Black fungi are recently described microorganisms and amongst the most stress-tolerant eukaryotes currently known. They are a taxonomically diverse, but morphologically similar group of filamentous fungi that share two distinct signature characteristics, i.e. melanisation of the cell wall and compact colony morphology, which confer them passive, constituent extremotolerance. Albeit morphologically undifferentiated, black fungi show extensive phylogenetic and ecological diversity. Due to their persistence in unfavourable niches, they are ubiquitous on deserts and in glaciers and are permanent settlers of rock and other atmosphere-exposed material surfaces as well as man-made environments like salterns, humidifiers and dishwashers, and thus widespread in temperate regions worldwide. Some members are devastating opportunistic pathogens of invertebrates or vertebrates, including humans; others show symbiotic potentials with co-occurring microorganisms in extreme ecosystems. Beside their interest for fundamental biology, black fungi are important for several applied applications, e.g. in biotechnology, astrobiology, bioremediation and material preservation. Despite recent advances in the study of these fungi, many biological questions remain to be clarified regarding the molecular mechanisms underlying persistence, their physiology and nutritional modes, and their specific interactions with putative symbiotic partners. Models for pathogenic and halotolerant black fungi are established; however, no model was yet available for rock- and material-inhabiting ones. This thesis introduces the strain Knufia petricola A95 as a suitable model to study rockinhabiting lifestyle. For this purpose, the strain was characterised at the physiological and molecular levels by phenotype microarrays, growth experiments and genome analyses as well as further methods. Cell-wall mutants of K. petricola A95 isolated during the course of this study were described and included in the comparative analysis to investigate effect of melanisation on physiology and stress tolerance. Direct comparisons were also performed between the model strain and the phylogenetically distant but ecologically, biogeographically and morphologically highly similar rock inhabitant Coniosporium apollinis. Preliminary observations of a model biofilm of K. petricola A95 and the photosynthetic cyanobacterium Nostoc punctiforme ATCC 29133 are introduced to study symbiotic interactions of rock-inhabiting microorganisms. Data presented here are a contribution to the understanding of ecophysiology and extremotolerance of rock-inhabiting black fungi.

ACKNOWLEDGMENTS IX

ABSTRACT XI

ZUSAMMENFASSUNG XIII

TABLE OF CONTENTS XV

1 INTRODUCTION 1

1.1 Life on the rocks – Some like it hot, cold, dry and frugal 1

1.2 Black fungi – Survival of the toughest 2

1.3 Aim of this study 5

2 MATERIALS AND METHODS 7

2.1 Chemicals, solutions and growth media 7

2.2 Microorganisms 10

2.3 Microbiological methods 12

2.4 Molecular biology methods 17

2.5 Biochemical and analytical methods 23

2.6 Microscopical and histological methods 29

2.7 Statistical analyses 30

Summarizing table 32

3 RESULTS 33

PART I – Preliminary results 33

PART II – Phenotypic characterisation of black fungi 37

PART III – Growth in oligotrophic media 83

PART IV – Biochemical and molecular biology results 91

4 DISCUSSION 109

4.1 Phenotypic characterisation of black fungi 110

4.2 Growth of Knufia petricola A95 in oligotrophic media 117

4.3 Description of mutants 119

4.4 Genome analysis of black-fungal strains 121

5 CONCLUSIONS AND OUTLOOK 125

5.1 Black to the future 125

5.2 Celebrating differences – A wealth of mutants 126

5.3 Team play – Analysis of the model subaerial biofilm 126

LITERATURE 129

APPENDIX 143

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