Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1 T)

Standards in Genomic Sciences

Volumn 6, Issue 1, 2012, Pages 94-103

  Han, Cliff ^a,b   Kotsyurbenko, Oleg ^c,d   Chertkov, Olga ^a,b   Held, Brittany ^a,b   Lapidus, Alla ^a   Nolan, Matt ^a   Lucas, Susan ^a   Hammon, Nancy ^a   Deshpande, Shweta ^a   Cheng, Jan Fang ^a   Tapia, Roxanne ^a,b   Goodwin, Lynne ^a,b   Pitluck, Sam ^a   Liolios, Konstantinos ^a   Pagani, Ioanna ^a   Ivanova, Natalia ^a   Mavromatis, Konstantinos ^a   Mikhailova, Natalia ^a   Pati, Amrita ^a   Chen, Amy ^e   Palaniappan, Krishna ^e   Land, Miriam ^a,f   Hauser, Loren ^a,f   Chang, Yun juan ^a,f   Jeffries, Cynthia D ^a,f   Brambilla, Evelyne Marie ^g   Rohde, Manfred ^h   Spring, Stefan ^g   Sikorski, Johannes ^g   Göker, Markus ^g   Woyke, Tanja ^a   Bristow, James ^a   Eisen, Jonathan A ^a,i   Markowitz, Victor ^e   Hugenholtz, Philip ^a,j   Kyrpides, Nikos C ^a   Klenk, Hans Peter ^g   Detter, John C ^a,b   more..

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c TECHNICAL UNIVERSITY OF BRAUNSCHWEIG   (Germany)

^d MOSCOW STATE UNIVERSITY   (Russian Federation)

^e LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^f OAK RIDGE NATIONAL LABORATORY   (United States)

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

^h HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j UNIVERSITY OF QUEENSLAND   (Australia)

more..

Author keywords

Chemolithoautotrophic; Facultatively anaerobic; GEBA; Gram negative; Helicobacteracea; Mesophilic; Microaerobic; Motile; Sulfur oxidizing

Indexed keywords

BACTERIAL RNA; PETROLEUM; RNA 16S; SULFUR DERIVATIVE;

ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL STRAIN; EPSILONPROTEOBACTERIA; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; SULFURICURVUM KUJIEINSE;

EPSILONPROTEOBACTERIA; HELICOBACTERACEAE; NEGIBACTERIA; SULFURICURVUM; SULFURICURVUM KUJIENSE;

EID: 84859069667     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.2456004     Document Type: Article

References (49)

1. Kodama Y, Watanabe K. Sulfuricurvum kujiense gen.nov., sp. nov., a facultatively anaerobic, chemolithoautotrophic, sulfur-oxidizing bacterium isolated from an underground crude-oil storage cavity. Int J Syst Evol Microbiol 2004; 54:2297-2300. PubMed http://dx.doi.org/10.1099/ijs.0.63243-0
2. Euzeby J. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590-592. PubMed http://dx.doi.org/10.1099/00207713-47-2-590
3. Kodama Y, Watanabe K. Isolation and characterization of a sulfur-oxidizing chemolithotroph growing on crude oil under anaerobic conditions. Appl Environ Microbiol 2003; 69:107-112. Pub-Med http://dx.doi.org/10.1128/AEM.69.1.107-112.2003
4. Campbell BJ, Engel AS, Porter ML, Takai K. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 2006; 4:458-468. PubMed http://dx.doi.org/10.1038/nrmicro1414
5. Porter ML, Engel AS. Diversity of uncultured Epsilonproteobacteria from terrestrial sulfidic caves and springs. Appl Environ Microbiol 2008; 74:4973-4977. PubMed http://dx.doi.org/10.1128/AEM.02915-07
6. Hubert CR, Oldenburg TBP, Fustic M, Gray ND, Larter SR, Penn K, Rowan AK, Seshadri R, Sherry A, Swainsbury R, et al. Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil. [PubMed]. Environ Microbiol 2011; (In press). PubMed
7. Altschul SF, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. [PubMed]. J Mol Biol 1990; 215:403-410. PubMed
8. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebastopol, 2003.
9. 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 http://dx.doi.org/10.1128/AEM.03006-05
10. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137.
11. Watanabe K, Watanabe K, Kodama Y, Syutsubo K, Harayama S. Molecular characterization of bacterial populations in petroleum-contaminated groundwater discharged from underground crude oil storage cavities. Appl Environ Microbiol 2000; 66:4803-4809. PubMed http://dx.doi.org/10.1128/AEM.66.11.4803-4809.2000
12. Haaijer SC, Harhangi HR, Meijerink BB, Strous M, Pol A, Smolders AJ, Verwegen K, Jetten MS, Op den Camp HJ. Bacteria associated with iron seeps in a sulfur-rich, neutral pH, freshwater eco-system. ISME J 2008; 2:1231-1242. PubMed http://dx.doi.org/10.1038/ismej.2008.75
13. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
14. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. [PubMed]. Mol Biol Evol 2000; 17:540-552. PubMed
15. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
16. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
17. 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. http://dx.doi.org/10.1007/978-3-642-02008-7_13
18. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
19. 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 http://dx.doi.org/10.1093/nar/gkp848
20. Sikorski J, Munk C, Lapidus A, Ngatchou Djao OD, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Han C, Cheng JF, et al. Complete genome sequences of Sulfurimonas autotrophica type strain (OK 10T). Stand Genomic Sci 2010; 3:194-202. PubMed
21. Baar C, Eppinger M, Raddatz G, Simon J, Lanz C, Klimmek O, Nandakumar R, Gross R, Rosinus A, Keller H, et al. Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci USA 2003; 100:11690-11695. PubMed http://dx.doi.org/10.1073/pnas.1932838100
22. Sikorski J, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, Saunders E, et al. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T). Stand Genomic Sci 2010; 2:149-157. PubMed http://dx.doi.org/10.4056/sigs.671209
23. Pati A, Gronow S, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Arcobacter nitrofigilis type strain (CIT). Stand Genomic Sci 2010; 2:300-308. PubMed http://dx.doi.org/10.4056/sigs.912121
24. Anderson I, Sikorski J, Zeytun A, Nolan M, Lapidus A, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, et al. Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1T). Stand Genomic Sci 2011; 4:322-330. PubMed http://dx.doi.org/10.4056/sigs.1844518
25. Meier-Kolthoff JP, Auch AF, Huson DH, Göker M. COPYCAT: Co-phylogenetic Analysis tool. Bioinformatics 2007; 23:898-900. PubMed http://dx.doi.org/10.1093/bioinformatics/btm027
26. Stamatakis A, Auch A, Meier-Kolthoff JP, Göker M. AxPcoords & Parallel AxParafit: Statistical co-phylogenetic analyses on thousands of taxa. BMC Bioinformatics 2007; 8:405. PubMed http://dx.doi.org/10.1186/1471-2105-8-405
27. Felsenstein J. Inferring phylogenies. Sinauer Associates Inc., Sunderland, Massachusetts, 2004.
28. 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 http://dx.doi.org/10.1038/nbt1360
29. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
30. 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 http://dx.doi.org/10.1073/pnas.87.12.4576
31. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
32. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. [PubMed]. Int J Syst Evol Microbiol 2006; 56:1-6. PubMed http://dx.doi.org/10.1099/ijs.0.64188-0
33. Garrity GM, Bell JA, Lilburn T. Class V. Epsilonproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 1145.
34. Garrity GM, Bell JA, Lilburn T. Order I. Campylobacterales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 1145.
35. Garrity GM, Bell JA, Lilburn T. Family II. Helicobacteraceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 1168.
36. BAuA. Classification of bacteria and archaea in risk groups. TRBA 466. p. 227. Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, Germany. 2010.
37. 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 http://dx.doi.org/10.1038/75556
38. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/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 http://dx.doi.org/10.1038/nature08656
40. List of growth media used at DSMZ: http//www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/list-of-media-for-microorganisms.html.
41. 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. Biopreserv Biobank 2011; 9:51-55. http://dx.doi.org/10.1089/bio.2010.0029
42. JGI website. http://www.jgi.doe.gov/.
43. The Phred/Phrap/Consed software package. 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 http://dx.doi.org/10.1101/gr.074492.107
45. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26-29, 2006: 141-146.
46. 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.
47. 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. Pub-Med http://dx.doi.org/10.1186/1471-2105-11-119
48. 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 http://dx.doi.org/10.1038/nmeth.1457
49. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393