Retrieval of Quantitative and Qualitative Information about Plant Pigment Systems from High Resolution Spectroscopy Susan L. Ustin 1, Gregory P. Asner 2, John A. Gamon 3, K. Fred Huemmrich 4, Stéphane Jacquemoud 5, Michael Schaepman 6, and Pablo Zarco-Tejada 7 1University of California Davis 95616 (USA), slustin@ucdavis.edu, 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 Photosynthesis Green Algae Eukaryotes 0% O 2 Prokaryotes 0.2% O 2 21% O 2 Prokaryote cells Green algal symbiont Red algal symbiont
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) carotenoides Energy Transfer (40~50%) Chl b Thermal Energy Transfer (40~50%) Thermal Chl a Emergy Transfer (100%) Fluorescence (650~800nm) Reaction Center Source : Ismaël Moya (LMD-IPSL)
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
chlorophylls Leaf Senescence Follows Consistent Pattern of Pigment Changes Anthocyanin Carotenoids Xanthophylls 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
Variability in Pigment Composition and FieldSpec FR portable spectroradiometer Concentration in Vegetation PIGMENTS LAI LAD EAU CARBON Source : Mid-America Remote Sensing Center - Murray State University
Chlorophyll a (ug/g) 4000.00 3500.00 3000.00 2500.00 2000.00 1500.00 1000.00 Salicornia virginica SAVI pigment Pigment comparison Concentration (phenology) y = 10.816x + 49.339 R 2 = 0.9477 y = 23.815x - 533.35 R 2 = 0.6966 B-Carotene, Fall Spring y = 11.379x + 20.117 R 2 = 0.9907 y = 10.656x + 105.64 R 2 = 0.9937 Xanthophyll, Fall Spring y = 7.3292x - 84.654 R 2 = 0.9076 y = 11.639x - 552.42 R 2 = 0.9658 y = 8.292x + 8.2362 R 2 = 0.9921 y = 8.9612x - 149.11 R 2 = 0.9912 Chlorophyll b, Fall Spring y = 3.181x - 3.221 R 2 = 0.9029 y = 2.8876x + 100.47 R 2 = 0.986 y = 3.0191x - 9.7034 R 2 = 0.9776 y = 3.1251x - 44.803 R 2 = 0.9894 94 Fall Xantho 94 Fall Chlo-b 94 Fall b-caro 94 Spring Xantho 94 SpringChlo-b 94 Spring b-caro 94 Fall Tubs Xantho 94 Fall Tubs Chlo-b 94 Fal Tubs b-caro 95 Spring Xantho 95 Spring Chlo-b 95 Spring b-caro 500.00 0.00 0.00 200.00 400.00 600.00 800.00 1000.00 1200.00 B-Carotene, Xanthophyll, Xanthophyll, Chlorophyll and b, b-carotene Chlorophyll concentrations b Concentrations (ug/g) (μg/g)
Chlorophyll a (ug/g) Spartina foliosa Pigment Concentration (salinity, phenology) 3500.00 3000.00 2500.00 2000.00 1500.00 1000.00 βcarotene Spring Mouth Spring River Fall River b-carotene SPFO pigment concentration (salinity) Xanthophyll Spring Mouth Spring River Fall River Xanthophyll Xanthophyll Chlorophyll b Chlorophyll Spring Mouth b b Spring River Fall River Fall river b-caro Fall river CHLO-b Fall river XANTHO Spring mouth b-caro Spring river b-caro Spring mouth CHLO-b Spring river CHLO-b Spring mouth XANTHO Spring river XANTHO 500.00 0.00 0.00 200.00 400.00 600.00 800.00 1000.00 1200.00 b-carotene, Chlorophyll b, Xanthophyll (ug/g)
Xanthophyll Cycle: Light Mediated Photosynthesis Zeaxanthin Antheraxanthin Antheraxanthin Violaxanthin
Pigment Indexes AVIRIS IMAGE CUBE ANTHOCYANINS CHLOROPHYLL RGB IMAGE: RED=ANTHOCYANINS GREEN=CHLOROPHYLL BLUE=CAROTENOIDS CAROTENOIDS See Rahman et al. 2001 Gamon & Colleagues, From Ustin et al., 2004
01/01/2005 01/01/2004 01/01/2003 01/01/2002 01/01/2001 0.0-0.1 PRI Chlorophyll index [Chl total]/[v+a+z+l] [Chl total]/[v+a+z+l] 2000 1000 0 PRI Chl index Pigments 0.3 0.2 0.1 0 4 3 2 1 4 3 2 1 PAR (μmolesm -2 s -1 ) Air temperature (C o ) Precipitation (mm) 0.0-0.1-0.2-0.3 PAR Air temp. ppt. drought year fire no data 60 40 20 0 200 150 100 50 PRI Chlorophyll index (a) (b) (c) PRI Chl index Pigments Adenostoma fasciculatum Adenostoma sparsifolium 0.4 0.3 0.2 0.1 Mean Diurnal cycle For Month 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 0.00 (a) (b) PRI -0.04 r ²=0.719 P=0.008-0.08 10 15 20 25 30 [Chl t]/([z]+0.5[a]) r ²=0.525 P=0.042 6 8 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 PRI CWR G. Asner et al., In Press Ecosystems CRI
Vegetation Indices Related to Vapor Pressure Deficit 0.90 2.0 NDVI PRI CRI Carotenoid Pigments (CRI) Canopy Greenness (NDVI) Canopy Light-use Water Retrieval Efficiency (μm (PRI) H O; CWR) 2 0.85 0.80 0.75 0.70 0.65 0.60 4500-0.0 2 4000-0.0 4 3500-0.0 6 3000-0.0 8 2500-0.1 0 2000 O h ia, S ite 1 O h ia, S ite 2 M y ric a, S ite 1 M y ric a, S ite 2 M ix e d O h ia - M y ric a VPD Hawai i Volcanoes National Park 1500-0.1 2 0.0 8/1/2004 10/1/2004 12/1/2004 2/1/2005 4/1/2005 0.0024 0.0 2.0 O h ia, S ite 1 0.0022 O h ia, S ite 2 M yrica, S ite 1 0.0020 M yrica, S ite 2 Mixed Ohia - Myrica 1.5 0.0018 VPD 0.0016 0.0014 0.0012 0.0010 0.0008 0.0006 0.0 8/1/2004 10/1/2004 12/1/2004 2/1/2005 4/1/2005 1.5 1.0 0.5 0.0 2.0 2.0 1.5 1.5 1.0 1.0 0.5 0.5 1.0 0.5 Weekly Vapor Pressure Deficit (k Pa) Weekly Mean Vapor Vapor Pressure Deficit (k (k Pa) Pa) Weekly Vapor Pressure Deficit (k Pa) Hawai i Volcanoes National Park Ohia, Site 1 (native) Myrica, Site 1 (n-fixing invasive) Myrica, Site 2 Mixed Ohia-Myrica Vapor Pressure Deficit
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 R d derive the area σ λ 0 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 Mean Spruce Needles Chl a/b Ratio 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 Ch a+b
Spectral Based Approaches: Spectral Identification Methods Reflectance Chlorophyll a Chlorophyll b Foreground/Background Vectors Claudia Castenada & Jorge Pinzon, et al.
Measured & Predicted Pigments Needle Class 1, 2: Chl a Measured Predicted Needle Class 1, 2: Chl b Measured Predicted Regression 95% C.I. Regression R 2 =0.57 R 2 =0.78 Needle Class 3, 4: Chl a Measured Predicted Needle Class 3, 4: Chl b Measured Predicted Regression Regression R 2 =0.50 R 2 =0.42
First strategy: Pigments chlorophyll a chlorophyll b β-carotene
The end S. Knap & N. Knight, 2001, Flora, Harry N Abrams, 80 pages.