A peer-reviewed version of this preprint was published in PeerJ on 19 April 2017. View the peer-reviewed version (peerj.com/articles/3162), which is the preferred citable publication unless you specifically need to cite this preprint. Gutiérrez-Preciado A, Vargas-Chávez C, Reyes-Prieto M, Ordoñez OF, Santos-García D, Rosas-Pérez T, Valdivia-Anistro J, Rebollar EA, Saralegui A, Moya A, Merino E, Farías ME, Latorre A, Souza V. 2017. The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions. PeerJ 5:e3162 https://doi.org/10.7717/peerj.3162 Exiguobacterium pavilionensis str. N139, a halotolerant, UV-B and metal resistant bacteria from a high-altitude Andean lake Ana Gutiérrez-Preciado Corresp., 1 , Carlos Vargas-Chávez 1 , Mariana Reyes-Prieto 1 , Omar F Ordoñez 2 , Diego Santos-García 3 , Tania Rosas-Pérez 1 , Jorge Valdivia-Anistro 4 , Eria A Rebollar 5 , Andrés Saralegui 6 , Andrés Moya 1 , Enrique Merino 7, 8 , María Eugenia Farías 9 , Amparo Latorre 1 , Valeria Souza 10 1 Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle Catedrático José Beltrán Martínez 2, 46980, Paterna, Valencia, Spain 2 Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Belgrano y Pasaje Caseros, 4000 , San Miguel de Tucumán, Argentina 3 Department of Entomology, Hebrew University of Jerusalem, Rehovot, Israel 4 Carrera de Biología, Faculta de Estudios Superiores Zaragoza, UNAM, Mexico City, Mexico 5 Department of Biology, James Madison University, Harrisonburg, Virginia, United States of America 6 Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México 7 Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, México 8 Molecular Microbiology, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Apdo. Postal 510-3, Mexico 9 Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas, Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Belgrano y Pasaje Caseros, 4000 , San Miguel de Tucumán, Argentina 10 Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, coyoacan, Mexico City, México Corresponding Author: Ana Gutiérrez-Preciado Email address: [email protected] We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three megaplasmids. The genome analysis suggests the presence of enzymes that confer E. pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals and high ultraviolet B radiation. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina . PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.2512v1 | CC BY 4.0 Open Access | rec: 10 Oct 2016, publ: 10 Oct 2016 1 Exiguobacterium pavilionensis str. N139, a halotolerant, 2 UV-B and metal resistant bacteria from a high-altitude Andean 3 lake 4 5 Ana Gutiérrez-Preciado1†, Carlos Vargas-Chávez1†, Mariana Reyes-Prieto1, Omar F Ordoñez2, Diego 6 Santos-Garcia1, Tania Rosas-Pérez1, Jorge Valdivia-Anistro3, Eria A Rebollar4, Andrés Saralegui5, Andrés 7 Moya1, Enrique Merino6, María Eugenia Farias2, Amparo Latorre1* and Valeria Souza3*. 8 9 *Corresponding authors: Amparo Latorre E-mail: [email protected]; Valeria Souza E-mail: [email protected] 10 †Equal contributors 11 1Unidad de Genética Evolutiva, Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Calle 12 Catedrático José Beltrán Martínez 2, 46980, Paterna, Spain 13 2Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales 14 Microbiológicos (PROIMI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Av. Belgrano y 15 Pasaje Caseros, 4000 San Miguel de Tucumán, Argentina 16 3Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, México D.F., 17 México 18 4Department of Biology, James Madison University, Harrisonburg, Virginia, 22801, United States of America 19 5Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 20 Apdo, Postal 510-3, Cuernavaca, Morelos 62250, México 21 6Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo, 22 Postal 510-3, Cuernavaca, Morelos 62250, México 23 24 Data deposition: This Whole Genome Shotgun project has been deposited at GenBank under the accession 25 JMEH00000000. The version described in this paper is version JMEH001000000.1; BioSample 26 SAMN02732272 27 Abstract 28 We report the genome sequence of Exiguobacterium pavilionensis str. N139, isolated 29 from a high-altitude Andean lake. The 2,952,588-bp genome contains one chromosome and three 30 megaplasmids. The genome analysis suggests the presence of enzymes that confer E. 31 pavilionensis str. N139 the ability to grow under multiple environmental extreme conditions, 32 including high concentrations of different metals and high ultraviolet B radiation. Moreover, the 33 regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, 34 and that these pathways might be fundamental in the amino acid metabolism of the microbial 35 community from Laguna Negra, Argentina. 36 37 38 39 40 Short title: Genome of E. pavilionensis str. N139 41 Keywords 42 Exiguobacterium, High Altitude Andean Lakes, UV resistance, Arsenic resistance, bacterial 43 metabolism, tryptophan biosynthesis, Extremophiles, Metals or Metalloids 44 Abbreviations 45 HAALs: high altitude Andean Lakes ANI: Average Nucleotide Identity LM: Lake Medium 46 SCCore: Single Copy Core SSGs: Strain Specific Genes HGT: Horizontal Gene Transfer 47 BCAA: Branched Chain Amino Acids PER: Photoenzymatic Repair 48 NER: Nucleotide Excision Repair PRR: Post Replication Repair 49 50 51 Introduction 52 The high altitude Andean Lakes (HAALs) from Puna, Argentina, are a group of lakes 53 located at 3000-6000 meters above sea level which are characterized by high ultraviolet (UV) 54 radiation and salinity, broad temperature variations, low nutrient concentrations and high 55 contents of metals and metalloids, mainly arsenic (Fernández-Zenoff et al., 2006; Fernández- 56 Zenoff, Siñeriz & Farías, 2006; Dib et al., 2008; Flores et al., 2009; Ordoñez et al., 2009; 57 Albarracín et al., 2011; Belfiore, Ordoñez & Farías, 2013). These environmental conditions are 58 considered to be extreme and might resemble those of the Earth's early atmosphere, as has been 59 stated by NASA (Cabrol et al., 2007; Farías et al., 2009). Hence, these geographical areas have 60 been proposed for studies on astrobiology (Farías et al., 2009). Despite being oligotrophic and 61 hostile, a great microbial diversity has been found in the HAALs, where bacteria from the genus 62 Exiguobacterium are one of the dominant taxa (Ordoñez et al., 2009, 2013; Sacheti et al., 2013). 63 The Exiguobacterium genus, a sister clade to the Bacillus genus, is currently 64 underexplored, and molecular studies of this genus from different sources are limited 65 (Vishnivetskaya, Kathariou & Tiedje, 2009). Exploring Exiguobacterium strains is of great 66 significance because understanding their strategies to adapt to diverse and extreme 67 environmental conditions will likely place them as model organisms involved in the remediation 68 of organic and inorganic pollutants. In particular, Exiguobacterium strains isolated from the 69 HAALs have the potential of becoming an attractive model system to study environmental stress 70 responses, as these microorganisms are able to grow efficiently in the laboratory (Ordoñez et al., 71 2009; Belfiore, Ordoñez & Farías, 2013). Moreover, Dib et al. suggested that these 72 microorganisms could harbor various stress defense associated systems (Dib et al., 2008). 73 The Exiguobacterium pavilionensis str. N139 was selected for genome sequencing due to 74 its stress defense mechanisms such as its tolerance to high UV-B radiation, salinity and 75 metalloids, particularly arsenic. This strain was isolated from the water column of Laguna Negra, 76 which belongs to the ‘Salar de la Laguna Verde’, a system of five shallow oligotrophic lakes 77 originated in the Tertiary (65 million to 1.8 million years ago). 78 In the present study we characterized the genome of E. pavilionensis str. N139, in order 79 to identify the strategies that this organism employs to cope with the extreme environmental 80 factors present in the aforementioned lake, mainly those related to metal and UV-B resistance. 81 Classification and features 82 Members of the Exiguobacterium genus are Firmicutes, Gram-positive, facultative 83 anaerobes with a low G + C content (Vishnivetskaya, Kathariou & Tiedje, 2009). 84 Exiguobacterium is widely distributed all over the