Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Australia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. The complete genome sequence is presented in this report

Guss, Adam M.

Hatmaker, E. Anne

Mormile, Melanie R.

O\u27Dell, Kaela B.

English

Missouri University of Science and Technology (Missouri S&T): Scholars' Mine

Missouri University of Science and Technology Scholars' Mine Biological Sciences Faculty Research & Creative Works Biological Sciences 01 Oct 2018 Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia Kaela B. O'Dell E. Anne Hatmaker Adam M. Guss Melanie R. Mormile Missouri University of Science and Technology, mmormile@mst.edu Follow this and additional works at: https://scholarsmine.mst.edu/biosci_facwork  Part of the Biology Commons Recommended Citation K. B. O'Dell et al., "Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia," Microbiology Resource Announcements, vol. 7, no. 13, American Society for Microbiology, Oct 2018. The definitive version is available at https://doi.org/10.1128/MRA.01047-18 This work is licensed under a Creative Commons Attribution 4.0 License. This Article - Journal is brought to you for free and open access by Scholars' Mine. It has been accepted for inclusion in Biological Sciences Faculty Research & Creative Works by an authorized administrator of Scholars' Mine. This work is protected by U. S. Copyright Law. Unauthorized use including reproduction for redistribution requires the permission of the copyright holder. For more information, please contact scholarsmine@mst.edu. Complete Genome Sequence of Salinisphaera sp. Strain LB1, aModerately Halo-Acidophilic Bacterium Isolated from LakeBrown, Western AustraliaKaela B. O’Dell,a E. Anne Hatmaker,a Adam M. Guss,a Melanie R. MormilebaBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USAbDepartment of Biological Sciences, Missouri University of Science and Technology, Rolla, Missouri, USAABSTRACT Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Aus-tralia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. The complete ge-nome sequence is presented in this report.Halo-acidophilic bacteria are gaining attention as a source of enzymes for use inindustrial processes that require efficient enzymatic activity within operatingconditions at low pH and high concentrations of salt (1). Members of the familySalinisphaeraceae are Gram-negative Gammaproteobacteria that are cocci or short rodshaped and halotolerant (2). Salinisphaera sp. strain LB1 was isolated from surface waterfrom Lake Brown, Western Australia, through enrichment cultures in modified growthmedium (3, 4) at pH 4.0 and with 5% (wt/vol) NaCl and plated onto phytagel-solidifiedmedium incubated at 37°C. A pure colony was subcultured in liquid medium forgenome sequencing.Genomic DNA was isolated from Salinisphaera sp. strain LB1 using the QiagenGenomic-tip 100/G extraction kit and bacterial protocol (Qiagen, Valencia, CA, USA).The genome was generated by the DOE Joint Genome Institute (JGI) using the PacBiosequencing technology (Menlo Park, CA, USA). A PacBio SMRTbell library of10 kb wasconstructed and sequenced on the PacBio RS II platform (5), which generated 92,798filtered subreads for a total of 597,839,667 bases. The reads were then assembled usingHierarchical Genome Assembly Process 3 (HGAP3; v2.3.0.p5) (6). The final assembly hadan input read coverage of 92.8. The genome includes a single, contiguous, circularchromosome 4,141,708 bp long, with an average GC content of 64%. The genomewas annotated using Rapid Annotations using Subsystem Technology (RAST) v2.0 (7)and is predicted to include 3,784 protein-coding sequences, 48 tRNAs, and 6 rRNAs in2 operons. DNA modification detection and motif analysis were performed by JGI usingthe PacBio single-molecule real-time (SMRT) analysis platform (pbsmrtpipe.pipelines.dsmodification motif analysis 0.1.0). Briefly, raw reads were filtered using SFilter to removeshort reads and reads derived from sequencing adapters. Filtered reads were aligned tothe reference genome for Salinisphaera sp. strain LB1 using BLASR (v5.3) (8). Modifiedsites were then identified through kinetic analysis of the aligned DNA sequence data (9)and grouped into motifs using MotifFinder. These motifs represent the recognitionsequences of methyltransferase genes active in the genome (10). One methylated motifwas identified, gAgnnnnnnnnTgcc, which showed 99.2% modification from a count of830 sites in the genome. All software used the default settings.Based on the 16S rRNA gene, Salinisphaera hydrothermalis was 96.13% similar overthe entire 1,542-bp gene to Salinisphaera sp. strain LB1 when matched using theEzBioCloud 16S database (11). According to JSpeciesWS (12), the ANIb value (calculatedby BLAST) of Salinisphaera sp. strain LB1 compared with that of Salinisphaera hydro-thermalis C41B8 is 81.15%, and the ANIm (calculated by MUMmer) value is 85.42%,Received 24 July 2018 Accepted 7 August2018 Published 4 October 2018Citation O’Dell KB, Hatmaker EA, Guss AM,Mormile MR. 2018. Complete genomesequence of Salinisphaera sp. strain LB1, amoderately halo-acidophilic bacterium isolatedfrom Lake Brown, Western Australia. MicrobiolResour Announc 7:e01047-18. https://doi.org/10.1128/MRA.01047-18.Editor David A. Baltrus, University of ArizonaCopyright © 2018 O’Dell et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Melanie R.Mormile, mmormile@mst.edu.K.B.O. and E.A.H. contributed equally to thiswork.GENOME SEQUENCEScrossmVolume 7 Issue 13 e01047-18 mra.asm.org 1 on March 26, 2019 by guesthttp://mra.asm.org/Downloaded from suggesting that strain LB1 and S. hydrothermalis are different species. The completegenome sequence of Salinisphaera sp. strain LB1 will be a critical tool enablingexperiments and analyses to uncover mechanisms of adaptation to polyextreme con-ditions and potential novel enzymes from these environments.Data availability. This complete genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession no. CP029488. PacBio reads were deposited at theNCBI Sequence Read Archive (SRA) under accession no. SRP156246.ACKNOWLEDGMENTSThis work was supported by the BioEnergy Science Center (BESC) and the Center forBioenergy Innovation (CBI), U.S. Department of Energy Bioenergy Research Centers,supported by the Office of Biological and Environmental Research in the DOE Office ofScience. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. DOEunder contract DE-AC05-00OR22725. The DNA sequencing work was conducted by theU.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility,which is supported by the Office of Science of the U.S. Department of Energy undercontract DE-AC02-05CH11231. The original isolation of Salinisphaera sp. strain LB1 wasfunded by NSF Biogeosciences Program grants EAR-0433040 and EAR-0433044. Thefunders had no role in study design, data collection and analysis, decision to publish,or preparation of the manuscript.We thank Jennifer Parks for technical assistance with this project.REFERENCES1. 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Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia

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Complete Genome Sequence of Salinisphaera sp. Strain LB1, a Moderately Halo-Acidophilic Bacterium Isolated from Lake Brown, Western Australia

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