Retrieval of Quantitative and
Qualitative Information about Plant
Pigment Systems from High
Resolution Spectroscopy
Susan L. Ustin1,
Gregory P. Asner2, John A. Gamon3,
K. Fred Huemmrich4, Stéphane Jacquemoud5,
Michael Schaepman6, and Pablo Zarco-Tejada7
1University of California Davis 95616 (USA), [email protected],
2Carnegie Institution of Washington, Stanford, CA, USA,
3California State University Los Angeles, CA, USA,
4NASA GSFC, Greenbelt, MA, USA,
5Institut de Physique du Globe de Paris,
6Wageningen University, NL,
7Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, ES
Photosynthesis
B-G Bacteria
0% O2
Photosynthesis
Green Algae
Eukaryotes
Prokaryotes 0.2% O2
Prokaryote cells
Green algal
symbiont
Red algal
symbiont
21% O2
Light Harvesting Complexes (Photosystems I, II)
Photosystem I
PS II
PS II
PS II
P700
RC
Absorption Coefficients for Common Photosynthetic Pigments
Characteristic of:
Blue-Green Bacteria
(cyanobacteria)
Red algae
Characteristic of:
Green algae & all Land
Plants
Photosynthetic pigments: excitation energy transfer
Visible Spectrum (400-700 nm)
Energy Transfer
(40~50%)
carotenoides
Chl b
Thermal
Emergy Transfer
(100%)
Energy Transfer
(40~50%)
Chl a
Thermal
Reaction Center
Source : Ismaël Moya (LMD-IPSL)
Fluorescence
(650~800nm)
Stress: Loss of
Chlorophyll & Increase
in Carotenoids
Chemical Structures of Pigments are Known
β-Cryptoxanthin
Lycopene
α-Carotene
β-Carotene
Xanthphylls:
Lutein
Zeaxanthin
Violaxanthin
Abtheraxathin
Anthocyanin +
glucose
β-carotene
Chlorophyll a, b, d
Leaf Senescence Follows Consistent Pattern of
Pigment Changes
Ì chlorophylls
Ê Anthocyanin
Ê Carotenoids
Ê Xanthophylls
Ê “Brown”
pigment
Wavelength, nm
Pigment Composition Varies between Species,
even Closely Related Ones
Mature Valley Oak (deciduous) vs. Coast Live Oak (evergreen)
Reflectance and Pigment Composition & Concentrations
Ustin et al. 1998
CARBON
EAU
PIGMENTS
LAI
LAD
Variability in Pigment Composition and
FieldSpec® FR portable spectroradiometer
Concentration
in Vegetation
Source : Mid-America Remote Sensing Center - Murray State University
4000.00
3500.00
Chlorophyll a (ug/g)
3000.00
SAVI pigment
comparison
Salicornia virginica
Pigment
Concentration (phenology)
94 Fall Xantho
y = 10.816x + 49.339 y = 11.379x + 20.117
R2 = 0.9477
R2 = 0.9907
y = 23.815x - 533.35 y = 10.656x + 105.64
R2 = 0.6966
R2 = 0.9937
B-Carotene
▲, ▲ Fall
▲ Spring
y = 7.3292x - 84.654
R2 = 0.9076
94 Fall Chlo-b
y = 11.639x - 552.42
R2 = 0.9658
94 Fall b-Caro
y = 8.292x + 8.2362
R2 = 0.9921
94 SpringChlo-b
y = 8.9612x - 149.11
R2 = 0.9912
94 Fall Tubs Xantho
94 Spring Xantho
94 Spring b-Caro
94 Fall Tubs Chlo-b
94 Fal Tubs b-Caro
2500.00
95 Spring Xantho
Xanthophyll
♦, ♦ Fall
♦ Spring
2000.00
95 Spring Chlo-b
95 Spring b-Caro
Chlorophyll b
1500.00
■, ■ Fall
■ Spring
1000.00
y = 3.181x - 3.221
R2 = 0.9029
y = 2.8876x + 100.47
R2 = 0.986
y = 3.0191x - 9.7034
R2 = 0.9776
y = 3.1251x - 44.803
R2 = 0.9894
500.00
0.00
0.00
200.00
400.00
600.00
800.00
1000.00
1200.00
Xanthophyll,
Chlorophylland
b, b-Carotene
concentrations
(ug/g)
B-Carotene,
Xanthophyll,
Chlorophyll
b Concentrations
(μg/g)
Spartina foliosa Pigment Concentration (salinity,
phenology)
SPFO pigment
concentration (salinity)
3500.00
3000.00
βCarotene
♦ Spring Mouth
▲Spring River
▲ Fall River ▲
b-Carotene
Chlorophyll a (ug/g)
▲▲
2500.00
Fall river b-CARO
Fall river CHLO-b
Xanthophyll
▲ ♦ Spring Mouth
▲ ▲Spring River
▲ Fall River
Xanthophyll
Xanthophyll
▲
Fall river XANTHO
Spring mouth b-CARO
Spring river b-CARO
▲
Spring mouth CHLO-b
Spring river CHLO-b
Spring mouth XANTHO
2000.00
1500.00
▲
▲
♦
♦
♦
♦♦
▲
▲
▲
▲
▲ ▲
♦
▲
▲
▲▲
♦ ♦
♦
Chlorophyll b
♦ Spring Mouth
Chlorophyll
Chlorophyll b b
▲Spring River
▲ Fall River
1000.00
500.00
Spring river XANTHO
♦
0.00
0.00
200.00
400.00
600.00
800.00
1000.00
b-Carotene, Chlorophyll b, Xanthophyll (ug/g)
1200.00
Xanthophyll Cycle: Light Mediated Photosynthesis
Zeaxanthin
Antheraxanthin
Antheraxanthin
Violaxanthin
Pigment Indexes
AVIRIS IMAGE CUBE
ANTHOCYANINS
CHLOROPHYLL
CAROTENOIDS
RGB IMAGE:
RED=ANTHOCYANINS
GREEN=CHLOROPHYLL
BLUE=CAROTENOIDS
See Rahman et al. 2001
Gamon & Colleagues,
From Ustin et al., 2004
drought
year
no
data
0
50
0.2
-0.2
Adenostoma
fasciculatum
0.1
4
3
2
1
(c)
PRI
Chl index
Pigments
0.3
PRI
0.0
0.2
-0.1
0.1
01
/0
1/
20
05
01
/0
1/
20
04
01
/0
1/
20
03
01
/0
1/
20
02
Adenostoma
sparsifolium
4
3
2
1
[Chl total]/[V+A+Z+L]
0.4
[Chl total]/[V+A+Z+L]
PRI
Chl index
Pigments
0.3
01
/0
1/
20
01
100
Mean
Diurnal cycle
For Month
0
(b)
-0.1
-0.3
150
Precipitation (mm)
20
fire
0
Air temperature (Co)
40
1000
0.0
PRI
60
Chlorophyll index
2000
200
(a)
Chlorophyll index
PAR (μmolesm-2s-1)
PAR
Air temp.
ppt.
José Alfonso
Silva
Sepúlveda,
2006
Honors
Thesis
CSU-LA
Leaf photochemical reflectance index (PRI)
versus
(a)de-epoxidation of the xanthophyll cycle pigments
normalized to chlorophyll and
(b) total xanthophylls cycle pigments normalized to chlorophyll
0.04
(a)
(b)
PRI
0.00
-0.04
P=0.008
r ²=0.719
-0.08
10
15
20
25
30
[Chl t]/([Z]+0.5[A])
r ²=0.525
6
8
P=0.042
10 12 14 16 18 20 22
[Chl t]/[V+A+Z]
Adenostoma fasciculatum (black circles)
Adenostoma sparsifolium (white circles)
Site: Skye Oaks, California; Chaparral
José Alfonso Silva Sepúlveda,
2006 Honors Thesis
CSU-LA
EO-1 Hyperion Hyperspectral
Physiological Indices
PRI = photochemical reflectance index
CRI = carotenoid reflectance index
NDVI = normalized difference vegetation index
CWR = canopy water retrieval (curve-fitting, not reflectance index)
NDVI
CWR
PRI
G. Asner et al.,
In Press Ecosystems
CRI
Vegetation Indices Related to Vapor Pressure Deficit
0 .9 0
1 .5
0 .8 0
0 .7 5
1 .0
0 .7 0
0 .5
0 .6 5
4- 00 .00 04
PRI
1 .0
3000
-0 .0 8
2500
Hawai’i Volcanoes National Park
1 .0
0 .5
-0 .1 0
2000
0 .5
1 0 /1 /2 0 0 4
1 2 /1 /2 0 0 4
2 /1 /2 0 0 5
O h ia , S it e 1
O h ia , S it e 2
M y r ic a , S it e 1
M y r ic a , S it e 2
M ix e d O h ia - M y r ic a
V P D
0 .0 0 2 2
Carotenoid Pigments (CRI)
1 .5
1 .5
3500
-0 .0 6
1- 05 .01 02
8 /1 /2 0 0 4
0 .0 0 2 4
CRI
0 .0
2 .0
2 .0
h ia , S it e 1
h ia , S it e 2
y r ic a , S it e 1
y r ic a , S it e 2
ix e d O h ia - M y r ic a
P D
0 .0 0 2 0
0 .0 0 1 8
0 .0
4 /1 /2 0 0 5
0 .0
2 .0
1 .5
0 .0 0 1 6
1 .0
0 .0 0 1 4
0 .0 0 1 2
0 .5
0 .0 0 1 0
0 .0 0 0 8
0 .0 0 0 6
8 /1 /2 0 0 4
1 0 /1 /2 0 0 4
1 2 /1 /2 0 0 4
2 /1 /2 0 0 5
Vapor Pressure Deficit
0 .0
4 /1 /2 0 0 5
Mean
Vapor
Pressure
Deficit
Pa)
Weekly
Vapor
Pressure
Deficit
(k(kPa)
O
O
M
M
M
V
2
Canopy
Light-use
Water Retrieval
Efficiency(μm
(PRI)
H O; CWR)
0 .6 0
4- 05 .00 02
Weekly Vapor Pressure Deficit (k Pa)
Canopy Greenness (NDVI)
NDVI
0 .8 5
Weekly Vapor Pressure Deficit (k Pa)
2 .0
Hawai’i
Volcanoes
National
Park
Ohia, Site 1 (native)
Myrica, Site 1
(n-fixing invasive)
Myrica, Site 2
Mixed Ohia-Myrica
Satellite Hyperspectral Physiological Indices vs.
Top-of-canopy Leaf Pigments Measured in the Field
PRI
CRI
PRI
CRI
Fitting Multiple Gaussian to Spectrum to Identify &
Quantify Multiple Pigments
Rd
derive
the area
σ
λ0
CSTARS
Acala Cotton Leaf Reflectance, ASD Data
Whiting et al.
Chronic stress - Crown
Transformation
a
b
c
Michael Schaepman
Norway spruce functional crown parts:
a/ juvenile part
b/ production part
c/ saturation part
Spruce Damage from Austria: Acid Deposition
Chl a/b Ratio
Mean Spruce Needles
Spruce Needle Damage Class
Spruce Branch Samples from Cliff Banninger, Gratz Austria
CSTARS: Pigment Analysis
Chlorophyll Retrieval from Indexes, ANMB, PROSPECT
T
e
s
t
i
n
g
d
a
t
a
Comparison of the RMSE between measured and retrieved Cha+b
Spectral Based Approaches:
Spectral Identification Methods
Reflectance
Chlorophyll a
Foreground/Background Vectors
Chlorophyll b
Claudia Castenada &
Jorge Pinzon, et al.
Measured & Predicted Pigments
Needle Class 1, 2: Chl a
Needle Class 1, 2: Chl b
Measured
Predicted
Measured
Predicted
Regression
95%
C.I.
R2=0.57
Regression
R2=0.78
Needle Class 3, 4: Chl a
Needle Class 3, 4: Chl b
Measured
Predicted
Measured
Predicted
Regression
R2=0.50
Regression
R2=0.42
First strategy: Pigments
chlorophyll a
chlorophyll b
β-carotene
The end
S. Knap & N. Knight, 2001, Flora,
Harry N Abrams, 80 pages.