Thermosediminibacter oceani (Lee et al. 2006) is the type species of the genus Thermosediminibacter in the family Thermoanaerobacteraceae. The anaerobic, barophilic, chemoorganotrophic thermophile is characterized by straight to curved Gram-negative rods. The strain described in this study was isolated from a core sample of deep sea sediments of the Peruvian high productivity upwelling system. This is the first completed genome sequence of a member of the genus Thermosediminibacter and the seventh genome sequence in the family Thermoanaerobacteraceae. The 2,280,035 bp long genome with its 2,285 protein-coding and 63 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain JW/IW-1228PT (= DSM 16646 = ATCC BAA-1034) is the type strain of Thermosediminibacter oceani, which is the type species of the genus Thermosediminibacter , one out of nineteen genera in the family Thermoanaerobacteraceae [2–4]. The generic name derives from the Greek word ‘thermos’ meaning ‘hot’, the Latin word ‘sediment’ and the Latin word ‘bacter’ meaning ‘a rod or staff’, referring to its origin and growth temperature . The species epithet is also derived from the Latin word ‘oceani’ meaning ‘of an ocean’, referring to its origin from the ocean . Strain JW/IW-1228PT was described in 2005 by Lee as T. oceani  and validly published in 2006 . Strain JW/IW-1228PT was isolated from a core sediment sample (core 201-1228E-1H-1) at 136–143 cm below the seafloor. The core sample was obtained from the outer shelf edge of the Peruvian high productivity upwelling system. The sea floor there was located at 252 m below the sea level with 12°C mud line temperature. Strain JW/IW-1228PT is of particular interest because it is able to ferment a significant number of polysaccharides . Moreover, the strain JW/IW-1228PT is able to use thiosulfate, elemental sulfur and MnO2 as electron acceptors for growth. The only other species in the genus Thermosediminibacter is T. litoriperuensis, the type strain of which was isolated from the Peru Trench at 5,086 m below sea level with a mud-line temperature of 2°C .
Here we present a summary classification and a set of features for T. oceani JW/IW-1228PT, together with the description of the complete genomic sequencing and annotation.
Classification and features
The 16S rRNA gene sequence of JW/IW-1228PT is 98.4% identical to that of T. litoriperuensis JW/YJL-1230-2T, the type strain of the only other described species with a validly published name in the genus. The sequence similarities between strain JW/IW-1228PT and the type strains of the members of the genera Fervidicola and Caldanaerovirga are 94.4%, with the closest sequence match being that with F. ferrireducens and C. acetigignens . Three significantly similar 16S rRNA gene sequences are known from uncultured clones of Thermovenabulum sp. from GenBank : B5_otu10 (96%, DQ097675), B14_otu11 (95%, DQ097676) and B8_otu12 (95%, DQ097677), all from the Kongdian bed of the Dagang oil field (Hebei province, China) [7,8]. No phylotypes from environmental screening or genomic surveys could be linked to the species T. oceani or even the genus Thermosediminibacter, indicating a rather rare occurrence of these in the habitats screened so far (as of July 2010).
Figure 1 shows the phylogenetic neighborhood of T. oceani JW/IW-1228PT in a 16S rRNA based tree. The sequences of the three 16S rRNA gene copies in the genome differ from each other by up to one nucleotide and differ by only one nucleotide from the previously published sequence (AY703478).
The cells of strain JW/IW-1228PT are straight to curved rods which occur singly, in pairs or in chains (Table 1 and Figure 2). They are between 0.2–0.7µm in diameter and 1.5–16 µm in length. In the late-exponential or stationary phase of growth the cells are swollen and subsequently form L-shaped autoplasts . Strain JW/IW-1228PT is Gram-negative, although Thermosediminibacter belongs to the Gram-positive Bacillus-Clostridium subphylum . The cells tend towards elongation and to form aggregates during growth. Motility has not been reported although flagella are observed on the cells (not visible in Figure 2), however, the cells are able to tumble , which might imply an impaired flagellar function. Strain JW/IW-1228PT is thermophilic and grows optimally at 68°C; the temperature range for growth is 52–76°C. The optimum pH25°C for growth is 7.5, with a range for growth at 6.3–9.3. The optimum salinity for growth is 1% (w/v), with a salinity range of 0–6% (w/v) . Yeast extract is required for growth. The growth of strain JW/IW-1228PT is not observed on H2/CO2 (80:20, v/v) . The strain produces α-glucosidase . The carbon and energy sources used by JW/IW-1228PT include beef extract, casamino acids, cellobiose, fructose, galactose, glucose, inositol, lactate, maltose, mannose, pyruvate, raffinose, sorbitol, sucrose, trehalose, tryptone and xylose when 0.02% w/v of yeast extract is present in growth medium . The fermentation product from glucose is acetate and occasionally trace amounts of propionate, isobutyrate and isovalerate. Acetate is a major product . Strain JW/IW-1228PT does not utilize xylitol . It is able to use thiosulfate, elemental sulfur and MnO2 as electron acceptors for growth. There is no indication that JW/IW-1228PT is able to grow chemolithoautotrophically; it does not reduce sulfate or Fe(III) .
The peptidoglycan structure of strain JW/IW-1228PT is still unknown. The phospholipid fatty acid composition of strain JW/IW-1228PT consists of branched and straight chain saturated acids: iso-C15:0 (56.2%), iso-C17:0 (9.6%), C16:0 (7.5%), anteiso-C15:0 (6.7%), C16:1ω9c (5.6%), C15:0 (5.0%), C18:1 ω 9c (3.3%) and iso-C16:0 (1.9%) .
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 Genome OnLine 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
T. oceani JW/IW-1228PT, DSM 16646, was grown anaerobically in DSMZ medium 664 (Thermotoga elfii medium)  at 68°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the standard protocol as recommended by the manufacturer, with modification st/LALMP for cell lysis as described in Wu et al. .
Genome sequencing and assembly
The genome was sequenced using a combination of Sanger, 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 2.0.0-PostRelease-07/15/2008 (Roche). The initial Newbler assembly consisted of 83 contigs in 32 scaffolds which was converted into a phrap assembly by making fake reads from the consensus. Illumina GAii sequencing data was assembled with Velvet  and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. Draft assemblies were based on 166.4 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 (http://www.phrap.com) was used for sequence assembly and quality assessment in the following finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 625 additional reactions and two shatter libraries were necessary to close gaps and to raise the quality of the finished sequence. Illumina data was 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 Sanger, Illumina and 454 sequencing platforms provided 65.0 ×coverage of the genome.
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, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform .
The genome consists of a 2,280,035 bp long chromosome with a 468% GC content (Table 3 and Figure 3). Of the 2,348 genes predicted, 2,285 were protein-coding genes, and 63 RNAs; eighty eight pseudogenes were also identified. The majority of the protein-coding genes (73.3%) 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.
Lee YJ, Wagner ID, Brice ME, Kevbrin VV, Mills GL, Romanek CS, Wiegel J. Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin. Extremophiles 2005; 9:375–383. PubMed doi:10.1007/s00792-005-0453-4
Validation list no. 132. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2010; 60:469–472. doi:10.1099/ijs.0.022855-0
Wiegel J. 2009. Family I. Thermoanaerobacteraceae fam. nov., p. 1225. In P De Vos, GM Garrity, D. Jones, NR Krieg, W Ludwig, FA Rainey, KH Schleifer, and W Whitman (eds), Bergey’s Manual of Systematic Bacteriology, second ed, vol. 3. Springer-Verlag, New York.
Garrity G. NamesforLife. Browser Tool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.
Validation list no. 109. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:925–927. PubMed doi:10.1099/ijs.0.64380-0
Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261. PubMed doi:10.1099/ijs.0.64915-0
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2009; 37:D26–D31. PubMed doi:10.1093/nar/gkn723
Nazina TN, Shestakova NM, Grigor’ian AA, Mikhailova EM, Turova TP, Poltaraus AB, Feng C, Ni F, Beliaev SS. Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang Oilfield (China). Mikrobiologiia 2006; 75:70–81. PubMed
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
Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R. The All-Species Living Tree project: A 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250. PubMed doi:10.1016/j.syapm.2008.07.001
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:10.1007/978-3-642-02008-713
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 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848
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
Garrity GM, Holt JG. 2001. The Road Map to the Manual, p. 119–169. In G.M. Garrity, D.R. Boone, and R.W. Castenholz (ed.), Bergey’s Manual of Systematic Bacteriology, 2 ed, vol. 1. Springer, New York.
Gibbons NE, Murrey RGE. Proposals concerning the higher taxa of bacteria. Int J Syst Bacteriol 1978; 28:1–6. doi:10.1099/00207713-28-1-1
Rainey FA. 2009. Class II. Clostridia class nov, p. 736. In: P De Vos, GM Garrity, D Jones, NR Krieg, W Ludwig, FA Rainey, KH Schleifer, W Whitman (eds), Bergey’s Manual of Systematic Bacteriology, second edition, vol. 3 (The Firmicutes), vol. 3. Springer, Dordrecht, Heidelberg, London, New York.
Wiegel J. Order III. Thermoanaerobacterales ord. nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer Verlag, New York, 2009, p. 1224.
Classification of bacteria and archaea in risk groups. TRBA 466.
D’Hondt SL, Jørgensen BB, Miller DJ, Aiello IW, Bekins B, Blake R, Cragg BR, Cypionka H, Dickens GR, Ferdelman T, et al. Init Repts, 201: College Station, TX (Ocean Drilling Program) 2003.
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
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.
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. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. HR Arabnia & H Valafar (eds), 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 Maren Schröder for growing T. oceani cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). 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 and SI 1352/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY.
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Pitluck, S., Yasawong, M., Munk, C. et al. Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228PT). Stand in Genomic Sci 3, 108–116 (2010). https://doi.org/10.4056/sigs.1133078
- upwelling system
- core sample
- deep sea sediment