Microbial Community Structure and Function in Coarse Woody Debris and Boreal Forest Soil after Intensified Biomass Harvests by Emily Elizabeth Smenderovac A thesis submitted in conformity with the requirements for the degree of Masters of Science in Forestry Faculty of Forestry University of Toronto © Copyright by Emily Smenderovac 2014 Microbial Community Structure and Function in Coarse Woody Debris and Boreal Forest Soils under Intensified Biomass Harvests Emily Smenderovac Masters of Science in Forestry Faculty of Forestry University of Toronto 2014 Abstract Intensified biomass harvesting could prove to be negative for forest ecological health through the impacts this type of forest management could exert on microbial community structure and function in forest soils and in CWD pools. Microbial community functional characteristics as well as community structure (through T-RFLP and pyrotag sequencing of ssu rRNA) were assayed soils in a boreal jack pine forest exposed to a clearcut intensified harvesting gradient. Microbial communities within CWD of various decay stages were also assessed in order to determine habitat specificity of the decomposer communities within them. Soil microbial communities were altered by harvesting, but intensification did not cause further disturbance. Soils in harvested sites were different from fire sites also assayed, meaning that these disturbance types may have different impacts on microbial community structure and functioning. CWD communities within logs had different characteristics in different sites. Intensification could reduce site specific organisms important in decay initiation. ii Acknowledgments I would like to acknowledge some associates with whom I have shared in the trials and tribulations of this Masters project. Without the excellent teachings of Michael Preston I don’t know if I would have been able to trust my own T-RFLP data. I must admit that the 80’s music thrumming through the lab was uplifting as well. The guidance of Caroline Sadlier through the intimidating process of learning QIIME turned the program equivalent of a ravenous lion into something closer to one of those inbred lions they use for photo opportunities in Florida. To my supervisor, Nathan Basiliko, you may think it was a huge inconvenience to get me to ship up and move to Sudbury when you switched Universities, but I’m glad you did, I have enjoyed my time here. Also, I appreciate how lucky I was to experience the rare opportunity of having both supervisors Nate Basiliko and John Caspersen visit the field with me. I enjoyed hearing about the professor perspective on academia and publishing while we were sampling CWD and soils; all while I was admiring their seemingly supernatural bug tolerance. I would also like to thank Genevieve Noyce for sampling assistance and for remembering where I was the entire time we were in the field. Also, many thanks to Phil Rudz who initially showed me how to identify decay stages. Without Kara Webster, Dave Morris, Rob Fleming, and Paul Hazlett at CFS, I would not have had the chance to work on the Island Lake sites. They are a beautiful experimental set up and I was very lucky to get a chance to work there. Also, I’d like to acknowledge Stephanie Wilson for completing my microbial biomass assays and teaching me how to conduct large scale enzyme assays and SIR at CFS. This research was funded by NSERC-CRD with industrial support from Tembec Inc., and community partners of the Northeast Superior Regional Chief’s Forum and the Northeast Superior Forest Communities. iii Table of Contents Acknowledgments .......................................................................................................................... iii Table of Contents ........................................................................................................................... iv General Introduction ....................................................................................................................... 1 Incentives for Intensifying Biomass Removal ........................................................................... 2 Forests as Global Carbon Stores ................................................................................................ 2 Ecological Functions of Coarse Woody Debris ......................................................................... 3 Nutritional Contributions to Forest Soils ............................................................................ 4 Biodiversity Maintenance ................................................................................................... 5 Potential Impacts of Harvesting Intensification ......................................................................... 6 Study Summary, Thesis Structure, and Co-Authorship Statement ............................................ 7 Research Objectives and Hypotheses ......................................................................................... 8 Chapter 1 Impacts of Intensified Harvesting on Microbial Community Structure and Function in Boreal Forest Soils ................................................................................................................. 9 1.1 Introduction ......................................................................................................................... 9 1.2 Methods ............................................................................................................................. 11 1.2.1 Study Site .............................................................................................................. 11 1.2.2 Sampling ............................................................................................................... 12 1.2.3 Laboratory Methods .............................................................................................. 12 1.2.4 Statistical Analysis ................................................................................................ 16 1.3 Results ............................................................................................................................... 17 1.3.1 Soil Chemistry and Microbial Biomass ................................................................ 17 1.3.2 T-RFLP based Microbial Richness and Diversity ................................................ 18 1.3.3 Microbial Community Structure and Functioning ................................................ 18 1.3.4 Species associated with harvesting treatments ..................................................... 19 1.4 Discussion ......................................................................................................................... 20 iv 1.4.1 Harvesting impacts on biomass, moisture and microbial community function .... 21 1.4.2 Microbial community structure doesn’t respond noticeably to intensification of clearcut harvesting on short term time scales ................................................... 22 1.4.3 Clear cut harvesting as an analog for fire disturbance .......................................... 25 1.5 Conclusion ........................................................................................................................ 26 Chapter 1 Figures .......................................................................................................................... 27 Chapter 1 Tables ........................................................................................................................... 39 Chapter 2 Coarse Woody Debris Microbial Community Dynamics in Boreal Hardwood and Temperate Mixedwood Forests ................................................................................................ 42 2.1 Introduction ....................................................................................................................... 42 2.2 Methods ............................................................................................................................. 44 2.2.1 Study Sites ............................................................................................................ 44 2.2.2 Decay Classification ............................................................................................. 45 2.2.3 Sampling ............................................................................................................... 46 2.2.4 Laboratory Techniques ......................................................................................... 46 2.2.5 Statistical Analysis ................................................................................................ 48 2.3 Results ............................................................................................................................... 49 2.3.1 Microbial Richness and Diversity ......................................................................... 50 2.3.2 Community Structure ............................................................................................ 50 2.3.3 Indicator Species ................................................................................................... 51 2.3.4 Wood Chemistry and Linkages to Community Structure ..................................... 52 2.4 Discussion ......................................................................................................................... 52 2.4.1 Microbial community change through the decay process ..................................... 52 2.4.2 Site specificity of microbial communities ...........................................................