The role of microorganisms in the nutrient cycling of subtropical savannah soils Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades einer Doktorin der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Katharina Julia Huber aus Erding 1. Referent: Professor Dr. Jörg Overmann 2. Referent: Professor Dr. Dieter Jahn eingereicht am: 03.09.2014 mündliche Prüfung (Disputation) am: 08.12.2014 Druckjahr 2015 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Huber, K. J.. Wüst, P. K., Grönemeyer, J. L., Burbano, C. S., Reinhold-Hurek, B. & Overmann, J. Microbiology - Mashare. In: Oldeland, J., Erb, C., Finckh, M. & Jürgens, N. [Eds.]: Environmental Assessments in the Okavango Region. Biodiversity & Ecology 5: 109– 111 (2013). Huber, K. J., Wüst, P. K., Rohde, M., Overmann, J. & Foesel, B. U. Aridibacter famidurans gen. nov., sp. nov. and Aridibacter kavangonensis, two novel members of subdivision 4 of the Acidobacteria isolated from semiarid savannah soil. IJSEM: 64: 1866-1875 (2014). Tagungsbeiträge Huber, K. J., Wüst, P. K., Fösel, B. U. & Overmann, J. Ammonification and nitrification rates depend on soil and land use type of subtropical savannah soils. (Poster) Vereinigung für Allgemeine und Angewandte Mikrobiologie Jahrestagung 2012, Tübbingen (2012). Huber, K. J., Wüst, P. K., Fösel, B. U. & Overmann, J. Soil and land use type affect the structure and function of bacterial community in subtropical savannah soils. (Poster) Vereinigung für Allgemeine und Angewandte Mikrobiologie Jahrestagung 2013, Bremen (2013). To my precious mother Anna and beloved sister Verena Contents Chapter 1 Summary ................................................................................................................. 1 Chapter 2 General Introduction ............................................................................................. 4 2.1. Microorganisms and their relevance for nutrient cycling .............................................. 4 2.2. Nutrient cycles ................................................................................................................ 5 2.2.1. Carbon cycle ............................................................................................................. 5 2.2.2. Nitrogen cycle .......................................................................................................... 6 2.2.3. Phosphorus cycle ...................................................................................................... 7 2.3. The ecosystem soil and its microbial community .......................................................... 8 2.4. Subsaharan Namibian and Angolan savannah soils and microbial community ............. 9 2.4.1. Soil types .................................................................................................................. 9 2.4.2. Land use types ........................................................................................................ 10 2.4.3. Climate and seasonal variability of water availability ........................................... 12 2.5. Analysis of soil microbial diversity and activity .......................................................... 12 2.5.1. Microbial diversity ................................................................................................. 12 2.5.2. Microbial activity ................................................................................................... 14 2.6. Aims and background information of the present study .............................................. 15 2.7. References .................................................................................................................... 16 Chapter 3 Variations and controls of hydrolytic exoenzyme activities in Subsaharan savannah soils ....................................................................................................... 21 3.1. Contribution of the authors .......................................................................................... 21 3.2. Abstract ........................................................................................................................ 22 3.3. Introduction .................................................................................................................. 23 3.4. Materials and Methods ................................................................................................. 25 3.4.1 Study site ................................................................................................................ 25 3.4.2 Soil sampling and characteristics ........................................................................... 27 3.4.3 Total cell counts ..................................................................................................... 27 3.4.4 Exoenzyme activity ................................................................................................ 28 3.4.5 Multivariate statistical analysis .............................................................................. 29 3.5. Results .......................................................................................................................... 31 3.5.1 Soil physicochemistry, bacterial cell numbers and land use .................................. 31 3.5.2 Microbial exoenzyme activities and kinetics ......................................................... 32 3.5.3 Multiple regression and multivariate statistical analysis ........................................ 35 3.6. Discussion .................................................................................................................... 39 3.6.1 Interrelation of geochemical soil conditions and bacterial activities in arenosols . 39 3.6.2 Specific bacterial responses to environmental conditions in arenosols ................. 41 3.6.3 Implications for land management ......................................................................... 42 3.7. Acknowledgement ........................................................................................................ 43 3.8. References .................................................................................................................... 44 3.9. Supplementary Tables .................................................................................................. 47 3.10. Supplementary Figures ................................................................................................. 50 Chapter 4 Environmental controls and microbial drivers of nutrient cycling in low-fertility semiarid savannah soils .......................................................................................... 53 4.1. Contribution of the authors .......................................................................................... 53 4.2. Abstract ........................................................................................................................ 54 4.3. Introduction .................................................................................................................. 55 4.4. Materials and Methods ................................................................................................. 57 4.4.1 Study sites .............................................................................................................. 57 4.4.2 Soil sampling .......................................................................................................... 59 4.4.3 Total bacterial cell numbers ................................................................................... 59 4.4.4 Exoenzyme activity assay ...................................................................................... 59 4.4.5 Nitrogen turnover rates (Pool Dilution Technique) ............................................... 60 4.4.6 Stimulation experiment and metatranscriptomics .................................................. 62 4.4.6.1. Field incubation ................................................................................................ 62 4.4.6.2. RNA extraction ................................................................................................ 63 4.4.6.3. Library preparation and Illumina sequencing .................................................. 64 4.4.6.3.1. ScriptSeq Libraries .............................................................................. 64 4.4.6.3.2. Amplicons ............................................................................................ 65 4.4.6.4. Bioinformatic analysis/Metatranscriptome pipeline ........................................ 66 4.5. Results .......................................................................................................................... 68 4.5.1. Soil physicochemistry and total cell numbers ........................................................ 68 4.5.2. Exoenzyme activities .............................................................................................. 68 4.5.3. Nitrogen turnover rates: ammonification and nitrification in subtropical savannah soils ......................................................................................................................... 69 4.5.4. Composition of the active soil microbial community ...........................................