Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar De Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance
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fmicb-08-00456 March 21, 2017 Time: 10:32 # 1 ORIGINAL RESEARCH published: 21 March 2017 doi: 10.3389/fmicb.2017.00456 Comparative Genomics Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals a Repertoire of Stress-Related Genes and Arsenic Resistance Juan Castro-Severyn1,2†, Francisco Remonsellez3†, Sandro L. Valenzuela2, Cesar Salinas1, Jonathan Fortt3, Pablo Aguilar3,4, Coral Pardo-Esté1, Cristina Dorador4,5, Raquel Quatrini6, Franck Molina7, Daniel Aguayo2,8, Eduardo Castro-Nallar2* and Claudia P. Saavedra1* 1 Laboratorio de Microbiología Molecular, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Edited by: Universidad Andres Bello, Santiago, Chile, 2 Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias Biológicas, Martin G. Klotz, Universidad Andrés Bello, Santiago, Chile, 3 Laboratorio de Tecnologías de Membranas, Biotecnología y Medio Ambiente, Queens College (CUNY), USA Departamento de Ingeniería Química, Facultad de Ingeniería y Ciencias Geológicas, Universidad Católica del Norte, Antofagasta, Chile, 4 Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta and Departamento Reviewed by: de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile, Adrian Gustavo Turjanski, 5 Centre for Biotechnology and Bioengineering, Antofagasta, Chile, 6 Laboratorio de Ecofisiología Microbiana, Fundación University of Buenos Aires, Argentina Ciencia and Vida, Santiago, Chile, 7 Sys2Diag CNRS/Bio-Rad UMR3145, Montpellier, France, 8 Centro Interdisciplinario de Tatiana A. Vishnivetskaya, Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile University of Tennessee, Knoxville, USA *Correspondence: The Atacama Desert hosts diverse ecosystems including salt flats and shallow Andean Eduardo Castro-Nallar lakes. Several heavy metals are found in the Atacama Desert, and microorganisms [email protected] Claudia P. Saavedra growing in this environment show varying levels of resistance/tolerance to copper, [email protected] tellurium, and arsenic, among others. Herein, we report the genome sequence and †These authors have contributed comparative genomic analysis of a new Exiguobacterium strain, sp. SH31, isolated equally to this work. from an altiplanic shallow athalassohaline lake. Exiguobacterium sp. SH31 belongs to Specialty section: the phylogenetic Group II and its closest relative is Exiguobacterium sp. S17, isolated This article was submitted to from the Argentinian Altiplano (95% average nucleotide identity). Strain SH31 encodes a Evolutionary and Genomic Microbiology, wide repertoire of proteins required for cadmium, copper, mercury, tellurium, chromium, a section of the journal and arsenic resistance. Of the 34 Exiguobacterium genomes that were inspected, only Frontiers in Microbiology isolates SH31 and S17 encode the arsenic efflux pump Acr3. Strain SH31 was able to Received: 09 August 2016 grow in up to 10 mM arsenite and 100 mM arsenate, indicating that it is arsenic resistant. Accepted: 06 March 2017 Published: 21 March 2017 Further, expression of the ars operon and acr3 was strongly induced in response to Citation: both toxics, suggesting that the arsenic efflux pump Acr3 mediates arsenic resistance Castro-Severyn J, Remonsellez F, in Exiguobacterium sp. SH31. Valenzuela SL, Salinas C, Fortt J, Aguilar P, Pardo-Esté C, Dorador C, Keywords: Exiguobacterium, polyextremophile, stress, comparative genomics, Chilean Altiplano Quatrini R, Molina F, Aguayo D, Castro-Nallar E and Saavedra CP (2017) Comparative Genomics INTRODUCTION Analysis of a New Exiguobacterium Strain from Salar de Huasco Reveals Extremophiles are microorganisms from all three domains of life (Bacteria, Archaea and Eukarya) a Repertoire of Stress-Related Genes and Arsenic Resistance. that grow in the most hostile environments found on Earth, where they must withstand conditions Front. Microbiol. 8:456. including extreme pH, temperature, salinity, pressure, UV radiation, and the presence of heavy doi: 10.3389/fmicb.2017.00456 metals or toxic compounds. In some cases, extremophiles face more than one extreme condition Frontiers in Microbiology| www.frontiersin.org 1 March 2017| Volume 8| Article 456 fmicb-08-00456 March 21, 2017 Time: 10:32 # 2 Castro-Severyn et al. New Arsenic Resistant Exiguobacterium simultaneously, and are called polyextremophiles (Seufferheld The Exiguobacterium genus (Collins et al., 1983) includes et al., 2008; Bowers et al., 2009; Farías et al., 2013; Kurth et al., psychrotrophic, mesophilic, and moderate thermophilic species 2015). To survive under extreme conditions, microbes finely tune with variable morphologies (ovoid, rods, double rods, and chains) gene expression, modulating the levels of proteins implicated in that grow in a wide range of habitats, including cold and hot the response to stress (Duché et al., 2002). Since their discovery, environments with temperatures ranging from −12 to 55◦C extremophiles have attracted researchers because of their unique (Vishnivetskaya and Kathariou, 2005; Vishnivetskaya et al., 2007). physiology, ability to adapt to different environments, and for Taxonomic and phylogenetic classification of the genus by 16S their potential use in biotechnology (Rothschild and Mancinelli, rRNA gene sequence analysis shows that Exiguobacterium forms 2001). two distinct groups: Group I includes strains isolated from cold or The Andean Plateau region in West Central South America, low temperature environments, and Group II from hot springs the Altiplano, hosts a rich microbial diversity and remains or slightly alkaline and marine environments (Vishnivetskaya an untapped resource for understanding the genetic diversity et al., 2009). One exception is Exiguobacterium sp. GIC31, which and distribution of polyextremophiles (Catalán et al., 2006). belongs to group II, but was isolated from a glacier in Greenland High-altitude Andean Lakes (HAALs) are exposed to some of (Vishnivetskaya et al., 2014). the highest levels of solar radiation on Earth (Albarracín et al., Members of the Exiguobacterium genus display traits that 2015). Further, water bodies found in the Altiplano (i.e., shallow could be of biotechnological interest, e.g., bioremediation and lakes, ponds, streams, etc.) are highly diverse, showing different agriculture applications. For example, strains Z8 and 2Sz can chemical compositions, temperatures, evaporation rates, and neutralize highly alkaline industry wastewater and remove depths, among other conditions. Together, these factors drive the pesticides, respectively (Lopez et al., 2005; Kumar et al., changing community structure of rich polyextreme microbiota 2006); strain WK6 reduces arsenate to arsenite (Anderson and that populates these lakes (Márquez-García et al., 2009; Dorador Cook, 2004), and other strains reduce chrome and mercury et al., 2013; Cordero et al., 2014). Despite these harsh conditions, in a wide range of temperatures, pH, and salt concentrations almost 500 strains of prokaryotes (archaea, cyanobacteria and (Pattanapipitpaisal et al., 2002; Petrova et al., 2002; Okeke, eubacteria) and lower eukaryotes (fungi and yeast) have been 2008); Exiguobacterium oxidotolerans T-2-2T shows high catalase isolated from bacterioplankton, benthos, microbial mats, and activity in response to H2O2 as a function of the growth phase and soils surrounding HAALs (Dib et al., 2008; Flores et al., 2009; oxygen levels, which could be used to remove peroxides used in Ordoñez et al., 2009; Di Capua et al., 2011; Lynch et al., 2012; Bull the bleaching industry (Takebe et al., 2007); Exiguobacterium sp. and Asenjo, 2013; Bull et al., 2016). Microbial communities that S17, isolated from Laguna Socompa in the Argentinian altiplanic evolved in HAALs tolerate a wide range of chemical and physical desert, tolerates high arsenic concentrations (Belfiore et al., 2013; stresses, including wide fluctuations in temperature, low nutrient Ordoñez et al., 2013). Further, members of the Exiguobacterium levels, alkalinity, and hypersalinity (up to 30%). Further, high genus are a source of enzymes that exhibit a broad range of concentrations of heavy metals and metalloids, especially arsenic thermal stability (Usuda et al., 1998; Suga and Koyama, 2000; (up to 200 ppm), are found in HAALs, primarily because of Hwang et al., 2005; Hara et al., 2007; Kasana and Yadav, 2007). the geological foundation (Fernandez-Zenoff et al., 2006; Zenoff In the present study, we aimed to understand the phylogenetic et al., 2006; Dib et al., 2009; Farias et al., 2009; Albarracín et al., placement and to identify genetic determinants required for 2012). the response to stress in a new psychro-halotolerant strain Salar de Huasco is a saline wetland located at 3,800 m above isolated from Salar de Huasco, Exiguobacterium sp. SH31. We sea level in the Chilean Altiplano (−20.303436, −68.880918) investigated whether Exiguobacterium sp. SH31 belongs to Group and is considered an athalassohaline system. It exhibits II, and to what extent species from this genus share functional typical conditions of the Altiplano: low temperatures (mean features based on the group to which they belong. Additionally, annual temperature <5◦C), low atmospheric pressure, high we searched the genomes of Exiguobacterium sp. SH31 and other solar radiation (up to 72 Wm−2 UVA radiation: Hernández species for the presence of genes encoding proteins known to et al., 2016), negative water balance, and variable