ESPM 129, Biometeorology, Dennis Baldocchi Instructor

Lecture 1, Introduction
1
Lecture 1. Introduction and Overview

August 25, 2010

ESPM/EPS 129, Biometeorology
MWF 11-12
306 Wellman Hall
University of California, Berkeley

Instructor: Dennis Baldocchi
Professor of Biometeorology
Ecosystem Science Division
Department of Environmental Science, Policy and Management
345 Hilgard Hall
University of California, Berkeley
Berkeley, CA 94720

Email: Baldocchi@nature.berkeley.edu
Phone: 510-642-2874
Fax: 510-643-5098
Web Site: http://nature.berkeley.edu/biometlab

Lecture 1 Outline

1. Introduction: What is Biometeorology?
2. Goals of the Course, Philosophy and Expectations
3. Course Outline


L1.1 Introduction

Biometeorology involves the study of interactions between the physical environment and
all of Life's forms, including terrestrial and marine vertebrates, invertebrates, plants,
funghi and bacteria. In ESPM/EPS 129, we will focus on a narrower aspect of
biometeorology: ‘how the terrestrial biosphere breathes?’

Principles taught in this course will serve students interested in quantitative and
qualitative aspects of environmental sciences. Lectures draw on principles derived from
a diverse but interconnected set of fields like atmospheric science, ecosystem ecology,
plant physiology, biogeochemistry, hydrology, soil physics, agriculture and forestry.
Agricultural and Forest Management problems that require biometeorological
information include integrated management of pests, frost and spray drift, irrigation
scheduling, crop modeling, vineyard, orchard and plantation site selection, optimal crop
design, wind breaks, and cultural practices (e.g. tillage practice, row orientation and soil
mulching). Science problems using biometeorological principles and data involve the
predicting and diagnosing weather and climate, biogeochemical cycles of carbon, water
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
2
and nutrients, water balance of watersheds and the growth and dynamics of forests and
ecosystems.

L1.2 Topic Overview

A link between climate and vegetation have long been recognized by farmers, foresters
and playwrights for hundreds, if not thousands, of years. The word climate is coined
from the Greek word for slope, ‘klima’. The Greeks understood that different types of
vegetation and weather occurred on different hill slopes.

Citations to plant-atmosphere interactions can also be drawn from more contemporary
literature. In the play, Uncle Vanya by Anton Checkov (1899), the Doctor refers to
plants and climate, with a modern sense:

"... forests tremble under the axe, millions of trees are lost, animals and birds
have to flee, rivers dry out, beautiful landscapes are lost forever.....waters are
polluted, wildlife disappears, the climate is harsher...".

In a latter passage he says:

"...the forest teaches us to appreciate beauty, it softens the harshness of the
climate",

The physical status of the atmosphere is defined by its temperature, humidity, wind
speed, and pressure. But how does the atmosphere maintain its physical state? To
answer this question we must assess the fluxes of heat, energy and momentum into and
out of the atmosphere, which is analogous to studying the flows of water into and out of a
bathtub to determine the level of water inside.

For an illustrative example, let’s consider the factors that control atmospheric humidity
(Figure 1). Its content in the atmosphere depends on gains by surface evaporation and
losses by precipitation (rain, snow) and dew formation. The pertinent question asked by
the biometeorologist is: what controls evaporation? To answer this question we must
start invoking explanations that involve plants. Plants intercept sunlight and the
intercepted sunlight heats the soil and leaves and drives transpiration and evaporation.
Plants also exert drag on the wind. This alters turbulent mixing and the transfer of
moisture from the surface to the atmosphere.
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
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Figure 1 Links between plants and the flow of heat, water, CO2 and sunlight.

The ability of plants to exert an influence on the humidity budget of the atmosphere also
depends upon how plants respond to their environment. The humidity of the air alters
the opening of stomata on leaves and rates of transpiration. The heat budget and the
consequential temperature of the leaves controls respiration (leaves, roots, microbes),
photosynthesis, trace gas volatilization, saturation vapor pressure, plant growth, kinetic
rates of biochemical reactions. Sunlight drives photosynthesis, which is linked to
stomatal conductance and growth. Photosynthesis and photorespiration depend upon
CO
2
levels. Finally, if moisture in the atmosphere condenses, it forms clouds and these
clouds can precipitate. On climatic time scales, the water balance of the soil affects
transpiration, stomatal conductance, photosynthesis, soil respiration, plant growth, plant
competition, species and leaf area.

The rates at which trace gases and energy are transferred between the biosphere and
atmosphere depend upon a complex and non-linear interplay among physiological,
ecological, biochemical, chemical and edaphic factors and meteorological conditions.
Contemporary theories consider the exchanges of energy and mass in concert. Flows of
energy need to be calculated because the biosphere requires energy to perform work. Gas
exchange activities requiring energy and work include biosynthesis, evaporation,
transport of nutrients and carbon dioxide fixation. Concurrently, these activities require
flows of substrate material. Water and carbon and nitrogen based compounds are the
most important forms of matter for the sustenance of life.

ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
4
Scale is an important concept we must concern ourselves with when studying
biometeorology. To understand why, let’s consider the functioning of a plant canopy, 1
m tall. It consists of leaves, an order of magnitude smaller, and it is the functioning of
the leaves, a smaller scale phenomenon, that helps us understand the functioning of the
canopy. Now the environment imposed on the canopy comes from a much larger scale,
that of the planetary boundary layer and regional weather, with scales of kilometers.

Another concept to consider is emergent processes. As we transcend scales new
processes emerge, while others may become less important. For example, the net
exchange of water vapor at the canopy scale is not simply the average rate of
transpiration of a leaf multiplied by the number of leaves and their area. We must also
consider soil evaporation. In addition, as one adds more and more leaves, their
contribution to canopy evaporation diminishes, as their upper neighbors have already
harvested most of the photons and solar energy that drives evaporation.

Issues relating to scale, non-linear, coupled processes and emergent processes are
important as they are attributes of complex systems, which are deterministic, but can
have chaotic responses, and are sensitive to initial conditions.

The plant, weather and climate processes of interest are associated with a huge range of
time and space scales.

Space scales of interest include:

1. cell: microns (10
-6
m)
2. leaf: 0.01 to 0.1 m (needles to broad-leaves)
3. plants and vegetation canopies: 0.1 to 100 m (grass to redwoods)
4. surface boundary layer (50 to 1000m): scale of individual fields
5. planetary boundary layers (100 to 3000m): scale of the planetary boundary layer,
where the earth surface affects the properties of the overlying atmosphere.
6. landscape: (1 km to 10 km): patch size of mosaic of extended fields, lakes and forests.
Patches are large enough to affect convection and advection.
7. region to globe (100 km to 10000km): the scale of biomes, continents and oceans,
scales of atmospheric waves, fronts and storms

Temporal scales of interest to us include:

1-10 hz: sunflecks and wind fluctuations:
30-500 s: coherent turbulent structures and sun patches:
100 to 3000 s: photosynthetic and stomatal inductance
3600-86400s: hourly and diurnal movement of earth/sun, water movement through stems,
convective cloud generation and dissipation:
~7 days: weekly sequence of frontal passages, swings in temperature, humidity
60 to 120 days: season variations in phenology, growth, adaptation, drought, frost, soil
temperature wave
year: 365 days: summation of seasonal effects
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
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decade: climate, inter-annual variability, El Nino, volcanos).

Overall, spatial and temporal information, of interest to biometeorologists span 8 to 10
orders of magnitude (10
-6
to 10
4
m; 10
-2
to 10
6
s).
canopy
landscape
region/biome
continent
s
e
c
o
n
d
s
d
a
y
s
y
e
a
r
s
c
e
n
t
u
r
i
e
s
Weather:
ppt, T, u,
R
g
Ecosystem Dynamics:
species, functional
type
Climate
Biogeo-
chemistry:
LAI, C/N, Vc
max Biophysics:
ìE, H, A, Gc

Figure 2 Conceptual diagram showing the link between biometeorological processes and time and
space scales

L1.3. Structure and Function

‘Form Follows Function’, Louis Henri Sullivan (1856-1924), architect

‘Form follows function―that has been misunderstood. Form and function should be one,
joined in a spiritual union’, Frank Lloyd Wright (1869-1959), protégé’ of Louis Henri
Sullivan and architect

On walking through the woods, one of the first impressions one draws is that a
forest is a structurally complex entity. If one is walking through a temperate hardwood or
tropical forest, one observes trees of multiple stature, age and species. Stopping and
looking upward into the canopy crown, one sees that many leaves are sunlit leaves, their
inclination angles are rather erect, they are rather thick and they tend to be arranged in
clumps (Parker, 1995). At eye-level, tree trunks, understory vines, saplings and shrubs
immediately come to view. Understory leaves are relatively thin and tend to be oriented
horizontally, to absorb as much light as possible, in the sun-dappled shade. Looking
downward one sees fresh and decomposing litter, soil, rocks, fallen logs, seedlings, herbs
and shrubs.
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
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Figure 3 A walk through the woods. Armstrong Redwoods State Preserve, Guerneville, CA. Ian
McCully, photo.
Walking through forests in seasonally dry climates, like the ponderosa pine
ecosystem of the western United States or oak woodland ecosystems in Mediterranean
climates, one observes a stand with fewer tree species, than a temperate or tropical forest.
The architecture of forest canopies in xeric environments is more complex due to
periodic fires and seasonal drought. Structurally, the forest canopy is a patch-work of
dense and clumped young trees, open spaces, tall and solitary old trees and a mat of
shrubs and herbs in and around gaps.

Unseen by the naked eye is functional complexity. As stomata open to allow CO
2

to diffuse into the mesophyll, water is lost, as photosynthesis, respiration, stomatal
conductance and transpiration operate in concert with one another. Biophysics,
competition and natural selection act as governors on the ultimate rates of photosynthesis
and transpiration that a leaf can achieve; these processes interact to constrain leaf
morphology, photosynthetic capacity, stomatal conductance, leaf water potential, root-
shoot allocation and resource acquisition (e.g. nutrients and soil moisture).

Structural and functional complexity of a forest is not static. On visiting a forest
many times over a year, one will observe both gradual and dramatic transitions in
structure and function. During the winter, the forest may be leafless or dormant and
respiring. With the occurrence of spring comes a flush of growth. Rapid changes in
biological activity and structure occur as leaves expand, nodes elongate, roots grow and
reproductive organs emerge. Coincidently, photosynthetic capacity of leaves changes
rapidly during this period, as chloroplast with nitrogen-rich RUBP are constructed.
During the summer, gradual changes in canopy structure, maximum stomatal
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
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conductance and physiological capacity occur as leaves age, experience water deficits,
acclimate, are eaten or drop due to prolonged drought. With the approach of autumn, the
face of the landscape changes yet again. Leaves re-translocate nitrogen back to stems,
their photosynthetic capacity diminishes, they senesce and they drop from the trees.

Understanding complexity in canopy structure and function are key to quantifying
carbon dioxide and water vapor exchange of forest stands, information that is used in
models that predict and diagnose weather, climate, biogeochemical cycling and forest
dynamics. This is because many structural and functional properties of plant canopies
alter: 1) wind and turbulence within and above the canopy, by exerting drag; 2) the
interception and scattering of photons throughout the canopy; 3) the heat load on
leaves and the soil; 4) the physiological resistances to water and CO
2
transfer and 5) the
biochemical capacity to consume or respire carbon dioxide.

Any study on canopy microclimate or mass and energy exchange is essentially
worthless, unless it is accompanied with information on canopy architecture, plant
structure and function. Such a folly would be equivalent to trying to study demographics
of a city without knowing the population. For example, how could you estimate the
water use of San Francisco without knowing the number of people, houses and toilets in
the city?

In this lecture we focus on the physical attributes of plant canopies and how they
relate to biometeorological variables and processes.

L1.4 Physical Attributes of Plant Canopies

Reviews on the topic of canopy structure define several specific terms (Parker, 1995).
Physiognomy is concerned with the shape of crowns. Architecture describes growth
patterns and forms of stems. Organization relates to the statistical distribution of canopy
components in time and space and texture refers to the crown units of the overstory. In a
broad sense, I define a plant canopy as an amalgam of herbs, shrubs, plants and
underlying soil that exists on a landscape.

Important attributes of a plant canopy that relate to mass and energy exchange, canopy
microclimate and ecosystem physiology and functioning include:

1) leaf area index of the canopy (the amount of leaf area per ground area);
2) shape and size of leaves (needles vs planar, projected vs surface area of needles and
shoot to total needle area);
3) vertical distribution of leaf area;
4) spatial distribution of leaves (are they dispersed in a random, clumped or regular
fashion?)
5) seasonal variation of leaf area (is the canopy evergreen or deciduous?)
6) leaf angle distribution (are leaves erect, planophile, spherical?; are they azimuthally
symmetric or asymmetric?)
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
8
7) canopy height (short and aerodynamically smooth vs tall and aerodynamically rough)
8) crown volume and shape (vertical and horizontal dimensions; conical, ellipsoidal,
spherical)
9) plant species (species number, functional types)
10) stem density (stems per hectare);
11) spatial distribution of plants (random, clumped, rows, regular);
12) photosynthetic pathway (C
3
, C
4
, CAM);
13) plant habit (deciduous/evergreen; woody/herb, annual/perennial)
14) age structure (disturbed/undisturbed, plantation, native, agriculture, even aged,
mixed aged)
15) exposure/acclimation (sunlit/shaded, thickness, clumping, angle);
16) woody biomass area index (silhouette woody biomass per unit area);
17) rooting depth, root architecture (fibrous, tap), accessible water and nutrient volume
18) history and type of disturbance (recent fires, logging, plowing, re-planting)

Different attributes of a plant canopy influence the state of the atmosphere and
components of mass and energy exchange in various ways.

Leaf size, shape and orientation affect:

1) the properties of the leaf boundary layer;
2) the reflectance and transmittance of light;
3) leaf’s energy balance;
4) Umbra and penumbra (full or partial shade);
5) Leaf or needle clumping;


Figure 4. Blue oak leaves (Quercus douglasii).

The thickness of the leaf boundary layer affects the rate diffusion of trace gas to and from
the leaf. The interception of light depends on leaf orientation, relative to the sun, and
how clumped the leaves or needles may be. If a leaf is big enough to block the solar disk,
as viewed by another leaf, full shade is cast. Otherwise the inferior leaf is exposed to
partial or penumbral shade. The optical properties of leaves affect how much intercepted
radiation is available for evaporating water, photosynthesis and heating a leaf. The
temperature of a leaf governs kinetic rates of many important biochemical processes like
photosynthesis, respiration, plus the production of secondary compounds like isoprene.
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
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Growth form and geometry of a canopy or group of plants affects mass and energy
exchange by how it traps photons, exerts drag and alters physiological functioning. Tall
plant stands are aerodynamically rougher, so turbulent mixing and transport is more
efficient. Tall plant stands also trap photons more efficiently, so they are optically
darker. This means they absorb more solar energy and hence have more energy
available to evaporate water and heat the air. Tall plants, on the other hand, exert a
stronger resistance to water transport through their xylem. So taller plants may impose
stronger physiological restraints on mass and energy exchange than may shorter plants.

The structure of a plant canopy is not static with time. It can vary over the course of a
year and over the course of the plant’s lifespan. Evergreeness and deciduousness are
two examples of seasonal behavior by plants. Evergreen shed older leaves after new
leaves unfold, so there is an annual cycling of foliage. On a shoot of a conifer, for
example, many years of needles will coexist. Their photosynthetic capacity diminishes
with age. We also know that the photosynthetic capacity of co-occurring deciduous and
evergreen plants of the same genus (e.g. Quercus) can differ by a factor of two, with
greater capacity being associated with the deciduous species.

Evergreen type often occurs in habitats where carbon assimilation is restricted by
unfavorable conditions, as in the boreal forest. But it can also occur in tropical regions
where there is essential little seasonality, hence no reason to become dormant and drop
leaves. Conifers also reside on soils with lower nutrient availability (Sprugel, 1989).

The deciduous type leaf is more productive and its dominance on the landscape is more
common when nutrients and water is plentiful. The seasonal pattern of having or
dropping leaves has dire impact on mass and energy exchange. The rates of sensible heat
and the reflectivity of a forest differ markedly if it has leaves or not.

Plant function, as identified by its photosynthetic pathway will affect its stomatal
conductance and the partitioning of energy into evaporating water and generating heat. It
will also affect the efficiency of photosynthesis.

A quantitative understanding about how plant functional and structural attributes affect
the canopy microclimate and mass and energy exchange can be gained by examining the
Conservation of Mass equation. A simplified version of the conservation of mass can
be used to demonstrate that the net flux density (moles m
-2
s
-1
) of carbon dioxide or water
vapor between a forest and the atmosphere (F) can be estimated by integrating the
source-sink strength with respect to height (S(z)):

F S z z
h
=
¯
( )A
0
(1

This assumption is valid as long as the forest is horizontally homogeneous and the
environmental conditions are not varying.

ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
10
Conceptually, the source-sink strength of vegetation is proportional to leaf area density
(a(z)) and the differences between the scalar concentration in the atmosphere (C
a
)
adjacent to leaves and that inside the leaves (C
i
). It is inversely proportional to the sum of
the aerodynamic (r
a
) and stomatal resistances (r
s
):

c
c
= = ÷
÷
+
F
z
S z a z
C z C
r r
i
a s
( ) ( )
( ( ) )
(2

For CO
2
, the daytime sink strength in a layer of canopy is determined by the balance
between a biochemical and physiologically-limited demand of leaves and the diffusional-
limited supply from the atmosphere and through the leaf boundary layer (Farquhar et al.,
1980).
Using Equation 1 as a framework, one can identify how physical and functional
attributes of single leaves, individual plants and plant stands impact carbon, water and
energy exchange through their impact on boundary layer (G
a
) and surface
conductances (G
s
), physiological sink capacity (C
i
) and photon transport through leaf
mesophyll and canopy foliage (P(0), the probability of beam penetration) (Table 1). As
this course develops over the course of this semester we focus on much of the material
presented in this table in greater detail.

Table 1 presents a summary of key leaf and plant characteristics, their attributes
and how these two features impact mass and energy exchange of plant canopies and
affect the local microclimate.

Table 1 Structural and functional attributes of leaves, plants and plant stands and their impact on carbon,
water and energy fluxes (Baldocchi et al., 2002; Horn, 1971; Nobel, 1999; Norman, Campbell, 1989; Ross,
1980). G
a
: aerodynamic conductance; G
s
: surface conductance; P(0): light transmission through a leaf or
canopy; o: albedo or reflectivity; C
i
: biochemical capacity
Characteristic Structural or Functional
Attribute
Primary Impacts on
Carbon, Water and
Energy Fluxes
Leaves


Photosynthetic pathway C
3
,C
4
,CAM, maximal stomatal
conductance
C
i
, G
s

Leaf size/shape Needle/planar/ shoot;
projected/surface area,
penumbra/umbra
G
a
, P(0)
Leaf inclination angle
distribution
Spherical, erectophile,
planophile
P(0)
Leaf azimuthal angle
distribution
Symmetric/asymmetric P(0)
Exposure Sunlit/shaded; acclimation
C
i
, G
s,
o
Optical properties Reflectance,transmittance,
emittance
o
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
11
Leaf thickness Photosynthetic capacity, supply
of CO
2
to chloroplast, optical
properties, Stomatal
conductance capacity
C
i
,G
s
, o
Stomatal distribution Amphistomatous/hypostomatous G
s


Plants/Trees





Crown volume shape Cone, ellipse, cylinder P(0), G
a

Plant species monoculture, mixed stand,
functional type
P(0), G
a
, G
s
, C
i

Spatial distribution of
leaves
Random, clumped, regular P(0)
Plant habit Evergreen/deciduous; woody
herbaceous; annual/perennial
G
a
, G
s
, o
Plant height Short (< 0.10 m)
tall (> 10 m)
G
a
, o
Rooting depth Accessible water and nutrients,
plant water relations
G
s

Leaf area/sapwood ratio Hydraulic Conductivity G
s
, C
i



Forest Stand


Leaf area index Open, sparse, closed P(0), G
s
, G
a

Vertical distribution of LAI Uniform, skewed G
a
, P(0)
Seasonal variation of LAI Evergreen/deciduous; winter or
drought deciduous
G
a
, G
s

Age structure Disturbed/undisturbed;
plantation; agriculture; regrowth
G
a
, G
s
, P(0)
Stem density Spatial distribution of plants
G
a
, o
Woody biomass index Amount of woody biomass G
a
, P(0)
Topography Exposure, site history, water
balance
G
a
, G
s

Site history Fires, logging, plowing, re-
growth
G
a
,G
s
,C
i
, o




As we walk through the country-side it become readily obvious that different types of
ecosystems, growing in different climates have different structural properties. To get a
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
12
sense of how micrometeorological and plant canopy attributes of different ecosystems
compare, we draw on compiled lists by the author and assorted references (Breuer et al.,
2003; Myneni et al., 1997; Saugier et al., 2001).

Table 2 Summary of Plant Attributes
Parameter grass/
cereal
shrub Broad-
leaved crop
savanna Broad-
leaved
forest
needle
leaved
forest
LAI 0-5 1-7 0-6 0-7 3-7 1-10
fraction of
ground
cover
1.0 0.2-0.6 0.1-1 0.2-0.4 >0.8 >0.7
understory
LAI
- - - 0-5 0-2 0-2
leaf normal
orientation
erecto
phile
uniform uniform uniform/
erectophi
le
uniform/
planophile/
clumped
uniform/
planophile/
clumped
fraction of
stems
- 0.05 0.10 0.10 0.15-20 0.15-0.20
leaf size (m) 0.05 0.05 0.10 0.10 0.10 0.01
crown size 4 by 4 10 by 10 7 by 7




Table 3 Survey of Biophysical parameters, Saugier et al. 2001, Breuer et al. 2003. zo is aerodynamic
roughness length.
biome albedo Height (m) Zo(m) LAI max Rooting
Depth
Tropical
forests
0.12-0.14 30-50 2-2.2 4-7.5 1-8
Temperate
forests
0.1-0.18 15-50 1-3 3-15 0.5-3
Boreal forests 0.1-0.3 2-20 1-3 1-6 0.5-1
Arctic tundra 0.2-0.8 < 0.5 < 0.05 0-3 0.4-0.8
Mediterranean
shrubland
0.12-0.2 0.3-10 0.03-0.5 1-6 1-6
Crops 0.1-0.2 variable variable 4 0.2-1.5
Tropical
savanna
0.07-0.4 0.3-9 variable 0.5-4 0.5-2
Temperate
grassland
0.15-0.25 0.1-1 0.02-0.1 1-3 0.5-1.5
desert 0.2-0.4 < 0.5 < 0.05 1 0.2-15
- -

ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
13


Table 4 Ecophysiological Parameters by Biome, Saugier et al. 2001., Breuer et al., 2003, gs is stomatal
conductance, ga is aerodynamic conductance, RUE is radiation use efficiency for photosynthesis.
biome Max g
s
g
a
Max CO
2

flux, day
Max CO
2

flux, night
RUE
Units mol m
-2
s
-1
mol m
-2
s
-1
umol m
-2
s
-1
umol m
-2
s
-1
G(DM)/ MJ
(PAR)
Tropical
forests
0.5-1 0-4 -25 5-8 0.9
Temperate
forests
0.5 1-4 -25 1-6 1
Boreal forests 0.2 10 -12 0-4 0.3-0.5
Arctic tundra -0.5 to -2 1-2
Mediterranean
shrubland
0.5-1 -12 to -15 6-7
Crops 1.2 1-3 -40 2-8 1-1.5
Tropical
savanna
0.2-1 0.1-4 -4 to -25 2-5 0.4-1.8
Temperate
grassland
0.4-1 0.2-1.5 -13 to -20 0.5-4




Having a general knowledge of these features will be critical later in the course when we
draw on these features to compute rates of transpiration, evaporation and photosynthesis.

Points to Ponder:

Does biodiversity and species matter when considering plant microclimates and mass and
energy exchange?

How does the plant microclimate and mass and energy exchange differ by substituting an
evergreen forest with a deciduous forest?; by substituting a forest with a grassland?

How has the evolution of the Earth’s climate affected the evolution of plant physiognomy
and ecosystem structure and function? Does leaf size, for instance, correlate with water
balance and climate?

Summary

- Physical attributes of a canopy include leaf area index, canopy height, and leaf
size.
- Physiological attributes of a canopy include photosynthetic pathway, stomatal
distribution (amphi or hypostomatous)
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
14
- Structural and functional properties of plant canopies alter: 1) wind and
turbulence within and above the canopy, by exerting drag; 2) the interception
and scattering of photons throughout the canopy; 3) the heat load on leaves and
the soil; 4) the physiological resistances to water and CO
2
transfer and 5) the
biochemical capacity to consume or respire carbon dioxide.
- The physical and physiological attributes of a canopy can vary in space (vertically
and horizontally) and in time (seasonally and decadally).


References/Bibliography

Baldocchi DD, Wilson KB, Gu L (2002) Influences of structural and functional
complexity on carbon, water and energy fluxes of temperate broadleaved
deciduous forest. Tree Physiology. 22, 1065-1077.
Breuer L, Eckhardt K, Frede H-G (2003) Plant parameter values for models in temperate
climates. Ecological Modelling 169, 237-293.
Horn HS (1971) The Adaptive Geometry of Trees Princeton Univeristy Press.
Myneni RB, Nemani RR, Running SW (1997) Estimation of global leaf area index and
absorbed par using radiative transfer models. Ieee Transactions on Geoscience
and Remote Sensing 35, 1380-1393.
Nobel PS (1999) Physicochemical and Environmental Plant Physiology Academic Press.
Norman JM, Campbell GS (1989) Canopy Structure. In: Plant Physiological Ecology.
Parker GG (1995) Structure and Microclimate of Forest Canopies. In: Forest Canopies,
pp. 73-106.
Ross J (1980) The Radiation Regime and Architecture of Plant Stands. Dr. W Junk, The
Hague.
Saugier B, Roy J, Mooney H (2001) Estimations of global terrestrial productivity:
converging toward a single number. In: Terrestrial Global Productivity (ed. J Roy
BS, HA Mooney), pp. 543-557. Academic Press.
Sprugel DG (1989) The Relationship of Evergreenness, Crown Architecture, and Leaf
Size. American Naturalist 133, 465-479.



L1.6 Educational Resources

Key Journal in the Field

Main Journals

Agricultural and Forest Meteorology
Boundary Layer Meteorology
Journal of Geophysical Research, Biogeosciences
Plant, Cell and Environment

Journals with Occasional Articles
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
15

Global Change Biology
Biogeosciences
Journal of Applied Meteorology
Tree Physiology
Journal of Hydrology
Water Resources Research
Oecologia
Ecological Applications
Ecology
Quarterly Journal of the Royal Meteorological Society
Atmospheric Environment
International journal of Biometeorology

Key Web pages

Key Societies and Organizations with Activities in Biometeorology and Agricultural
and Forest Meteorology:

American Meteorological Society: http://www.ametsoc.org/AMS/

American Geophysical Union: http://www.agu.org/

Ecological Society of American: http://esa.sdsc.edu/
Physiological Ecology Section: http://www.biology.duke.edu/jackson/ecophys/

International Society of Biometeorology: http://www.es.mq.edu.au/ISB/

American Agronomy Society: http://www.agronomy.org/

International Society for Agrometeorology: http://www.agrometeorology.org/

World Meteorological Organization, Commission for Agricultural Meteorology:
http://www.wmo.ch/web/wcp/agm/agmp.html

Biospheric Aspects of the Hydrological Cylcle, IGBP: http://www.pik-potsdam.de/~bahc/

Canadian Society of Agricultural Meteorology: http://www.uoguelph.ca/~csam/

Key Text books, Biometeorology, Micrometeorology, Environmental Physics,
Ecophysiology, Ecohydrology.

Arya, S. P. 1988. Introduction to Micrometeorology. Academic Press.

Bonan, G. 2002. Ecological Climatology. Cambridge University Press

ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
16
Campbell,G.S. and Norman, J.M. 1998. An Introduction to Environmental Biophysics.
Springer.

Eagleson P.S. 2002. Ecohydrology. Cambridge University Press.

Garratt, J.R. 1992. The Atmosphere Boundary Layer. Cambridge Press.

Grace, J. 1983. Plant-Atmosphere Relations. Chapman and Hall.

Jones, H.G. 1992. Plants and Microclimate. Cambridge Press

Kaimal, J.C. and J.J. Finnigan. 1994. Atmospheric Boundary Layer Flows: Their
Structure and Measurement. Oxford Press.

Larcher W. 1975. Physiological Plant Ecology. Springer-Verlag. Berlin. 252 pp.

Monteith, J.L. and M.H. Unsworth. 1990. Principles of Environmental Physics. E.A.
Arnold.

Nobel, P.S. 1991. Physiochemical and Environmental Plant Physiology. Academic Press

Oke, T.R. 1987. Boundary Layer Climates. Metheun.

Panofsky, H.A. and J.A. Dutton. 1984. Atmospheric Turbulence. Wiley and Sons, 397
pp.

Stull, R.B. 1988. An Introduction to Boundary Layer Meteorology, Kluwer Academic
Publishers.

Rosenberg, N.J., B.L. Blad and S.B.Verma. 1983. Microclimate. J. Wiley and Sons.

Tindall, J.A. and J.R. Kunkel. 1999. Unsaturated Zone Hydrology for Scientists and
Engineers. Prentice Hall.624 pp.

Specialized Proceedings

Andreae, M.O. and D.S. Schimel. 1989. Exchange of Trace Gases between Terrestrial
Ecosystems and the Atmosphere. Dahlem Workshop. J. Wiley.

Barfield, B.J. and J.F. Gerber. 1979. Modification of the Aerial Environment of Plants.
ASAE Monograph. St. Joseph, MI

Brutsaert, W.H. 1982. Evaporation into the Atmosphere. D. Reidel Pub.

Ehleringer, J.R. and C.B. Field. 1993. Scaling Physiological Processes: Leaf to Globe.
Academic Press.
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
17

Gash, JHC, C. Nobre, J. Roberts and R. Victoria. 1996. Amazonian Deforestation and
Climate. J. Wiley.

Grace, J, E.D. Ford and P.G. Jarvis. 1980. Plants and Their Atmospheric Environment.
Blackwell. Oxford.

Griffiths, J.F (eds). 1994. Handbook of agricultural meteorology. New York : Oxford
University Press, 1994

Hutchison, B.A. and B.B. Hicks. 1985. Forest-Atmosphere Interactions. D. Reidel.

Moore, B. and D.S. Schimel. 1992. Trace Gases and the Biosphere. NCAR.

Noormets Phenology book

Ross, J. 1981. The Radiation Regime and Architecture of Plant Stands. Dr. Junk, The
Hague.

Roy, J., Saugier, B. Mooney, H. 2001. Terrestrial Global Productivity. Academic Press.

Steffen, W.L. and O.T. Denmead. 1988. Flow and Transport in the Natural Environment:
Advances and Applications. Springer-Verlag.

Sharkey, T.D., E.A. Holland and H.A. Mooney. 1991. Trace Gas Emission by Plants.
Academic Press.

Tenhunen, J. and P. Kabat. 1999. Integrating Hydrology, Ecosystem Dynamics and
Biogeochemistry in Complex Landscapes. Dahlem Konferenzen

Valentini Carbo Europe Book

Varlet-Grancher, C., R. Bonhomme and H. Sinoquet. 1993. Crop Struction and Light
Microclimate. INRA, France.

Von Caemmerer, S. 2000. Biochemical models of leaf photosynthesis. CSIRO
Publishing.

Woodward, I. 1986. Climate and Plant Distributions. Cambridge

Methods

Fritschen, L.J. and L.W. Gay. 1979. Environmental Instrumentation. Springer Verlag.

Hall, D.O. et al. 1993. Photosynthesis and Production in a Changing Environment: a
Field and Laboratory Manual. Chapman and Hall.
ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
18

Matson, P.A. and R.C. Harriss. 1995. Biogenic Trace Gases: Measuring Emissions from
Soil and Water. Blackwell.

Pearcy, R.W., J. Ehleringer, H.A. Mooney and P.W. Rundel. 1985. Plant Physiological
Ecology: Field Methods and Instrumentation. Chapman Hall.

Classic Books

Baver, L.D., W.H. Gardner and W.R. Gardner. 1972. Soil Physics. John Wiley and Sons.
New York. 497 pp.

Brooks, F.A. 1960. Physical Microclimatology. University of California, Davis.

Budyko, M.I. 1974. Climate and Life. Academic Press.

deVries, D.A. and N.H. Afgan. 1975. Heat and Mass Transfer in the Biosphere. John
Wiley and Sons

Geiger, R. 1961. The Climate Near the Ground. Harvard University Press.

Haugen et al. 1973. Workshop on Micrometeorology, American Meteorological Society,
Boston

Lowry, W.P. 1969. Weather and Life: an Introduction to Biometeorology.

Lumley, J.L. and H.A. Panofsky. 1964. The Structure of Atmospheric Turbulence. John
Wiley and Son. New York.

Monin, A.S. and A.M. Yaglom. 1975. Statistical Hydrodynamics. MIT Press. Cambridge.

Monteith, J.L. 1975. Vegetation and the Atmosphere, I, Academic Press. London.

Monteith, J.L. 1975. Vegetation and the Atmosphere, II, Academic Press, London

Munn, R.E. 1966. Descriptive Micrometeorology. Academic Press. New York.

Pasquill, F.A. 1974. Atmospheric Diffusion. Wiley.

Rose, CW. 1966. Agricultural Physics. Pergamon Press. 230 pp.

Sestak, Z., J. Catsky and P.G. Jarvis. 1971. Plant Photosynthetic Production: Manual of
Methods. Dr. W Junk, The Hague.

Setlik et al. 1970. Prediction and measurement of Photosynthetic Productivity. Pudoc.

ESPM 129, Biometeorology, Dennis Baldocchi Instructor
Lecture 1, Introduction
19
Sutton, O.G. 1953. Micrometeorology. McGraw-Hill.

But how does the atmosphere maintain its physical state? To answer this question we must assess the fluxes of heat. wind speed.waters are polluted.". foresters and playwrights for hundreds. snow) and dew formation. let’s consider the factors that control atmospheric humidity (Figure 1).ESPM 129. forests tremble under the axe. energy and momentum into and out of the atmosphere. Plants intercept sunlight and the intercepted sunlight heats the soil and leaves and drives transpiration and evaporation. beautiful landscapes are lost forever. and pressure. water balance of watersheds and the growth and dynamics of forests and ecosystems. Dennis Baldocchi Instructor Lecture 1. the climate is harsher. Biometeorology.. 2 . The Greeks understood that different types of vegetation and weather occurred on different hill slopes... if not thousands. Citations to plant-atmosphere interactions can also be drawn from more contemporary literature. Introduction and nutrients. rivers dry out. humidity.. ‘klima’. the Doctor refers to plants and climate.2 Topic Overview A link between climate and vegetation have long been recognized by farmers. Plants also exert drag on the wind. which is analogous to studying the flows of water into and out of a bathtub to determine the level of water inside.. of years.the forest teaches us to appreciate beauty. with a modern sense: ". wildlife disappears. animals and birds have to flee. L1. millions of trees are lost. In the play. Its content in the atmosphere depends on gains by surface evaporation and losses by precipitation (rain. This alters turbulent mixing and the transfer of moisture from the surface to the atmosphere. Uncle Vanya by Anton Checkov (1899). In a latter passage he says: ". The word climate is coined from the Greek word for slope. The pertinent question asked by the biometeorologist is: what controls evaporation? To answer this question we must start invoking explanations that involve plants.... For an illustrative example.. it softens the harshness of the climate". The physical status of the atmosphere is defined by its temperature..

photosynthesis. Concurrently. photosynthesis. Water and carbon and nitrogen based compounds are the most important forms of matter for the sustenance of life. The humidity of the air alters the opening of stomata on leaves and rates of transpiration. On climatic time scales. evaporation. biochemical. Contemporary theories consider the exchanges of energy and mass in concert. kinetic rates of biochemical reactions. trace gas volatilization. plant growth. transport of nutrients and carbon dioxide fixation. saturation vapor pressure. The ability of plants to exert an influence on the humidity budget of the atmosphere also depends upon how plants respond to their environment. Photosynthesis and photorespiration depend upon CO2 levels. plant growth. ecological. Biometeorology. Sunlight drives photosynthesis. which is linked to stomatal conductance and growth. roots. microbes). The rates at which trace gases and energy are transferred between the biosphere and atmosphere depend upon a complex and non-linear interplay among physiological. stomatal conductance. CO2 and sunlight. soil respiration. if moisture in the atmosphere condenses. The heat budget and the consequential temperature of the leaves controls respiration (leaves. water. plant competition. species and leaf area. Dennis Baldocchi Instructor Lecture 1. the water balance of the soil affects transpiration. 3 . it forms clouds and these clouds can precipitate. Finally. chemical and edaphic factors and meteorological conditions. Flows of energy need to be calculated because the biosphere requires energy to perform work. these activities require flows of substrate material.ESPM 129. Introduction Figure 1 Links between plants and the flow of heat. Gas exchange activities requiring energy and work include biosynthesis.

6. growth. Issues relating to scale. frost. and are sensitive to initial conditions. surface boundary layer (50 to 1000m): scale of individual fields 5. leaf: 0. drought. while others may become less important. a smaller scale phenomenon. It consists of leaves. Biometeorology. Space scales of interest include: 1. fronts and storms Temporal scales of interest to us include: 1-10 hz: sunflecks and wind fluctuations: 30-500 s: coherent turbulent structures and sun patches: 100 to 3000 s: photosynthetic and stomatal inductance 3600-86400s: hourly and diurnal movement of earth/sun. swings in temperature. adaptation. with scales of kilometers. their contribution to canopy evaporation diminishes. coupled processes and emergent processes are important as they are attributes of complex systems. that helps us understand the functioning of the canopy. cell: microns (10-6m) 2. but can have chaotic responses. planetary boundary layers (100 to 3000m): scale of the planetary boundary layer. landscape: (1 km to 10 km): patch size of mosaic of extended fields. Patches are large enough to affect convection and advection. For example. where the earth surface affects the properties of the overlying atmosphere.ESPM 129.1 to 100 m (grass to redwoods) 4. To understand why. as one adds more and more leaves. Now the environment imposed on the canopy comes from a much larger scale. soil temperature wave year: 365 days: summation of seasonal effects 4 . As we transcend scales new processes emerge. 1 m tall. the net exchange of water vapor at the canopy scale is not simply the average rate of transpiration of a leaf multiplied by the number of leaves and their area. and it is the functioning of the leaves. Dennis Baldocchi Instructor Lecture 1. which are deterministic. convective cloud generation and dissipation: ~7 days: weekly sequence of frontal passages. Another concept to consider is emergent processes. scales of atmospheric waves. continents and oceans. The plant. region to globe (100 km to 10000km): the scale of biomes. lakes and forests. In addition. 7. plants and vegetation canopies: 0. as their upper neighbors have already harvested most of the photons and solar energy that drives evaporation. We must also consider soil evaporation. humidity 60 to 120 days: season variations in phenology. that of the planetary boundary layer and regional weather. an order of magnitude smaller.01 to 0. let’s consider the functioning of a plant canopy. non-linear. water movement through stems.1 m (needles to broad-leaves) 3. Introduction Scale is an important concept we must concern ourselves with when studying biometeorology. weather and climate processes of interest are associated with a huge range of time and space scales.

If one is walking through a temperate hardwood or tropical forest. herbs and shrubs. Dennis Baldocchi Instructor Lecture 1. one of the first impressions one draws is that a forest is a structurally complex entity. in the sun-dappled shade.3. H. architect ‘Form follows function―that has been misunderstood. joined in a spiritual union’. rocks. soil. 1995). their inclination angles are rather erect. At eye-level. saplings and shrubs immediately come to view. tree trunks. Climate Ecosystem Dynamics: species. one observes trees of multiple stature. inter-annual variability. Biometeorology. understory vines. C/N. age and species. Vcmax continent region/biome Weather: ppt. Gc canopy centuries Figure 2 Conceptual diagram showing the link between biometeorological processes and time and space scales L1. Overall. they are rather thick and they tend to be arranged in clumps (Parker. to absorb as much light as possible. spatial and temporal information. of interest to biometeorologists span 8 to 10 orders of magnitude (10-6 to 104 m. 5 seconds years days . Introduction decade: climate. volcanos). T.ESPM 129. seedlings. Frank Lloyd Wright (1869-1959). Form and function should be one. fallen logs. functional type Biogeochemistry: LAI. protégé’ of Louis Henri Sullivan and architect On walking through the woods. A. Looking downward one sees fresh and decomposing litter. El Nino. Structure and Function ‘Form Follows Function’. Stopping and looking upward into the canopy crown. Louis Henri Sullivan (1856-1924). u. 10-2 to 106 s). one sees that many leaves are sunlit leaves. Understory leaves are relatively thin and tend to be oriented horizontally. Rg landscape Biophysics: E.

nutrients and soil moisture). Dennis Baldocchi Instructor Lecture 1. With the occurrence of spring comes a flush of growth. The architecture of forest canopies in xeric environments is more complex due to periodic fires and seasonal drought. these processes interact to constrain leaf morphology. On visiting a forest many times over a year.g. Structural and functional complexity of a forest is not static. stomatal conductance and transpiration operate in concert with one another. leaf water potential. Introduction Figure 3 A walk through the woods. Guerneville. Structurally. one will observe both gradual and dramatic transitions in structure and function. photosynthetic capacity. During the winter. photosynthetic capacity of leaves changes rapidly during this period. than a temperate or tropical forest. one observes a stand with fewer tree species. like the ponderosa pine ecosystem of the western United States or oak woodland ecosystems in Mediterranean climates. As stomata open to allow CO2 to diffuse into the mesophyll. Biophysics. water is lost. Armstrong Redwoods State Preserve. stomatal conductance. Rapid changes in biological activity and structure occur as leaves expand. Ian McCully. the forest canopy is a patch-work of dense and clumped young trees. During the summer. nodes elongate. the forest may be leafless or dormant and respiring. rootshoot allocation and resource acquisition (e. maximum stomatal 6 . Coincidently. as photosynthesis. as chloroplast with nitrogen-rich RUBP are constructed. Unseen by the naked eye is functional complexity. tall and solitary old trees and a mat of shrubs and herbs in and around gaps. roots grow and reproductive organs emerge. CA. open spaces. respiration. photo. competition and natural selection act as governors on the ultimate rates of photosynthesis and transpiration that a leaf can achieve.ESPM 129. gradual changes in canopy structure. Biometeorology. Walking through forests in seasonally dry climates.

3) vertical distribution of leaf area. Important attributes of a plant canopy that relate to mass and energy exchange. Dennis Baldocchi Instructor Lecture 1. Biometeorology. This is because many structural and functional properties of plant canopies alter: 1) wind and turbulence within and above the canopy. houses and toilets in the city? In this lecture we focus on the physical attributes of plant canopies and how they relate to biometeorological variables and processes. Understanding complexity in canopy structure and function are key to quantifying carbon dioxide and water vapor exchange of forest stands. spherical?. planophile. For example. canopy microclimate and ecosystem physiology and functioning include: 1) leaf area index of the canopy (the amount of leaf area per ground area). unless it is accompanied with information on canopy architecture. clumped or regular fashion?) 5) seasonal variation of leaf area (is the canopy evergreen or deciduous?) 6) leaf angle distribution (are leaves erect. experience water deficits. shrubs. by exerting drag. Such a folly would be equivalent to trying to study demographics of a city without knowing the population. the face of the landscape changes yet again. Leaves re-translocate nitrogen back to stems. 1995). how could you estimate the water use of San Francisco without knowing the number of people. With the approach of autumn.ESPM 129. are they azimuthally symmetric or asymmetric?) 7 . Architecture describes growth patterns and forms of stems. I define a plant canopy as an amalgam of herbs. plant structure and function. 2) the interception and scattering of photons throughout the canopy. 2) shape and size of leaves (needles vs planar. L1. climate. 4) the physiological resistances to water and CO2 transfer and 5) the biochemical capacity to consume or respire carbon dioxide. acclimate. Any study on canopy microclimate or mass and energy exchange is essentially worthless. information that is used in models that predict and diagnose weather. Introduction conductance and physiological capacity occur as leaves age. biogeochemical cycling and forest dynamics. plants and underlying soil that exists on a landscape. 4) spatial distribution of leaves (are they dispersed in a random. Physiognomy is concerned with the shape of crowns. projected vs surface area of needles and shoot to total needle area). 3) the heat load on leaves and the soil. they senesce and they drop from the trees. are eaten or drop due to prolonged drought. In a broad sense.4 Physical Attributes of Plant Canopies Reviews on the topic of canopy structure define several specific terms (Parker. Organization relates to the statistical distribution of canopy components in time and space and texture refers to the crown units of the overstory. their photosynthetic capacity diminishes.

tap). clumped. C4. Umbra and penumbra (full or partial shade). Otherwise the inferior leaf is exposed to partial or penumbral shade. respiration. The interception of light depends on leaf orientation. native. Blue oak leaves (Quercus douglasii). accessible water and nutrient volume 18) history and type of disturbance (recent fires. even aged. mixed aged) 15) exposure/acclimation (sunlit/shaded. and how clumped the leaves or needles may be. CAM). 8 . thickness. leaf’s energy balance. annual/perennial) 14) age structure (disturbed/undisturbed. 12) photosynthetic pathway (C3. photosynthesis and heating a leaf. Dennis Baldocchi Instructor Lecture 1. Figure 4. woody/herb. If a leaf is big enough to block the solar disk. clumping. plowing. The thickness of the leaf boundary layer affects the rate diffusion of trace gas to and from the leaf. the reflectance and transmittance of light. 17) rooting depth. plantation. conical. ellipsoidal. relative to the sun. plus the production of secondary compounds like isoprene. The optical properties of leaves affect how much intercepted radiation is available for evaporating water. 11) spatial distribution of plants (random. 13) plant habit (deciduous/evergreen. functional types) 10) stem density (stems per hectare). full shade is cast. rows. Biometeorology.ESPM 129. re-planting) Different attributes of a plant canopy influence the state of the atmosphere and components of mass and energy exchange in various ways. Leaf size. root architecture (fibrous. agriculture. Leaf or needle clumping. Introduction 7) canopy height (short and aerodynamically smooth vs tall and aerodynamically rough) 8) crown volume and shape (vertical and horizontal dimensions. spherical) 9) plant species (species number. as viewed by another leaf. The temperature of a leaf governs kinetic rates of many important biochemical processes like photosynthesis. 16) woody biomass area index (silhouette woody biomass per unit area). regular). logging. shape and orientation affect: 1) 2) 3) 4) 5) the properties of the leaf boundary layer. angle).

The structure of a plant canopy is not static with time. many years of needles will coexist. so there is an annual cycling of foliage. 9 . Evergreen shed older leaves after new leaves unfold.g. on the other hand. It will also affect the efficiency of photosynthesis. Introduction Growth form and geometry of a canopy or group of plants affects mass and energy exchange by how it traps photons. It can vary over the course of a year and over the course of the plant’s lifespan. Evergreeness and deciduousness are two examples of seasonal behavior by plants. This means they absorb more solar energy and hence have more energy available to evaporate water and heat the air. with greater capacity being associated with the deciduous species. A quantitative understanding about how plant functional and structural attributes affect the canopy microclimate and mass and energy exchange can be gained by examining the Conservation of Mass equation. Conifers also reside on soils with lower nutrient availability (Sprugel. Dennis Baldocchi Instructor Lecture 1. 1989).ESPM 129. as in the boreal forest. for example. The rates of sensible heat and the reflectivity of a forest differ markedly if it has leaves or not. Biometeorology. On a shoot of a conifer. exerts drag and alters physiological functioning. exert a stronger resistance to water transport through their xylem. So taller plants may impose stronger physiological restraints on mass and energy exchange than may shorter plants. The deciduous type leaf is more productive and its dominance on the landscape is more common when nutrients and water is plentiful. Tall plants. Evergreen type often occurs in habitats where carbon assimilation is restricted by unfavorable conditions. Tall plant stands also trap photons more efficiently. Plant function. as identified by its photosynthetic pathway will affect its stomatal conductance and the partitioning of energy into evaporating water and generating heat. hence no reason to become dormant and drop leaves. Their photosynthetic capacity diminishes with age. so they are optically darker. A simplified version of the conservation of mass can be used to demonstrate that the net flux density (moles m-2 s-1) of carbon dioxide or water vapor between a forest and the atmosphere (F) can be estimated by integrating the source-sink strength with respect to height (S(z)): F   S ( z )z (1 0 h This assumption is valid as long as the forest is horizontally homogeneous and the environmental conditions are not varying. But it can also occur in tropical regions where there is essential little seasonality. Tall plant stands are aerodynamically rougher. Quercus) can differ by a factor of two. We also know that the photosynthetic capacity of co-occurring deciduous and evergreen plants of the same genus (e. so turbulent mixing and transport is more efficient. The seasonal pattern of having or dropping leaves has dire impact on mass and energy exchange.

Ci: biochemical capacity Characteristic Structural or Functional Attribute Primary Impacts on Carbon.C4.. projected/surface area. Nobel. : albedo or reflectivity. Horn. Water and Energy Fluxes Leaves Photosynthetic pathway Leaf size/shape C3. Norman.. Gs Ga. Table 1 Structural and functional attributes of leaves. physiological sink capacity (Ci) and photon transport through leaf mesophyll and canopy foliage (P(0). plants and plant stands and their impact on carbon. planophile Symmetric/asymmetric Sunlit/shaded. Campbell. individual plants and plant stands impact carbon. P(0): light transmission through a leaf or canopy.CAM. Using Equation 1 as a framework. It is inversely proportional to the sum of the aerodynamic (ra) and stomatal resistances (rs): F (C ( z )  Ci )  S ( z)  a ( z) z ra  rs (2 For CO2. water and energy fluxes (Baldocchi et al.  10 . Introduction Conceptually. water and energy exchange through their impact on boundary layer (Ga) and surface conductances (Gs).transmittance. 1971. P(0) Leaf inclination angle distribution Leaf azimuthal angle distribution Exposure Optical properties P(0) P(0) Ci. emittance Ci . 1999. 2002. As this course develops over the course of this semester we focus on much of the material presented in this table in greater detail. Dennis Baldocchi Instructor Lecture 1.ESPM 129. 1980). Gs: surface conductance. their attributes and how these two features impact mass and energy exchange of plant canopies and affect the local microclimate. the daytime sink strength in a layer of canopy is determined by the balance between a biochemical and physiologically-limited demand of leaves and the diffusionallimited supply from the atmosphere and through the leaf boundary layer (Farquhar et al. acclimation Reflectance. Ga: aerodynamic conductance. 1980). erectophile. Biometeorology. the source-sink strength of vegetation is proportional to leaf area density (a(z)) and the differences between the scalar concentration in the atmosphere (Ca) adjacent to leaves and that inside the leaves (Ci). penumbra/umbra Spherical. Table 1 presents a summary of key leaf and plant characteristics. one can identify how physical and functional attributes of single leaves. Gs. the probability of beam penetration) (Table 1). Ross. 1989. maximal stomatal conductance Needle/planar/ shoot.

logging. P(0) Ga. Ga.ESPM 129. agriculture. skewed Evergreen/deciduous. regrowth Spatial distribution of plants Amount of woody biomass Exposure.Ci. mixed stand.  Gs Gs. Ci Forest Stand Leaf area index Vertical distribution of LAI Seasonal variation of LAI Age structure Stem density Woody biomass index Topography Site history Open. supply Ci . Ci P(0) Ga. clumped.  of CO2 to chloroplast.Gs. water balance Fires. P(0) Ga. Ga Ga. Gs.  Ga. plantation. winter or drought deciduous Disturbed/undisturbed. Gs. Biometeorology. Gs Ga. growing in different climates have different structural properties. ellipse.  As we walk through the country-side it become readily obvious that different types of ecosystems. regular Evergreen/deciduous. optical properties. Gs Ga. plowing.Gs. closed Uniform. Introduction Leaf thickness Photosynthetic capacity. Gs. cylinder monoculture. Dennis Baldocchi Instructor Lecture 1. site history. plant water relations Hydraulic Conductivity P(0).10 m) tall (> 10 m) Accessible water and nutrients. To get a 11 . sparse. Ga. regrowth P(0). Stomatal conductance capacity Amphistomatous/hypostomatous Gs Stomatal distribution Plants/Trees Crown volume shape Plant species Spatial distribution of leaves Plant habit Plant height Rooting depth Leaf area/sapwood ratio Cone. annual/perennial Short (< 0. P(0) Ga. woody herbaceous. functional type Random. Gs. Ga P(0).

2-0.6 0-7 0.2-1..07-0.5-1 0.ESPM 129. Introduction sense of how micrometeorological and plant canopy attributes of different ecosystems compare.01 7 by 7 0.10 10 by 10 0-2 uniform/ planophile/ clumped 0.5 3-15 1-6 0-3 1-6 4 0. 2001).1-0.2 0.5 Zo(m) 2-2.5 variable variable 0. Table 2 Summary of Plant Attributes Parameter grass/ cereal 0-5 1.05 0.15-20 0. 2003. Saugier et al.10 4 by 4 0-2 uniform/ planophile/ clumped 0.03-0.20 0. Breuer et al.4-0. zo is aerodynamic roughness length.5-4 1-3 1 - Rooting Depth 1-8 0.3-10 variable 0.02-0.4 0.10 0.05 - LAI max 4-7.12-0.2-0.0 shrub Broadleaved crop 0-6 0.1 < 0.1-1 savanna LAI fraction of ground cover understory LAI leaf normal orientation fraction of stems leaf size (m) crown size 1-7 0.4 Height (m) 30-50 15-50 2-20 < 0.8 needle leaved forest 1-10 >0.5 0. Dennis Baldocchi Instructor Lecture 1.15-0. Myneni et al.18 0.05 0.3 0.2-0.05 uniform uniform 0-5 uniform/ erectophi le 0..1-0. we draw on compiled lists by the author and assorted references (Breuer et al.2 0. Biometeorology. biome Tropical forests Temperate forests Boreal forests Arctic tundra Mediterranean shrubland Crops Tropical savanna Temperate grassland desert albedo 0. 2003.5 0.5 0.3-9 0.25 0.4 Broadleaved forest 3-7 >0.1-1 < 0.14 0.7 erecto phile 0.10 Table 3 Survey of Biophysical parameters. Saugier et al.2-15 12 .5-3 0.05 0..12-0. 1997.15-0.10 0. 2001.1-0.2-0.8 1-6 0.2 1-3 1-3 < 0.8 0.5-1.5-2 0.

5 1-3 0. Introduction Table 4 Ecophysiological Parameters by Biome. Breuer et al.5 1-1.. 2001. Points to Ponder: Does biodiversity and species matter when considering plant microclimates and mass and energy exchange? How does the plant microclimate and mass and energy exchange differ by substituting an evergreen forest with a deciduous forest?. by substituting a forest with a grassland? How has the evolution of the Earth’s climate affected the evolution of plant physiognomy and ecosystem structure and function? Does leaf size. Biometeorology. ga is aerodynamic conductance.5-4 RUE G(DM)/ MJ (PAR) 0. correlate with water balance and climate? Summary   Physical attributes of a canopy include leaf area index. RUE is radiation use efficiency for photosynthesis.2 0.2 0. Physiological attributes of a canopy include photosynthetic pathway.9 1 0..5-1 1.5 0.4-1.5 to -2 -12 to -15 -40 -4 to -25 -13 to -20 Max CO2 flux.8 Having a general knowledge of these features will be critical later in the course when we draw on these features to compute rates of transpiration.ESPM 129. evaporation and photosynthesis. for instance.5 0. biome Units Tropical forests Temperate forests Boreal forests Arctic tundra Mediterranean shrubland Crops Tropical savanna Temperate grassland Max gs mol m-2 s-1 0. Saugier et al. canopy height. day mol m-2 s-1 -25 -25 -12 -0.4-1 ga mol m-2 s-1 0-4 1-4 10 Max CO2 flux.2-1. and leaf size. night mol m-2 s-1 5-8 1-6 0-4 1-2 6-7 2-8 2-5 0.5-1 0. Dennis Baldocchi Instructor Lecture 1. 2003.1-4 0. gs is stomatal conductance.2-1 0.3-0. stomatal distribution (amphi or hypostomatous) 13 .

Breuer L. Horn HS (1971) The Adaptive Geometry of Trees Princeton Univeristy Press. 237-293. 1380-1393. Norman JM. HA Mooney). Saugier B. Mooney H (2001) Estimations of global terrestrial productivity: converging toward a single number.6 Educational Resources Key Journal in the Field Main Journals Agricultural and Forest Meteorology Boundary Layer Meteorology Journal of Geophysical Research. Biogeosciences Plant. Crown Architecture. Myneni RB. water and energy fluxes of temperate broadleaved deciduous forest. Nemani RR. Introduction  Structural and functional properties of plant canopies alter: 1) wind and turbulence within and above the canopy. 22. pp. 465-479. 4) the physiological resistances to water and CO2 transfer and 5) the biochemical capacity to consume or respire carbon dioxide. Ecological Modelling 169. Academic Press. Ross J (1980) The Radiation Regime and Architecture of Plant Stands. and Leaf Size. L1. Eckhardt K.  References/Bibliography Baldocchi DD.ESPM 129. Ieee Transactions on Geoscience and Remote Sensing 35. 1065-1077. In: Forest Canopies. Tree Physiology. W Junk. by exerting drag. The Hague. Running SW (1997) Estimation of global leaf area index and absorbed par using radiative transfer models. Frede H-G (2003) Plant parameter values for models in temperate climates. 543-557. pp. 73-106. Gu L (2002) Influences of structural and functional complexity on carbon. Sprugel DG (1989) The Relationship of Evergreenness. 3) the heat load on leaves and the soil. In: Plant Physiological Ecology. J Roy BS. Nobel PS (1999) Physicochemical and Environmental Plant Physiology Academic Press. Campbell GS (1989) Canopy Structure. Dr. American Naturalist 133. Biometeorology. Parker GG (1995) Structure and Microclimate of Forest Canopies. Cell and Environment Journals with Occasional Articles 14 . Roy J. Dennis Baldocchi Instructor Lecture 1. In: Terrestrial Global Productivity (ed. Wilson KB. 2) the interception and scattering of photons throughout the canopy. The physical and physiological attributes of a canopy can vary in space (vertically and horizontally) and in time (seasonally and decadally).

edu.html Biospheric Aspects of the Hydrological Cylcle.org/AMS/ American Geophysical Union: http://www.edu/jackson/ecophys/ International Society of Biometeorology: http://www.ESPM 129.ch/web/wcp/agm/agmp.mq. Bonan. 2002. Cambridge University Press 15 . Ecophysiology. Commission for Agricultural Meteorology: http://www.ca/~csam/ Key Text books.au/ISB/ American Agronomy Society: http://www.de/~bahc/ Canadian Society of Agricultural Meteorology: http://www. Arya.wmo. 1988. P. Introduction to Micrometeorology. Introduction Global Change Biology Biogeosciences Journal of Applied Meteorology Tree Physiology Journal of Hydrology Water Resources Research Oecologia Ecological Applications Ecology Quarterly Journal of the Royal Meteorological Society Atmospheric Environment International journal of Biometeorology Key Web pages Key Societies and Organizations with Activities in Biometeorology and Agricultural and Forest Meteorology: American Meteorological Society: http://www.edu/ Physiological Ecology Section: http://www.es.agronomy.agu.org/ International Society for Agrometeorology: http://www. Ecohydrology.org/ Ecological Society of American: http://esa.sdsc.biology. Micrometeorology. S.pik-potsdam. IGBP: http://www. Biometeorology.agrometeorology.duke. G.ametsoc. Ecological Climatology.uoguelph. Environmental Physics.org/ World Meteorological Organization. Biometeorology. Dennis Baldocchi Instructor Lecture 1. Academic Press.

Physiochemical and Environmental Plant Physiology. B. B. Ehleringer. Introduction Campbell.C. Specialized Proceedings Andreae. 1979. and J. Atmospheric Boundary Layer Flows: Their Structure and Measurement. Stull. An Introduction to Environmental Biophysics. Microclimate. Panofsky. Exchange of Trace Gases between Terrestrial Ecosystems and the Atmosphere. Jones. Nobel. J.A. Schimel. Dutton. Ecohydrology.A. R. Wiley. Reidel Pub. and J. and J.J. An Introduction to Boundary Layer Meteorology. N. M. J. 1998. Gerber. Finnigan. Joseph.G. Blad and S. 2002.J. D. Metheun. St. J. 1991.B. 252 pp.L. Prentice Hall. Wiley and Sons. 1999.L. Kluwer Academic Publishers. and C. ASAE Monograph. 397 pp. Eagleson P. Springer-Verlag. Tindall.J. Springer. Principles of Environmental Physics. Plants and Microclimate. Scaling Physiological Processes: Leaf to Globe. Oxford Press. The Atmosphere Boundary Layer.M.ESPM 129.G. 1987. W. Berlin. 1992. Evaporation into the Atmosphere. Kunkel. Cambridge Press Kaimal. 1975. Wiley and Sons. 1982. 1992.R. Garratt.F.H. Dahlem Workshop.S. and Norman. H.H. Field. Rosenberg. 1993.S. MI Brutsaert. Unsaturated Zone Hydrology for Scientists and Engineers.R. 16 . Atmospheric Turbulence. Larcher W. J. 1994. 1983. Modification of the Aerial Environment of Plants. J. 1989. Biometeorology. T.B. and D.624 pp.R.A. 1990. 1983.A.B. Barfield. P. Arnold. E.S. J. Monteith. Grace. J. Boundary Layer Climates. Plant-Atmosphere Relations. Cambridge Press. Cambridge University Press. Academic Press Oke.Verma. 1984. Physiological Plant Ecology. Academic Press. Dennis Baldocchi Instructor Lecture 1. and J.O. J. H. 1988. Unsworth.R..S. J. Chapman and Hall. and M.

1994 Hutchison. Introduction Gash. and P. Tenhunen. 1988. 1994. Woodward. 1986. B. J. New York : Oxford University Press. Blackwell. Cambridge Methods Fritschen. Roy.. Victoria. D. R. B. Noormets Phenology book Ross. Trace Gases and the Biosphere. INRA. L. Mooney. Sharkey. J. Ecosystem Dynamics and Biogeochemistry in Complex Landscapes. Flow and Transport in the Natural Environment: Advances and Applications. 1999. Von Caemmerer. Griffiths.L. Roberts and R. 1993. 1992. J. J. 1979. Crop Struction and Light Microclimate.B. The Hague. Nobre. J.F (eds). 2000.W. Hicks. Grace. Jarvis. 1993. Biochemical models of leaf photosynthesis. C. W. J.A.S.D. 1981. Environmental Instrumentation. and D.T. France. Terrestrial Global Productivity. Trace Gas Emission by Plants. Sinoquet. et al. 1996. Springer-Verlag. NCAR. Schimel. The Radiation Regime and Architecture of Plant Stands. E. Forest-Atmosphere Interactions. Chapman and Hall. Denmead. D. Amazonian Deforestation and Climate. Ford and P.. and L.A.A. Integrating Hydrology. T. Moore. Climate and Plant Distributions. 1991. C. JHC. Dennis Baldocchi Instructor Lecture 1. J. Springer Verlag. I. Saugier. 1985. Biometeorology. Oxford.D. Holland and H. Junk.O.ESPM 129. Gay. Mooney. Dahlem Konferenzen Valentini Carbo Europe Book Varlet-Grancher. Dr. Wiley.G. Reidel. Hall..J. 17 . Steffen. Bonhomme and H. Photosynthesis and Production in a Changing Environment: a Field and Laboratory Manual. Plants and Their Atmospheric Environment. B. 2001. Kabat. and B. Academic Press. H. Academic Press. 1980. CSIRO Publishing. and O. S. E. Handbook of agricultural meteorology.

Sestak. deVries.. Heat and Mass Transfer in the Biosphere. P. Dennis Baldocchi Instructor Lecture 1. New York. W. and H. Pasquill. Mooney and P. J. Plant Photosynthetic Production: Manual of Methods.. John Wiley and Sons Geiger. John Wiley and Sons. 230 pp. The Structure of Atmospheric Turbulence. Climate and Life.L. 18 . Academic Press. Plant Physiological Ecology: Field Methods and Instrumentation. Afgan. 497 pp.H. R.D. Boston Lowry.A. 1960. 1975. 1972. Vegetation and the Atmosphere. Prediction and measurement of Photosynthetic Productivity. Rundel. II.W. New York. Academic Press. CW. Gardner. London Munn. Pudoc. London. J.A. I. Z. 1975. 1971.A. The Hague. 1966.G. Introduction Matson. MIT Press. Statistical Hydrodynamics. Physical Microclimatology. Gardner and W. 1974. Academic Press. F. R. Monin. The Climate Near the Ground. Classic Books Baver. Descriptive Micrometeorology.P. F. American Meteorological Society. J. Workshop on Micrometeorology. Ehleringer. H. L. Pergamon Press.W.I. 1985. W Junk. 1964. Yaglom. W. J.A.ESPM 129. Biometeorology. and A. 1975. Cambridge. Harriss.. University of California. Academic Press.S. Vegetation and the Atmosphere.A. 1973. Soil Physics. 1961. Monteith. 1974. Pearcy. A.H. Rose. 1975. Harvard University Press. Lumley. D.C.M. Weather and Life: an Introduction to Biometeorology. M.R. New York. Atmospheric Diffusion.E. Haugen et al. Setlik et al. Chapman Hall. and R. Monteith. Panofsky. J. Catsky and P.L. Brooks.A. 1969. Jarvis. and N. 1966. Budyko. Wiley. Davis. Agricultural Physics. Biogenic Trace Gases: Measuring Emissions from Soil and Water. Dr. R.L. Blackwell. John Wiley and Son. 1995. 1970.

1953. Introduction Sutton. Dennis Baldocchi Instructor Lecture 1.G. McGraw-Hill.ESPM 129. Micrometeorology. 19 . O. Biometeorology.

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