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The Natural Ecology of Saccharomyces Yeasts

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The Natural Ecology of Saccharomyces Yeasts The natural ecology of Saccharomyces yeasts Dissertation in fulfillment of the requirements for the degree "Dr. rer. nat." of the Faculty of Mathematics and Natural Sciences at the Christian Albrechts University of Kiel submitted by Vienna Kowallik Kiel, December 2015 First referee: Dr. Duncan Greig Second referee: Prof. Dr. Hinrich Schulenburg Date of the oral examination: Approved for publication: Table of Contents Abstract ................................................................................................................................................................................... 1 Zusammenfassung ........................................................................................................................................................ 3 General Introduction .................................................................................................................................................. 5 1. General information about Saccharomyces yeasts ................................................................................... 5 1.1. What are yeasts? ........................................................................................................................... 5 1.2. Saccharomyces taxonomy ............................................................................................................. 6 1.3. Saccharomyces life cycle ................................................................................................................ 7 2. S. cerevisiae: humanity's pet yeast ..................................................................................................................... 8 3. S. cerevisiae: the laboratory model organism .............................................................................................. 9 3.1. The early days of yeast research .................................................................................................... 9 3.2. S. cerevisiae´s establishment as model organism ........................................................................ 10 4. The natural ecology of Saccharomyces yeast ............................................................................................. 11 4.1. The problematic lack of ecology knowledge – Why should we care? ......................................... 11 4.1.1. One caveat: the domestication problem of S. cerevisiae .................................................... 12 4.2. The natural environment of Saccharomyces yeast ...................................................................... 13 4.2.1. Saccharomyces: adapted to a fruit habitat? ....................................................................... 14 4.2.2. Saccharomyces: adapted to oak habitat? ........................................................................... 18 4.2.3. Saccharomyces adapted to both; fruit and oak habitat? .................................................... 19 4.2.4. Saccharomyces: not adapted to any specific habitat .......................................................... 20 Scope of this thesis ...................................................................................................................................................... 22 Chapter I The interaction with Saccharomyces paradoxus with its natural competitors on oak bark – published manuscript ............................................................... 22 Supporting Information Chapter I ............................................................................................................................. 39 Table of Contents Chapter II Analysis of the interactions between Saccharomyces paradoxus and two oak bark bacteria (follow up study to Chapter I) ............................................................................................................................................................................ 44 1. Introduction ................................................................................................................................................................. 44 1.1. Background .................................................................................................................................. 44 1.2. Microbial communities remain poorly understood. .................................................................... 45 1.3. The paradox of high biodiversity within microbial communities................................................. 45 1.4. The complexity of microbial communities and the interactions between members .................. 47 1.5. Determining the mechanisms of the interactions between S. paradoxus and two oak bark bacteria ..................................................................................................................................................... 48 2. Methods .......................................................................................................................................................................... 50 2.1. Estimating the effects of the microbial species on each other in competition ........................... 50 2.2. Characterizing the interaction between S. paradoxus and Pseudomonas .................................. 51 2.3. Competition of S. paradoxus with Mucilaginibacter using different initial frequencies…………………………………………………………………………………………………………………………….……………52 2.4. Characterizing the interaction between S. paradoxus and Mucilaginibacter on a temperature gradient ..................................................................................................................................................... 52 2.5. Conditioned media experiments ................................................................................................. 53 3. Results ............................................................................................................................................................................. 53 3.1. Pseudomonas dominates the interaction with S. paradoxus ...................................................... 53 3.2. S. paradoxus and Mucilaginibacter both benefit from the interaction ....................................... 54 3.3. Conditioned media has little effect on the growth of S. paradoxus ............................................ 57 4. Discussion ...................................................................................................................................................................... 58 4.1. S. paradoxus and Pseudomonas interaction is uni-directional with a resulting killing of the yeast..........................................................................................................................................................58 4.2. The interaction between S. paradoxus and Pseudomonas is not frequency-dependent nor strongly regulated by temperature ........................................................................................................... 58 4.3. The killing effect from Pseudomonas depends on the direct presence of the bacterium…. ....... 59 Table of Contents 4.4. The interaction between S. paradoxus and Mucilaginibacter benefits the yeast´s growth……………...…………………………………………………………………………………………………………………………………60 4.5. The interaction of S. paradoxus and Mucilaginibacter is independent of the organism´s frequency but strongly influenced by temperature.................................................................................. 61 4.6. No big effects on S. paradoxus growth using conditioned medium ............................................ 61 4.7. A more natural medium allowed us the detection of more complex interactions ..................... 62 5. Conclusion ..................................................................................................................................................................... 63 6. Supplemental Material ........................................................................................................................................... 64 Chapter III Is the Crabtree effect an adaptation to high sugar environments? ............................................................................................................................................................... 65 1. Introduction ................................................................................................................................................................. 65 1.1. The aerobic and anaerobic metabolism of Saccharomyces spp. ................................................. 65 1.2. The Crabtree effect: an adaptation to high sugar environments? .............................................. 68 1.3. Competition studies in the scientific literature and their interpretation problem ..................... 70 1.4. Use of a Crabtree positive and negative strain in our study ........................................................ 71 1.5. Project aim ................................................................................................................................... 73 2. Methods .......................................................................................................................................................................... 73 2.1. Transformation of drug resistance genes into yeast strains ........................................................ 73 2.2. Experimental design .................................................................................................................... 74 2.3. Testing
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