 

2. Concepts

a. Boundary Layers

            i. Planetary Boundary Layer

            ii. Surface Boundary Layer

            iii. Internal Boundary Layer (constant flux layer)

            iv. Nocturnal Boundary Layer

b. Logarithmic Wind Profiles

c. Zero plane displacement and Roughness Length

            i. Variations of zo and d with LAI

d. Aerodynamic Resistance

e. Conservation equation for wind

f.  Role of stability on wind profiles

g. Monin Obuhkov theory; Richardson number

                                               

B. Turbulence

            1. Observations

a. Time series of w,u,T,Q,C

b. Sweep and ejections.

            c. Counter-gradient transfer

2. Concepts

            a.  Definition of Turbulence

b. Reynold’s Number

            3. Statistical Representation of Turbulence

a. Reynold’s averaging

b. Variances ( turbulence intensities)

c. Covariances

                        d. Power Spectra/ Co-spectra

            4. Measures of turbulence and turbulent transfer

a. Friction velocity

b. momentum transfer

c. observations of turbulence statistics

            5. Spectrum of turbulence

                        a. inertial subrange

            6. Conservation of Equations for turbulent transfer of mass, momentum and continuity

 

Topic 10 Conservation Budget for Mass and Energy

 

1. Continuity Equation, the Conservation of mass of a small volume of air, representing an isothermal system

            a. concept

b. derivation

c. local and total derivatives

            d. constant density, incompressible flow

 

2. Conservation of mass for multicomponent system, stationary and rectangular coordinates, still air

            a. mass and molar densities and fractions

            b. diffusive flux densities on molar and mass bases

c. Fick’s First Law

            d. Fick's Second Law

 

3. Conservation of Mass, turbulent flow

            a. bulk flux density on molar and mass bases

b. Reynolds decomposition

            c. derivation

 

Topic 11, Leaf Boundary Layers and their Resistances.

            1. Schmidt Number

            2. Grasshof Number

            3. Nusselt Number

4. Prandtl Number

5. Sherwood Number

6. Form Drag

            7. Skin Friction

            8. Laminar and Turbulent Flow

            9. Role of clumping and characteristic length

 

Topic 12, Leaf Energy Balance

 

A. Convection, Conduction and Radiation

B. Resistance Networks and Theory

C. Steady-State Linear Theory, Iterative model for leaf temperature and evaporation

1. amphistomatous

2. hypostomatous

3. leaf over soil

D. Quadratic, Quartic Equations

E. Response surfaces, leaf-air temperature differences

            1. leaf width

            2. transpiration

F. Dynamic Responses

G. Jarvis McNaughton Coupling theory

 

Topic 13, Stomatal Conductance  

 

A. Observations

            1. Diurnal variations of stomata

                        a. ample soil moisture

                        b. soil moisture deficits

            2. Response of stomata to environmental forcings

                        a. light

                        b. humidity deficits

                        c. temperature

                        d. CO2

                        e. soil moisture

3. Reponse of stomata to physiological variables

            a. photosynthesis

            b. leaf nitrogen

            c. plant functional relations

 

B. Simple Models

1. Jarvis Algorithm

2. Ball Berry Algorithm

3. Cowan/Farquhar theory

4. Theories of Mott and Parkhurst, Monteith (conductance is a function of transpiration

5. Optimal use of water with time, Makela, Farquhar

6. Tardieu et al. (ABA)

 

Topic 14, Canopy Evaporation and Transpiration

 

A. Penman Monteith Equation

            1 Canopy Conductance versus Canopy Stomatal Conductance

B. Equilibrium Evaporation, Priestly-Taylor Relation

C. Coupling Theory

D. Sensitivity to abiotic and biotic variables

            1. Role of Functional types, radiation and humidity deficits

            2. Roles of LAI, leaf N and soil moisture deficits, links with carbon and nutrient cycles.

E. Dew fall.

F. Evaporation from wet canopies

            1. Rainfall interception

G. Soil evaporation

H. Two Layer models, Shuttleworth-Wallace, Van den Hurk-McNaughton, Dolman

 

Topic 15, Canopy Fluxes of Mass and Energy

 

A. Fluxes of sensible and latent heat, G and Can storage

            1. Observations, Crops/Forests/Grassland.

2. Diurnal and seasonal patterns

                            well watered, soil mositure deficits

                        grass, boreal forests, temperate forests, C3 crop, C4 crop, xeric woodland