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Soil Microbial Communities in Bioenergy Cropping Systems: Unearthing Relationships Across a Heterogeneous Agroecosystem Sarah Kate Hargreaves Iowa State University

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Soil Microbial Communities in Bioenergy Cropping Systems: Unearthing Relationships Across a Heterogeneous Agroecosystem Sarah Kate Hargreaves Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2014 Soil microbial communities in bioenergy cropping systems: unearthing relationships across a heterogeneous agroecosystem Sarah Kate Hargreaves Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Ecology and Evolutionary Biology Commons, Microbiology Commons, and the Soil Science Commons Recommended Citation Hargreaves, Sarah Kate, "Soil microbial communities in bioenergy cropping systems: unearthing relationships across a heterogeneous agroecosystem" (2014). Graduate Theses and Dissertations. 14003. https://lib.dr.iastate.edu/etd/14003 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Soil microbial communities in bioenergy cropping systems: unearthing relationships across a heterogeneous agroecosystem by Sarah Kate Hargreaves A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Ecology and Evolutionary Biology Program of Study Committee: Kirsten S. Hofmockel, Major Professor Michael J. Castellano Larry J. Halverson Thomas M. Isenhart Timothy P. Parkin Iowa State University Ames, Iowa 2014 Copyright © Sarah Kate Hargreaves, 2014. All rights reserved. ii TABLE OF CONTENTS Page LIST OF TABLES ..................................................................................................... iv LIST OF FIGURES ................................................................................................... vi ACKNOWLEDGEMENTS ....................................................................................... ix ABSTRACT………………………………. .............................................................. xii CHAPTER 1. GENERAL INTRODUCTION 1 Thesis Organization ............................................................................................. 4 References ......................................................................................................... 6 CHAPTER 2. PHYSIOLOGICAL SHIFTS IN THE MICROBIAL COMMUNITY DRIVE CHANGES IN ENZYME ACTIVITY IN A PERENNIAL AGROECOSYSTEM .............................................................................................. 8 Abstract ......................................................................................................... 8 Introduction ......................................................................................................... 9 Methods ......................................................................................................... 12 Results ......................................................................................................... 17 Discussion ......................................................................................................... 20 Conclusions ......................................................................................................... 26 Acknowledgements ............................................................................................. 26 References ......................................................................................................... 27 Tables ......................................................................................................... 36 Figures ......................................................................................................... 38 Supplementary Materials ..................................................................................... 41 Supplementary Materials (not included in publication) ....................................... 42 CHAPTER 3. A MODIFIED INCUBATION METHOD REDUCES ANALYTICAL VARIATION OF SOIL HYDROLASE ASSAYS ......................... 44 Abstract ......................................................................................................... 44 Introduction ......................................................................................................... 45 Materials and methods ........................................................................................ 46 Results ......................................................................................................... 49 Discussion ......................................................................................................... 50 Acknowledgements ............................................................................................. 52 iii Page References ......................................................................................................... 52 Figures ......................................................................................................... 54 Supplementary Materials ..................................................................................... 55 Supplementary Materials (not included for publication) ..................................... 57 CHAPTER 4. HIERARCHICAL INFLUENCES OF TOPOGRAPHY, CROPPING SYSTEM, AND RHIZOSPHERE ON SOIL MICROBIAL COMMUNITIES IN PERENNIAL AND ANNUAL AGROECOSYSTEM ........... 60 Abstract ......................................................................................................... 60 Introduction ......................................................................................................... 61 Materials and methods ........................................................................................ 64 Results ......................................................................................................... 68 Discussion ......................................................................................................... 71 Conclusions ......................................................................................................... 74 Acknowledgments ............................................................................................... 75 References ......................................................................................................... 75 Tables ......................................................................................................... 81 Figures ......................................................................................................... 82 Supplementary Materials ..................................................................................... 86 CHAPTER 5. FINE-SCALE ENVIRONMENTAL HETEROGENEITY STRUCTURES MICROBIAL COMMUNITIES WITHIN AND ACROSS LAND USE ......................................................................................................... 89 Abstract ......................................................................................................... 89 Introduction ......................................................................................................... 90 Materials and methods ........................................................................................ 93 Results ......................................................................................................... 102 Discussion ......................................................................................................... 106 Conclusions ......................................................................................................... 111 Acknowledgements ............................................................................................. 112 References ......................................................................................................... 113 Tables ......................................................................................................... 119 Figures ......................................................................................................... 122 Supplementary Materials ..................................................................................... 131 CHAPTER 6. SUMMARY AND CONCLUSIONS ............................................. 158 iv LIST OF TABLES Page CHAPTER 2 Table 1. Soil characteristics at three sampling dates from an annual (continuous corn) and perennial (switchgrass) agroecosystem (n = 9) ......................... 36 Table 2. Microbial biomass and specific activity in an annual (continuous corn) and perennial (switchgrass) agroecosystem throughout the growing season in 2011 (n = 9) ........................................................................................... 37 Table S1. Pearson correlation coefficients (r) between enzyme activity, microbial activity, and soil physical and chemical properties .................................. 41 Table S2. Microbial biomass and extracellular enzyme activity in a rotated crop agroecosystem (sorghum/triticale) throughout the growing season in 2011 ....................................................................................................... 42 Table S3. Microbial biomass carbon and nitrogen in an annual (continuous corn), perennial (switchgrass) and rotated crop (sorghum/triticale) agroecosystem throughout the growing season in 2012 ............................ 43 CHAPTER 3 Table S1. Selected soil properties and assay buffers used ......................................... 57 CHAPTER 4 Table 1. Significance of ANOVA for microbial richness,
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