Complete genome sequence of oceanithermus profundus type strain (506 T)

Standards in Genomic Sciences

Volumn 4, Issue 2, 2011, Pages 210-220

  Pati, Amrita ^a   Zhang, Xiaojing ^b   Lapidus, Alla ^a   Nolan, Matt ^a   Lucas, Susan ^a   del Rio, Tijana Glavina ^a   Tice, Hope ^a   Cheng, Jan Fang ^a   Tapia, Roxane ^a,b   Han, Cliff ^a,b   Goodwin, Lynne ^a,b   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Pagani, Ioanna ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Chen, Amy ^c   Palaniappan, Krishna ^c   Hauser, Loren ^a,d   Jeffries, Cynthia D ^a,d   Brambilla, Evelyne Marie ^e   Röhl, Alina ^f   Mwirichia, Romano ^g   Rohde, Manfred ^h   Tindall, Brian J ^e   Sikorski, Johannes ^e   Wirth, Reinhard ^f   Göker, Markus ^e   Woyke, Tanja ^a   Detter, John C ^a,b   Bristow, James ^a   Eisen, Jonathan A ^a,i   Markowitz, Victor ^c   Hugenholtz, Philip ^a,j   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^e   Land, Miriam ^a,d   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^d OAK RIDGE NATIONAL LABORATORY   (United States)

^e LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^f UNIVERSITY OF REGENSBURG   (Germany)

^g JOMO KENYATTA UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Kenya)

^h HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j UNIVERSITY OF QUEENSLAND   (Australia)

more..

Author keywords

Chemolithoheterotrophic; GEBA; Gram negative; Hydrothermal vent; Microaerophilic; Moderate thermo philic; Neutrophilic; Nitrate reducing; Non motile; Thermaceae

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; OCEANITHERMUS; OCEANITHERMUS PROFUNDUS; THERMACEAE;

EID: 80053514179     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1734292     Document Type: Article

References (49)

1. Miroshnichenko ML, L'haridon S, Jeanthon C, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA. Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2003; 53:747-752. PubMed doi:10.1099/ijs.0.02367-0
2. Da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Bergey's Manual of Systematic Bac-teriology 2001. Boone DR, Castenholz RW, Garri-ty GM (eds), 2nd edn, vol. 1, pp. 403-404. New York: Springer.
3. Mori K, Kakegawa T, Higashi Y, Nakamura K, Maruyama A, Hanada S. Oceanithermus desulfu-rans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chim-ney in Suiyo Seamount. Int J Syst Evol Microbiol 2004; 54:1561-1566. PubMed doi:10.1099/ijs.0.02962-0
4. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a Chimera-checked 16S rRNA gene database and workbench compat-ible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi:10.1128/AEM.03006-05
5. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137.
6. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
7. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
8. 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
9. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. doi:10.1111/j.1095-8312.2007.00864.x
10. 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
11. 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
12. Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Rio TGD, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiother-mus silvanus type strain (VI-R2T). Stand Genomic Sci 2010; 3:37-46. PubMed doi:10.4056/sigs.1042812
13. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Rio TGD, Nolan M, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meio-thermus ruber type strain (21T). Stand Genomic Sci 2010; 3:26-36. PubMed doi:10.4056/sigs.1032748
14. Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Deshpande S, Cheng JF, Tapia R, et al. Complete genome sequence of Truepera radiovictrix type strain (RQ-24T). Stand Genomic Sci 2011; 4:91-99. PubMed doi:10.4056/sigs.1563919
15. Brock TD, Edwards MR. Fine structure of Thermus aquaticus, an extreme thermophile. J Bacteriol 1970; 104:509-517. PubMed
16. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, An-giuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
18. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 2 - The Bacteria: Phyla Aquificae, Thermotogae, Thermodesulfobacteria, Deino-coccus-Thermus, Chrysiogenetes, Chloroflexi, Thermomicrobia, Nitrospira, Deferribacteres, Cyanobacteria, and Chlorobi. http://www.taxonomicoutline.org/index.php/toba/article/view/187/211 2007.
19. Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construc-tion. Syst Appl Microbiol 1989; 11:128-134. PubMed
20. Garrity GM, Holt JG. Class I. Deinococci class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 1, Springer, New York, 2001, p. 395.
21. List Editor. Validation List no. 85. Validation of publication of new names and new combinations previously effectively published outside the IJ-SEM. Int J Syst Evol Microbiol 2002; 52:685-690.PubMed doi:10.1099/ijs.0.02358-0
22. Rainey FA, da Costa MS. Order II. Thermales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriolo-gy, Second Edition, Volume 1, Springer, New York, 2001, p. 403.
23. da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteri-ology, Second Edition, Volume 1, Springer, New York, 2001, p. 403-404.
24. Classification of bacteria and archaea in risk groups. http://www.baua.deTRBA 466.
25. Ashburner M, Ball CA, Blake JA, Botstein D, But-ler 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
26. Fedosov DV, Podkopaeva DA, Miroshnichenko ML, Bonch-Osmolovskaya EA, Lebedinsky AV, Grabovich MY. Metabolism of the thermophilic bacterium Oceanithermus profundus. Microbiolo-gy 2008; 77:159-165. PubMed doi:10.1134/S0026261708020069
27. Donato MM, Seleiro EA, Da Costa MS. Polar lipid and fatty acid composition of strains of the genus Thermus. Syst Appl Microbiol 1990; 13:234-239.
28. Donato MM, Seleiro EA, Da Costa MS. Polar lipid and fatty acid composition of strains of Thermus ruber. Syst Appl Microbiol 1991; 14:235-239.
29. Yang YL, Yang FL, Jao SC, Chen MY, Tsay SS, Zou W, Wu SH. Structural elucidation of phosphogly-colipids from strains of the bacterial thermophiles Thermus and Meiothermus. J Lipid Res 2006; 47:1823-1832. PubMed doi:10.1194/jlr.M600034-JLR200
30. Steinsbu BO, Tindall BJ, Torsvik VL, Ingunn H, Thorseth IH, Daae FL, Pedersen RB. Rhabdother-mus arcticus gen. nov., sp. nov., a novel member of the family Thermaceae isolated from a hydro-thermal vent chimney from Soria Moria vent field at the Arctic Mid-Ocean Ridge. Int J Syst Evol Mi-crobiol 2010
31. Miroshnichenko ML, L'Haridon S, Nercessian O, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C. Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 2003; 53:1143-1148. PubMed doi:10.1099/ijs.0.02579-0
32. Embley TM, O'Donnell AG, Wait R, Rostron J. Lipid and cell wall amino acid composition in the classification of members of the genus Deinococ-cus. Syst Appl Microbiol 1987; 10:20-27.
33. Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, Da Costa MS. Deinococcus geothermalis sp. nov. and Deino-coccus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 1997; 47:939-947. PubMed doi:10.1099/00207713-47-4-939
34. Hensel R, Demharter W, Kandler O, Kroppenstedt RM, Stackebrandt E. Chemotaxonomic and mole-cular-genetic studies of the genus Thermus: evi-dence for a phylogenetic relationship of Thermus aquaticus and Thermus ruber to the genus Deino-coccus. Int J Syst Bacteriol 1986; 36:444-453. doi:10.1099/00207713-36-3-444
35. Chung AP, Rainey F, Nobre MF, Burghardt J, Da Costa MS. Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids. Int J Syst Bacteriol 1997; 47:1225-1230. PubMed doi:10.1099/00207713-47-4-1225
36. Sako Y, Nakagawa S, Takai K, Horikoshi K. Mari-nithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2003; 53:59-65. PubMed doi:10.1099/ijs.0.02364-0
37. Ekman JV, Raulio M, Busse HJ, Fewer DP, Salki-noja-Salonen M. Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill. Int J Syst Evol Microbiol 2011; 61:540-548. PubMed doi:10.1099/ijs.0.017970-0
38. 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
39. 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
40. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
41. Gemeinholzer B, Dröge G, Zetzsche H, Haszpru-nar 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
42. DOE Joint Genome Institute. http://www.jgi.doe.gov
43. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
44. 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
45. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. PubMed doi:10.4056/sigs.761
46. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
47. Hyatt D, Chen GL, LoCascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
48. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
49. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393