Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2017 Scaling approach to microbial interactions in soil across three bioenergy cropping systems Racheal Nichole Upton(Erb) Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Microbiology Commons Recommended Citation Upton(Erb), Racheal Nichole, "Scaling approach to microbial interactions in soil across three bioenergy cropping systems" (2017). Graduate Theses and Dissertations. 16295. https://lib.dr.iastate.edu/etd/16295 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]. Scaling approach to microbial interactions in soil across three bioenergy cropping systems by Racheal Nichole Upton (Racheal Nichole Erb) A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Microbiology Program of Study Committee: Kirsten Hofmockel, Co-Major Professor Brian Wilsey, Co-Major Professor Laura Jarboe Leonor Leandro Torey Looft The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2017 ii TABLE OF CONTENTS Page LIST OF FIGURES ..……………………………………………………………………. iv LIST OF TABLES ………………………………………………………………………. vi ACKNOWLEDGEMENTS ……………………………………………………………… viii ABSTRACT……………………………………………………………………………….. x CHAPTER 1 GENERAL INTRODUCTION ……………………………………………. 1 CHAPTER 2 BELOWGROUND RESPONSE OF PRAIRIE RESTORATION AND RESILIENCY TO DROUGHT…………………………………………. 8 Abstract ..…………………….…………………………………………………… 8 Introduction ...……………………………………………………………………….. 9 Methods ……………….………………………………………………………….. 14 Results ….……………………………………………………………………….. 20 Discussion ……………….………………………………………………………….. 26 References …………………………….…………………………………………….. 32 Tables ……………………………….………………………………………….. 42 Figures .………………………………………………………………………….. 53 Supplemental……………………...…………………………………………………. 58 CHAPTER 3 LOCAL INTERACTIONS OF FUNGAL COMMUNITIES AND SPECIFIC PLANT SPECIES IN IOWAN PRAIRIES……...…………. 59 Abstract ..………………………………………….……………………………… 59 Introduction …………………………………...…………………………………….. 60 Methods …….…………………………………………………………………….. 65 Results ………………………….……………………………………………….. 72 Discussion ………………………………………………….……………………….. 74 References ………………….……………………………………………………….. 81 Tables……………………………………………………………..………………….. 90 Figures ……………………….………………………………………………….. 95 Supplemental…………………………………………………………………………. 99 iii CHAPTER 4 SPATIO-TEMPORAL MICROBIAL COMMUNITY DYNAMICS WITHIN SOIL AGGREGATES …………………………………….. 100 Abstract ..……………………………………………….…………………...…. 100 Introduction ……………………………………………………………………….. 101 Methods ……………………………………..………………………………….. 105 Results ……..………………………………………………………………….. 109 Discussion ……………………………..………………………………………….. 112 References ……………………………………..………………………………….. 117 Figures ………………………………………..……………………………….. 127 Tables ……………………………………..………………………………….. 134 Supplemental ……………………………………………………..……………….. 142 CHAPTER 5 FLUORESCENTLY LABELED CELLULOSE NANOCRYSTALS PROVIDE THE MEANS TO ISOLATE LIVE CELLULOSE DEGRADING CELLS FROM A COMPLEX COMMUNITY ….….. 150 Abstract ..……………………………..………………………………………… 150 Introduction ……………………………………………………………………….. 150 Methods …………………………………………..…………………………….. 152 Results …………..…………………………………………………………….. 158 Discussion ………………………………………..……………………………….. 159 References ……………………………………..………………………………….. 161 Tables ……..………………………………………………………………….. 165 Figures ……………………………..………………………………………….. 166 Supplemental ……………………..………………………………………….. 169 CHAPTER 6 GENERAL CONCLUSIONS ………………………………………… 170 iv LIST OF FIGURES Page Figure 2.1 : Relative mean abundance (%) of fungal classes by cropping system and sampling year……………………………………………………………… 53 Figure 2.2 : PCoA ordinations on Bray-Curtis Dissimilarity of fungal community sequence data with T-normal ordination ellipses…………………………. 54 Figure 2.3 : PCoA ordinations on Bray-Curtis Dissimilarity of bacterial community sequence data with T-normal ordination ellipses…………………………. 55 Figure 2.4 : Mean fungal community richness, evenness, and Shannon’s Diversity Index across cropping systems and sampling year………………………………. 56 Figure 2.5 : Mean bacterial community richness, evenness, and Shannon’s Diversity Index across cropping systems and sampling year…………..……………. 57 Figure 3.1 : Relative mean abundance (%) of fungal classes by cropping system……...… 95 Figure 3.2 : Mean % cover of legumes and fungal richness...............…………………….. 96 Figure 3.3 : PCoA ordinations on Bray-Curtis Dissimilarity of fungal community sequence by abundance of legumes…………………….…………………. 97 Figure 3.4 : Mean fungal community richness by targeted plant functional group……….. 98 Figure 4.1 : PCoA ordinations on Bray-Curtis Dissimilarity of fungal community sequence, by soil aggregate fraction and ecosystem…….………………... 127 Figure 4.2 : PCoA ordinations on Bray-Curtis Dissimilarity of bacterial community sequence, by soil aggregate fraction and ecosystem…….………..………. 128 Figure 4.3 : Mean fungal diversity measurements across soil aggregate fraction and sampling season…………………………………......……………………. 129 Figure 4.4 : Mean bacterial diversity measurements across soil aggregate fraction and sampling season………………………………………….……….………. 130 v Figure 4.5 : Mean fungal diversity measurements across ecosystem treatments………………………………………......……………………. 131 Figure 4.6 : Mean bacterial diversity measurements across ecosystem treatments………………………………………......……………………. 132 Figure 4.7 : Conceptual model of increases in diversity across our field site…………… 133 Figure 5.1 : Cumulative respiration over time………...…….…………………………... 166 Figure 5.2 : Optical density over time…………….…….………..……………………… 167 Figure 5.3 : Fluorescently labeled cells microscopic images, pre-sorting by FACS …… 168 Figure S5.1 : Methods overview of cellulose nancrystal incubation experiment........…...169 vi LIST OF TABLES Page Table 2.1 : Extracellular enzyme activity assay enzymes and substrates…………...……… 42 Table 2.2 : Results of main model effects on fungal and bacterial diversity measurements, abundant phyla, and potential extracellular enzyme activity………………. 43 Table 2.3 : Mean resiliency indices for bacterial and fungal richness and extracellular enzyme activity…………..…………...……………………………………. 45 Table 2.4 : Mean abundance of fungal phyla………………………………………………. 45 Table 2.5 : Indicator fungal families by cropping system and sampling year..…………….. 46 Table 2.6 : Mean abundance of bacterial phyla………………………..…………...………. 48 Table 2.7 : Indicator bacterial families by cropping system and sampling year……..…….. 50 Table 2.8 : Mean potential extracellular enzyme activity by cropping system and sampling year……………………………...……………………………….. 52 Table S2.1 : Environmental data from each sampling year..………………………………. 58 Table 3.1 : Plant functional group and plant species in study…………………………........ 90 Table 3.2 : Extracellular enzyme activity assay enzymes and substrate…………..……….. 92 Table 3.3 : Table of plant species only found in one of the prairie treatments…………….. 92 Table 3.4 : Indicator fungal families in the presence/absence of legumes………...……….. 93 Table 3.5 : Mean potential extracellular enzyme activity in targeted specific plant species/functional groups…………………………………………………... 94 Table S3.1 : Results of correlation test to determine inter-dependency of plant functional groups…………………………………………………………………..…... 99 Table 4.1 : Mean relative abundance of fungal phyla by soil aggregate fraction, ecosystem, and sampling season……….....................…………………….. 134 vii Table 4.2 : Mean relative abundance of bacterial phyla by soil aggregate fraction, ecosystem, and sampling season…………..….………..………………... 137 Table 4.3 : Results of main model effects (soil aggregate fraction, ecosystem treatment, sampling season, and sampling year) on fungal and bacterial diversity measurements…………………………....……………………. 141 Table S4.1 : Mean aggregate size distribution by ecosystem and sampling season and year…………………………..………………………….……….………. 142 Table S4.2 : Indicator fungal families by in the large marcoaggregate soil fraction by sampling season…..……………………………......……………………. 144 Table S4.3 : Indicator fungal families by in the small mircoaggregate soil fraction by sampling season…..……………………………......……………………. 145 Table S4.4 : Indicator bacterial families by in the large marcoaggregate soil fraction by sampling season…..……………………………......……………………. 146 Table S4.5 : Indicator bacterial families by in the small mircoaggregate soil fraction by sampling season…..……………………………......……………………. 148 Table 5.1 : Sorting event counts by rep for unlabeled and labeled events ..……………... 165 viii ACKNOWLEDGEMENTS I would like to thank my major professor, Kirsten Hofmockel, for all the support and cheerleading she has provided. Kirsten allowed me to explore a whole range of research topics and experiences that I would not have the opportunity to experience without her. I would also like to thank my committee, Brian Wilsey, Torey Looft, Leonor Leandro, and Laura Jarboe for their thoughtful insights