Open access
17 December 2015

Draft Genome Sequence of Thermophilic Geobacillus sp. Strain Sah69, Isolated from Saharan Soil, Southeast Algeria


Geobacillus spp. are potential sources of novel enzymes, such as those involved in the degradation of recalcitrant polymers. Here, we report a Geobacillus genome that may help reveal genomic differences between this strain and publicly available representatives of the same genus from diverse niches.


Thermophilic environments such as desert soils contain a diverse consortia of microbial taxa, which span both archaeal and bacterial lineages (1, 2). Efforts have focused on isolation of thermophilic archaea, principally due to their potential biotechnological applications (3). However, more recently, the need to identify novel thermostable hydrolytic enzymes has led to renewed interest in isolating Geobacillus spp., due to their capacity to degrade complex carbohydrates for application in bioethanol production (4). We sequenced the genome of a novel isolate from a hot Saharan soil in order to further understand the metabolic capacity of this genus. Geobacillus spp. are thermophilic, Gram-positive, spore-forming aerobic bacteria, many of which have demonstrated broad-specificity, carbohydrate-degradative traits (5).
Geobacillus sp. strain Sah69 was grown on nutrient agar and incubated at 55°C for 24 h. Genomic DNA was obtained from the isolate using a modification of the method first described by Miller and colleagues (6). The 16S rRNA gene was amplified and sequenced, confirming that isolate Sah69 belongs to the genus Geobacillus. Genomic DNA was sent for sequencing on an Illumina MiSeq DNA at MR DNA, Shallowater, TX, USA. The library preparation and sequencing was done as described elsewhere (7). The genome was assembled using DNAStar SeqMan NGen software, and annotated using the Rapid Annotation using Subsystems Technology (RAST) server ( (8). The draft genome had a total of 73 contigs with protein-encoding genes, 2,998,191 nucleotides, and a G+C content of 52.58%. RAST annotation revealed 102 RNAs and 3,372 coding sequences. One intact and one incomplete phage genome was predicted using the PHAST (Phage Search Tool) server (9). The genome was shown to possess the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR-associated) elements of the Csn1, Cas1, and Cas2 families (10). These elements are essential for the acquisition of resistance by bacteria against foreign genetic elements through the excision and integration of a genome fragment from invading DNA into its CRISPR arrays.
These data will help provide knowledge about the mechanisms behind microorganisms that thrive in extreme environments.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LLKS00000000. The version described in this paper is the first version, LLKS01000000.


We thank the National Research Foundation of South Africa, the Genomics Research Institute (University of Pretoria), and the Research Development Programme (University of Pretoria) for financial support.


Amend JP, Shock EL. 2001. Energetics of overall metabolic reactions of thermophilic and hyperthermophilic archaea and bacteria. FEMS Microbiol Rev 25:175–243.
Stetter KO. 1996. Hyperthermophilic procaryotes. FEMS Microbiol Rev 18:149–158.
Hatzenpichler R, Lebedeva EV, Spieck E, Stoecker K, Richter A, Daims H, Wagner M. 2008. A moderately thermophilic ammonia-oxidizing crenarchaeote from a hot spring. Proc Nalt Acad Sci USA 105:2134–2139.
Taylor MP, van Zyl L, Tuffin IM, Leak DJ, Cowan DA. 2011. Genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts. Microb Biotechnol 4:438–448.
Brumm PJ, De Maayer P, Mead DA, Cowan DA. 2015. Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies. Front Microbiol 6 [Epub ahead of print.].
Miller DN, Bryant JE, Madsen EL, Ghiorse WC. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715–4724.
Gosse JT, Hill P, Dowd SE, Boddy CN. 2015. Draft genome sequence of streptomyces sp. strain PBH53, isolated from an urban environment. Genome Announc 3(4):e00859-15.
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214.
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: A fast phage search Tool. Nucleic Acids Res 39:W347–W352.
Sander JD, Joung JK. 2014. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32:347–355.

Information & Contributors


Published In

cover image Genome Announcements
Genome Announcements
Volume 3Number 631 December 2015
eLocator: 10.1128/genomea.01447-15


Received: 20 October 2015
Accepted: 27 October 2015
Published online: 17 December 2015



Oliver K. I. Bezuidt
Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
Thulani P. Makhalanyane
Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
Mohamed A. Gomri
Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments, INATAA, Université Frères Mentouri, Constantine, Algeria
Karima Kharroub
Equipe Métabolites des Extrêmophiles, Laboratoire de Recherche Biotechnologie et Qualité des Aliments, INATAA, Université Frères Mentouri, Constantine, Algeria
Don A. Cowan
Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa


Address correspondence to Don A. Cowan, [email protected].

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