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

257 Pages·2014·3.75 MB·English
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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 project report. I also reserve the right to use in future works (such as articles or books) all or part of this thesis, 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 publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that this copy is being made available in this form by the authority of the copyright owner solely for the purpose of private study and research and may not be copied or reproduced except as permitted 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

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Sudbury Region. This study aimed at identifying the fungal species and abundance in limed and study (Swer, Dkhar & Kayang, 2011). This lends
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