Genome analysis of Bacillus safensis RP10, a strain from the soil of Atacama Desert in northern Chile, reflects a bacterium adapted to live in soil containing high levels of heavy metals, high salt conditions, and low carbon and energy sources

Fuentes, Derie

McClelland, Michael

Pedroso, Inti

Ponce, Raul

Strahsburger, Erwin

Tapia, Paz

Valdes, Jorge

Zapata, Felipe

English

eScholarship - University of California

UC IrvineUC Irvine Previously Published WorksTitleDraft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, ChilePermalinkhttps://escholarship.org/uc/item/7894v1jdJournalMicrobiology Resource Announcements, 8(44)ISSN2576-098XAuthorsStrahsburger, ErwinZapata, FelipePedroso, Intiet al.Publication Date2019-10-31DOI10.1128/mra.01150-19 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of CaliforniaDraft Genome Sequence of Bacillus safensis RP10, Isolatedfrom Soil in the Atacama Desert, ChileErwin Strahsburger,a,c Felipe Zapata,b Inti Pedroso,b Derie Fuentes,b Paz Tapia,b Raul Ponce,a Michael McClelland,cJorge ValdesbaDoctoral Program in Agronomy in Desert and Arid Zones, Molecular Biotechnology Laboratory, Faculty of Renewal Natural Resources, Universidad Arturo Prat, Iquique,ChilebBio-Computing and Applied Genetics Division, Center for Systems Biotechnology, Fraunhofer Chile Research Foundation, Santiago, ChilecDepartment of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, California, USAABSTRACT Genome analysis of Bacillus safensis RP10, a strain from the soil of Ata-cama Desert in northern Chile, reflects a bacterium adapted to live in soil con-taining high levels of heavy metals, high salt conditions, and low carbon and en-ergy sources.The Atacama Desert of Chile is the driest desert in the world (1, 2) and has soilsnaturally enriched in heavy metals and salts, which affects local agricultural activ-ities (3). These soils also harbor species of the genus Bacillus (4, 5). This genus is adaptedto live in many different environments (6, 7), and it has been used for biocontrol ofagricultural plagues (8), for phytoremediation (9, 10), and as a probiotic (11). With theaim of understanding how Bacillus species have adapted to conditions in the AtacamaDesert, we isolated Bacillus strains by mixing 1 g of soil with 9 ml of NaCl 0.8% andincubating at 50°C for 1 h. The solution was decanted, and 1 ml of the supernatant wasspread on Luria broth (LB) agar and incubated at 37°C for 4 days under aerobicconditions. One of the colonies recovered was named RP10, and its genome wassequenced. The genomic DNA was purified using a QuickExtract bacterial DNA extrac-tion kit (Epibio), and the library was constructed using a Nextera XT kit (Illumina).Whole-genome shotgun sequencing was performed using 2  250- bp (paired-end)reads on an Illumina MiSeq platform. A total of 14.2 million reads was obtained. Readswere filtered for a Phred quality score of at least 20 and assembled using the A5pipeline (2015 Linux, default parameters) (12). Open reading frame prediction andannotation were performed using Prokka software version 1.11 (13).Bacillus species identification was achieved by using the JSpeciesWS server onlinewith BLAST (14) average nucleotide identity (ANIb) and MUMmer average nucleotideidentity (ANIm) analysis (15–17). The RP10 strain was identified as a member of thespecies Bacillus safensis, and the highest identities were with B. safensis FO-36b (16SrRNA, 99.2%; ANIb, 98.83%; ANIm, 99.07%) and B. safensis JPL-MERTA-8-2 (ANIb, 98.7%;ANIm, 99.00%). Both strains were isolated from clean rooms at the Jet PropulsionLaboratory at NASA (Pasadena, CA). (18–19). A genome comparison between thesethree strains by Mauve software (20) and the Rapid Annotation using SubsystemTechnology (RAST)-National Microbial Pathogen Database Resource (NMPDR) serverwith SEED view indicated that the RP10 genome contained an island enriched inphage-related genes (60 kb), an arsenic resistance operon, and other uncharacterizedmetabolic operons not found in the other two genomes.The draft genome of Bacillus safensis RP10 consists of 3,813,379 bp distributed in 102contigs, with an average GC content of 41.7%. The draft genome comprises 75 tRNAsand 20 T box leader sequences that are probably involved in a riboswitch mechanismdescribed for Gram-positive bacteria (21). The RAST-NMPDR server with SEED viewCitation Strahsburger E, Zapata F, Pedroso I,Fuentes D, Tapia P, Ponce R, McClelland M,Valdes J. 2019. Draft genome sequence ofBacillus safensis RP10, isolated from soil in theAtacama Desert, Chile. Microbiol ResourAnnounc 8:e01150-19. https://doi.org/10.1128/MRA.01150-19.Editor John J. Dennehy, Queens CollegeCopyright © 2019 Strahsburger et al. This is anopen-access article distributed under the termsof the Creative Commons Attribution 4.0International license.Address correspondence to ErwinStrahsburger, estrahsb@unap.cl.Received 24 September 2019Accepted 14 October 2019Published 31 October 2019GENOME SEQUENCEScrossmVolume 8 Issue 44 e01150-19 mra.asm.org 1indicates that this strain carries genes and operons for resistance to arsenic (arsRRBC),lead (epsABCDEFFHIKLMN and cadA), copper (copZA), and manganese (mntP, mnH,and mntABC) and an operon with potential antimicrobial activity and 34% identity withthe bacteriocin operon AS-48 of Enterococcus faecalis. Finally, the genome encodesdiverse capabilities for synthesizing several vitamins, siderophores, and aromatic com-pounds, including tryptophan (trpEDCFBA) and several multidrug efflux pumps,which are potentially associated with the ability to survive under saline soil conditionswith a low content of energy and carbon sources.Data availability. This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under the accession number MKXN00000000 with contigs underaccession numbers MKXN01000001 to MKXN01000102, and the raw reads are availablein the SRA under the accession number PRJNA345377.ACKNOWLEDGMENTSThis work was supported by funds from academic innovation project DE1549,sustained by the Academic Vicerectory, by internal grants VRIIP0123-15 and VRIIP0218-15,supported by the Vicerectory of Research, Innovation, and Postgraduate (VRIIP) ofUniversidad Arturo Prat, and by the program of InnovaChile CORFO for Attraction ofInternational Centers of Excellence (grant FCR-CSB 09CEII-6991).REFERENCES1. Olson DM, Dinerstein E. 1998. The global 200: a representationapproach to conserving the Earth’s most biologically valuable ecore-gions. Conserv Biol 12:502–515. https://doi.org/10.1046/j.1523-1739.1998.012003502.x.2. Betancourt JL, Latorre C, Rech JA, Quade J, Rylander KA. 2000. 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Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile

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Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile.

Draft Genome Sequence of Bacillus safensis RP10, Isolated from Soil in the Atacama Desert, Chile.

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