Impact of Rain Forest Transformation on Roots and Functional Diversity of Root-Associated Fungal Communities Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades "Doctor rerum naturalium" der Georg-August-Universit¨atG¨ottingen im Promotionsprogramm "Grundprogramm Biologie" der Georg-August University School of Science (GAUSS) vorgelegt von: Josephine Sahner aus Berlin G¨ottingen,2016 Betreuungsausschuss Prof. Dr. Andrea Polle, Department of Forest Botany and Tree Physiology, B¨usgen- Institute Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology Mitglieder der Pr¨ufungskommission Referentin: Prof. Dr. Andrea Polle, Department of Forest Botany and Tree Physiology, B¨usgen-Institute Korreferent: Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology Weitere Mitglieder der Pr¨ufungskommission: Prof. Dr. Holger Kreft, Biodiversity, Macroecology & Conservation Biogeography Group, Faculty of Forest Sciences and Forest Ecology Prof. Dr. Edzo Veldkamp, Soil Science of Tropical and Subtropical Exosystems, B¨usgen- Institute Prof. Dr. Thomas Friedl, Experimental Phycology and Culture Collection of Algae at the University of G¨ottingen PD Dirk Gansert, Centre of biodiversity and sustainable land use, Section: Biodiversity, ecology and nature conservation Tag der m¨undlichenPr¨ufung:13.12.2016 placeholder Table of Contents List of Figures ix List of Tables xi List of Abbreviations xiii Summary 1 1 General Introduction 6 1.1 Anthropogenic Land Use { a Driver for Global Change . 7 1.2 Deforestation in The Tropics . 7 1.3 Rubber Trees and Oil Palms { Main Actors for Land Use Changes in Indonesia . 8 1.4 The Impact of Land Use Changes on Plant Diversity . 10 1.5 Plants and their Associated Microorganisms . 11 1.6 Plant Root-Associated Fungal Communities . 12 1.6.1 Mycorrhizal Fungi . 13 1.6.2 Plant Pathogenic Fungi . 14 1.6.3 Saprotrophic Fungi . 14 1.7 Metagenomics and Functional Trait-Based Approaches to Investigate Hyper- divers Communities . 15 1.8 Scope of this Thesis . 15 1.9 References . 17 2 Degradation of Root Community Traits as Indicator for Transformation of Tropical Lowland Rain Forests into Oil Palm an Rubber Plantations 27 2.1 Introduction . 27 2.2 Materials and Methods . 29 2.2.1 Site Description . 29 2.2.2 Sampling and Export Permission . 29 2.2.3 Sampling Design . 31 2.2.4 Sample Preparation . 32 2.2.5 Analysis of Root Vitality and Ectomycorrhizal Colonization . 33 2.2.6 Arbuscular Mycorrhizal Colonization . 33 iv TABLE OF CONTENTS 2.2.7 Determination of Arbuscular Mycorrhizal Spore Abundance . 34 2.2.8 Element Analysis in Plant and Soil fractions . 35 2.2.9 Determination of Soil pH . 36 2.2.10 Maps of the Sampling Site . 36 2.2.11 Data Analysis . 36 2.2.12 Data Deposition and Availability . 37 2.3 Results . 37 2.3.1 Root Community-Weighed Traits are Massively Affected by the Land Use System . 37 2.3.2 Root Community-Weighed Traits Indicate Transformation Intensity . 38 2.3.3 Transformation Intensity is Linked with Ecosystem Properties . 42 2.4 Discussion . 46 2.4.1 Root Community-Weighed Traits and Soil Properties Vary with Forest Transformation . 46 2.4.2 Degradation of Root Health is Related to Accumulation of Plant Toxic Elements . 48 2.5 Acknowledgments . 50 2.6 Author Contributions . 50 2.7 References . 51 3 The Impact on Roots and Functional Diversity of Root-Associated Fungal Communities 57 3.1 Introduction . 58 3.2 Material and Methods . 61 3.2.1 Sites . 61 3.2.2 Sampling . 62 3.2.3 Sampling and Export Permission . 63 3.2.4 Calculation of Land Use Intensity Index . 65 3.2.5 DNA Extraction from Root Communities . 65 3.2.6 Amplicon Library Preparation for Illumina Sequencing . 66 3.2.7 Sequencing Processing . 68 3.2.8 Statistical Analysis . 69 3.3 Results . 72 v TABLE OF CONTENTS 3.3.1 Diversity and Composition of Root-Associated Fungal Communities in Four Different Land Use Systems . 72 3.3.2 Taxonomic Composition of Root-Associated Fungal Communities . 79 3.3.3 Land Use Intensity of the Investigated Core Plots . 81 3.3.4 Dissimilarities of Root-Associated Fungal Communities Referring to Land Use . 83 3.3.5 Assignment of Root-Associated Fungal OTUs to Guilds and Functional Groups . 85 3.3.6 Contribution of Specific Fungal Genera Assigned to an Ecological Guild to Dissimilarities Among Root-associated Fungal Communities From Different Land Use Systems . 86 3.3.7 Shifts Among Functional Groups Referring to Different Land Use Systems 90 3.3.8 Dissimilarities Within the Communities of Different Functional Groups . 93 3.4 Discussion . 95 3.4.1 Research on Fungal Diversity Conducted in Tropical Region . 95 3.4.2 Differences of Fungal OTU Richness Across Land Use Systems . 96 3.4.3 Different Patterns in OTU Richness of Root-Associated Fungal Com- munities in Land Use Systems of the Two Landscapes . 97 3.4.4 Root-Associated Fungal Community Composition was Affected by Land Use Change . 98 3.4.5 Ecological Fungal Guilds: Abundances in and Shift Between Land Use Systems . 99 3.5 References . 102 4 Comparisons of Illumina Sequencing and 454 Pyrosequencing on Fungal Community Samples 110 4.1 Introduction . 111 4.2 Materials and Methods . 116 4.2.1 Study Sites and Sampling . 116 4.2.2 DNA Extraction . 117 4.2.3 Primer Choice for 454 Pyrosequencing and Illumina MiSeq Sequencing 117 4.2.4 Amplicon Library Preparation for 454 Pyrosequencing . 118 4.2.5 Amplicon Library Preparation for Illumina MiSeq Sequencing . 120 vi TABLE OF CONTENTS 4.2.6 Sequence Processing . 120 4.2.7 Data Analyses . 121 4.3 Results . 123 4.3.1 Higher OTU Richness and Sequence Richness of Root-Associated Fun- gal Communities Analyzed by Illumina Sequencing . 123 4.3.2 Alpha and Beta-Diversity of Root-Associated Fungal Communities are not Influenced by the Applied NGS Technique and Related Differential Barcoding of Fungal DNA . 129 4.3.3 Taxonomic Composition of Root-Associated Fungal Communities were Similar Between Root Community Samples Analyzed by Illumina Se- quencing and 454 Pyrosequencing . 132 4.3.4 The Applied NGS Technique had no Influence on the Relative Abun- dance of Selected Fungal Orders and Genera . 135 4.4 Discussion . 138 4.4.1 Effect of Applied NGS Technique and Related Sequenced Fungal Bar- code on Obtained Results on Fungal OTU and Sequence Richness . 138 4.4.2 Effects of the Applied NGS Techniques and Related Differing Sequenced Fungal Barcode Regions on Alpha- and Beta-Diversity . 139 4.4.3 The Detection of the Taxonomic Composition of Root-Associated Fun- gal Communities is Affected by the Applied NGS Techniques and Dif- ferent DNA Barcode Regions . 140 4.4.4 Taxonomic Overlap and Distinctness of Root-Associated Fungal Com- munities Investigated by Two Different NGS Techniques . 141 4.4.5 Validation of Data on Relative Abundances of Fungal OTUs Belonging to Selected Fungal Genera with a Proven Ecological Function . 142 4.5 References . 143 5 Synthesis 148 5.1 The Broader Frame of this Thesis . 149 5.2 Relationship Between Root Community Traits, Fungal OTU Richness and Eco- logical Functions . 150 5.3 Conclusion and Outlook . 155 5.4 References . 156 vii TABLE OF CONTENTS 6 Supplements xiv Declaration of the Authors Own Contributions xxxiv Acknowledgments xxxv Curriculum Vitae xxxvii Eidestattliche Erkl¨arung xxxviii viii List of Figures 1.2.1 Changes in Land Coverage with Forest and Deforestation in Sumatra. 8 1.3.1 Extensive and Intensive Rubber Cultivation in Sumatra . 9 1.3.2 Oil Palm Cultivation in Sumatra . 10 1.5.1 Plants and their Associated Microorganisms . 12 2.2.1 Maps of the Province Jambi (A) with the Landscapes Bukit12 (B) and Harapan (C) on Sumatra (Indonesia) . 30 2.3.1 Chemical Composition of Roots in Different Land Use Systems . 40 2.3.2 Performance Parameters of Roots in Different Land Use Systems . 41 2.3.3 Principle Component Analysis of Root Community-Weighed Traits . 42 2.3.4 Non-Metric Multidimensional Scaling (NMDS) of Root Community-Weighed Traits . 44 3.2.1 Maps of the Province of Jambi (A) with the Bukit12 (B) and Harapan (C) landscapes on Sumatra (Indonesia) . 62 3.2.2 Setup for Freeze Drying and Storage of Fine Root Material . 64 3.3.1 Richness of Rarified Fungal Sequences and OTUs on Land Use Landscape Level . 75 3.3.2 Rarefaction Curve on Core Plot Level Rarified to 12.789 Sequences in the Two Different Landscapes . 76 3.3.3 Fungal OTU Richness of Samples Rarified to 12.789 Sequences . 77 3.3.4 Venn Diagram of Shared and Unique Shared Fungal OTUs Among the Four Different Land Use Systems . 78 3.3.5 Relative Abundances of Fungal Phyla (A) and Orders (B) in Four Different Land Use Systems . 80 3.3.6 Land Use Intensity of the Four Investigated Different Land Use Systems . 83 3.3.7 Non-Metric Multidimensional Scaling (NMDS) of Fungal OTU Communities Based on Bray Curtis Distance Matric . 84 3.3.8 Relative Abundances of Fungal Genera Assigned to Ecological Guilds in Four Different Land Use Systems . 87 3.3.9 Contribution of Fungal Genera to the Dissimilarity of Whole Fungal Com- munities in the Four Different Land Use Systems . ..