UNIVERSITÀ DEGLI STUDI DI TRIESTE XXXI CICLO DEL DOTTORATO DI RICERCA IN AMBIENTE E VITA TITOLO DELLA TESI Phylogenetic relationships among extremotolerant rock- inhabiting fungi and their associations with algae Settore scientifico-disciplinare: BIO/01 DOTTORANDO Claudio Gennaro Ametrano COORDINATORE Prof. Giorgio Alberti SUPERVISORE DI TESI Dr.ssa Lucia Muggia, PhD ANNO ACCADEMICO 2017/2018 Summary Thesis abstract .............................................................................................................................................. 3 Riassunto della tesi ....................................................................................................................................... 4 General introduction ..................................................................................................................................... 5 Chapter 1 .................................................................................................................................................... 7 Extremotolerant black fungi from rocks and lichens .............................................................................. 7 Abstract ........................................................................................................................................................ 7 Introduction .................................................................................................................................................. 7 Phylogenetic relationships of black fungi within Dothideomycetes and Eurotiomycetes ............................. 8 Important features of extremotolerant fungi ............................................................................................... 10 Life styles of black fungi ............................................................................................................................ 14 Links to lichen symbiosis ........................................................................................................................... 15 Omics approaches for the study of black fungi ........................................................................................... 19 Acknowledgments ...................................................................................................................................... 21 References .................................................................................................................................................. 21 Chapter 2 .................................................................................................................................................. 26 Phylogenetic relationships of rock-inhabiting black fungi belonging to the widespread genera Lichenothelia and Saxomyces ................................................................................................................... 26 Abstract ...................................................................................................................................................... 26 Introduction ................................................................................................................................................ 26 Matherials and methods .............................................................................................................................. 28 Results ........................................................................................................................................................ 40 Taxonomy .................................................................................................................................................. 47 Discussion .................................................................................................................................................. 65 Acknowledgements .................................................................................................................................... 67 Funding ...................................................................................................................................................... 67 References .................................................................................................................................................. 67 Chapter 3 .................................................................................................................................................. 71 A standardized approach for co-culturing Dothidealean rock-inhabiting fungi and lichen photobionts in vitro ................................................................................................................................... 71 Abstract ...................................................................................................................................................... 71 Introduction ................................................................................................................................................ 72 Material and Methods ................................................................................................................................. 73 Results ........................................................................................................................................................ 76 Discussion .................................................................................................................................................. 81 Acknowledgments ...................................................................................................................................... 82 References .................................................................................................................................................. 82 1 Chapter 4 .................................................................................................................................................. 84 Genome-scale data suggest an ancestral rock-inhabiting life-style of Dothideomycetes (Ascomycota) ................................................................................................................................................................... 84 Abstract ...................................................................................................................................................... 84 Introduction ................................................................................................................................................ 84 Materials and methods ................................................................................................................................ 85 Results ........................................................................................................................................................ 87 Discussion .................................................................................................................................................. 92 References .................................................................................................................................................. 94 Appendix ................................................................................................................................................... 99 DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy; PLoS One, 13(3), e0194489. ................................................................................................................................................... 99 Abstract ...................................................................................................................................................... 99 Ongoing project - preliminary title: “Trends in diversity and dispersal of airborne spores and pollens are highlighted by one-year survey and DNA metabarcoding” ........................................................................ 99 General conclusions and future perspectives ....................................................................................... 101 Supplementary materials of the manuscript .............................................................................................. 103 Phylogenetic relationships of rock-inhabiting black fungi belonging to the widespread genera Lichenothelia and Saxomyces ................................................................................................................... 103 Supplementary materials for the manuscript ............................................................................................ 121 Genome-scale data suggest an ancestral rock-inhabiting life-style of Dothideomycetes (Ascomycota) ... 121 2 Thesis abstract Fungi with dark-coloured mycelia - also known as black fungi - form a ubiquitous fraction of microbial communities on rock surfaces all over the world. These organisms show a high capacity to adapt to a wide range of ecological conditions, including those peculiar of extreme environments. Their high tolerance to multiple abiotic stresses, such as solar radiation and osmotic stress is assured by the production of melanin pigments and osmoprotective compounds. The cosmopolitan genera Lichenothelia and Saxomyces were taken as iconic representatives of polyextremotolerant rock-inhabiting black fungi. I investigated their phylogenetic relationships with an extended taxon sampling within the class Dothideomycetes, the most diverse