Effects of Liming on Soil Respiration, Fungi Diversity and Abundance in a Metal-Contaminated

257 Pages·2014·3.75 MB·English

Effects of Liming on Soil Respiration, Fungi Diversity and Abundance in a Metal-Contaminated
Region in Northern Ontario

By
Kassandre Goupil

Thesis submitted in partial fulfillment
of the requirements for the degree of
Master of Science (MSc) in Biology

School of Graduate Studies
Laurentian University
Sudbury, Ontario

© Kassandre Goupil, 2014
THESIS DEFENCE COMMITTEE/COMITÉ DE SOUTENANCE DE THÈSE

Laurentian Université/Université Laurentienne
School of Graduate Studies/École des études supérieures

Title of Thesis
Titre de la thèse EFFECTS OF LIMING ON SOIL RESPIRATION, FUNGI DIVERSITY AND
ABUNDANCE IN A METAL-CONTAMINATED REGION IN NORTHERN
ONTARIO

Name of Candidate
Nom du candidat Goupil, Kassandre

Degree
Diplôme Master of Science

Department/Program Date of Defence
Département/Programme Biology Date de la soutenance April 28, 2014

APPROVED/APPROUVÉ

Thesis Examiners/Examinateurs de thèse:

Dr. Kabwe Nkongolo
(Supervisor/Directeur de thèse)

Dr. Peter Beckett
(Committee member/Membre du comité)
Approved for the School of Graduate Studies
Dr. Graeme Spiers Approuvé pour l’École des études supérieures
(Committee member/Membre du comité) Dr. David Lesbarrères
M. David Lesbarrères
Dr. Nandakumar Kanavillil Director, School of Graduate Studies
(External Examiner/Examinateur externe) Directeur, École des études supérieures

ACCESSIBILITY CLAUSE AND PERMISSION TO USE

I, Kassandre Goupil, hereby grant to Laurentian University and/or its agents the non-exclusive license to archive
and make accessible my thesis, dissertation, or project report in whole or in part in all forms of media, now or for the
duration of my copyright ownership. I retain all other ownership rights to the copyright of the thesis, dissertation or
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dissertation, or project report. I further agree that permission for copying of this thesis in any manner, in whole or in
part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their
absence, by the Head of the Department in which my thesis work was done. It is understood that any copying or
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by the copyright laws without written authority from the copyright owner.

ii
Abstract
At present, little is known concerning the fungi communities inhabiting the Greater
Sudbury Region. This study aimed at identifying the fungal species and abundance in limed and
unlimed areas contaminated with metals. Samples were collected from the LFH soil layer from
Wahnapitae Hydro-Dam, Daisy Lake, Kingsway, Kelly Lake, Hagar, Onaping Falls and Capreol.
Limed and unlimed areas were compared for soil metals, pH, fungi diversity, abundance and
seasonal soil respiration. Fungi from soil samples were cultured using Sabouraud Dextrose Agar
and Malt Extract Agar. A total of 52 fungi species from 34 genera were identified. There was a
significantly higher fungal diversity in the limed areas compared to the samples from unlimed
sites based on SDA medium data. Fungi abundance followed the same trend. Significantly higher
soil respiration rates were recorded for limed sites compared to unlimed sites. Summer soil
respiration rates correlated (r = 0.50) with total fungal abundance.

iii
Acknowledgements
I would first like to thank my supervisor, Dr. Nkongolo, for his constant devotion,
guidance and expertise towards fulfilling this research project. I am also greatly appreciative
towards Dr. Nasserulla’s help in identifying many of the fungi species. I also must sincerely
thank my committee members, Dr. Spiers and Dr. Beckett, for their assistance and knowledge in
completing this research project. Furthermore, I would like to express gratitude towards Irene
McAuley for her added support concerning this research project. Her knowledge regarding the
safe operation of the laboratory equipment, safety regulations in the laboratory and media
preparation proved greatly helpful to me. Equally, I am grateful to all my esteemed labmates for
their continued assistance throughout this research project. Their support is greatly appreciated.

iv
Table of Contents
Abstract .................................................................................................................................. iii
Acknowledgments ................................................................................................................. iv
Table of Contents ................................................................................................................... v
List of Figures ....................................................................................................................... vii
List of Tables ......................................................................................................................... ix
Chapter 1: Literature Review .............................................................................................. 1
1.1 Metal Contamination in the Greater Sudbury Region (Ontario, Canada) ............. 1
1.2 Fungi and Soil Elements ........................................................................................ 4
1.3 Fungi and Soil Liming ........................................................................................... 6
1.4 Soil Amendment in the Sudbury Region ............................................................... 8
1.5 Soil Respiration .................................................................................................... 10
1.6 Government Regulations and Revegetation......................................................... 13
1.7 Objectives ............................................................................................................ 14

Chapter 2: Soil Metal Analysis in Limed and Unlimed Areas in the Greater Sudbury
Region (Ontario, Canada) ................................................................................................... 15
2.1 Introduction .......................................................................................................... 15
2.2 Materials and Methods ......................................................................................... 16
2.2.1 Site Description and Substrate Sampling / Collection ....................................... 16
2.2.2 Soil pH and Metal Analysis .............................................................................. 17
2.2.3 Statistical Analysis ............................................................................................ 19
2.3 Results .................................................................................................................. 19
2.3.1 Total Metals ...................................................................................................... 20
2.3.2 Bioavailable Metals .......................................................................................... 20
2.3.3 Effect of Liming ................................................................................................ 21
2.4 Discussion ............................................................................................................ 28

Chapter 3: Analysis of Soil Fungi Diversity and Abundance in Limed and Unlimed Areas
Contaminated with Metals in the Greater Sudbury Region (Ontario, Canada) ........... 32

3.1 Introduction .......................................................................................................... 32
3.2 Materials and Methods ......................................................................................... 33
3.2.1 Soil Sampling and Processing ........................................................................... 33
3.2.2 Fungal Isolation Method ................................................................................... 34
3.2.3 Slide Preparation ............................................................................................... 35
3.2.4 Statistical Analysis ............................................................................................ 35
3.3 Results .................................................................................................................. 36
3.3.1 Fungi Diversity ................................................................................................. 36
3.3.2 Fungi Phylum Identification ............................................................................. 37
3.3.3 Fungi Species Identification ............................................................................. 38
3.3.4 Fungi Diversity ................................................................................................. 41
3.3.5 Fungi Abundance .............................................................................................. 42
3.4 Discussion ............................................................................................................ 68

v
Chapter 4: Analysis of Soil Respiration as an Indicator of Soil Microbial Activity in Limed
and Unlimed Areas in the Greater Sudbury Region (Ontario, Canada) ....................... 77
4.1 Introduction .......................................................................................................... 77
4.2 Materials and Methods ......................................................................................... 78
4.2.1 Assessment of Soil Respiration ........................................................................ 78
4.2.2 Statistical Analysis ............................................................................................ 79
4.3 Results .................................................................................................................. 79
4.3.1 Analysis of Temperature and Rainfall .............................................................. 79
4.3.2 Seasonal Soil Respiration and Relationship to Fungal Abundance .................. 79
4.4 Discussion ............................................................................................................ 86

Chapter 5: General Conclusions......................................................................................... 91
Literature Cited ................................................................................................................... 95
Appendices………………………………………………………………………………...103
Appendix A - Illustrations of fungi species on agar media ..................................... 104
Appendix B - Illustrations of fungi species via microscope .................................... 108
Appendix C - Photographs of sites used in the study .............................................. 112
Appendix D - Sudbury soil horizons ....................................................................... 114
Appendix E - Professional soil test interpretation by Solvita .................................. 115
Appendix F - Sample calculation for abundance of fungi species ........................... 116
Appendix G - Compendium of tables showcasing species in their corresponding
replicates and dilution factors, species abundance as well as their time of appearance,
colony description on agar plate and species description via microscope ............... 117

vi
List of Figures

Figure 1: Location of sampling area from the Greater Sudbury Region ............................... 18
Figure 2: Venn diagram illustrating common fungi species among limed areas based on SDA
and MEA medium analysis ........................................................................................ 54
Figure 3: Venn diagram illustrating common fungi species among unlimed areas based on SDA
and MEA medium analysis ........................................................................................ 55
Figure 4: Venn diagram illustrating common fungi species among reference sites based on
SDA and MEA medium analysis ............................................................................... 56
Figure 5: Fungi phyla present in limed areas ......................................................................... 60
Figure 6: Fungi phyla present in unlimed areas ..................................................................... 60
Figure 7: Fungi phyla present in reference sites .................................................................... 61
Figure 8: Fungi diversity identified in limed and unlimed samples on SDA medium for all
targeted sites with standard error bars ....................................................................... 63
Figure 9: Fungi diversity identified in limed and unlimed samples on MEA medium for all
targeted sites with standard error bars ....................................................................... 64
Figure 10: Fungal abundance for different dilution factors for unlimed and limed areas of all
targeted sites based on SDA medium analysis with standard error bars on logarithmic
scale............................................................................................................................ 65
Figure 11: Fungal abundance for different dilution factors for unlimed and limed areas of all
targeted sites based on MEA medium analysis with standard error bars on logarithmic
scale............................................................................................................................ 66
Figure 12: Mean summer soil respiration rates for unlimed, limed and reference sites in the
Greater Sudbury Region with standard error bars ..................................................... 84
Figure 13: Mean fall soil respiration rates for unlimed, limed and reference sites in the Greater
Sudbury Region with standard error bars .................................................................. 84
Figure 14: Mean June and November soil respiration rates for the Greater Sudbury Region
with standard error bars ............................................................................................. 85
Figure 15: Photographs of the Wahnapitae Hydro-Dam site, demonstrating limed and unlimed
areas utilized for soil samples .................................................................................. 112
vii
Figure 16: Photographs of the Kingsway site, demonstrating limed and unlimed areas utilized
for soil samples ........................................................................................................ 113
Figure 17: Sudbury soil horizons demonstrating LFH layer to be used for fungal analysis.114

viii
List of Tables

Table 1: Mean total concentrations of elements in selected soil horizons from sites in the
Greater Sudbury region (concentrations are in mg kg-1, dry weight) ........................ 22
Table 2: Bio-available nutrients and metals in selected soil horizons from sites in the
Greater Sudbury region (concentrations are in mg kg-1, dry weight) ....................... 23
Table 3: Total nutrient and metal content in the organic surface horizon (LFH) of limed and
unlimed sites from the Greater Sudbury region sites (concentrations are in mg kg-1,
dry weight) ................................................................................................................ 24
Table 4: Bio-available nutrients and metals in the organic surface horizon (LFH) of limed and
unlimed sites from the Greater Sudbury region sites (concentrations are in mg kg-1,
dry weight) ................................................................................................................ 24
Table 5: Proportion of bioavailable relative to total elements for the LFH horizon of soils from
the Greater Sudbury region sites ................................................................................ 25
Table 6: Correlation between total and bio-available metal and nutrient content in soil
profiles from the Greater Sudbury region sites .......................................................... 26
Table 7: The pH of the LFH layer from the Greater Sudbury region sites ............................ 27
Table 8: Fungi species isolated from the different sites within the Greater Sudbury
Region ........................................................................................................................ 46
Table 9: Fungi species and phyla identified in samples from sites within the GSR .............. 57
Table 10: Number of different fungi species within medium for limed and unlimed soil
samples ....................................................................................................................... 61
Table 11: Number of different fungi species within medium for limed, unlimed and
reference sites............................................................................................................. 62
Table 12: Mean fungi abundance within media for limed and unlimed soil samples ........... 67
Table 13: Mean fungi abundance within media for limed, unlimed and reference soil
samples ....................................................................................................................... 67
Table 14: Weekly mean temperature and total rainfall for May 11 – June 11 2012-13 in
Sudbury ...................................................................................................................... 81

ix
Table 15: Weekly mean temperature and total rainfall for Nov. 9 - Dec. 9 2013 in
Sudbury ...................................................................................................................... 81
Table 16: Total fungi abundance and soil respiration for limed, unlimed and reference sites
in the GSR .................................................................................................................. 82
Table 17: Fall soil respiration rates for limed, unlimed and reference sites in the GSR ....... 83
Table 18: Fungi species isolated from samples from limed area at Dam using
SDA medium ........................................................................................................... 117
Table 19 Fungi species isolated from samples from unlimed area at Dam using
SDA medium ........................................................................................................... 118
Table 20: Fungi species isolated from samples from limed area at Dam using
MEA medium........................................................................................................... 119
Table 21: Fungi species isolated from samples from unlimed area at Dam using
MEA medium........................................................................................................... 120
Table 22: Fungi species isolated from samples from limed area at Daisy Lake using
SDA medium ........................................................................................................... 121
Table 23: Fungi species isolated from samples from unlimed area at Daisy Lake using
SDA medium ........................................................................................................... 122
Table 24: Fungi species isolated from samples from limed area at Daisy Lake using
MEA medium........................................................................................................... 123
Table 25: Fungi species isolated from samples from unlimed area at Daisy Lake using
MEA medium........................................................................................................... 124
Table 26: Fungi species isolated from samples from limed area at Kingsway using SDA
medium .................................................................................................................... 125
Table 27: Fungi species isolated from samples from unlimed area at Kingsway using SDA
medium .................................................................................................................... 127
Table 28: Fungi species isolated from samples from limed area at Kingsway using MEA
medium .................................................................................................................... 128
Table 29: Fungi species isolated from samples from unlimed area at Kingsway using MEA
medium ................................................................................................................... 129
Table 30: Fungi species isolated from samples from unlimed area at Kelly Lake using
SDA medium ........................................................................................................... 130
x