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Complete genome sequence of Desulfurococcus mucosus type strain (O7/1T)
Standards in Genomic Sciences volume 4, pages173–182(2011)
Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus Desulfurococcus, which belongs to the crenarchaeal family Desulfurococcaceae. The species is of interest because of its position in the tree of life, its ability for sulfur respiration, and several biotechnologically relevant thermostable and thermoactive extracellular enzymes. This is the third completed genome sequence of a member of the genus Desulfurococcus and already the 8th sequence from a member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain O7/1T (= DSM 2162 = ATCC 35584 = JCM 9187) is the type strain of the species Desulfurococcus mucosus , which is the type species of its genus Desulfurococcus. The genus currently consists of five species with a validly published name . For the genus name the Neo-Latin ‘desulfo-’ meaning ‘desulfuricating’ is used to characterize the dissimilatory sulfate-reducing feature of this spheroid-shaped ‘coccus’ . The species epithet is derived from the Latin word ‘mucosus’ (slimy) . Strain O7/1T was isolated from an acidic hot spring in Askja, Iceland and the name of the species was effectively published by Zillig et al. in 1982 ; valid publication of the name followed in 1983 . The strain was an early target for phylogenetic studies of the domain Archaea (at that time termed ‘Archaebacteria’) via DNA-rRNA cross-hybridizations [4,5], as well as studies on the archaeal DNA-dependent RNA polymerase structure  and Archaea-specific quinones . Subsequently, strain O7/1T was used for studies on thermostable extracellular enzymes such as proteinase  and pullulanase . Here we present a summary classification and a set of features for D. mucosus strain O7/1T, together with a description of the complete genome sequencing and annotation.
Classification and features
The single genomic 16S rRNA sequence of strain O7/1T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem ) were determined. The five most frequent genera were Sulfolobus (27.8%), Aeropyrum (11.3%), Desulfurococcus (11.3%), Ignicoccus (6.5%) and Vulcanisaeta (6.2%) (100 hits in total). Regarding the five hits to sequences from other members of the genus, the average identity within HSPs was 96.7%, whereas the average coverage by HSPs was 97.4%. Among all other species, the one yielding the highest score was Desulfurococcus mobilis, which corresponded to an identity of 100.0% and an HSP coverage of 100.0%. The highest-scoring environmental sequence was AB462558 (‘Microbial production and energy source hyperthermophilic prokaryotes geothermal hot spring pool clone DDP-A01’), which showed an identity of 95.8% and a HSP coverage of 98.2%. The five most frequent keywords within the labels of environmental samples which yielded hits were ‘spring’ (9.2%), ‘microbi’ (6.8%), ‘hot’ (6.2%), ‘nation/park/yellowston’ (5.4%) and ‘popul’ (4.8%) (150 hits in total), indicating a good fit to the original habitat of D. mucosus. Environmental samples which yielded hits of a higher score than the highest scoring species were not found.
Figure 1 shows the phylogenetic neighborhood of D. mucosus in a 16S rRNA based tree. A 16S rRNA reference sequence for D. mucosus has not been previously published.
The non-motile cells of strain O7/1T are spheroid with diameters of 0.3 to 2.0 µm  (Figure 2), sometimes up to 10 µm , surrounded by a slimy mucoid layer, which covers the envelope and consists of neutral sugars and a small fraction of amino sugars  (Figure 2). In growing cultures, cells of strain O7/1T were often found in pairs  (Table 1). Cells of strain O7/1T can be differentiated from those of D. mobilis, the closest relative of D. mucosus, which are mobile by monopolar polytrichous flagella and devoid of the mucous polymer surrounding the D. mucosus cells [1,23]. Strain O7/1T can utilize yeast extract and casein or its tryptic digests, but not casamino acids as the sole carbon source, by sulfur respiration with the production of H2S and CO2, or by fermentation . Growing cultures synthesize a strong smelling uncharacterized product . Cultures require little or no NaCl in growth media [1,23]. The temperature range for growth of strain O7/1T is 76 to 93°C, with an optimum at 85°C [1,23]. At the optimal growth temperature, the generation time of strain O7/1T was about four hours . The pH range is 4.5 to 7.0, with an optimum at 6.0 [1,23]. Sugars, starch, glycogen, alcohols and intermediary metabolites are also not utilized . Strain O7/1T lacks an intron in the 23S RNA gene, which has been described for its close relative D. mobilis .
According to Zillig et al. 1982 , the cell envelope of the strain O7/1T is flexible and probably composed of two layers of which at least the outer one appears to consist of subunits perpendicular to the surface . Scarce information is available regarding the lipid composition of D. mucosus. The lipids in the strain O7/1T are composed of phytanol and C40 polyisoprenoid dialcohols . The polar lipid profile of the closely related D. mobilis has been studied and the structure of its three complex lipids has been elucidated in detail .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position , and is part of the Genomic Encyclopedia of Bacteria and Archaea project . The genome project is deposited in the Genomes On Line Database  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
D. mucosus strain 07/1T, DSM 2162, was grown anaerobically in DSMZ medium 184 (Desulfurococcus medium)  at 85°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA kit (Qiagen 10262) following the standard protocol as recommended by the manufacturer, with no modification. DNA is available through the DNA Bank Network .
Genome sequencing and assembly
The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website . Pyrosequencing reads were assembled using the Newbler assembler version 2.5-internal-10Apr08-1-threads (Roche). The initial Newbler assembly consisting of three contigs in one scaffold was converted into a phrap assembly  by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (99.5 Mb) were assembled with Velvet  and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 546.5 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package  was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution , Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 12 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI . The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 120.5 × coverage of the genome. The final assembly contained 264,988 pyrosequence and 1,310,055 Illumina reads.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform .
The genome consists of a 1,314,639 bp long chromosome with a G+C content of 53.1% (Table 3 and Figure 3). Of the 1,421 genes predicted, 1,371 were protein-coding genes, and 50 RNAs; 26 pseudogenes were also identified. The majority of the protein-coding genes (65.5%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Zillig W, Stetter KO, Prangishvilli D, Schäfer W, Wunderl S, Janekovic D, Holz I, Palm P. Desulfurococcaceae, the second family of the extremely thermophilic, anaerobic, sulfur-respiring Thermoproteales. Zentralbl Bakteriol 1982; 3:304–317.
Garrity G. Names for Life. Browser Tool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
List Editor. Validation List no. 10. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol 1983; 33:438–440. doi:10.1099/00207713-33-2-438
Tu JK, Prangishvilli D, Huber H, Wildgruber G, Zillig W, Stetter KO. Taxonomic relations between Archaebacteria including 6 novel genera examined by cross hybridization of DNAs and 16S rRNAs. Mol Evol 1982; 18:109–114. PubMed doi:10.1007/BF01810829
Klenk HP, Haas B, Schwass V, Zillig W. Hybridization homology: a new parameter for the analysis of phylogenetic relations, demonstrated with the urkingdom of the Archaebacteria. J Mol Evol 1986; 24:167–173. doi:10.1007/BF02099964
Prangishvilli D, Zillig W, Gierl A, Biesert L, Holz I. DNA-dependent RNA polymerase of thermoacidophilic archaebacteria. Eur J Biochem 1982; 122:471–477. PubMed doi:10.1111/j.1432-1033.1982.tb06461.x
Thurl S, Witke W, Buhrow I, Schäfer W. Quinones from archaebacteria, II. Different types of quinones from sulphur-dependent archaebacteria. Biol Chem Hoppe Seyler 1986; 367:191–197. PubMed doi:10.1515/bchm3.1986.367.1.191
Cowan DA, Smolenski KA, Daniel RM, Morgan HW. An extracellular proteinase from a strain of the archaebacterium Desulfurococcus growing at 88 degrees C. Biochem J 1987; 247:121–133. PubMed
Duffner F, Bertoldo C, Andersen JT, Wagner K, Antranikian G. A new thermoactive pullulanase from Desulfurococcus mucosus: cloning, sequencing, purification, and characterization of the recombinant enzyme ofter expression in Bacillus subtilis. J Bacteriol 2000; 182:6331–6338. PubMed doi:10.1128/JB.182.22.6331-6338.2000
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K, Huber T, Dalevi D, Hu P, Andersen G. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05
Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137. doi:10.1108/eb046814
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-7_13
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2009; 38:D346–D354. PubMed doi:10.1093/nar/gkp848
Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG. Complete genome sequence of the anaerobic, proteindegrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. J Bacteriol 2009; 191:2371–2379. PubMed doi:10.1128/JB.01525-08
Anderson IJ, Sun H, Lapidus A, Copeland A, Glavina Del Rio T, Tice H, Dalin E, Lucas S, Barry K, Land M, et al. Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1. Stand Genomic Sci 2009; 1: 183–188. PubMed doi:10.4056/sigs.30527
Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP. The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic crenarchaeote growing up to 108°C. Archaea 2007; 2:127–135. PubMed doi:10.1155/2007/745987
Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, et al. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1T). Stand Genomic Sci 2010; 3:66–75. PubMed doi:10.4056/sigs.1072907
Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, et al. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 2008; 9:R158. PubMed doi:10.1186/gb-2008-9-11-r158
Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, et al. Complete genome sequence of Thermosphaera aggregans type strain (M11TLT). Stand Genomic Sci 2010; 2:245–259. PubMed doi:10.4056/sigs.821804
Huber H, Stetter KO. 2006. Desulfurococcales In: M Dworkin, S Falkow, E Rosenberg, KH Schleifer E Stackebrandt (eds), The Prokaryotes, 3. ed, vol. 3. Springer, New York, p. 52–68.
Stetter KO, Zillig W. 1985. Thermoplasma and the thermophilic sulfur-dependent archaebacteria. In: Woese CR, and Wolfe RS (eds) The Bacteria. Academic Press. New York, NY. 8:100–201.
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576
Validation list 85: Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol 2002; 52:685–690. PubMed doi:10.1099/ijs.0.02358-0
Garrity GM, Holt JG. 2001. Phylum AI. Crenarchaeota phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, p. 169–210.
Reysenbach AL. 2001. Class I. Thermoprotei class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, p. 169.
Huber H, Stetter O. 2001. Order II. Desulfurococcales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, p. 179–180.
Burggraf S, Huber H, Stetter KO. Reclassification of the crenarchael orders and families in accordance with 16S rRNA sequence data. Int J Syst Bacteriol 1997; 47:657–660. PubMed doi:10.1099/00207713-47-3-657
Perevalova AA, Svetlichny VA, Kublanov IV, Chernyh NA, Kostrikina NA, Tourova TP, Kuznetsov BB, Bonch-Osmolovskaya EA. Desulfurococcus fermentans sp. nov., a novel hyperthermophilic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococcus. Int J Syst Evol Microbiol 2005; 55:995–999. PubMed doi:10.1099/ijs.0.63378-0
Classification of Bacteria and Archaea in risk groups. www.baua.de TRBA 466.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556
Kjems J, Garrett RA. Novel splicing mechanism for the ribosomal RNA intron in the archaebacterium Desulfurococcus mobilis. Cell 1988; 54:693–703. PubMed doi:10.1016/S0092-8674(88)80014-X
Lanzotti V, De Rosa M, Trincone A, Basso AL, Gambacorta A, Zillig W. Complex lipids from Desulfurococcus mobilis, a sulfur-reducing archaebacterium. Biochim Biophys Acta 1987; 922:95–102.
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656
List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51–55. doi:10.1089/bio.2010.0029
DOE Joint Genome Institute. http://www.jgi.doe.gov
Phrap and Phred for Windows, MacOS, Linux, and Unix. http://www.phrap.com
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107
Han C, Chain P. 2006. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26–29, 2006: 141–146.
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393
We would like to gratefully acknowledge the help of Olivier D. Ngatchou-Djao (HZI) in preparing the manuscript. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.
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Wirth, R., Chertkov, O., Held, B. et al. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1T). Stand in Genomic Sci 4, 173–182 (2011). https://doi.org/10.4056/sigs.1644004
- sulfur respiration
- extracellular enzymes