Greenhouse Gas Production and Consumption in Soils of the Canadian High Arctic

150 Pages·2015·3.12 MB·English

by  Martin Brummell

Greenhouse Gas Production and Consumption in Soils of the
Canadian High Arctic

A Dissertation 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
By
Martin Earl Brummell

© Copyright Martin Earl Brummell, January, 2015. All rights reserved.
PERMISSION TO USE

In presenting this 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
dissertation in any manner, in whole or in part, for scholarly purposes may be granted by the
professor or professors who supervised my dissertation work or, in their absence, by the Head of
the Department or the Dean of the College in which my dissertation work was done. It is
understood that any copying or publication or use of this 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 the University of Saskatchewan in any scholarly use which
may be made of any material in my dissertation.
Requests for permission to copy or to make other uses of materials in this dissertation in
whole or part should be addressed to:

Head of the Department of Soil Science
Agriculture Building
University of Saskatchewan
51 Campus Dr.
Saskatoon, Saskatchewan S7N 5A8
Canada

OR

Dean
College of Graduate Studies and Research
University of Saskatchewan
107 Administration Place
Saskatoon, Saskatchewan S7N 5A2
Canada
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DISCLAIMER

Reference in this dissertation to any specific commercial products, process, or service by
trade name, trademark, manufacturer, or otherwise, does not consistute or imply its endorsement,
recommendation, or favouring by the University of Saskatchewan. The views and opinions of the
author expressed herein do not state or reflect those of the University of Saskatchewan, and shall
not be used for advertising or product endorsement purposes.

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ABSTRACT
Micro-organisms living in the soils of the Canadian High Arctic produce and consume
the greenhouse gases (GHGs) CO , CH , and N O, contributing to global nutrient and GHG
2 4 2
cycles; however, different vegetation and soil communities differ in their net productions of each
gas and the total emissions from the ecosystem. The range of Arctic vegetation communities
spans wetlands, tundras, and deserts differing in their soil water contents and other properties
such as organic matter content. Previous estimates of total GHG emissions are often imprecise
relative to the scale of microbial processes that result in these emissions. Deserts have extremely
low levels of both water and organic matter, yet I found that deserts produce nearly as much
GHGs as wetter, more fully vegetated tundras. To test the hypothesis that this unexpectedly
strong source of GHGs in deserts was a consequence of recently-thawed, organic-rich
permafrost, I measured GHG net production throughout the active layer of polar desert soils;
both production and consumption of CH and N O, as well as soil respiration were found
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throughout the profile, indicating no link to thawed permafrost and suggesting these high GHG
activities are characteristic features of Arctic polar deserts rather than transient effects of recent
warming.
I studied the community of microorganisms of the Arctic deserts by examining DNA
from soil samples collected from three deserts on Ellesmere Island using DNA microarrays
targeted for the functional genes AmoA and pmo. Using Structural Equation Modeling (SEM) I
evaluated the hypotheses that the community of ammonia-oxidizers would be causally linked to
the observed patterns of N O net production, and that methane-oxidizers would be causally
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linked to CH net production. The SEM showed the expected link for CH production, but not
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N O production. Available nitrogen in Arctic desert soils is primarily in the form of
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ammonia/ammonium, thus I find it surprising that no link could be found to the nitrifying
community. Subsequent analysis of the occurence patterns of nitrous oxide reductase, a gene
present in denitrifying bacteria and the only known biological sink for N O, revealed only a
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weak association. Thus it remains unknown which organisms are responsible for the high levels
of N O emitted from Arctic polar desert soils. Furthermore, I observed several cases of unusual
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GHG processes, including a positive correlation between net CO and net N O production in
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only some soils and some soil layers that consumed both CH and N O.
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ACKNOWLEDGEMENTS
I am very grateful for the support and encouragement from my supervisor, Dr. Steven
Siciliano, and my advisory committee, Drs. Richard Ferrell, Reynald Lemke, and Alec Aitken.
All of these professors provided extensive and very useful advice regarding all parts of my PhD
project from start to finish.
Financial support for my research was provided by the Natural Sciences and Engineering
Research Council of Canada through grants to Dr. Siciliano. Personal support was provided by
NSERC through a Canada Graduate Scholarship.
The field campaigns that form the foundation of my work were cooperative ventures and
the 2009 field team, especially Dr. Heather Stuart and Dr. Greg Henry and his assistants allowed
me to undertake the experiments that led to the foundational discoveries about the polar deserts.
The 2010 team, especially Sarah Hardy and Aaron Betts, were similarly crucial for the follow-up
season. The Polar Continental Shelf Project in Ottawa and in Resolute Bay provided logistical
support in the form of flights and material coordination during both field campaigns.
I am especially thankful to Dr. Derek Peak for his mentorship during my involvement
with the Environmental Science Capstone course, and I am grateful to the staff at the Gwenna
Moss Centre for Teaching Effectiveness for their help during that course as well.

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DEDICATION
I dedicate this dissertation to Charlie Roy. Thank you, My Love.
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TABLE OF CONTENTS

Permission to Use ............................................................................................................................ i
Disclaimer ....................................................................................................................................... ii
Abstract .......................................................................................................................................... iii
Acknowledgements ........................................................................................................................ iv
Dedication ....................................................................................................................................... v
Table of Contents ........................................................................................................................... vi
List of Tables ................................................................................................................................. ix
List of Figures ................................................................................................................................. x
List of Abbreviations ................................................................................................................... xiv
1. Introduction ................................................................................................................................. 1
1.1 Organization of the Dissertation ............................................................................................... 3
2. Literature Review........................................................................................................................ 5
2.1 Arctic Soils................................................................................................................................ 5
2.2 Greenhouse Gases ..................................................................................................................... 9
2.3 Measuring Soil Gases ............................................................................................................. 19
3. Greenhouse Gas Soil Production and Surface Fluxes at a High Arctic Polar Oasis ................. 22
3.1 Preface..................................................................................................................................... 22
3.2 Abstract ................................................................................................................................... 23
3.3 Introduction ............................................................................................................................. 23
3.4 Materials and Methods ............................................................................................................ 25
3.4.1 Study Location .............................................................................................................. 25
3.4.2 Soil Gas Profile and Surface Flux Measurements ........................................................ 26
3.4.3 CO , CH , and N O Production .................................................................................... 29
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4.3.4 Soil Sampling and Analysis .......................................................................................... 30
3.4.5 Data Analysis ................................................................................................................ 32
3.5 Results ..................................................................................................................................... 33
3.5.1 Soil Characteristics ....................................................................................................... 33
3.5.2 GHG Flux, Profile Concentration, and Net Production ................................................ 33
3.6 Discussion ............................................................................................................................... 35
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3.6.1 Soil Carbon Dioxide Production Profile ....................................................................... 40
3.6.2 Methane and Nitrous Oxide Production ....................................................................... 40
3.6.3 Conclusions .................................................................................................................. 44
4. Greenhouse Gas Production and Consumption in High Arctic Deserts ................................... 47
4.1 Preface..................................................................................................................................... 47
4.2 Abstract ................................................................................................................................... 48
4.3 Introduction ............................................................................................................................. 48
4.4 Materials and Methods ............................................................................................................ 49
4.4.1. Study Sites and Field Sampling ................................................................................... 49
4.4.2 Data Analysis ................................................................................................................ 50
4.4.3 Soil Analysis ................................................................................................................. 53
4.5 Results ..................................................................................................................................... 55
4.6 Discussion ............................................................................................................................... 60
4.6.1 Production and Consumption of Gases ........................................................................ 60
4.6.2 Conclusions .................................................................................................................. 65
5. Soil factors influence archaeal ammonia oxidizers but not methanotrophs in Arctic Polar
Desert Soils ................................................................................................................................... 66
5.1 Preface..................................................................................................................................... 66
5.2 Abstract ................................................................................................................................... 67
5.3 Introduction ............................................................................................................................. 67
5.4 Materials and Methods ............................................................................................................ 70
5.4.1 Soil Collection Locations ............................................................................................. 70
5.4.2 Amplification of Target Sequences .............................................................................. 71
5.4.3 DNA Microarrays ......................................................................................................... 72
5.4.4 Data Analysis ................................................................................................................ 73
5.5 Results ..................................................................................................................................... 74
5.6 Discussion ............................................................................................................................... 81
5.6.1 Conclusions .................................................................................................................. 83
6. Summary, Conclusions, and Future Considerations ................................................................. 84
6.1 Summary of Methodology and Findings ................................................................................ 84
6.1.1 Novel and Refined Methods ......................................................................................... 84
6.1.2 Summary of Findings ................................................................................................... 88
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6.2 Unexplored Avenues ............................................................................................................... 89
6.2.1 Co-consumption of CH and N O ................................................................................ 89
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6.2.2 CO , N O, and Light ..................................................................................................... 91
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6.2.3 Measuring Gases in Freezing Soil ................................................................................ 92
6.3 Future Research Directions ..................................................................................................... 92
6.3.1 Gas-Gas Interactions..................................................................................................... 93
6.3.2 Microbial Ecology ........................................................................................................ 94
6.3.3 The Changing Arctic .................................................................................................... 95
7. References ................................................................................................................................. 96
Appendices .................................................................................................................................. 127
Appendix 1 .................................................................................................................................. 128
Error Propagation ................................................................................................................ 128
Appendix 1 References ........................................................................................................ 129
Appendix 2 .................................................................................................................................. 130
Appendix 3 .................................................................................................................................. 131

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LIST OF TABLES
Table 3.1. Vegetation communities included in the 2009 greenhouse gas study. ....................... 27
Table 3.2. Depth profiles of soil variables in the vegetation communities at Alexandra Fjord... 34
Table 3.3. Mean calculated diffusivities (D ) for each studied gas in the soil profiles. .............. 43
e
Table 4.1. Surface characteristics of three deserts on Ellesmere Island. ..................................... 57
Table 4.2. GHG fluxes at three deserts on Ellesmere Island. ...................................................... 57
Table 4.3. Soil parameters in the active layer at three polar desert sites on Ellesmere
Island. ............................................................................................................................... 58
Table 5.1. Correlations between Fast Unifrac PCoA axes and edaphic variables. ...................... 80

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