pathways of abiotic humification as catalyzed by - eCommons

276 Pages·2008·5.95 MB·English

by  Ailsa Hardie

PATHWAYS OF ABIOTIC HUMIFICATION AS CATALYZED BY
MINERAL COLLOIDS

A thesis submitted to the College of Graduate Studies and Research
in partial fulfillment of the requirements for the degree of Doctor of Philosophy
in the Department of Soil Science, University of Saskatchewan, Saskatoon, Canada

By

Ailsa Ghillainé Hardie

Keywords: abiotic humification pathways, polyphenol-Maillard reaction, soil mineral colloids,
biomolecules, humic substances, rhodochrosite, catalysis, NEXAFS

© Copyright Ailsa Ghillainé Hardie, August 2008. All rights reserved.
PERMISSION TO USE
In presenting this thesis/dissertation in partial fulfillment of the requirements for a
Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this
University may make it freely available for inspection. I further agree that permission for
copying of this thesis/dissertation in any manner, in whole or in part, for scholarly purposes may
be granted by the professor or professors who supervised my thesis/dissertation work or, in their
absence, by the Head of the Department or the Dean of the College in which my thesis work was
done. It is understood that any copying or publication or use of this thesis/dissertation or parts
thereof for financial gain shall not be allowed without my written permission. It is also
understood that due recognition shall be given to me and to the University of Saskatchewan in
any scholarly use which may be made of any material in my thesis/dissertation.

Requests for permission to copy or to make other uses of materials in this
thesis/dissertation in whole or part should be addressed to:

Head of the Department of Soil Science
University of Saskatchewan
51 Campus Drive
Saskatoon, Saskatchewan S7N 5A8
Canada
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ABSTRACT
The polyphenol pathway and Maillard reaction (polycondensation of sugars and amino
acids) are regarded as important pathways in natural humification. The significance of linking
the Maillard reaction and polyphenol pathways into an integrated humification pathway has been
addressed. However, the ability of mineral colloids commonly occurring in tropical and
temperate environments to promote the Maillard reaction and integrated polyphenol-Maillard
humification pathways remained to be uncovered. Furthermore, the effect of the nature and
relative abundance of biomolecules on humification and associated reaction products remained
to be studied.
The results of this study show that the structure of polyphenols and the relative molar ratio
of polyphenol, glucose and glycine, significantly affected humification processes and the
associated carbonate formation in the integrated polyphenol-Maillard reaction catalyzed by
birnessite. Increasing the molar ratio of ortho-polyphenols (catechol and pyrogallol) to Maillard
reagents in the polyphenol-Maillard pathway catalyzed by birnessite enhanced humification
while suppressing the formation of rhodochrosite (MnCO ). The opposite trend of MnCO
3 3
formation was observed in the meta-polyphenol (resorcinol)-Maillard reaction system. Increasing
the amount of glucose in the integrated catechol-Maillard system under the catalysis of birnessite
promoted the formation of Maillard reaction-type humic acid in the supernatant and MnCO in
3
the solid phase.
The catalytic abilities of commonly occurring mineral colloids from temperate and tropical
regions greatly differed in influencing humification processes and products in the Maillard
reaction and integrated polyphenol-Maillard pathways. Compared with layer silicate colloids, the
poorly ordered Fe and Mn oxides were by far the strongest catalysts of humification reactions in
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the Maillard and catechol-Maillard pathways. This accounted for the significant difference in
reactivity between the sesquioxide-rich Oxisol clay from the high rainfall region of South Africa
and the Mollisol clay from the Canadian Prairies. Furthermore, the nature of the mineral colloids
also affected the extent of organic C accumulation in the solid phase upon humification, and
related mineral surface alteration. The metal oxide- and Oxisol clay-catalyzed Maillard and
catechol-Maillard reaction systems had the highest accumulation of organic C in the solid phase,
indicating their significance in contributing to C sequestration in the environment.
The findings obtained in this study are of fundamental significance in understanding the
influence of the atomic bonding, structural configuration and related surface properties of
mineral colloids, and the nature and abundance of biomolecules on the abiotic humification
pathways and related reaction products in natural environments.

iii
ACKNOWLEDGEMENTS
I would like to thank my supervisor, Dr P.M. Huang, for giving me this opportunity and
for all his guidance and encouragement throughout this project. I wish to thank all the members
of my PhD Advisory Committee, Drs D.W. Anderson, D.E. Ward, D. Peak and L.M. Kozak, for
their invaluable suggestions and inputs. I would like to thank The Natural Sciences and
Engineering Research Council of Canada for financial support and the University of
Saskatchewan for the awards of PhD Tuition Scholarship and PhD Devolved Scholarship.
The NEXAFS spectroscopy research described in this thesis was performed at the
Canadian Light Source (CLS), which is supported by NSERC, NRC, CIHR, and the University
of Saskatchewan. I would like to thank J.J. Dynes, Environment Canada/McMaster University,
for assisting me with the NEXAFS spectroscopy data collection at the CLS. I would like to thank
Edwige Otero, Department of Chemistry, University of Saskatchewan, for helping to prepare the
gold-coated silicon mounts used in the NEXAFS experiments. I would like to thank the SGM
beamline staff, Tom Regier and Robert Blyth, and the PGM beamline staff, Yongfeng Hu and
Lucia Zuin, at the CLS for their assistance with the NEXAFS experiments.
I would like to thank Barry Goetz for his assistance using the atomic absorption
spectrometer. I would like to thank Arlette Seib and Lori Phillips for training me and assisting
me with the aseptic techniques used in my experiments. I would like to thank my fellow graduate
students at the University of Saskatchewan, Mohammad Tahir, Dani Xu, Christian Dedzoe and
Adam Gillespie, for all their help and suggestions during my project.

iv
DEDICATION

To my parents, Caryle and Stewart Hardie.
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TABLE OF CONTENTS
PERMISSION TO USE .................................................................................................................. i 
ABSTRACT .................................................................................................................................... ii 
ACKNOWLEDGEMENTS ......................................................................................................... iv 
TABLE OF CONTENTS ............................................................................................................. vi 
LIST OF TABLES ........................................................................................................................ ix 
LIST OF FIGURES ...................................................................................................................... xi 
1  INTRODUCTION.................................................................................................................. 1 
2  LITERATURE REVIEW ..................................................................................................... 5 
2.1  Introduction .................................................................................................................... 5 
2.2  Current Concepts on the Nature of Humic Substances ............................................. 8 
2.3  Decomposition of Organic Residues in the Environment ........................................ 11 
2.3.1  Organisms Involved in Degradation Processes ..................................................................... 11 
2.3.2  Degradation Processes in the Formation of Substrates and Preservation Products ............... 13 
2.3.3  Decomposition of Organic Material by Fire and Charcoal Formation .................................. 23 
2.4  Pathways of Humic Substance Formation ................................................................. 24 
2.4.1  Selective preservation pathways of humification .................................................................. 24 
2.4.2  Synthesis pathways of humification ...................................................................................... 28 
2.5  Biotic Catalysis of Synthetic Humification Pathways ............................................... 37 
2.5.1  Enzymes ................................................................................................................................ 37 
2.5.2  Microorganisms ..................................................................................................................... 40 
2.6  Abiotic Catalysis of Synthetic Humification Pathways ............................................ 42 
2.6.1  Oxides, Oxyhydroxides and Short-Range Ordered Minerals ................................................ 46 
2.6.2  Clay Size Layer Silicates....................................................................................................... 51 
2.6.3  Primary Minerals ................................................................................................................... 54 
2.6.4  Natural Soils .......................................................................................................................... 55 
2.7  Comparison of the Mechanisms and Significance of Biotic and Abiotic Catalyses
of Humification Reactions in Natural Environments ................................................... 57 
2.7.1  Comparison of the Mechanisms of Biotic and Abiotic Catalyses of Synthetic
Humification Reactions ......................................................................................................... 57 
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2.7.2  Comparison of the Products of Biotic and Abiotic Catalyses of Synthetic Humification
Reactions ............................................................................................................................... 60 
2.7.3  The Effect of Environmental Particles on Activity of Biotic Catalysts ................................ 61 
2.7.4  The Significance of Biotic and Abiotic Catalysts in Synthetic Humification Reactions in
Natural Environments ........................................................................................................... 64 
2.8  Conclusions and Future Research Prospects ............................................................ 64 
3  EXPERIMENTS, RESULTS AND DISCUSSION ........................................................... 67 
3.1  Research Unit 1: The effect of catechol interaction with the Maillard reaction on
abiotic humification as catalyzed by birnessite ................................................................ 67 
3.1.1  Introduction ........................................................................................................................... 67 
3.1.2  Materials and Methods .......................................................................................................... 68 
3.1.3  Results and Discussion .......................................................................................................... 72 
3.1.4  Conclusions ........................................................................................................................... 92 
3.2  Research Unit 2: Biomolecule-induced formation of rhodochrosite in the birnessite-
polyphenol-Maillard humification pathway .................................................................... 94 
3.2.1  Introduction ........................................................................................................................... 94 
3.2.2  Materials and Methods .......................................................................................................... 95 
3.2.3  Results and Discussion .......................................................................................................... 98 
3.2.4  Conclusions ......................................................................................................................... 110 
3.3  Research Unit 3: The influence of polyphenols on the integrated polyphenol-
Maillard humification pathway as catalyzed by birnessite ............................................ 111 
3.3.1  Introduction ......................................................................................................................... 111 
3.3.2  Materials and Methods ........................................................................................................ 114 
3.3.3  Results ................................................................................................................................. 117 
3.3.4  Discussion ........................................................................................................................... 137 
3.3.5  Conclusions ......................................................................................................................... 145 
3.4  Research Unit 4: The role of glucose in the integrated polyphenol-Maillard
humification pathway as catalyzed by birnessite ........................................................... 147 
3.4.1  Introduction ......................................................................................................................... 147 
3.4.2  Materials and Methods ........................................................................................................ 148 
3.4.3  Results and Discussion ........................................................................................................ 152 
3.4.4  Conclusions ......................................................................................................................... 169 
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3.5  Research Unit 5: Catalysis of the Maillard and polyphenol-Maillard humification
pathways by poorly crystalline Al and Fe oxides ........................................................... 171 
3.5.1  Introduction ......................................................................................................................... 171 
3.5.2  Materials and Methods ........................................................................................................ 172 
3.5.3  Results and Discussion ........................................................................................................ 176 
3.5.4  Conclusions ......................................................................................................................... 193 
3.6  Research Unit 6: Catalysis of the Maillard and polyphenol-Maillard humification
pathways by pure layer silicates and natural soil clays ................................................. 195 
3.6.1  Introduction ......................................................................................................................... 195 
3.6.2  Materials and Methods ........................................................................................................ 196 
3.6.3  Results and Discussion ........................................................................................................ 201 
3.6.4  Conclusions ......................................................................................................................... 221 
4  GENERAL DISCUSSION AND CONCLUSIONS ........................................................ 224 
5  REFERENCES ................................................................................................................... 229 
6  APPENDICES .................................................................................................................... 249 

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LIST OF TABLES
Table 2.1 Definitions of environmental organic matter and humic substances (Modified from
Stevenson 1994). ................................................................................................................. 7 
Table 2.2 Mechanisms of chemical recalcitrance of primary and secondary sources of organic
matter (adapted from von Lützow et al. 2006). ................................................................ 13 
Table 2.3 Regression analyses for combined andesite-granite (AN) and granite (GR) data
explaining total C content (n = 6)† (Rasmussen et al. 2005). ........................................... 22 
Table 2.4 Correlation of δ13C values of charred plant fragments, humic and fulvic acids, and
whole soils (Shindo et al. 2005). ....................................................................................... 24 
Table 2.5 Summary of research conducted on mineral catalysis of abiotic humification
reactions (updated from Wang et al. 1986). ...................................................................... 42 
Table 2.6 Release of CO in oxide-pyrogallol systems in air or N atmosphere at the end of
2 2
90-h reaction period (Wang and Huang 2000b). .............................................................. 49 
Table 2.7 Effects of clay minerals on the synthesis of humic acids (HA) at an initial pH of 5.5
at the end of 7 days (Shindo and Huang 1985b). .............................................................. 53 
Table 2.8 Release of carbon dioxide in the nontronite-polyphenol systems at the end of a 90-h
reaction period (Wang and Huang 1994). ......................................................................... 54 
Table 2.9 Effects of primary minerals on the synthesis of HA at an initial pH of 5.5 at the end
of 7 days (Shindo and Huang 1985a). ............................................................................... 55 
Table 2.10 Immobilization of laccase and horseradish peroxidase on different supports
(Gianfreda and Bollag 1994). ........................................................................................... 62 
Table 3.1.1 Effect of birnessite on the final pH and redox status (pH + pE) of the Maillard
reaction, catechol only and equimolar catechol-Maillard systems. .................................. 73 
Table 3.1.2 Assignment of the FTIR absorption bands of the purified HA fractions from the
supernatants of the Maillard, integrated catechol-Maillard and catechol only systems
reacted in the presence of birnessite. ................................................................................ 82 
Table 3.1.3 Total carbon contents of the solid residues from selected reaction systems ............. 84 
Table 3.1.4 Interpretation of the Py-FIMS results of the solid residues from the Maillard (0.05
mole glucose + 0.05 mole glycine), equimolar catechol-Maillard (0.05 mole catechol +
0.05 mole glucose + 0.05 mole glycine) and catechol only (0.05 mole catechol)
systems catalyzed by birnessite. ....................................................................................... 90 
Table 3.1.5 Interpretation of the Py-GC/MS results of the solid residue from the integrated
equimolar catechol-Maillard system reacted in the presence of birnessite. ...................... 91 
Table 3.2.1 The solution pH, visible absorbance (400 and 600 nm) and Mn concentration of
the Maillard reaction, catechol-only and selected integrated catechol-Maillard systems
in the presence or absence of birnessite. ........................................................................... 99 
Table 3.2.2 Assignments of FTIR absorption bands of the solid residues of the Maillard
reaction, catechol-Maillard and catechol only systems shown in Fig. 3.2.3. ................. 104 
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