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Patrick Neuberger Anthropogenic disturbance alters the microbial biodiversity of permafrost soils by Patrick Neuberger A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Microbiology and Biotechnology Department of Biological Sciences University of Alberta © Patrick Neuberger, 2018 Abstract Anthropogenic climate change and increasing industrial activity is impacting Northern Canada and accelerating permafrost thaw. While research into the impact of permafrost thaw on microbial community dynamics is burgeoning, there has been little investigation into how human activities alter the resident microbial communities of permafrost. To examine the effect of anthropogenically-induced permafrost thaw on living microbial communities, I surveyed a site where permafrost thaw was induced by stripping the area’s vegetation and topsoil in preparation for gold mining near Dominion Creek, Yukon, Canada. I analysed a set of permafrost cores, as well as surface soil samples, across a disturbance gradient from undisturbed forest active layer to disturbed soils, composed of recently thawed permafrost, to a newly formed thermokarst pond. I identified three distinct community groupings within the dataset: (1) undisturbed active layer, (2) lower active layer, disturbed active layer, and disturbed permafrost, and (3) intact permafrost. These groupings indicate that disturbance alters the microbial community of surface soils. Biotic interactions drove differences across these groupings, while within group variation was controlled primarily by pH. This study suggests a strong microbial community response to anthropogenic permafrost disturbance under field conditions and that this response occurs prior to shifts in the measured soil edaphic parameters. Both anthropogenic and natural disturbances to permafrost may induce significant microbial community changes, impacting carbon budgets and carbon feedbacks in permafrost-affected soils. ii Preface This thesis is an original work by Patrick Neuberger. No part of this thesis has been previously published. iii Acknowledgements My sincerest thanks go out to Dr. Brian Lanoil for his guidance, useful advice, as well as his indispensable knowledge and patience. I would also like to thank my committee members, Dr. Duane Froese, Dr. Yan Boucher, and Dr. Suzanne Tank, for their input and advice. Thank you to my friends and lab mates, William Kirby, Alireza Saidi-Mehrabad, and Helena Magaldi, for their support and assistance throughout my Undergraduate and Graduate studies. I also need to extend a thank you to my parents, Herbert Neuberger and Jacqueline Neuberger, as well as my two brothers, Daniel Neuberger and Mitchell Neuberger, for their understanding and encouragement. As well, I am grateful to Marissa Chow, for her love and compassion throughout my studies. Finally, thank you to UAlberta North, Natural Sciences and Engineering Research Council (NSERC), and the Department of Biology for their financial support. iv Table of Contents List of Tables ........................................................................................................................ viii List of Figures .......................................................................................................................... ix Chapter 1: Literature Review ................................................................................................. 1 1.1 Introduction ...................................................................................................................... 1 1.2 Permafrost and Active Layer as Periglacial Soils ............................................................ 4 1.2.1 Geological response of permafrost and active layer to climate change and anthropogenic disturbance .................................................................................................. 7 1.2.2 The chemical response of permafrost subsidence ................................................... 10 1.3.0 Soil Microbiology ....................................................................................................... 13 1.3.1 Drivers of the soil microbiome ................................................................................ 14 1.3.2 The role of biodiversity and community composition in soils ................................ 17 1.3.3 Ecosystem function of soil microbial communities ................................................ 19 1.4.0 Microbial Ecology in Permafrost-Affected Soils ........................................................ 21 1.4.1 Microbial adaptations to the periglacial environment ............................................. 22 1.4.2 Structure and importance of microbial communities in permafrost-affected soils . 23 1.4.3 Distinction of live and dead microorganisms .......................................................... 30 1.5.0 Microbial Responses to Climate Change and Disturbance ......................................... 35 1.5.1 Climate Change in the Arctic .................................................................................. 35 1.5.2 Greenhouse Gas Concentrations .............................................................................. 36 1.5.3 Microbial community responses to permafrost thaw .............................................. 36 1.5.4 Permafrost Carbon Feedback and Microbial Activity ............................................. 42 1.6.0 Research Project .......................................................................................................... 44 1.6.1 The Changing Permafrost Microbial Community ................................................... 44 1.6.2 Research Question and Hypothesis ......................................................................... 44 1.6.3 Aims and Objectives ................................................................................................ 45 1.6.4 Experimental Design ............................................................................................... 45 v Chapter 2: Bacterial community composition changes independently of soil edaphic parameters with anthropogenic permafrost thaw .............................................................. 47 2.1 Originality-Significance Statement ................................................................................ 48 2.2 Abstract .......................................................................................................................... 49 2.3 Introduction .................................................................................................................... 51 2.4 Methods .......................................................................................................................... 55 Field Site and Sampling Procedure .................................................................................. 55 Soil Chemistry Subsampling and Analysis ...................................................................... 59 Biological Subsampling .................................................................................................... 60 Contamination Detection .................................................................................................. 61 16S rRNA Gene Amplicon Sequencing and Analysis ..................................................... 62 Microbiological Diversity, Taxonomy and Assembly ..................................................... 63 Mock Community Analysis .............................................................................................. 65 Cell Enumeration .............................................................................................................. 66 2.5 Results ............................................................................................................................ 67 Edaphic Parameter Analysis ............................................................................................. 67 Viability is negatively impacted by disturbance ............................................................... 70 Diversity of disturbed soil resembles active layer soils ................................................... 73 Microbial community composition shifts with disturbance ............................................. 75 Persistence of permafrost indicator OTUs in disturbed permafrost soils ......................... 79 Community membership of disturbed soils resembles active layer soils ......................... 82 Assembly processes change with disturbance .................................................................. 86 2.6 Discussion ...................................................................................................................... 88 Summary ........................................................................................................................... 88 Anthropogenic Disturbance does not reliably shift edaphic parameters .......................... 89 Drivers of Microbial Community Composition are biotic ............................................... 92 Taxonomic profiles resemble other regional studies across the Arctic ............................ 94 Viability and survivability in permafrost .......................................................................... 95 vi Analogues of natural disturbances .................................................................................... 96 Conclusions ...................................................................................................................... 97
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