Estimation of Pyrrolizidine Alkaloids in native and invasive - ITC

89 Pages·2010·3.55 MB·English

Estimation of Pyrrolizidine Alkaloids in native
and invasive weed species of the Netherlands
using reflectance spectroscopy

Fatemeh Eghbali Moghaddam
January, 2010
Course Title: Geo-Information Science and Earth Observation
for Environmental Modelling and Management

Level: Master of Science (Msc)

Course Duration: April 2008 - January 2010

Consortium partners: University of Southampton (UK)
Lund University (Sweden)
University of Warsaw (Poland)
International Institute for Geo-Information Science
and Earth Observation (ITC) (The Netherlands)
GEM thesis number: 2010-05
Estimation of Pyrrolizidine Alkaloids in native and invasive weed species of the
Netherlands using reflectance spectroscopy

by

Fatemeh Eghbali Moghaddam

Thesis submitted to the International Institute for Geo-information Science and Earth
Observation in partial fulfilment of the requirements for the degree of Master of
Science in Geo-information Science and Earth Observation for Environmental
Modelling and Management

Thesis Assessment Board

Chair: Prof. Dr. Andrew Skidmore
External Examiner: Prof. Dr. Terry Dawson  
First Supervisor: Dr. Martin Schlerf
Second Supervisor: Prof. Dr. Andrew Skidmore
Member : M.Sc. Andre Kooiman
Advisor: M.Sc. Sabrina Carvalho

International Institute for Geo-Information Science and Earth Observation
Enschede, the Netherlands
Disclaimer

This document describes work undertaken as part of a programme of study at
the International Institute for Geo-information Science and Earth Observation.
All views and opinions expressed therein remain the sole responsibility of the
author, and do not necessarily represent those of the institute.

Dedicated to my dearest husband Ehsan
For his continuous support
With love and gratitude
Abstract
Pyrrolizidine Alkaloids (PAs) are secondary metabolites which are
frequently found in some genera of genus Senecionea. Senecio species have been
studied extensively for their alkaloid content, which are generally hazardous to
herbivores, and to the fact that some of these species are becoming a plague in The
Netherlands and becoming invasive abroad. Linking plant population biochemistry
variation with differences in spectral reflectance properties is a new and promising
tool to understand and monitor plant population dynamics and plant – soil
interactions because these interactions affect the plants chemical variation.
The overall aim of this research is to find the Pyrrolizidine Alkaloids
spectral signals and correlate PAs concentration from the leaf spectral reflectance.
Different water and nutrient treatments were fashioned on 200 samples of Jacobaea
vulgaris, Senecio inaequidens and Senecio erucifolius to find the potential effects of
the water/nutrients on the reflectance pattern and concentration of alkaloids. An
ASD Integrating Sphere was used to collect the spectral data of their leaves in the
spectroscopy lab in July and August 2009.
The ANOVA test and T-test were applied on the PAs and spectral data to
check the nutrient effects on the PAs concentration and spectral reflectance of the
species. To study the relationship between the species spectral reflectance and the
leaves PA concentrations, PLSR (Partial Least Squares Regression) method was
used to find the important wavelengths related to Pyrrolizidine Alkaloids.
The results of ANOVA test indicated that the PAs concentrations and PAs
chemotypes were significantly different in the species. The results of the T-test
showed that increasing the nutrient led to increasing the absorption of light in visible
domain in both fresh and dry levels thus a shift in red edge to the increased
wavelengths. The results of the PLSR indicated that, there were possibly two
wavebands (2105 nm and 2355 nm) identified by PLSR B coefficients as the
indicators of PAs in Jacobaea vulgaris and one wavelength (710 nm) as indicator
for PAs in Senecio inaequidens.
In fresh level, the best model for Jacobaea vulgaris achieved the highest R2
=0.64 with an RMSE of 42%, the best model for Senecio inaequidens achieved only
R2= 0.14 with an RMSE of 66%. In dry samples, the best model for Jacobaea
vulgaris achieved an R2=0.60 with an RMSE of 44%, the best model for Senecio
inaequidens the highest R2=0.81 with an RMSE of 31%.

Key words: Pyrrolizidine Alkaloids, nutrient effects, Jacobaea vulgaris, Senecio
inaequidens, Senecio erucifolius, T-test, ANOVA test, PLSR.
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Acknowledgements
All the worship and adoration to almighty God, the beneficent, the
merciful, Without His divine grace the successful accomplishment of this research
was impossible.
I am greatly indebted to the European Union through the Erasmus Mundus
scheme for awarding me the scholarship to undertake this study. What a splendid
opportunity I had to study in four European countries. The course would not have
been effective without the commitment of the consortium leaders Prof. Terry
Dawson of Southampton University, Prof. Petter Pilesjo of Lund University, Prof.
Katarzyna Dabrowska of Warsaw University and Prof. Andrew Skidmore of ITC.
The lecturers in the four universities can not go unnoticed for their dedication to the
professionalism.
My utmost gratitude goes to my supervisors: Dr. Martin Schlerf and Prof.
Andrew Skidmore, for their invaluable inputs, expert guidance and moral support.
All your great ideas helped me maintain the focus during all phases of the research
for which I thank you.
My deep gratitude goes to my advisor Sabrina Carvalho. She gave me
invaluable advice and help on the design of the experiment, the lab-work and
statistical analyzing.
I am grateful to Prof. Wim Van Der Putten and Dr. Mirka Macel from
NIOO for critical advises, coordinating to fieldwork and sharing their knowledge in
plants-ecology.
I specially thank GEM-2008 classmates for their lovely friendship. You
were wonderful classmates indeed. Living, studding and travelling together yielded
comradeship, fellow-feeling cordiality and unity.
My heartfelt thanks go to my husband for his dedicated love,
encouragement and support, without him all these would not have been achievable.
Let it herewith be officially recorded that you are the best.

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Table of contents
1. Introduction ............................................................................................ 1
1.1. Invasive species ............................................................................ 1
1.1.1. Toxic content ............................................................................ 1
1.1.2. Natural Enemies of invasive plants .......................................... 2
1.2. The role of Pyrrolizidine Alkaloids and how thay are affected by
nutrient supply ............................................................................................ 2
1.2.1. Spectroscopy as tool to detect PAs ........................................... 4
1.3. Research Objectives ...................................................................... 6
1.3.1. General Objective ..................................................................... 6
1.3.2. Specific Objectives ................................................................... 6
1.4. Research Questions and Hypothesis ............................................. 6
2. Methods and Materials ........................................................................... 8
2.1. Research workflow and the steps .................................................. 9
2.2. Study area ..................................................................................... 9
2.3. Fertilizing experimant ................................................................. 10
2.3.1. Soil collection and sterilization .............................................. 10
2.3.2. Seed germination .................................................................... 10
2.3.3. Plants growing phase in greenhouse ....................................... 11
2.3.4. Leaf spectral measurements with ASD Integrating Sphere .... 11
2.4. PAs concentration measurements ............................................... 16
2.5. Data preprocessing and Statistical analysis ................................ 17
2.5.1. Deletion of the noisy bands .................................................... 17
2.5.2. Testing the outliers ................................................................. 17
2.5.3. Testing the Normality of PA data ........................................... 17
2.6. Two-way ANOVA ...................................................................... 17
2.7. T-test 2 ........................................................................................ 18
2.8. Partial Least Squares Regression (PLSR) ................................... 18
2.8.1. Determination of optimum PLS factors .................................. 19
2.8.2. Selection of spectral processing methods ............................... 20
2.8.3. Important wavelengths for predicting PAs ............................. 22
2.9. Employed software ..................................................................... 22
3. Results .................................................................................................. 23
3.1. PAs measurments ........................................................................ 24
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3.1.1. Summery statistics of the PA .................................................. 24
3.1.2. Testing the outliers ................................................................. 24
3.1.3. Testing the normality of the PA data ...................................... 25
3.2. Leaf spectral measurements ........................................................ 25
3.3. Soil nutrient effects on leaf PAs concentrations ......................... 27
3.4. Soil nutrient affects on leaf reflectance ....................................... 30
3.4.1. Fresh samples ......................................................................... 30
3.4.2. Dry samples ............................................................................ 34
3.5. Relations between leaf spectral reflectance and leaf PAs ........... 38
3.5.1. PLSR models accuracy ........................................................... 38
3.5.2. Determination of important wavelength on PLSR models ..... 42
4. Discussion ............................................................................................ 46
4.1. Soil nutrient effects on leaf PAs concentrations ......................... 46
4.2. Soil nutrient effects on leaf spectral reflectance ......................... 47
4.2.1. Fresh samples ......................................................................... 47
4.2.2. Dry samples ............................................................................ 48
4.3. Relation between the leaf spectral reflectance and the leaf PAs . 49
4.3.1. Comparison of PLSR model performances for three species at
the fresh and dry levels ......................................................................... 49
4.3.2. Important wavelengths for predicting of PAs in Jacobaea
vulgaris ……………………………………………………………….50
4.3.3. Important wavelengths for predicting of PAs in Senecio
inaequidens ........................................................................................... 51
4.4. Assumptions and source of errors ............................................... 52
5. Conclusions and Recommendations ..................................................... 53
5.1. Conclusions ................................................................................. 53
5.2. Recommendations ....................................................................... 55
6. References ............................................................................................ 56
7. Appendices ........................................................................................... 62
7.1. Appendix I: Shrub and leaf structure of the studied plants. ........ 63
7.2. Appendix II: Testing the outliers. ............................................... 64
7.3. Appendix III: PA data. ................................................................ 67
7.4. Appendix IV: The spectral reflectances of all samples in fresh and
dry level. ................................................................................................... 70
7.5. Appendix V: Nutrient effects on fresh samples, group one. ....... 71
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