Dependence of soil microbial community structure and function on land use types and management regimes Dissertation for the award of the degree ―Doctor rerum naturalium‖ of the Georg-August-Universität Göttingen within the doctoral program Microbiology & Biochemistry of the Georg-August University School of Science (GAUSS) submitted by Kristin Kaiser from Melsungen Göttingen, 2016 Thesis Committee / Members of the Examination Board Prof. Dr. Rolf Daniel, Genomic and Applied Microbiology, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen PD Dr. Michael Hoppert, General Microbiology, Institute for Microbiology and Genetics, Georg- August-Universität Göttingen Prof. Dr. Scheu, Animal Ecology, J.F. Blumenbach Institute for Zoology and Anthropology, Georg-August-Universität Göttingen Further members of the Examination Board Prof. Dr. Kai Heimel, Microbial Cell Biology, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen Prof. Dr. Stefan Vidal, Agricultural Entomology, Department for Cropsciences, Georg- August-Universität Göttingen Prof. Dr. Stefanie Pöggeler, Genetics of Eucaryotic Microorganisms, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen Date of oral examination: 07.07.2016 To my Mom, one of the strongest and most inspiring persons I know, and my Dad, for always believing in me. TABLE OF CONTENTS TABLE OF CONTENTS I. SUMMARY ....................................................................................................................... 9 II. GENERAL INTRODUCTION ..................................................................................... 13 II.1. THE SOIL HABITAT AND ITS MICROBIAL COMMUNITIES ......................................... 14 II.2. PLANT-ASSOCIATED MICROBIAL COMMUNITIES .................................................... 15 II.3. BIODIVERSITY AND BIODIVERSITY LOSS ................................................................. 17 II.4. STUDY REGIONS AND FRAMEWORKS ....................................................................... 19 II.4.1. The German Biodiversity Exploratories .............................................................. 19 II.4.2. The Grassland Management Experiment (GrassMan) ......................................... 23 II.4.3. The Vicia faba L. and Triticum aestivum L. Intercropping Experiment (IMPAC³) ......................................................................................................................... 25 II.5. GENERAL STUDY AIMS ............................................................................................. 25 III. PUBLICATIONS ........................................................................................................... 27 III.1. EFFECTS OF NUCLEIC EXTRACTION METHODS ........................................ 29 Abstract…………………………………………………………………………… 31 Introduction……………………………………………………………………….. 31 Materials and Methods……………………………………………………………. 31 Results……………………………………………………………………………. 35 Discussion………………………………………………………………………… 40 Acknowledgements……………………………………………………………….. 41 References………………………………………………………………………… 41 III.2. DRIVERS OF SOIL BACTERIA ........................................................................... 44 Abstract……………………………………………………………………………. 46 Introduction…………….…………………………………………………………. 46 Results and Discussion..…………………………………………………………... 47 Conclusion……………………………………………………………………….... 53 Materials and Methods…………………………………………………………… .54 References……………………………………………………………………….... 55 Acknowledgements……………………………………………………………….. 57 TABLE OF CONTENTS III.3. TREE SPECIES EFFECTS ON SOIL MICROBIAL COMMUNITIES ............. 58 Abstract .................................................................................................................... 60 Introduction .............................................................................................................. 60 Materials and Methods ............................................................................................. 63 Results and Discussion ............................................................................................. 68 Conclusion ................................................................................................................ 80 Acknowledgements .................................................................................................. 81 References ................................................................................................................ 82 III.4. GROUP-SPECIFIC EFFECTS OF GRASSLAND LAND USE ON SADS ......... 94 Summary .................................................................................................................. 97 Introduction .............................................................................................................. 98 Material and Methods ............................................................................................. 101 Results .................................................................................................................... 106 Discussion .............................................................................................................. 110 Conclusions ............................................................................................................ 114 Acknowledgements ................................................................................................ 115 References .............................................................................................................. 116 III.5. FOREST MANAGEMENT AND BIODIVERSITY ............................................ 122 Abstract .................................................................................................................. 125 Introduction ............................................................................................................ 126 Methods .................................................................................................................. 129 Results and Discussion ........................................................................................... 133 Acknowledgements ................................................................................................ 140 References .............................................................................................................. 141 III.6. BACTERIAL ENDOPHYTES IN IMPORTANT GRASS SPECIES ................ 146 Abstract .................................................................................................................. 148 Introduction ............................................................................................................ 148 Materials and Methods ........................................................................................... 150 Results and Discussion ............................................................................................153 TABLE OF CONTENTS Conclusion .............................................................................................................. 167 References .............................................................................................................. 168 III.7. SOIL ARCHAEAL COMMUNITIES UNDER DIFFERENT CROPPING REGIMES ................................................................................................................ 175 Abstract .................................................................................................................. 177 Introduction ............................................................................................................ 177 Materials and Methods ........................................................................................... 179 Results and Discussion ........................................................................................... 183 Conclusion .............................................................................................................. 195 Acknowledgements ................................................................................................ 196 References .............................................................................................................. 197 III.8. MICROBIAL COMMUNITIES UNDER CROPPING REGIMES ................... 204 Abstract .................................................................................................................. 206 Introduction ............................................................................................................ 206 Material and Methods ............................................................................................. 208 Results and Discussion ........................................................................................... 213 Conclusion .............................................................................................................. 231 References .............................................................................................................. 233 IV. GENERAL DISCUSSION ........................................................................................... 243 IV.1. TERRESTRIAL MICROBES ......................................................................... 246 IV.1.1. Soil bacterial communities and their response to land use intensity .............. 246 IV.1.2. Soil bacterial communities in response to environmental parameters ........... 251 IV.1.3. Bacterial functioning in grasslands