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Diversity and Function of Root-Associated Fungal Communities in Relation to Nitrogen Nutrition in Temperate Forests

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Diversity and Function of Root-Associated Fungal Communities in Relation to Nitrogen Nutrition in Temperate Forests DIVERSITY AND FUNCTION OF ROOT-ASSOCIATED FUNGAL COMMUNITIES IN RELATION TO NITROGEN NUTRITION IN TEMPERATE FORESTS Dissertation In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (PhD) of the Faculty of Forest Sciences and Forest Ecology, Georg-August-University of Göttingen, Germany Submitted by Quang Dung Nguyen Born in Hanoi, Vietnam Göttingen, 2018 Referee: Prof. Dr. Andrea Polle Co-referee: Prof. Dr. Konstantin V. Krutovsky Date of examination: 18 July 2018 Table of Contents List of abbreviations ............................................................................................................ iv List of figures ...................................................................................................................... vii List of tables ........................................................................................................................ ix Summary ............................................................................................................................. 1 CHAPTER 1 ...................................................................................................................... 10 GENERAL INTRODUCTION ............................................................................................. 10 1.1 Temperate forest ecosystems .................................................................................. 11 1.2 Climate change and its effects on temperate forests ................................................ 12 1.3 Nitrogen in temperate forests ................................................................................... 13 1.4 Root-associated fungi .............................................................................................. 15 1.5 Goals of this thesis................................................................................................... 16 1.6 References .............................................................................................................. 16 CHAPTER 2 ...................................................................................................................... 20 IMPACT OF ECTOMYCORRHIZAL COMMUNITY COMPOSITION AND SOIL TREATMENT ON INORGANIC NITROGEN NUTRITION AND PERFORMANCE OF BEECH (FAGUS SYLVATICA L.) PROVENANCES .......................................................... 20 CHAPTER 3 ...................................................................................................................... 21 BEECH AND FUNGAL TRANSCRIPTOMES IN RESPONSE ........................................... 21 TO DIFFERENT BIOGEOGRAPHICAL ENVIRONMENTS IN TEMPERATE FORESTS ... 21 3.1 Introduction .............................................................................................................. 22 3.2 Materials and methods ............................................................................................. 23 3.2.1 Plant materials and experimental design ........................................................... 23 3.2.2 Harvest .............................................................................................................. 24 3.2.3 RNA extraction .................................................................................................. 25 3.2.4 Library preparation and RNA sequencing .......................................................... 27 3.2.5 Data analysis ..................................................................................................... 27 3.3 Results..................................................................................................................... 28 3.3.1 RNA-Seq output and read mapping ................................................................... 28 3.3.2 Analysis of transcript abundance ....................................................................... 30 3.3.3 Analysis of Gene Ontology (GO) terms.............................................................. 32 3.3.4 Beech and fungal genes related to nitrogen uptake and assimilation ................. 34 3.4 Discussion ............................................................................................................... 39 3.4.1 Limitations of RNA-Seq of beech roots .............................................................. 39 3.4.2 Differentially expressed genes of beech in three biogeographical regions ......... 40 i 3.4.3 N-related genes of beech and fungi ................................................................... 41 3.5 References .............................................................................................................. 42 CHAPTER 4 ...................................................................................................................... 48 ROOT-ASSOCIATED FUNGAL COMMUNITIES AND THEIR RELATIONSHIPS WITH SOIL AND ROOT NITROGEN AND CARBON AVAILABILITY IN TEMPERATE FORESTS .......................................................................................................................................... 48 4.1 Introduction .............................................................................................................. 49 4.2 Materials and methods ............................................................................................. 51 4.2.1 Study site description ........................................................................................ 51 4.2.2 Root and soil sampling ...................................................................................... 53 4.2.3 Analysis of root and soil carbon and nitrogen .................................................... 53 4.2.4 Analysis of non-structural carbohydrates ........................................................... 53 4.2.5 Analysis of soil and root ammonium and nitrate ................................................. 54 4.2.6 Measuring soil pH and soil moisture .................................................................. 55 4.2.7 DNA extraction and amplification of ITS2 .......................................................... 55 4.2.8 Sequence processing and analyses .................................................................. 56 4.2.9 Statistical analysis and calculations ................................................................... 57 4.3 Results..................................................................................................................... 58 4.3.1 Soil and root chemistry varies among biogeographic regions ............................ 58 4.3.2 Characterization of the abundance and richness of root-associated fungi ......... 60 4.3.3 Taxonomic and trophic community structures of root-associated fungi .............. 62 4.3.4 Drivers for the changes in root-associated fungal communities in three biogeographic regions ................................................................................................ 64 4.4 Discussion ............................................................................................................... 67 4.4.1 Differentiation in taxonomic and trophic communities of root-associated fungi across the three biogeographical regions .......................................................... 67 4.4.2 Root and soil factors correlated with trophic and taxonomic groups of root- associated fungi ......................................................................................................... 68 4.5 References .............................................................................................................. 70 CHAPTER 5 ...................................................................................................................... 77 CONCLUSION AND OUTLOOK ........................................................................................ 77 5.1 Conclusion ............................................................................................................... 78 5.2 Outlook .................................................................................................................... 80 APPENDICES ................................................................................................................... 81 Declarations of the author’s contributions ........................................................................ 106 Scientific activities during the PhD studies ...................................................................... 107 Curriculum vitae .............................................................................................................. 109 ii Acknowledgments ........................................................................................................... 110 Declaration of originality and certificate of authorship ...................................................... 112 iii List of abbreviations 15 15 + 15Am whole plant N content after labeling with NH4 15Am_R_S relative aboveground allocation of plant 15N after labeling with ammonium 15 15 - 15Ni whole plant N content after labeling with NO3 15Ni_R_S relative aboveground allocation of plant 15N after lableling with nitrate A Schwäbische Alb AGI arabidopsis genome initiative AIC Akaike's information criterion ANOSIM Analyses of similarity ANOVA analysis of variance BM whole plant biomass BTE beech transplantation experiment C carbon Cege Cenococcum geophilum DEG differentially expressed genes DFG German Research Foundation DNA deoxyribonucleic acid dNTPs deoxynucleotide EC enzyme commission EEA European Environment Agency EH species evenness EM ectomycorrhiza
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