Villalobos, Alvaro (2018) Diversity and taxonomic novelty of Actinobacteria isolated from the Atacama Desert and their potential to produce antibiotics. (PhD/ Doctoral thesis), Christian-Albrechts-Universität Kiel, Kiel, Germany, 172 pp.

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Abstract

Actinobacteria were isolated from selected environments of the Chilean Altiplano, from the rhizosphere of different plants near Socaire, from two hyper-saline lakes of the Atacama Desert, and from Llullaillaco Volcano Lake. The phylogenetic diversity and the potential of production of antibiotics were studied in a total of 79 isolates. Quite characteristically, each of the studied environments contained a different variety of actinobacteria. Actinobacteria isolated from the rhizosphere of plants close to Socaire revealed the presence of genera known as habitants in the rhizosphere of other plants, promoting its growth both directly and indirectly. Salar de Huasco showed a high diversity of Actinobacteria with Nocardiopsis as the most abundant genus, together with halophile actinobacteria, which are often found in saline environments. Isolates from Salar de Llamará belong exclusively to the micromonosporaceae family, exhibiting similarity with strains obtained from mangroves and marine sediments. Actinobacteria obtained from these environments showed a high number of putative novel species. One of the strains from Salar de Llamará, strain Llam7T, was characterised as a novel genus and species of the Micromonosporaceae family with the name Superstesspora tarapacensis. Another isolate originating from Llullaillaco Volcano Lake was described as a novel species with name Subtercola vilae and type strain DB165T. The characteristics of S. vilae allowing it to survive the cold environmental conditions of Llullaillaco Volcano Lake were identified through functional annotation of its genome, revealing an extensive repertoire of genes involved in membrane modulation, degradation of reactive oxygen species, and ice-binding proteins. More than half of the isolates have the capacity to produce antibiotic substances active against Gram-positive and Gram-negative bacteria. The genomic potential of 7 of the strains affiliated with Streptomyces, Kribbella and Superstesspora tarapcensis was studied and revealed the potential to produce natural products. Most of the biosynthetic gene clusters for natural products revealed only low homology in their gene synteny with entries in databases, and hence might be coding for novel natural product compounds. It is concluded that the Atacama Desert and its actinobacteria constitute a promising source of taxonomic and chemical novelty, providing a cornerstone for future taxonomic studies and secondary metabolite analyses.

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