BOREAS TE-08 Aspen Bark Chemistry Data

Summary

The BOREAS TE-08 team collected pigment density data from aspen bark and leaves 
from four sites within the BOREAS SSA from 24-May-1994 to 16-Jun-1994 (IFC-1), 
19-Jul-1994 to 08-Aug-1994 (IFC 2), and 30-Aug-1994 to 19-Sep-1994 (IFC-3). One 
to nine trees from each site were sampled during the three IFCs. Each tree was 
sampled in five different locations for bark pigment properties: basal stem 
section, which was any bark sample taken below one-half the tree height; upper 
stem section, which was any bark sample taken from the main stem above one-half 
the tree height; bark taken from branches up to 3 years old; a 2-year old branch 
segment; and a 1-year old branch segment. Additionally, a limited number of 
leaves were collected. Bark samples were removed from the stem of the tree, 
placed in ziplock bags, and transported to UNH, where they were processed and 
analyzed by a spectrophotometer. 

In each data file, samples are identified by Site, date, Tree#, and Sample 
Location (see 1st paragraph above). Pigment density values are normalized to 
mg/m2. Density values for the following pigments are provided: Chl a, Chl b, 
Total Chl (Chl a+b), Carotenoids, Chl a to b ratio, and the Total Chl to 
carotenoids ratio. 

Table of Contents

   *  1 Data Set Overview
   *  2 Investigator(s)
   *  3 Theory of Measurements
   *  4 Equipment
   *  5 Data Acquisition Methods
   *  6 Observations
   *  7 Data Description
   *  8 Data Organization
   *  9 Data Manipulations
   *  10 Errors
   *  11 Notes
   *  12 Application of the Data Set
   *  13 Future Modifications and Plans
   *  14 Software
   *  15 Data Access
   *  16 Output Products and Availability
   *  17 References
   *  18 Glossary of Terms
   *  19 List of Acronyms
   *  20 Document Information

1. Data Set Overview

1.1 Data Set Identification

BOREAS TE-08 Aspen Bark Chemistry Data

1.2 Data Set Introduction
 
These data are pigment densities for aspen bark samples and aspen leaf samples 
collected from four sites within the BOReal Ecosystem-Atmosphere Study (BOREAS) 
Southern Study Area (SSA) during the three Intensive Field Campaigns (IFCs) of 
1994. Each tree was divided into five different bark sampling locations: basal 
stem, upper stem, branch, 2-year old branches, and 1-year old branches. 
Additionally, several leaves were also measured for pigment density for 
comparison to bark data.

1.3 Objective/Purpose

The purpose of this work was to understand the potential influence of aspen bark 
photosynthesis on bark spectra and on the carbon budget of boreal aspen stands.

1.4 Summary of Parameters

Each data set contains the sample location, the chlorophyll (chl) A density, chl 
B density,  total chl density, carotenoid density, ratio of chl A/chl B, and the 
ratio of total chl/carotenoid.

1.5 Discussion

The bark of aspen (Populus tremuloides) is green and photosynthetic. The 
phenomenon of bark photosynthesis in aspen has been studied extensively; it has 
been shown that bark photosynthesis can account for between 5-40% of whole tree 
photosynthesis. BOREAS used remote sensing systems as a primary means for data 
collection to better understand the ecosystem-atmosphere interactions. Aspen is 
a dominant forest cover type, especially in the SSA. Therefore, bark spectral 
properties could significantly affect data collected and analyzed by remote 
sensing instruments in BOREAS. The photosynthetic pigment content of the bark 
affects the spectral properties, and the pigments densities were quantified.

This study was undertaken to quantify the pigment and spectral properties of 
aspen bark samples (spectral data are presented in separate files with a 
separate documentation file). The results of this study provide an initial 
understanding of the potential influence of aspen bark photosynthesis on 
remotely collected data and carbon budget for aspen stands. A more intensive 
study should be conducted to scale lab-based spectral measurements to airborne 
and spaceborne platforms. Additionally, direct measurements of bark 
photosynthesis would be required to determine the significance to the boreal 
carbon budget.

The quality of the pigment data is believed to be good. Comparisons with data 
reported by other researchers who have studied aspen bark photosynthesis show 
similar results. Additionally, leaf pigment samples correspond to measurements 
taken by other BOREAS researchers, showing that the bark samples should be of 
good quality.

1.6 Related Data Sets

BOREAS TE-08 Aspen Bark Spectral Reflectance Data
BOREAS TE-09 NSA Leaf Chlorophyll Density
BOREAS TE-10 Leaf Chemistry Data

2. Investigator(s)

2.1 Investigator(s) Name and Title

Dr. Slava Kharuk, Scientist

Dr. Barret N. Rock, Associate Professor

2.2 Title of Investigation

Aspen Bark Input in Tree-Atmosphere Interactions

2.3 Contact Information

Contact 1:
Mr. Shannon Spencer
Complex Systems Research Center
University of New Hampshire
Durham, NH 
(603) 862-1792
(603) 862-0188 fax
shannon.spencer@unh.edu

Contact 2:
Dr. Barret N. Rock
Department of Natural Resources
Complex Systems Research Center
University of New Hampshire
Durham, NH 
(603) 862-1792
barry.rock@unh.edu

Contact 3:
Andrea Papagno
Raytheon ITSS
NASA GSFC
Greenbelt, MD 
(301) 286-3134
(301) 286-2039 (fax)
Andrea.Papagno@gsfc.nasa.gov

3. Theory of Measurements

Bark pigment characteristics, primarily chlorophylls a and b, are important 
molecule complexes in the process of photosynthesis and carbon assimilation. 
Therefore, in order to better understand the phenomenon of bark photosynthesis 
and how it relates to the bark spectral properties, pigment extractions were 
made of bark and leaf samples. These samples were taken at the same time and 
place as spectral samples (see BOREAS TE-08 Aspen Bark Spectral Reflectance 
Data).

4. Equipment

4.1 Sensor/Instrument Description

A Beckman DU-7 spectrophotometer was used to make absorbance measurements. 
Calibrated 1-cm quartz vials were used for measurements within the 
spectrophotometer.

4.1.1 Collection Environment

Bark and leaf samples were collected from the field.  Measurements took place in 
laboratory conditions.

4.1.2 Source/Platform

None given.

4.1.3 Source/Platform Mission Objectives

None given.

4.1.4 Key Variables

Chl a, chl b, carotenoid densities.

4.1.5 Principles of Operation

Absorption due to light extinction (see Lichtenthaler, 1987; Gregory, 1989).

4.1.6 Sensor/Instrument Measurement Geometry

None given.

4.1.7 Manufacturer of Sensor/Instrument

Beckman Spectrophotometer, Model DU-7
Beckman Coulter, Inc.
4300 N. Harbor Boulevard 
P.O. Box 3100 
Fullerton, CA 92834-3100
(800) 742-2345
(800) 634-4366 (fax)

4.2 Calibration

4.2.1 Specifications

Absorption is calibrated based on use of a 100% dimethyl sulfoxide (DMSO) blank 
in a standard 1 cm quartz cuvette.

4.2.1.1 Tolerance

None given.

4.2.2 Frequency of Calibration

A 100% DMSO blank was used for calibration once every 10 measurements.

4.2.3 Other Calibration Information

None.

5. Data Acquisition Methods

Bark samples from different locations within the tree were collected and 
analyzed to determine chl a, chl b, total chl (chl a+b), and carotenoid 
concentrations.  At the Paddockwood field site, within a day following 
collection, bark and leaf samples were removed from the tree using a cork borer 
of known diameter.  Bark sections were peeled off the stem or branch wood, 
placed in ziplock bags with wet napkins, and kept cool until samples could be 
processed. These samples were then cut into pieces and added to 4 ml DMSO in 
capped glass vials, a standard procedure described by Lichtenthaler (1987) and 
Hixcox and Israelstam (1979) for chlorophyll extraction. Samples were allowed to 
extract in darkened conditions for 48 hours and were then kept frozen until 
processing could take place at the University of New Hampshire (UNH). Vials were 
kept frozen during transport to UNH and were measured within 1 week of arrival 
(except for IFC-1 samples; see Section 6.1).  

At UNH, the extracted solutions were refrigerated for 30 minutes prior to 
measurement.  The spectrophotometer was calibrated using 100% DMSO in a quartz 
cuvette.  Four ml of extract were placed in a 1-cm quartz cuvette, and 
absorption was measured at four different wavelength positions.  The sample was 
returned to the glass vial.  The quartz cuvette was rinsed between samples with 
80% acetone and the spectrophotometer was recalibrated every 10 samples.  
Extract solution absorbance was measured with a Beckman DU-7 spectrophotometer 
at 470.0 nm, 646.8 nm, 663.2 nm, and 750.0 nm (Lichtenthaler, 1987; Spencer, 
1996).  The results were printed and then entered into a spreadsheet.  
Absorbance values were used to calculate pigment concentrations using standard 
extinction equations reported by Lichtenthaler (1987) (see also Spencer, 1996). 
Absorption at 750.0 nm (value at 750 should be made equal to zero and the 
difference is applied to the other wavelengths) was used to calibrate other 
absorbance values (Middleton, personal communication; Spencer, 1996). Pigment 
concentration values were then normalized to mg/dm2 using the known amount of 
extraction used and the original surface area of the sample extracted.

6. Observations

6.1 Data Notes

Samples from IFC-1 were measured shortly after returning from Canada. However, 
data were erroneous because of a malfunctioning siphon that was initially used 
to fill and rinse the cuvette with the sample solution. This problem was noted 
and corrected. IFC-1 samples had been stored at 4 C and were remeasured in 
early August 1994 following correction of the problem.

The authors conducted some preliminary research on bark area leaf area ratios 
that is not reported here.  This information can be found in Spencer, 1996.

6.2 Field Notes

Samples were collected at field sites, placed in ziplock bags, and kept cool 
until processing. Extractions were conducted at the field lab and were then 
frozen (about 4 C) until they were measured with the spectrophotometer at UNH.

7. Data Description

7.1 Spatial Characteristics

7.1.1 Spatial Coverage

Four sites were sampled during the three 1994 IFCs. Not all sites were sampled 
during each IFC because of destructive sampling logistics. Two BOREAS tower 
sites were used: Old Aspen (SSA-9OA) and Young Aspen (YA). Additionally, the 
originally identified BOREAS YA site was sampled during all three IFCs and is 
identified in these data sets as the Young Aspen-Auxiliary 04 site (YA-AUX04), 
and a non-BOREAS mixed aspen and white spruce site is identified as YA-AUX07. 
One to five trees were destructively harvested during each IFC.

The following is sample collection information at the four SSA locations:

1) SSA-9OA: One tree was harvested during IFC-2. Branch samples only were 
collected during IFC-1, and no samples were collected from the SSA-9OA during 
IFC-3 because of the logistics of destructive sampling.

2) YA-AUX04: Three trees were destructively harvested during each of the three 
IFCs.

3) YA: Five trees were harvested during IFC 2 and 3.

4) YA-AUX07: This is a non-BOREAS site that exists within the BOREAS SSA and was 
established in order to harvest a second mature (>60 yr. old tree) aspen stand 
for TE-08 research. This site was a mixed site of mature aspen overstory and 
white spruce understory. It was located on the property of Snow Castle Lodge 
approximately 3 km N of the SSA-YA site (see Spencer, 1996, for more details). 
One tree was harvested from this site during IFC-3.

The SSA measurement sites and their associated North American Datum of 1983 
(NAD83) coordinates are:

SSA-9OA, site id C3B7T, Lat/Long: 53.62889 N, 106.19779 W, Universal Tranverse 
Mercator (UTM) Zone 13, N: 5,942,899.9 E: 420,790.5.

YA, site id D0H4T, Lat/Long: 53.65601 N, 105.32314 W, UTM Zone 13, N: 
5,945,298.9 E: 478,644.1.

YA-AUX04, site id D6H4A, Lat/Long: 53.70828 N, 105.31546 W, UTM Zone 13, N: 
5,951,112.1 E: 479,177.5.

YA-AUX07, Located 3 km N of SSA-YA on the property of Snow Castle Lodge, UTM 
Zone 13.  This was a mixed site of mature aspen overstory (>60 yrs) and white 
spruce understory.  

7.1.2 Spatial Coverage Map

Not available here.  See Spencer, 1996.

7.1.3 Spatial Resolution

These data are point measurements at the given location.

7.1.4 Projection

None given.

7.1.5 Grid Description

None given.

7.2 Temporal Characteristics

7.2.1 Temporal Coverage

These data were collected from 24-May-1994 to 16-Jun-1994 (IFC-1), 19-Jul-1994 
to 08-Aug-1994 (IFC-2), and 30-Aug-1994 to 19-Sep-1994 (IFC-3).

7.2.2 Temporal Coverage Map

None given.

7.2.3 Temporal Resolution

Each site was visited once.

7.3 Data Characteristics

Data characteristics are defined in the companion data definition file 
(te08bchm.def).

7.4 Sample Data Record

Sample data format shown in the companion data definition file (te08bchm.def).

8. Data Organization

8.1 Data Granularity

All of the bark chemistry data are in one file.

8.2 Data Format(s)

The data files contain ASCII numerical and character fields of varying length 
separated by commas. The character fields are enclosed with single apostrophe 
marks. There are no spaces between the fields. Sample data records are shown in 
the companion data definition file (te08bchm.def).

9. Data Manipulations
  
9.1 Formulae

Absorption data were calibrated with absorption data from the 750 nm band and 
were then input into the extinction equations listed in Section 9.1. These 
values were then normalized for the amount of solution used and the surface area 
of the sample to arrive at a figure in mg/dm2.  See section 9.2.1 for further 
details.

Extinction coefficients are from Lichtenthaler (1987):

[chl a]=12.25A(663.2)-2.79A(646.8)                                   (1)
[chl b]=21.50A(646.8)-5.10A(663.2)                                   (2)
[chl a+b]=[chl a]+[chl b]                                            (3)
[carotenoids]=(1000A(470)-1.82[chl a]-85.02[chl b])/198              (4)

where A(wavelength) is the absorption at the specified wavelength.

9.1.1 Derivation Techniques and Algorithms

Not applicable.

9.2 Data Processing Sequence

9.2.1 Processing Steps

1) Absorption results were entered into a spreadsheet.

2) Absorption at 750.0 nm (value at 750 was made equal to zero and the 
difference was applied to the other wavelengths) was used to calibrate other 
absorbance values (Middleton, personal communication; Spencer, 1996). 

3) Pigment concentration values were then normalized to mg/dm2 using the known 
amount of extraction used and the original surface area of the sample extracted.

4) Absorbance values were used to calculate pigment concentrations using 
standard extinction equations reported by Lichtenthaler (1987) (see also 
Spencer, 1996).

5) As part of its data integration efforts, BORIS staff converted the pigment 
concentration values to mg/m2 to be compatible with other similar measurements.

9.2.2 Processing Changes

None given.

9.3 Calculations

9.3.1 Special Corrections/Adjustments
      
Data were corrected with the measurement at 750 nm because of the purity of the 
DMSO and the possibility for debris in the extract solution. The value at 750 nm 
should be equal to zero for chlorophyll and pigment absorption. If the 
absorption value at 750 nm was greater than 0.01, the sample was rerun or 
discarded.

9.3.2 Calculated Variables

See Sections 9.1 and 9.3.1.

9.4 Graphs and Plots

None given.

10. Errors

10.1 Sources of Error
    
Error could have been created by the calibration discussed in Section 9.3.1. The 
extraction solution should have been filtered to avoid this problem. However, 
discussions with other BOREAS teams measuring chlorophyll concentration showed 
TE-08s calibration method discussed in Section 9.3.1 to be an acceptable 
practice.

10.2 Quality Assessment

Several tests were conducted to be sure that consistent, reliable data were 
collected by the instrument.  The tests included comparisons of light absorption 
to a standard of 100% DMSO and comparisons of results with those of TE-10.  Our 
data appear to be consistent with TE-10s results.

10.2.1 Data Validation by Source

10.2.2 Confidence Level/Accuracy Judgment

The data appear to be good. Leaf chlorophyll data were checked against those of 
TE-10 and found to be not significantly different.

10.2.3 Measurement Error for Parameters

None given.

10.2.4 Additional Quality Assessments

All data were checked for potential problems and discarded if problems were 
evident.

10.2.5 Data Verification by Data Center

Data were examined for general consistency and clarity.

11. Notes

11.1 Limitations of the Data

These data are calculated on an area basis rather than a weight basis because of 
the bark tissue heterogeneity.

11.2 Known Problems with the Data

None given.

11.3 Usage Guidance

None given.

11.4 Other Relevant Information

None given.

12. Application of the Data Set

These data provide information on the chlorophyll density of aspen bark. This 
information can be scaled up to the whole tree level to determine the amount of 
whole tree chlorophyll found in the bark tissue. This gives a preliminary 
indication as to the importance of bark photosynthesis on a whole tree/stand 
level. More work should be done in this area to determine bark photosynthesis 
significance to aspen carbon dynamics. Gas exchange measurements should be 
conducted on aspen bark during different times of the year. See Spencer, 1996, 
for more discussion.

13. Future Modifications and Plans

These data have been presented in more detail in Spencer, 1996.

14. Software

14.1 Software Description

Quattro Pro 4.0 was used for most analyses and then Excel 5.0 was used for the 
final and summative analyses. For a statistical package TE-08 used Stata Pro 
4.0.

14.2 Software Access

None given.

15. Data Access

Ms. Beth Nelson
BOREAS Data Manager
NASA GSFC
Greenbelt, MD
(301) 286-4005
(301) 286-0239 (fax)
Elizabeth.Nelson@gsfc.nasa.gov

15.2 Data Center Identification

See Section 15.1.

15.3 Procedures for Obtaining Data

Users may place requests by telephone, electronic mail, or fax.

15.4 Data Center Status/Plans

The TE-08 bark chemistry data are available from the Earth Observing System Data 
and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed 
Active Archive Center (DAAC).  The BOREAS contact at ORNL is:

ORNL DAAC User Services
Oak Ridge National Laboratory
(865) 241-3952
ornldaac@ornl.gov
ornl@eos.nasa.gov


16. Output Products and Availability

16.1 Tape Products

None.

16.2 Film Products

None.

16.3 Other Products

Tabular ASCII file.

17. References

17.1 Platform/Sensor/Instrument/Data Processing Documentation

Beckman Spectrophotometer Manual, Beckman Spectrophotometer, Model DU-7, Beckman 
Coulter, Inc.,Fullerton, CA 92834-3100.

17.2 Journal Articles and Study Reports

Gregory, R.P. 1989. Photosynthesis. Chapman and Hall. NY, NY. 160 pp.

Hixcox, J.D. and G.F. Israelstam. 1979. A method for the extraction of 
chlorophyll from leaf tissue without maceration. Can. J. Bot. 57:1332-1334.

Lichtenthaler, H.K. 1987. Chlorophylla and carotenoids:  pigments of 
photosynthetic biomembranes.  Methods in Enzymology. 148:349-382.

Rock, B.N. et al. High-spectral resolution field and laboratory optical 
reflectance measurements of red spruce and eastern hemlock needles and branches.  
1994. Remote Sensing of Environment. 47:176-189.

Sellers, P. and F. Hall.  1994.  Boreal Ecosystem-Atmosphere Study:  Experiment 
Plan.  Version 1994-3.0, NASA BOREAS REPORT (EXPLAN 94).

Sellers, P., F. Hall, H. Margolis, B. Kelly, D. Baldocchi, G. den Hartog, J. 
Cihlar, M.G. Ryan, B. Goodison, P. Crill, K.J. Ranson, D. Lettenmaier, and D.E. 
Wickland.  1995.  Boreal Ecosystem-Atmosphere Study (BOREAS): an overview and 
early results from the 1994 field year.  Bulletin of the American Meteorological 
Society. V76: 1549-1577.

Sellers, P., F. Hall, and K.F. Huemmrich.  1996.  Boreal Ecosystem-Atmosphere 
Study:  1994 Operations.  NASA BOREAS REPORT (OPS DOC 94).

Sellers, P. and F. Hall.  1996.  Boreal Ecosystem-Atmosphere Study:  Experiment 
Plan.  Version 1996-2.0, NASA BOREAS REPORT (EXPLAN 96).

Sellers, P., F. Hall, and K.F. Huemmrich.  1997.  Boreal Ecosystem-Atmosphere 
Study:  1996 Operations.  NASA BOREAS REPORT (OPS DOC 96).

Sellers, P.J., F.G. Hall, R.D.  Kelly, A.  Black, D.  Baldocchi, J. Berry, M.  
Ryan, K.J.  Ranson, P.M.  Crill, D.P.  Lettenmaier, H. Margolis, J. Cihlar, J. 
Newcomer, D. Fitzjarrald, P.G.  Jarvis, S.T. Gower, D. Halliwell, D. Williams, 
B. Goodison, D.E. Wickland, and F.E. Guertin. 1997. BOREAS in 1997: Experiment 
Overview, Scientific Results and Future Directions. Journal of Geophysical 
Research 102 (D24):28,731-28,770.

Spencer, S.L. 1996. Anatomical, Pigment, and Spectral Evidence of Cortical 
Photosynthesis in Populus tremuloides from the Canadian Boreal Region. Master's 
Thesis, Dept. Nat. Res., University of New Hampshire, 186 pp.

Spencer, S.L. and B.N. Rock. 1996. Assessing aspen bark carbon assimilation in 
the boreal region. In Proceedings of 22nd Conference on Agricultural and Forest 
Meteorology with Symposium on Fire and Forest Meteorology. 28 January-2 
February, 1996, Atlanta, Georgia. American Meteorological Society, pp:86-89.

17.3 Archive/DBMS Usage Documentation

None.

18. Glossary of Terms

None.

19. List of Acronyms

    ASCII   - American Standard Code for Information Interchange
    BOREAS  - BOReal Ecosystem-Atmosphere Study
    BORIS   - BOREAS Information System
    CHL     - Chlorophyll
    CD-ROM  - Compact Disk-Read-Only Memory
    DAAC    - Distributed Active Archive Center
    DMSO    - Dimethyl Sulfoxide
    EOS     - Earth Observing System
    EOSDIS  - EOS Data and Information System
    FOV     - Field-of-View
    GSFC    - Goddard Space Flight Center
    HTML    - HyperText Markup Language
    IFC     - Intensive Field Campaign
    NAD83   - North American Datum of 1983
    NASA    - National Aeronautics and Space Administration
    NOAA    - National Oceanic and Atmospheric Administration
    NSA     - Northern Study Area
    OA      - Old Aspen
    ORNL    - Oak Ridge National Laboratory
    PANP    - Prince Albert National Park
    SSA     - Southern Study Area
    TE      - Terrestrial Ecology
    UNH     - University of New Hampshire
    URL     - Uniform Resource Locator
    UTM     - Universal Transverse Mercator
    YA      - Young Aspen
    YA-AUX  - Young Aspen-Auxilliary

20. Document Information

20.1 Document Revision Date(s)

     Written:       21-May-1997
     Last Updated:  09-Feb-1999

20.2 Document Review Date(s)

     BORIS Review:   25-Oct-1998
     Science Review: 26-May-1998

20.3 Document ID

None.

20.4 Citation

Shannon L. Spencer and Barrett N. Rock, both of the Complex Systems Research 
Center at UNH.

20.5 Document Curator

20.6 Document URL

Keywords
Aspen
Bark chlorophyll 
Bark photosynthesis
Chlorophyll
Pigment absorption
Populus tremuloides

TE08_Bark_Chem.doc
03/03/99