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Complete Genome Sequence of the Antarctic Halorubrum Lacusprofundi Type Strain ACAM 34 Iain J

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Complete Genome Sequence of the Antarctic Halorubrum Lacusprofundi Type Strain ACAM 34 Iain J Anderson et al. Standards in Genomic Sciences (2016) 11:70 DOI 10.1186/s40793-016-0194-2 SHORT GENOME REPORT Open Access Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34 Iain J. Anderson1, Priya DasSarma2*, Susan Lucas1, Alex Copeland1, Alla Lapidus1, Tijana Glavina Del Rio1, Hope Tice1, Eileen Dalin1, David C. Bruce3, Lynne Goodwin3, Sam Pitluck1, David Sims3, Thomas S. Brettin3, John C. Detter3, Cliff S. Han3, Frank Larimer1,4, Loren Hauser1,4, Miriam Land1,4, Natalia Ivanova1, Paul Richardson1, Ricardo Cavicchioli5, Shiladitya DasSarma2, Carl R. Woese6 and Nikos C. Kyrpides1 Abstract Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. WereportherethecompletegenomesequenceofH. lacusprofundi type strain ACAM 34 and its annotation. This genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea. Keywords: Archaea, Halophile, Halorubrum, Extremophile, Cold adaptation, Tree of life Abbreviations: TE, Tris-EDTA buffer; CRITICA, Coding region identification tool invoking comparative analysis; PRIAM, PRofils pour l’Identification Automatique du Métabolisme; KEGG, Kyoto Encyclopedia of Genes and Genomes; COG, Clusters of Orthologous Groups; TMHMM, Transmembrane hidden Markov model; CRISPR, Clustered regularly interspaced short palindromic repeats Introduction 2006 Joint Genome Institute Community Sequencing Halorubrum lacusprofundi is an extremely halophilic Program project because of its ability to grow at low archaeon belonging to the class Halobacteria within the temperature and its phylogenetic distance from other phylum Euryarchaeota. The species is represented by halophiles with sequenced genomes (Fig. 2). the type strain, ACAM 34 (= DSM 5036 = ATCC 49239 = JCM 8891), and a second strain, ACAM 32, both of which were isolated from Deep Lake, Antarctica [1]. This organ- Organism information ism was first described as Halobacterium lacusprofundi Classification and features Halorubrum lacusprofundi but was later transferred to the genus Halorubrum [2]. ACAM 34 was isolated from Members of the genus Halorubrum have been found not a water-sediment sample from Deep Lake, Antarctica only in Antarctica, but also in Africa [3], Asia [4], and [1]. The water-sediment sample was incubated in the North America [5], where they are usually found in saline light at 18 °C, and after 3 months developed a reddish H. lacusprofundi lakes or salterns. Most members of the genus are neutro- color. was isolated from the sample by philes, but some are haloalkaliphiles [6, 7]. H. lacuspro- streaking on Deep Lake vitamin agar, which was com- fundi (Fig. 1) was proposed for sequencing as part of a posed of Lake Deep water with 1 g/L yeast extract, 15 g/L agar, and vitamin solution. The physiological * Correspondence: [email protected] characteristics of H. lacusprofundi were described as 2 Institute of Marine and Environmental Technology, Columbus Center, follows [1]. Cells were pleomorphic. Motility was not University of Maryland School of Medicine, University System of Maryland, Baltimore, MD 21202, USA observed, and no flagella were present. Cells grew at a Full list of author information is available at the end of the article temperature range of −1°Cto40°Cwithanoptimal © 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Anderson et al. Standards in Genomic Sciences (2016) 11:70 Page 2 of 6 and ethanol. Growth was not stimulated by addition of glycine. Acid was not produced from sugars. Genome sequencing information Genome project history H. lacusprofundi was selected for sequencing based upon its phylogenetic position relative to other haloarchaea and its cold tolerance (Table 1). It is part of a 2006 Joint Genome Institute Community Sequencing Program pro- ject that included six diverse archaeal genomes. Sequen- cing was done at the JGI Production Genomics Facility. Finishing was done at Los Alamos National Laboratory. Annotation was done at Oak Ridge National Labora- tory and JGI. The complete genome sequence was fin- ished in September, 2008 and was released to the public in GenBank in February, 2009. A summary of the project information is shown in Table 2. Fig. 1 Photomicrograph of H. lacusprofundi type strain ACAM 34 cells. The cells were grown in Franzmann et al. [1] medium. The image was taken using a phase microscope (Nikon Labphot) with Growth conditions and genomic DNA preparation 1000× magnification. The scale bar represents 10 μm H. lacusprofundi ATCC 49239 was grown in Franzmann medium (180 g NaCl, 75 g MgCl2 · 6H2O, 7.4 g MgSO4 · 7H2O, 7.4 g KCl, 1 g CaCl2 ·2H2O, 10 g C4H4O4Na2 · growth temperature of 36 °C [8]. Growth was observed 6H2O per liter, pH 7.4 with addition of 10 ml vitamin at NaCl concentration of 1.5 M to 4.5 M with an solution) [1]. The vitamin solution contained 0.1 g biotin, optimum salt concentration of 3.5 M. Cells lysed in dis- 0.1 g cyanocobalamin, and 0.1 g thiamine HCl per liter. tilled water. The optimum magnesium concentration for Cells were grown with shaking at 220 rpm at 4 °C with growth was 0.1 M. No growth was observed at magnesium illumination. concentrations of 0 M or 1.0 M. Ammonium could not be The DNA extraction method was modified from [9]. used as a nitrogen source; complex media such as yeast Cells were grown to OD600 = 0.8, collected by centrifuga- extract or peptone was required. Growth was stimulated tion at 8000 rpm for 10 min at 4 °C, resuspended in 1/20 by addition of glucose, galactose, mannose, ribose, lactose, volume basal salts and lysed by addition of 2 volumes of glycerol, succinate, lactate, formate, acetate, propionate, deionized water and mixing at room temperature. Next, Fig. 2 Phylogenetic tree of DNA-directed RNA polymerase subunit A’ of select haloarchaea. Sequence alignment and tree construction were carried out with Clustal W [39]. The tree was visualized with njplot [40]. Positions with gaps were excluded during tree construction. Methanosarcina acetivorans was used as the outgroup. The numbers indicate bootstrap values based on 1000 replicates Anderson et al. Standards in Genomic Sciences (2016) 11:70 Page 3 of 6 Table 1 Classification and general features of Halorubrum lacusprofundi ACAM 34T [31] MIGS ID Property Term Evidence codea Classification Domain Archaea TAS [32] Phylum Euryarchaeota TAS [33, 34] Class Halobacteria TAS [35] Order Halobacteriales TAS [36] Family Halobacteriaceae TAS [37] Genus Halorubrum TAS [3] Species Halorubrum lacusprofundi TAS [1] Gram stain Unknown Cell shape Pleomorphic TAS [1] Motility Non-motile TAS [1] Sporulation Nonsporulating NAS Temperature range −1–40 °C TAS [1] Optimum temperature 36 °C TAS [1] pH range, optimum Unknown Carbon source Sugars, organic acids, ethanol TAS [1] MIGS-6 Habitat Saline lake TAS [1] MIGS-6.3 Salinity 10–25 % NaCl TAS [1] MIGS-22 Oxygen requirement Aerobic TAS [1] MIGS-15 Biotic relationship Free-living TAS [1] MIGS-14 Pathogenicity Non-pathogen NAS MIGS-4 Geographic location Deep Lake, Antarctica TAS [1] MIGS-5 Sample collection 1988 TAS [1] MIGS-4.1 MIGS-4.2 Latitude-Longitude Unknown MIGS-4.4 Altitude Unknown aEvidence codes–IDA Inferred from Direct Assay, TAS Traceable Author Statement (i.e., a direct report exists in the literature), NAS Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [38] Table 2 Project information proteinase K was added to a final concentration of MIGS ID Property Term 100 μg/ml, mixed gently, and incubated for 1 h at 37 °C. MIGS-31 Finishing quality Finished The lysate was extracted using an equal volume of phenol, MIGS-28 Libraries Used 3 kb, 8 kb, and fosmid DNA mixed gently by inverting at room temperature for 5 min, and then spinning at 8000 g for 15 min at 4 °C. The MIGS-29 Sequencing platforms ABI3730 aqueous and interphase was collected and the phenol MIGS-31.2 Fold coverage 12.5× extraction was repeated twice more. The aqueous and Sequencing quality Less than one error per 50 kb interphase were then dialyzed against TE overnight at 4 °C MIGS-30 Assemblers Phrap with one change of buffer. The dialyzed solution was col- MIGS-32 Gene calling method CRITICA, GLIMMER, GenePRIMP lected and RNase A was added to a final concentration of μ Locus tag Hlac 50 g/ml, the solution was mixed and incubated for 2 h at 37 °C with gentle shaking. Proteinase K was added to a GenBank IDs CP001365, CP001366, CP001367 final concentration of 100 μg/ml, mixed and incubated for GenBank date of release February 4, 2009 an additional hour at 37 °C. The RNase A and proteinase GOLD ID Gc00952 K steps were repeated. The DNA was then dialyzed over- BIOPROJECT PRJNA18455 night against TE at 4 °C with one buffer change. NCBI project ID 18455 IMG Taxon ID 643692025 Genome sequencing and assembly The genome of H. lacusprofundi was sequenced at the MIGS-13 Source material identifier ATCC 49239, DSM 5036 Joint Genome Institute using a combination of 3 kb, Project relevance Tree of Life, cold adaptation 8 kb, and fosmid DNA libraries.
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