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Nitrogen Cycling Processes and Microbial Communities In NITROGEN CYCLING PROCESSES AND MICROBIAL COMMUNITIES IN RECONSTRUCTED OIL-SANDS SOILS by Jacynthe Masse B.Sc., Université de Montréal, 2009 M.Sc., Université de Montréal, 2011 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in THE FACULTY OF GRADUATE AND POSTDOCTORAL STUDIES (Forestry) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) July 2016 © Jacynthe Masse, 2016 Abstract Covering 140,200 square km, the Athabasca Oil Sands deposit in Alberta is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil- like profiles that can support the previous land capabilities. The overall objective of this thesis was to measure, compare and understand processes underlying nitrogen cycling rates and microbial communities in 20- to 30- year-old reconstructed oil-sands soils and in natural boreal- forest soils. The use of 15N tracer methods in combination with massively parallel sequencing techniques of the 16S and ITS genes identified key dissimilarities between reconstructed and + natural boreal-forest soils. In reconstructed soils, NH4 was mainly cycled through the + recalcitrant organic-N pool. In natural soils, NH4 was produced from the recalcitrant organic-N pool, but predominantly consumed in the labile organic-N pool, suggesting greater prominence of microbial N-cycling activity in the natural soils compared to the reconstructed soils. - Reconstructed soils also produced more NO3 than they immobilized it resulting in net nitrification rates. Prokaryotic and fungal β-diversity, but not α-diversity, differed between reconstructed and natural forest soils. Microorganisms associated with a copiotrophic lifestyle were more abundant in reconstructed soils, whereas microorganisms associated with an oligotrophic lifestyle were more abundant in natural forest soils. Vegetation cover was the main factor influencing prokaryotic and fungal α-diversity in reconstructed and natural forest soils. Nitrogen deposition, pH, soil nutrient content and plant cover influenced prokaryotic and fungal β-diversity. The results of this thesis deepen our understanding of the distinct pedological environments of oil-sands reconstructed soils and highlighted the importance of above- and below-ground interactions in reconstructed and natural ecosystems. ii Preface This study stemmed from an NSERC Collaborative Research and Development grant (PI Sylvie Quideau). As such, Sylvie Quideau, Cindy Prescott and Sue Grayston have identified key research questions and helped in the development of the general research design. Together with Jeff Anderson, Jacynthe Masse selected the specific research sites. Sampling design, soil description and soil collection was done by Jacynthe Masse with the help of Jeff Anderson, Meghan Laidlaw and research assistants (Hannah Mei and Eli Rechtschaffen). Vegetation survey on all sites was done solely by Jeff Anderson. Meghan Laidlaw was the main researcher to carry the microbial biomass measurements. Laboratory work was done by Jacynthe Masse with the help of research assistants. Sébastien Renaut suggested using the massively parallel sequencing techniques for microbial community analyses. Statistical work, data analyses and discussion of the results were done by Jacynthe Masse. Chapters were written by Jacynthe Masse with manuscript edits provided by Cindy Prescott and Sue Grayston. Chapter 2 has been accepted for publication in Geoderma. Masse J., Prescott, C.E., Müller, C., Grayston, S.J. (accepted Geoderma) “Gross nitrogen transformation rates differ in reconstructed oil-sand soils from natural boreal forest soils as revealed using a 15N tracing method” iii • Jacynthe Masse planned the experimental design, did the soil description, soil sampling and laboratory analyses. She also performed the statistical work, data analyses and wrote the manuscript • Cindy Prescott helped with the experimental design and provided manuscript edits. • Christoph Müller designed the original 15N tracing model and used the data provided by J.Masse to model the gross rates of N transformation. He also provided manuscript edits • Sue Grayston helped with the experimental design and provided manuscript edits. Chapter 2 will be submitted: Masse J., Prescott, C.E., Renaut S., Terrat, Y., Grayston S.J. “Vegetation cover and nitrogen deposition as drivers of α- and β- prokaryotic diversity in reconstructed oil-sand soils and in natural boreal forest soils” • Jacynthe Masse planned the experimental design, did the soil description, soil sampling and laboratory analyses. She also performed the statistical work, data analyses and wrote the manuscript • Cindy Prescott helped with the experimental design and provided manuscript edits. • Sébastien Renaut suggested the use of massively parallel techniques to analyze the microbial community and provided help with the bioinformatics work and with the manuscript edits • Yves Terrat provided helped with bioinformatics work and manuscript edits • Sue Grayston helped with the experimental design and provided manuscript edits. iv Table of Contents Abstract .......................................................................................................................................... ii Preface ........................................................................................................................................... iii Table of Contents .......................................................................................................................... v List of Tables ................................................................................................................................ xi List of Figures .............................................................................................................................. xii Acknowledgements ................................................................................................................... xvii Dedication ................................................................................................................................... xix Chapter 1: Introduction ..........................................................................................................................1 1.1 The oil sands in Canada ...........................................................................................................1 1.1.1 The resource .......................................................................................................................................2 1.1.2 The history of the oil sands development in Alberta .........................................................................2 1.1.3 The challenge of ecological restoration in the oil sands ....................................................................5 1.2 Nitrogen cycle ..........................................................................................................................6 1.2.1 Nitrogen fixation ................................................................................................................................8 1.2.2 Depolymerization .............................................................................................................................11 1.2.3 Mineralization ..................................................................................................................................12 1.2.4 Nitrification ......................................................................................................................................13 1.2.5 Denitrification ..................................................................................................................................15 1.2.6 Other nitrogen transformations in soil .............................................................................................17 1.3 Measuring nitrogen cycling processes ...................................................................................19 1.3.1 Measuring pools of N .......................................................................................................................19 v 1.3.2 Measuring net fluxes of N ................................................................................................................20 1.3.3 Measuring gross fluxes of N using analytical methods ...................................................................20 1.3.4 Measuring gross fluxes of N using analytical methods ...................................................................22 1.3.5 Comparison between analytical and numerical methods to measure gross fluxes of N ..................24 1.4 The microbial role in the nitrogen cycle: does diversity matter? ...........................................25 1.5 Impacts of tree species on soil processes and microbial communities ..................................27 1.6 Impacts of forest fire on the nitrogen cycle and soil microbial communities ........................29 1.7 Restoration ecology ................................................................................................................31 1.8 Reclamation of soil nitrogen cycling processes in the Athabasca Region .............................32 1.9 Objectives and hypotheses .....................................................................................................34 Chapter 2: Gross nitrogen transformation rates differ in reconstructed oil-sands soils and natural boreal-forest soils as revealed using a 15N tracing method
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