Uncultivated magnetotactic cocci from Yuandadu Park in Beijing, China

Applied and Environmental Microbiology

Volumn 75, Issue 12, 2009, Pages 4046-4052

  Lin, Wei ^a,b   Pan, Yongxin ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE SEQUENCE; BEIJING , CHINA; FIRST-ORDER REVERSAL CURVE DIAGRAMS; FLUORESCENCE IN SITU HYBRIDIZATION; FRESHWATER POND; LOW TEMPERATURES; MAGNETIC INTERACTIONS; MAGNETIC MEASUREMENTS; MAGNETOSOME CRYSTALS; MAGNETOSOMES; MAGNETOTACTIC BACTERIA; NOVEL LINEAGES; SEQUENCE IDENTITY; SHAPE FACTOR; SINGLE-DOMAIN SIZE; VERWEY TRANSITIONS;

BACTERIOLOGY; FLUORESCENCE MICROSCOPY; MAGNETIC PROPERTIES; OXIDE MINERALS; TRANSMISSION ELECTRON MICROSCOPY;

MAGNETITE;

FRESH WATER; RNA 16S;

BACTERIUM; FLUORESCENCE; FRESHWATER ECOSYSTEM; GENETIC ANALYSIS; LOW TEMPERATURE; MAGNETIC PROPERTY; MAGNETITE; MICROSCOPY; NOMENCLATURE; PHYLOGENETICS; POND; RNA;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL STRAIN; BACTERIUM CULTURE; CHINA; CONTROLLED STUDY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE SEQUENCE; MAGNETIC FIELD; MAGNETOCOCCUS YUANDADUCUM; MICROMORPHOLOGY; MICROSCOPY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS; TRANSMISSION ELECTRON MICROSCOPY; WATER SAMPLING;

ALPHAPROTEOBACTERIA; CHINA; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; FRESH WATER; IN SITU HYBRIDIZATION, FLUORESCENCE; LOCOMOTION; MAGNETICS; MICROSCOPY; MICROSCOPY, ELECTRON; MOLECULAR SEQUENCE DATA; ORGANELLES; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

ASIA; BEIJING [CHINA]; CHINA; EURASIA; FAR EAST; YUANDADU PARK;

ALPHAPROTEOBACTERIA; COCCOIDEA; MAGNETOCOCCUS;

EID: 67149088377     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00247-09     Document Type: Article

References (53)

1. Amann, R., L. Krumholz, and D. A. Stahl. 1990. Fluorescent- oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770. (Pubitemid 20070387)
2. Amann, R., J. Peplies, and D. Schüler. 2006. Diversity and taxonomy of magnetotactic bacteria. Springer, Berlin, Germany.
3. Bazylinski, D. A., and R. B. Frankel. 2004. Magnetosome formation in prokaryotes. Nat. Rev. Microbiol. 2:217-230.
4. Blakemore, R. P., D. Maratea, and R. S. Wolfe. 1979. Isolation and pure culture of a freshwater magnetic spirillum in chemically defined medium. J. Bacteriol. 140:720-729. (Pubitemid 10170130)
5. Brandl, M. T., B. Quinones, and S. E. Lindow. 2001. Heterogeneous transcription of an indoleacetic acid biosynthetic gene in Erwinia herbicola on plant surfaces. Proc. Natl. Acad. Sci. USA 98:3454-3459.
6. Chang, S. B. R., and J. L. Kirschvink. 1989. Magnetofossils, the magnetization of sediments, and the evolution of magnetite biomineralization. Annu. Rev. Earth Planet. Sci. 17:169-195.
7. Chen, A. P., R. Egli, and B. M. Moskowitz. 2007. First-order reversal curve (FORC) diagrams of natural and cultured biogenic magnetic particles. J. Geophys. Res. doi:10.1029/2006JB004575.
8. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2003. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31:442-443. (Pubitemid 36150424)
9. Cox, B. L., R. Popa, D. A. Bazylinski, B. Lanoil, S. Douglas, A. Belz, D. L. Engler, and K. H. Nealson. 2002. Organization and elemental analysis of P-, S-, and Fe-rich inclusions in a population of freshwater magnetococci. Geomicrobiol. J. 19:387-406.
10. Faivre, D., and D. Schüler. 2008. Magnetotactic bacteria and magnetosomes. Chem. Rev. 108:4875-4898.
11. Fischer, H., G. Mastrogiacomo, J. F. Loffler, R. J. Warthmann, P. G. Weidler, and A. U. Gehring. 2008. Ferromagnetic resonance and magnetic characteristics of intact magnetosome chains in Magnetospirillum gryphiswaldense. Earth Planet. Sci. Lett. 270:200-208.
12. Flies, C. B., J. Peplies, and D. Schüler. 2005. Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments. Appl. Environ. Microbiol. 71:2723-2731.
13. 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. (Pubitemid 27337634)
14. Greenberg, M., K. Canter, I. Mahler, and A. Tornheim. 2005. Observation of magnetoreceptive behavior in a multicellular magnetotactic prokaryote in higher than geomagnetic fields. Biophys. J. 88:1496-1499. (Pubitemid 40975976)
15. Grünberg, K., E. C. Muller, A. Otto, R. Reszka, D. Linder, M. Kube, R. Reinhardt, and D. Schüler. 2004. Biochemical and proteomic analysis of the magnetosome membrane in Magnetospirillum gryphiswaldense. Appl. Environ. Microbiol. 70:1040-1050.
16. Horner-Devine, M. C., K. M. Carney, and B. J. M. Bohannan. 2004. An ecological perspective on bacterial biodiversity. Proc. R. Soc. Lond. Ser. B Biol. Sci. 271:113-122.
17. Kawaguchi, R., J. G. Burgess, and T. Matsunaga. 1992. Phylogeny and 16S rRNA sequence of Magnetospirillum sp. AMB-1, an aerobic magnetic bacterium. Nucleic Acids Res. 20:1140.
18. Komeili, A. 2007. Molecular mechanisms of magnetosome formation. Annu. Rev. Biochem. 76:27.1-27.16.
19. Kopp, R. E., and J. L. Kirschvink. 2008. The identification and biogeochemical interpretation of fossil magnetotactic bacteria. Earth Sci. Rev. 86:42-61.
20. Kopp, R. E., B. P. Weiss, A. C. Maloof, H. Vali, C. Z. Nash, and J. L. Kirschvink. 2006. Chains, clumps, and strings: magnetofossil taphonomy with ferromagnetic resonance spectroscopy Earth Planet. Sci. Lett. 247:10-25.
21. Li, J., Y. Pan, G. Chen, Q. Liu, L. Tian, and W. Lin. 2009. Magnetite magnetosome and fragmental chain formation of Magnetospirillum magneticum AMB-1: transmission electron microscopy and magnetic observations. Geophys. J. Int. 177:33-42.
22. Lin, W., J. Li, D. Schüler, C. Jogler, and Y. Pan. 2009. Diversity analysis of magnetotactic bacteria in Lake Miyun, northern China, by restriction fragment length polymorphism. Syst. Appl. Microbiol. doi:10.1016/j.syapm.2008. 10.005.
23. 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.
24. Meldrum, F., S. Mann, B. R. Heywood, R. B. Frankel, and D. A. Bazylinski. 1993. Electron microscopy study of magnetosomes in a cultured coccoid magnetotactic bacterium. Proc. R. Soc. Lond. B 251:231-236.
25. Moskowitz, B. M. 1988. Magnetic properties of magnetotactic bacteria. J. Magn. Magn. Mater. 73:273-288.
26. Moskowitz, B. M., D. A. Bazylinski, R. Egli, R. B. Frankel, and K. J. Edwards. 2008. Magnetic properties of marine magnetotactic bacteria in a seasonally stratified coastal pond (Salt Pond, MA, USA). Geophys. J. Int. 174:75-92.
27. Moskowitz, B. M., R. B. Frankel, and D. A. Bazylinski. 1993. Rock magnetic criteria for the detection of biogenic magnetite. Earth Planet. Sci. Lett. 120:283-300.
28. Moskowitz, B. M., R. B. Frankel, D. A. Bazylinski, H. W. Jannasch, and D. R. Lovley. 1989. A comparison of magnetite particles produced anaerobically by magnetotactic and dissimilatory iron-reducing bacteria. Geophys. Res. Lett. 16:665-668.
29. Murray, R. G. E., and K. H. Schleifer. 1994. Taxonomic notes: a proposal for recording the properties of putative taxa of prokaryotes. Int. J. Syst. Bacteriol. 44:174-176.
30. Murray, R. G. E., and E. Stackebrandt. 1995. Taxonomic note: implementation of the provisional status Candidatus for incompletely described prokaryotes. Int. J. Syst. Bacteriol. 45:186-187.
31. Pan, H. M., K. L. Zhu, T. Song, K. Yu-Zhang, C. Lefevre, S. Xing, M. Liu, S. J. Zhao, T. Xiao, and L. F. Wu. 2008. Characterization of a homogeneous taxonomic group of marine magnetotactic cocci within a low tide zone in the China Sea. Environ. Microbiol. 10:1158-1164.
32. Pan, Y., N. Petersen, A. Davila, L. Zhang, M. Winklhofer, Q. Liu, M. Hanzlik, and R. Zhu. 2005. The detection of bacterial magnetite in recent sediments of Lake Chiemsee (southern Germany). Earth Planet. Sci. Lett. 232:109-123.
33. Pan, Y., N. Petersen, M. Winklhofer, A. Davila, Q. Liu, T. Frederichs, M. Hanzlik, and R. Zhu. 2005. Rock magnetic properties of uncultured magnetotactic bacteria. Earth Planet. Sci. Lett. 237:311-325.
34. Pernthaler, J., F. O. Glockner, W. Schonhuber, and R. Amann. 2001. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol. 30:207-226. (Pubitemid 33287422)
35. Petersen, N., T. von Dobeneck, and H. Vali. 1986. Fossil bacterial magnetite in deep-sea sediments from the South Atlantic Ocean. Nature 320:611-615. (Pubitemid 16268833)
36. Pike, C. R., A. P. Roberts, and K. L. Verosub. 2001. First-order reversal curve diagrams and thermal relaxation effects in magnetic particles. Geophys. J. Int. 145:721-730.
37. Pósfai, M., B. M. Moskowitz, B. Arato, D. Schüler, C. Flies, D. A. Bazylinski, and R. B. Frankel. 2006. Properties of intracellular magnetite crystals produced by Desulfovibrio magneticus strain RS-1. Earth Planet. Sci. Lett. 249:444-455.
38. Prozorov, R., T. Prozorov, S. K. Mallapragada, B. Narasimhan, T. J. Williams, and D. A. Bazylinski. 2007. Magnetic irreversibility and the Verwey transition in nanocrystalline bacterial magnetite. Phys. Rev. B doi:10.1103/ PhysRevB.76.054406.
39. 8) using first-order reversal curve diagrams. J. Geophys. Res. doi:10.1029/2006JB004715.
40. Roberts, A. P., C. R. Pike, and K. L. Verosub. 2000. First-order reversal curve diagrams: a new tool for characterizing the magnetic properties of natural samples. J. Geophys. Res. Solid Earth 105:28461-28475.
41. 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.
42. Schüler, D. 2008. Genetics and cell biology of magnetosome formation in magnetotactic bacteria. FEMS Microbiol. Rev. 32:654-672.
43. Schumann, D., T. D. Raub, R. E. Kopp, J. L. Guerquin-Kern, T. D. Wu, I. Rouiller, A. Smirnov, S. K. Sears, U. Lücken, S. M. Tikoo, R. Hesse, J. L. Kirschvink, and H. Vali. 2008. Gigantism in unique biogenic magnetite at the Paleocene-Eocene thermal maximum. Proc. Natl. Acad. Sci. USA doi:10.1073/pnas.0803634105.
44. Snowball, I., P. Sandgren, and G. Petterson. 1999. The mineral magnetic properties of an annually laminated Holocene lake-sediment sequence in northern Sweden. Holocene 9:353-362. (Pubitemid 29216018)
45. Snowball, I., L. Zillen, and P. Sandgren. 2002. Bacterial magnetite in Swedish varved lake-sediments: a potential bio-marker of environmental change. Quat. Int. 88:13-19.
46. Spring, S., R. Amann, W. Ludwig, K.-H. Schleifer, D. Schüler, K. Poralla, and N. Petersen. 1994. Phylogenetic analysis of uncultured magnetotactic bacteria from the alpha-subclass of Proteobacteria. Syst. Appl. Microbiol. 17:501-508.
47. Spring, S., R. Amann, W. Ludwig, K. H. Schleifer, H. van Gemerden, and N. Petersen. 1993. Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment. Appl. Environ. Microbiol. 59:2397-2403.
48. Tamura, K., J. Dudley, M. Nei, and S. Kumar. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599.
49. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. (Pubitemid 24354800)
50. Ullrich, S., M. Kube, S. Schubbe, R. Reinhardt, and D. Schüler. 2005. A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. J. Bacteriol. 187:7176-7184.
51. Vali, H., O. Forster, G. Amarantidis, and N. Petersen. 1987. Magnetotactic bacteria and their magnetofossils in sediments. Earth Planet. Sci. Lett. 86:389-400.
52. Weiss, B., S. Kim, J. Kirschvink, R. Kopp, M. Sankaran, A. Kobayashi, and A. Komeili. 2004. Ferromagnetic resonance and low-temperature magnetic tests for biogenic magnetite. Earth Planet. Sci. Lett. 224:73-89.
53. Zhou, J. Z., B. C. Xia, D. S. Treves, L. Y. Wu, T. L. Marsh, R. V. O'Neill, A. V. Palumbo, and J. M. Tiedje. 2002. Spatial and resource factors influencing high microbial diversity in soil. Appl. Environ. Microbiol. 68:326-334.