Diversity and taxonomic novelty of Actinobacteria isolated from the Atacama Desert and their potential to produce antibiotics Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel Vorgelegt von Alvaro S. Villalobos Kiel 2018 Referent: Prof. Dr. Johannes F. Imhoff Korreferent: Prof. Dr. Ute Hentschel Humeida Tag der mündlichen Prüfung: Zum Druck genehmigt: 03.12.2018 gez. Prof. Dr. Frank Kempken, Dekan Table of contents Summary .......................................................................................................................................... 1 Zusammenfassung ............................................................................................................................ 2 Introduction ...................................................................................................................................... 3 Geological and climatic background of Atacama Desert ............................................................. 3 Microbiology of Atacama Desert ................................................................................................. 5 Natural products from Atacama Desert ........................................................................................ 9 References .................................................................................................................................. 12 Aim of the thesis ............................................................................................................................ 16 Chapter I: Diversity and antibiotic activity of Actinobacteria isolated from the rhizosphere of endemic plants near Socaire, Chile ................................................................................................ 17 Abstract ....................................................................................................................................... 18 Introduction ................................................................................................................................ 19 Materials and methods ................................................................................................................ 20 Samples ................................................................................................................................... 20 Isolation of Actinobacteria ...................................................................................................... 20 16S rRNA gene sequencing, identification, and phylogenetic analysis ................................. 21 Antibiotic activity ................................................................................................................... 21 Results ........................................................................................................................................ 22 Discussion ................................................................................................................................... 29 References .................................................................................................................................. 30 Chapter II: Phylogenetic diversity and antibiotic activity of Actinobacteria from hypersaline lakes in the Atacama Desert, Chile. ......................................................................................................... 33 Abstract ....................................................................................................................................... 34 Introduction ................................................................................................................................ 35 Materials and methods ................................................................................................................ 36 Sampling ................................................................................................................................. 36 Isolation of Actinobacteria ...................................................................................................... 36 Antimicrobial activity test ....................................................................................................... 38 Results ........................................................................................................................................ 39 Isolation and identification of Actinobacteria ......................................................................... 39 Antimicrobial activity ............................................................................................................. 47 Discussion ................................................................................................................................... 49 Conclusions ................................................................................................................................ 53 Acknowledgements .................................................................................................................... 53 References .................................................................................................................................. 54 Chapter III: Superstesspora tarapacensis gen. nov., sp. nov., a new member of the Micromonosporaceae family from the hypersaline Salar de Llamará, Chile ................................ 61 Abstract ....................................................................................................................................... 62 Introduction ................................................................................................................................ 63 Phenotypic and chemotaxonomic characterisation ..................................................................... 63 Phylogeny ................................................................................................................................... 69 Proposal of Superstesspora gen. sp. nov. ................................................................................... 71 Description of Superstesspora gen. nov. .................................................................................... 77 Description of Superstesspora tarapacensis sp. nov. ................................................................. 77 Protologue ................................................................................................................................... 78 Author Statements ...................................................................................................................... 78 Abbreviations .............................................................................................................................. 78 References .................................................................................................................................. 79 Chapter IV: Subtercola vilae sp. nov., a new Actinobacterium from an extremely high-altitude cold volcano lake in Chile .............................................................................................................. 83 Abstract ....................................................................................................................................... 84 Introduction ................................................................................................................................ 85 Materials and methods ................................................................................................................ 85 Isolation and cell morphology ................................................................................................ 85 Physiological characteristics ................................................................................................... 86 Chemotaxonomic analyses ...................................................................................................... 86 DNA base composition ........................................................................................................... 86 Phylogenetic analyses ............................................................................................................. 87 Results ........................................................................................................................................ 87 Chemotaxonomic characteristics ............................................................................................ 90 16S rRNA gene sequence analyses ......................................................................................... 92 Discussion ................................................................................................................................... 93 Description of Subtercola vilae sp. nov. ..................................................................................... 97 Acknowledgements .................................................................................................................... 98 References .................................................................................................................................. 99 Chapter V: Cold-adaptation of Subtercola vilae DB165T an isolate from a high-altitude cold volcano lake as revealed by its genome analysis ......................................................................... 102 Abstract ....................................................................................................................................