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Diversity and Taxonomic Novelty of Actinobacteria Isolated from The 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 ....................................................................................................................................
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