Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification

Applied and Environmental Microbiology

Volumn 76, Issue 5, 2010, Pages 1480-1485

  Arakaki, Atsushi ^a   Shibusawa, Mie ^a   Hosokawa, Masahito ^a   Matsunaga, Tadashi ^a  

^a TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA SEQUENCES; AQUATIC ENVIRONMENTS; BACTERIAL COMMUNITY; BACTERIAL STRAINS; COMPLETE GENOMES; DISPLACEMENT AMPLIFICATION; ENVIRONMENTAL SAMPLE; GENE AMPLIFICATION; GENETIC INFORMATION; GENOMIC DNA; MAGNETIC CELL SEPARATIONS; MAGNETIC PARTICLE; MAGNETOTACTIC BACTERIA; MORPHOTYPES; MULTIPLE DISPLACEMENT AMPLIFICATIONS; NEW STRATEGY; PREPARATION METHOD; PURE CULTURE; QUANTITATIVE PCR; SINGLE SPECIES; UNCULTURED MAGNETOTACTIC BACTERIA;

AMPLIFICATION; BACTERIA; BACTERIOLOGY; CELL CULTURE; DNA; FLOW CYTOMETRY; GENE EXPRESSION; MAGNETIC SEPARATION; RNA; SOFTWARE ARCHITECTURE;

BIOINFORMATICS;

BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

BACTERIUM; DNA; FLOW CYTOMETRY; GENOME; PHYLOGENY; POLYMERASE CHAIN REACTION;

ALPHAPROTEOBACTERIA; ARTICLE; CHEMISTRY; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MAGNETISM; METHODOLOGY; MICROBIOLOGICAL EXAMINATION; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEIC ACID AMPLIFICATION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY;

ALPHAPROTEOBACTERIA; BACTERIOLOGICAL TECHNIQUES; DNA, BACTERIAL; DNA, RIBOSOMAL; MAGNETICS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; WATER MICROBIOLOGY;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); MAGNETOCOCCUS; MAGNETOSPIRILLUM; MAGNETOSPIRILLUM MAGNETICUM AMB-1; UNCULTURED MAGNETOCOCCUS SP.;

EID: 77649200047     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02124-09     Document Type: Article

References (33)

1. Abulencia, C. B., D. L. Wyborski, J. A. Garcia, M. Podar, W. Q. Chen, S. H. Chang, H. W. Chang, D. Watson, E. L. Brodie, T. C. Hazen, and M. Keller. 2006. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl. Environ. Microbiol. 72: 3291-3301.
2. Blakemore, R. 1975. Magnetotactic bacteria. Science 190: 377-379.
3. Burgess, J. G., R. Kawaguchi, T. Sakaguchi, R. H. Thornhill, and T. Matsunaga. 1993. Evolutionary relationships among Magnetospirillum strains inferred from phylogenetic analysis of 16S rDNA sequences. J. Bacteriol. 175: 6689-6694.
4. Button, D. K., B. R. Robertson, and F. Juttner. 1996. Microflora of a subalpine lake: bacterial populations, size and DNA distributions, and their dependence on phosphate. FEMS Microbiol. Ecol. 21: 87-101.
5. Dean, F. B., S. Hosono, L. Fang, X. Wu, A. F. Faruqi, P. Bray-Ward, Z. Sun, Q. Zong, Y. Du, J. Du, M. Driscoll, W. Song, S. F. Kingsmore, M. Egholm, and R. S. Lasken. 2002. Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl. Acad. Sci. U. S. A. 99: 5261-5266.
6. Dean, F. B., J. R. Nelson, T. L. Giesler, and R. S. Lasken. 2001. Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11: 1095-1099.
7. Flies, C. B., J. Peplies, and D. Schuler. 2005. Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments. Appl. Environ. Microbiol. 71: 2723-2731.
8. Frankel, R. B., D. A. Bazylinski, M. S. Johnson, and B. L. Taylor. 1997. Magneto-aerotaxis in marine coccoid bacteria. Biophys. J. 73: 994-1000.
9. Hongoh, Y., V. K. Sharma, T. Prakash, S. Noda, T. D. Taylor, T. Kudo, Y. Sakaki, A. Toyoda, M. Hattori, and M. Ohkuma. 2008. Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc. Natl. Acad. Sci. U. S. A. 105: 5555-5560.
10. Hutchison, C. A., III, H. O. Smith, C. Pfannkoch, and J. C. Venter. 2005. Cell-free cloning using phi29 DNA polymerase. Proc. Natl. Acad. Sci. U. S. A. 102: 17332-17336.
11. Ishoey, T., T. Woyke, R. Stepanauskas, M. Novotny, and R. S. Lasken. 2008. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 11: 198-204.
12. Jogler, C., W. Lin, A. Meyerdierks, M. Kube, E. Katzmann, C. Flies, Y. X. Pan, R. Amann, R. Reinhardt, and D. Schüler. 2009. Toward cloning of the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl. Environ. Microbiol. 75: 3972-3979.
13. Kawaguchi, R., J. G. Burgess, T. Sakaguchi, H. Takeyama, R. H. Thornhill, and T. Matsunaga. 1995. Phylogenetic analysis of a novel sulfate-reducing magnetic bacterium, RS-1, demonstrates its membership of the delta-Proteobacteria. FEMS Microbiol. Lett. 126: 277-282.
14. Kvist, T., B. K. Ahring, R. S. Lasken, and P. Westermann. 2007. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl. Microbiol. Biotechnol. 74: 926-935.
15. Lin, W., L. Tian, J. Li, and Y. Pan. 2008. Does capillary racetrack-based enrichment reflect the diversity of uncultivated magnetotactic cocci in environmental samples? FEMS Microbiol. Lett. 279: 202-206.
16. Lins, U., F. Freitas, C. N. Keim, H. Lins de Barros, D. M. S. Esquivel, and M. Farina. 2003. Simple homemade apparatus for harvesting uncultured magnetotactic microoganisms. Braz. J. Microbiol. 34: 111-116.
17. Marcy, Y., T. Ishoey, R. S. Lasken, T. B. Stockwell, B. P. Walenz, A. L. Halpern, K. Y. Beeson, S. M. Goldberg, and S. R. Quake. 2007. Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet. 3: 1702-1708. (Pubitemid 47510262)
18. Marcy, Y., C. Ouverney, E. M. Bik, T. Losekann, N. Ivanova, H. G. Martin, E. Szeto, D. Platt, P. Hugenholtz, D. A. Relman, and S. R. Quake. 2007. Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc. Natl. Acad. Sci. U. S. A. 104: 11889-11894.
19. Matsunaga, T., Y. Okamura, Y. Fukuda, A. T. Wahyudi, Y. Murase, and H. Takeyama. 2005. Complete genome sequence of the facultative anaerobic magnetotactic bacterium Magnetospirillum sp. strain AMB-1. DNA Res. 12: 157-166.
20. Matsunaga, T., T. Sakaguchi, and F. Tadokoro. 1991. Magnetite formation by a magnetic bacterium capable of growing aerobically. Appl. Microbiol. Biotechnol. 35: 651-655.
21. Ohkuma, M., T. Sato, S. Noda, S. Ui, T. Kudo, and Y. Hongoh. 2007. The candidate phylum 'Termite Group 1' of bacteria: phylogenetic diversity, distribution, and endosymbiont members of various gut flagellated protists. FEMS Microbiol. Ecol. 60: 467-476.
22. Raghunathan, A., H. R. Ferguson, Jr., C. J. Bornarth, W. Song, M. Driscoll, and R. S. Lasken. 2005. Genomic DNA amplification from a single bacterium. Appl. Environ. Microbiol. 71: 3342-3347.
23. Sakaguchi, T., A. Arakaki, and T. Matsunaga. 2002. Desulfovibrio magneticus sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles. Int. J. Syst. Evol. Microbiol. 52: 215-221.
24. Schleifer, K.-H., D. Schüler, S. Spring, M. Weizenegger, R. Amann, W. Ludwig, and M. Kohler. 1991. The genus Magnetospirillum gen. nov., description of Magnetospirillum gryphiswaldense sp. nov. and transfer of Aquaspirillum magnetotacticum to Magnetospirillum magnetotacticum comb. nov. Syst. Appl. Microbiol. 14: 379-385.
25. Simmons, S. L., D. A. Bazylinski, and K. J. Edwards. 2007. Population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qPCR. Environ. Microbiol. 9: 2162-2174.
26. Simmons, S. L., S. M. Sievert, R. B. Frankel, D. A. Bazylinski, and K. J. Edwards. 2004. Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond. Appl. Environ. Microbiol. 70: 6230-6239.
27. Spring, S., and K.-H. Schleifer. 1995. Diversity of magnetotactic bacteria. Syst. Appl. Microbiol. 18: 147-153.
28. Stepanauskas, R., and M. E. Sieracki. 2007. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc. Natl. Acad. Sci. U. S. A. 104: 9052-9057.
29. Thornhill, R. H., J. G. Burgess, and T. Matsunaga. 1995. PCR for direct detection of indigenous uncultured magnetic cocci in sediment and phylogenetic analysis of amplified 16S ribosomal DNA. Appl. Environ. Microbiol. 61: 495-500.
30. Thornhill, R. H., J. G. Burgess, T. Sakaguchi, and T. Matsunaga. 1994. A morphological classification of bacteria containing bullet-shaped magnetic particles. FEMS Microbiol. Lett. 115: 169-176.
31. Wolfe, R. S., R. K. Thauer, and N. Pfennig. 1987. A 'capillary racetrack' method for isolation of magnetotactic bacteria. FEMS Microbiol. Lett. 45: 31-35.
32. Yokouchi, H., Y. Fukuoka, D. Mukoyama, R. Calugay, H. Takeyama, and T. Matsunaga. 2006. Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ. Microbiol. 8: 1155-1163.
33. Zhang, K., A. C. Martiny, N. B. Reppas, K. W. Barry, J. Malek, S. W. Chisholm, and G. M. Church. 2006. Sequencing genomes from single cells by polymerase cloning. Nat. Biotechnol. 24: 680-686.