Genome sequence of the Leisingera aquimarina type strain (DSM 24565T), a member of the marine Roseobacter clade rich in extra chromosomal elements

Standards in Genomic Sciences

Volumn 8, Issue 3, 2013, Pages

  Riedel, Thomas ^a   Teshima, Hazuki ^b   Petersen, Jörn ^c   Fiebig, Anne ^c   Davenport, Karen ^b   Daligault, Hajnalka ^b   Erkkila, Tracy ^b   Gu, Wei ^b   Munk, Christine ^b   Xu, Yan ^b   Chen, Amy ^d   Pati, Amrita ^e   Ivanova, Natalia ^e   Goodwin, Lynne A ^b,e   Chain, Patrick ^b   Detter, John C ^b,e   Rohde, Manfred ^a   Gronow, Sabine ^c   Kyrpides, Nikos C ^e   Woyke, Tanja ^e   Göker, Markus ^c   Brinkhoff, Thorsten ^f   Klenk, Hans Peter ^c   more..

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

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

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e DOE JOINT GENOME INSTITUTE   (United States)

^f Institute for Chemistry and Biology of the Marine Environment (ICBM)   (Germany)

Author keywords

Alphaproteobacteria; Biofilm; Carbon monoxide utilization; Halotolerant; Heterotrophic; Marine; Ovoid shaped; Plasmid; Quorum sensing; Rhodobacteraceae; Thiosulfate oxidation

Indexed keywords

EXTRACHROMOSOMAL DNA; GENOMIC DNA; RNA 16S;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM; CHEMOTAXONOMY; DNA ISOLATION; GENETIC ASSOCIATION; GENOME; LEISINGERA AQUIMARINA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; ROSEOBACTER; SCANNING ELECTRON MICROSCOPY;

EID: 84881031716     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3858183     Document Type: Article

References (57)

1. Vandecandelaere I, Segaert E, Mollica A, Faimali M, Vandamme P.Leisingera aquimarina sp. nov., isolated form a marine electroactive biofilm, and emended descriptions of Leisingera methylohalidivorans Schaefer et al. 2002, Phaeobacter daeponensis Yoon et al. 2007 and Phaeobacter inhibens Martens et al. 2006. Int J Syst Evol Microbiol 2008; 58:2788-2793.[doi:10.1099/ijs.0.65844-0] [pmid:19060059]
2. Schaefer JK, Goodwin KD, McDonald IR, Murrell JC, Oremland RS. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide. Int J Syst Evol Microbiol 2002; 52:851-859. [doi:10.1099/ijs.0.01960-0] [pmid:12054249]
3. Sun F, Wang B, Liu X, Lai Q, Du Y, Li G, Luo J, Shao Z. Leisingera nanhaiensis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2010; 60:275-280. [doi:10.1099/ijs.0.010439-0] [pmid:19651744]
4. Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol 2005; 71:5665-5677. [doi:10.1128/AEM.71.10.5665-5677.2005] [pmid:16204474]
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410.[pmid:2231712]
6. Korf I, Yandell M, Bedell J. BLAST, O'Reilly, Sebastopol, 2003.
7. 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 Compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072.[doi:10.1128/AEM.03006-05] [pmid:16820507]
8. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130-137.
9. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464.[doi:10.1093/bioinformatics/18.3.452] [pmid:11934745]
10. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552.[doi:10.1093/oxfordjournals.molbev.a026334] [pmid:10742046]
11. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758-771.[doi:10.1080/10635150802429642] [pmid:18853362]
12. 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]
13. 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]
14. Swofford DL. PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
15. Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The GenomesOnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2012; 40:D571-D579.[doi:10.1093/nar/gkr1100] [pmid:22135293]
16. Ruiz-Ponte C, Cilia V, Lambert C, Nicolas JL. Roseobacter gallaciensis sp. nov., a marine bacterium isolated from rearings and collectors of the scallop Pecten maximus. Int J Syst Bacteriol 1998; 48:537-542. [doi:10.1099/00207713-48-2-537] [pmid:9731295]
17. Moran MA, Buchan A, González JM, Heidelbarg JF, Witman WB, Kiene JR, Henriksen JR, King GM, Belas R, Fuqua C, et al. Genome sequence of Silicibacter pomeroyi reveals adaptation to the marine environment. Nature 2004; 432:910-913. [doi:10.1038/nature03170] [pmid:15602564]
18. 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. [doi:10.1038/nbt1360] [pmid:18464787]
19. Woese CR, Kandler O, Weelis ML. Towards a natural system of organisms. Proposal for the domains Archaea and Bacteria. Proc Natl Acad Sci USA 1990; 87:4576-4579.[doi:10.1073/pnas.87.12.4576] [pmid:2112744]
20. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl nov. In: Brenner DJ, Krieg NR, Stanley JT, Garrity GM (eds), Bergey's Manual of Sytematic Bacteriology, second edition. Vol. 2 (The Proteobacteria), part B (The Gammaproteobacteria), Springer, New York, 2005, p. 1.
21. Garrity GM, Bell JA, Lilburn T. Class I. Alphaproteobacteria class. nov. In: Brenner DJ, Krieg NR, Stanley JT, Garrity GM (eds), Bergey's Manual of Sytematic Bacteriology, second edition. Vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York, 2005, p. 1.
22. Validation list No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1-6. [doi:10.1099/ijs.0.64188-0] [pmid:16403855]
23. Garrity GM, Bell JA, Lilburn T. Order III. Rhodobacterales ord. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition. vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York, 2005, p. 161.
24. Garrity GM, Bell JA, Lilburn T. Family I. Rhodobacteraceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, second edition. vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria), Springer, New York, 2005, p. 161.
25. Schaefer JK, Goodwin KD, McDonald IR, Murrell JC, Oremland RS. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide. Int J Syst Evol Microbiol 2002; 52:851-859. [doi:10.1099/ijs.0.01960-0] [pmid:12054249]
26. Martens T, Heidorn T, Pukall R, Simon M, Tindall BJ, Brinkhoff T. Reclassification of Roseobacter gallaeciensis Ruiz-Ponte et al. 1998 as Phaeobacter gallaeciensis gen. nov., comb. nov., description of Phaeobacter inhibens sp. nov., reclassification of Ruegeria algicola (Lafay et al. 1995) Uchino et al. 1999 as Marinovum algicola gen. nov., comb. nov., and emended descriptions of the genera Roseobacter, Ruegeria and Leisingera. Int J Syst Evol Microbiol 2006; 56:1293-1304.[doi:10.1099/ijs.0.63724-0] [pmid:16738106]
27. BAuA. Classification of Bacteria and Archaea in risk groups. TRBA 2010; 466:93.
28. 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. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29.[doi:10.1038/75556] [pmid:10802651]
29. Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP. Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 2012; 7:e34846. [doi:10.1371/journal.pone.0034846] [pmid:22536335]
30. Yoon JH, Kang SJ, Lee SY, Oh TK. Phaeobacter daeponensis sp. nov., isolated from a tidal flat of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2007; 57:856-861.[doi:10.1099/ijs.0.64779-0] [pmid:17392219]
31. List of growth media used at the DSMZ: http://www.dmsz.de/catalogues/cataloque-microorganisms/culture-technology/list-of-media-for-microorganisms.html.
32. 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.[doi:10.1089/bio.2010.0029]
33. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433-438.[doi:10.1517/14622416.5.4.433] [pmid:15165179]
34. The DOE Joint Genome Institute. www.jgi.doe.gov
35. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res 2008; 18:810-820.[doi:10.1101/gr.7337908] [pmid:18340039]
36. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829.[doi:10.1101/gr.074492.107] [pmid:18349386]
37. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
38. 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.[doi:10.1186/1471-2105-11-119] [pmid:20211023]
39. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 2009; 1:63-67.[doi:10.4056/sigs.632] [pmid:21304638]
40. 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. [doi:10.1038/nmeth.1457] [pmid:20436475]
41. 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. [doi:10.1093/bioinformatics/btp393] [pmid:19561336]
42. del Solar G, Giraldo R, Ruiz-Echevarria MJ, Espinosa M, Diaz-Orejes R. Replication and control of circular bacterial plasmids. Microbiol Mol Biol Rev 1998; 62:434-464.[pmid:9618448]
43. Petersen J, Brinkmann H, Berger M, Brinkhoff T, Päuker O, Pradella S. Origin and evolution of a novel DnaA-like plasmid replication type in Rhodobacterales. Mol Biol Evol 2011; 28:1229-1240. [doi:10.1093/molbev/msq310] [pmid:21097494]
44. Petersen J. Phylogeny and compatibility: plasmid classification in the genomics era. Arch Microbiol 2011; 193:313-321.[pmid:21374058]
45. Petersen J, Brinkmann H, Pradella S. Diversity and evolution of repABC type plasmids in Rhodobacterales. Environ Microbiol 2009; 11:2627-2638. [doi:10.1111/j.1462-2920.2009.01987.x] [pmid:19601964]
46. Zielenkiewicz U, Ceglowski P. Mechanisms of plasmid stable maintenance with special focus on plasmid addiction systems. Acta Biochim Pol 2001; 48:1003-1023. [pmid:11995964]
47. Giraud MF, Naismith JH. The rhamnose pathway. Curr Opin Struct Biol 2000; 10:687-696.[doi:10.1016/S0959-440X(00)00145-7] [pmid:11114506]
48. Petersen J, Frank O, Göker M, Pradella S. Extrachromosomal, extraordinary and essential-the plasmids of the Roseobacter clade. Appl Microbiol Biotechnol 2013; 97:2805-2815.[doi:10.1007/s00253-013-4746-8] [pmid:23435940]
49. Lawley TD, Klimke WA, Gubbins MJ, Frost LS. F factor conjugation is a true type IV secretion system. FEMS Microbiol Lett 2003; 224:1-15.[doi:10.1016/S0378-1097(03)00430-0] [pmid:12855161]
50. Zech H, Thole S, Schreiber K, Kalhöfer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R. Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics 2009; 9:3677-3697.[doi:10.1002/pmic.200900120] [pmid:19639587]
51. Petersen J, Brinkmann H, Bunk B, Michael V, Päuker O, Pradella S. Think pink: photosynthesis, plasmids and the Roseobacter clade. Environ Microbiol 2012; 14:2661-2672.[doi:10.1111/j.1462-2920.2012.02806.x] [pmid:22732061]
52. Fürch T, Preusse M, Tomasch J, Zech H, Wagner-Döbler I, Rabus R, Wittmann C. Metabolic fluxes in the central carbon metabolism of Dinoroseobacter shibae and Phaeobacter gallaeciensis, two members of the marine Roseobacter clade. BMC Microbiol 2009; 9:209.[doi:10.1186/1471-2180-9-209] [pmid:19788729]
53. Schwarz S, Hood RD, Mougous JD. What is type VI secretion doing in all those bugs? Trends Microbiol 2010; 18:531-537.[doi:10.1016/j.tim.2010.09.001] [pmid:20961764]
54. Wagner-Döbler I, Thiel V, Eberl L, Allgaier M, Bodor A, Meyer S, Ebner S, Hennig A, Pukall R, Schulz S. Discovery of complex mixtures of novel long-chain quorum sensing signals in free-living and host-associated marine alphaproteobacteria. ChemBioChem 2005; 6:2195-2206.[doi:10.1002/cbic.200500189] [pmid:16283687]
55. Auch AF, Von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117-134.[doi:10.4056/sigs.531120] [pmid:21304684]
56. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142-148.[doi:10.4056/sigs.541628] [pmid:21304686]
57. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60.[doi:10.1186/1471-2105-14-60] [pmid:23432962]