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Permanent Draft Genome Sequence of Desulfurococcus Mobilis Type Strain

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Permanent Draft Genome Sequence of Desulfurococcus Mobilis Type Strain Susanti et al. Standards in Genomic Sciences (2016) 11:3 DOI 10.1186/s40793-015-0128-4 SHORT GENOME REPORT Open Access Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland Dwi Susanti1, Eric F. Johnson2, Alla Lapidus3,4, James Han5, T. B. K. Reddy5, Manoj Pilay6, Natalia N. Ivanova5, Victor M. Markowitz6, Tanja Woyke5, Nikos C. Kyrpides5,7 and Biswarup Mukhopadhyay1,2,8* Abstract This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species. Keywords: Desulfurococcus, Sulfur-reducing crenarchaeon, Thermophile, Acidic hot spring Introduction Among known desulfurococci, D. mobilis is a closer Desulfurococcus mobilis type strain DSM 2161 was iso- relative of Desulfurococcus mucosus which is also a pep- lated from acidic hot springs in Hveravellir, Iceland [1]. tide degrader [1, 3]. D. mucosus genome was sequenced This hyperthermophilic crenarchaeaon utilizes casein in 2011 under the Genomic Encyclopedia of Bacteria and peptides present in yeast extract, and tryptic digest and Archaea program [3]. In addition to D. mobilis and of casein as energy and carbon source [1]. In the pres- D. mucosus, three desulfurococci are known, and these ence of sulfur as electron acceptor, D. mobilis undergoes are Desulfurococcus fermentans [4, 5], Desulfurococcus sulfur respiration generating H2S and CO2, whereas in amylolyticus [6], and Desulfurococcus kamchatkensis [7]. the absence of sulfur it performs peptide oxidation All of these organisms degrade peptides. As far as coupled to hydrogen production for regeneration of other substrates for growth, starch is used only by electron carriers [1, 2]. Growth in the presence of sulfur Desulfurococcus fermentans and Desulfurococcus amy- yields five times more cell density compared to that lolyticus whereas sugars can be used by Desulfurococ- without sulfur [1]. cus fermentans and Desulfurococcus kamchatkensis. TheonlycellulosedegradingDesulfurococcus is Desul- furococcus fermentans [4, 5]. The Desulfurococcus fer- * Correspondence: [email protected] mentans and Desulfurococcus kamchatkensis genomes 1Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA 2Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061, USA have been sequenced by the US Department of Energy Full list of author information is available at the end of the article © 2016 Susanti et al. 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. Susanti et al. Standards in Genomic Sciences (2016) 11:3 Page 2 of 7 Joint Genome Institute and the Russian Academy of three orders namely Desulfurococcales, Sulfolobales and Sciences Centre “Bioengineering”, respectively [5, 7]. Thermoproteales have been recognized. A phylogenetic Almost all organisms that belong to the genus Desulfur- tree based on 16S-ribosomal DNA sequences (Fig. 1) ococcus are dependent on or stimulated by sulfur [1–3, 7]. shows the position of D. mobilis relative to its neigh- Sulfur is used as a terminal electron acceptor. The only bours. Desulfurococcus mobilis is closely related to exception is Desulfurococcus fermentans [4, 5] as elemen- Desulfurococcus mucosus. The value of ANI between tal sulfur does not influence the growth of this organism Desulfurococcus mobilis and Desulfurococcus mucosus is and it is also the only Desulfurococcus species for which 99.88. Such a high ANI value suggested that these the growth is not inhibited by the presence of hydrogen. organisms should be considered as two strains of the The draft genome sequence of D. mobilis together with same species. the complete genome sequence of D. mucosus, Desulfuro- Desulfurococcus mobilis is a Gram-negative spherical coccus fermentans and Desulfurococcus kamchatkensis coccus, with diameter about 0.1-1 μm [1]. Unlike Desul- could give insight into the finer differences between pep- furococcus mucosus, Desulfurococcus mobilis is motile tide, starch and cellulose metabolism systems of these [1]. The latter possesses monopolar polytrichus flagella closely related desulfurococci leading to the discoveries of that form bundle of 12.5 nm diameter (Fig. 2). Classifica- new thermophilic enzymes and pathways. Similar inquiries tion and general features of Desulfurococcus mobilis are could be made for their differences in elemental sulfur shown in Table 1. requirements as well as their responses to the presence of H2 in their environment. Genome Sequencing Information Genome project history Organism Information D. mobilis was selected for sequencing by the Joint Classification and features Genome Institute Community Sequencing Program in Desulfurococcus mobilis belongs to the phylum Cre- 2009 as part of a genome comparison project for the genus narchaeota and class of Thermoprotei. Within this class, Desulfurococcaceae. Project information is available in the Desulfurococcus amyloliticus Z-533T (NZ_AZUU00000000) 86 T 100 Desulfurococcus kamchatkensis 1221n (NC_011766.1) T 98 Desulfurococcus fermentans DSM 16532 (NC_018001.1) Desulfurococcus mobilis DSM 2161T (NZ_AUQX00000000.1) 59 98 Desulfurococcus mucosus O7/1T (NC_014961.1) Staphylothermus marinus F1T (NC_009033.1) 59 T 73 Aeropyrum pernix K1 (BA000002 AP000058-AP000064) Desulfurococcales Hyperthermus butylicus DSM 5456T (NC_008818.1) 46 36 Ignicoccus hospitalis KIN4/IT (NC_009776.1) Sulfolobus acidocaldarius SUSAZ (NC_023069) 72 100 Sulfolobus tokodaii str. 7T (NC_003106.2) (NZ_ACUK000000000.1) Sulfolobus solfataricus 98/2 Sulfolobales Thermoproteus uzoniensis 768-20 (NC_015315.1) 100 T 90 Thermoproteus tenax Kra1 (NC_01535.1) pendens Hrk 5 (NC_008696.1) Thermoproteales 0.02 Fig. 1 A 16S ribosomal DNA sequence-based phylogenetic tree showing the position of Desulfurococcus mobilis DSM 2161 (shown in bold) relative to other Desulfurococcus species and other organisms from Sulfolobales and Thermoproteales orders. Alignment and trimming of genes encoding 16S rRNA (aligned size of 1112 bp) were performed by the use of Muscle 3.8.31 [33] and Gblocks 0.91, respectively. The tree was constructed using Maximum Likelihood method, dnaml, in the Phylip-3.696 package [34] and viewed by the use of FigTree (http://tree.bio.ed.ac.uk/), as previously described [35]. Type strains are indicated with the superscript T. NCBI accession numbers for genome sequence are presented within parenthesis. Methanocaldococcus jannaschii, a euryarchaeon (not shown), was used as an outgroup [36]. Number in each branch shows a percentage of bootstrap value from 100 replicates. The bar indicates 0.02 substitutions per nucleotide position Susanti et al. Standards in Genomic Sciences (2016) 11:3 Page 3 of 7 Table 1 Classification and general features of Desulfurococcus mobilis DSM 2161T [37] MIGS ID Property Term Evidence codea Classification Domain Archaea TAS [38] Phylum Crenarchaeota TAS [38] Class Thermoprotei TAS [39] Order Desulfurococcales TAS [40] Family Desulfurococcaceae TAS [1] Genus Desulfurococcus TAS [1] Species Desulfurococcus TAS [1] mobilis Type strain DSM TAS [1] 2161/ATCC 35582 Gram stain Negative TAS [1] Cell shape Coccus TAS [1] Fig. 2 An electron micrograph of Desulfurococcus mobilis type strain Motility Motile TAS [1] DSM 2161 showing unipolar polytrichus archaella. The picture has Sporulation Not reported been reproduced from [1] with permission Temperature 55-97 °C TAS [1] range GenomesOnLineDatabase(Table2)[8].DRAFTsequen- Optimum 85 °C TAS [1] cing, initial gap closure and annotation were performed by temperature the DOE Joint Genome Institute using state-of-the-art pH range; 2.2-6.5; 5.5-6.0 TAS [1] Optimum sequencing technology [9]. The draft genome was partly assembled and annotated in 2012 and was deposited in the Carbon Yeast extract, bactotryptone, TAS [1] source a tryptic-digest of casein Integrated Microbial Genome Data Management System or casein [10] in 2012. Energy Chemoorganotroph TAS [1] source Growth conditions and genomic DNA preparation Terminal Elemental
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