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      First Report on the Plasmidome From a High-Altitude Lake of the Andean Puna

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          Abstract

          Mobile genetic elements, including plasmids, drive the evolution of prokaryotic genomes through the horizontal transfer of genes allowing genetic exchange between bacteria. Moreover, plasmids carry accessory genes, which encode functions that may offer an advantage to the host. Thus, it is expected that in a certain ecological niche, plasmids are enriched in accessory functions, which are important for their hosts to proliferate in that niche. Puquio de Campo Naranja is a high-altitude lake from the Andean Puna exposed to multiple extreme conditions, including high UV radiation, alkalinity, high concentrations of arsenic, heavy metals, dissolved salts, high thermal amplitude and low O 2 pressure. Microorganisms living in this lake need to develop efficient mechanisms and strategies to cope under these conditions. The aim of this study was to characterize the plasmidome of microbialites from Puquio de Campo Naranja, and identify potential hosts and encoded functions using a deep-sequencing approach. The potential ecological impact of the plasmidome, including plasmids from cultivable and non-cultivable microorganisms, is described for the first time in a lake representing an extreme environment of the Puna. This study showed that the recovered genetic information for the plasmidome was novel in comparison to the metagenome derived from the same environment. The study of the total plasmid population allowed the identification of genetic features typically encoded by plasmids, such as resistance and virulence factors. The resistance genes comprised resistances to heavy metals, antibiotics and stress factors. These results highlight the key role of plasmids for their hosts and impact of extrachromosomal elements to thrive in a certain ecological niche.

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          Most cited references79

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          ISfinder: the reference centre for bacterial insertion sequences

          ISfinder () is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.
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            Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

            The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.
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              INTEGRALL: a database and search engine for integrons, integrases and gene cassettes.

              INTEGRALL is a freely available, text-based search system developed with the aim of collecting and organizing information on integrons in a single database. The current release (1.2) contains more than 4800 integron sequences and provides a public genetic repository for sequence data and nomenclature, offering scientists an easy and interactive access to integron's DNA sequences, their molecular arrangements as well as their genetic contexts.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                23 June 2020
                2020
                : 11
                : 1343
                Affiliations
                [1] 1Planta Piloto de Procesos Industriales Microbiológicos, Consejo Nacional de Investigaciones Científicas y Técnicas , San Miguel de Tucumán, Argentina
                [2] 2Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen , Göttingen, Germany
                [3] 3Línea Tecnológica Biocorrosión, Corporación para la Investigación de la Corrosión C.I.C. , Piedecuesta, Colombia
                [4] 4Facultad de Bioquímica, Química y Farmacia, Instituto de Microbiología, Universidad Nacional de Tucumán , San Miguel de Tucumán, Argentina
                Author notes

                Edited by: Jesse G. Dillon, California State University Long Beach, United States

                Reviewed by: Dariusz Bartosik, University of Warsaw, Poland; Christopher Morton Thomas, University of Birmingham, United Kingdom

                *Correspondence: Rolf Daniel, rdaniel@ 123456gwdg.de

                This article was submitted to Extreme Microbiology, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2020.01343
                7324554
                32655530
                9179c688-ae6c-4b5a-b456-94faabaad193
                Copyright © 2020 Perez, Kurth, Farías, Soria, Castillo Villamizar, Poehlein, Daniel and Dib.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 11 January 2020
                : 26 May 2020
                Page count
                Figures: 8, Tables: 1, Equations: 0, References: 97, Pages: 15, Words: 0
                Funding
                Funded by: Consejo Nacional de Investigaciones Científicas y Técnicas 10.13039/501100002923
                Funded by: Agencia Nacional de Promoción Científica y Tecnológica 10.13039/501100003074
                Categories
                Microbiology
                Original Research

                Microbiology & Virology
                plasmidome,extreme environment,resistance,high-altitude lake,andean puna,functional profile

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