Metagenomic analysis reveals unexpected subgenomic diversity of magnetotactic bacteria within the phylum nitrospirae

Applied and Environmental Microbiology

Volumn 77, Issue 1, 2011, Pages 323-326

  Lin, Wei ^a   Jogler, Christian ^b,c   Schüler, Dirk ^b   Pan, Yongxin ^a  

^a INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^b UNIVERSITY OF MUNICH   (Germany)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BEIJING , CHINA; COMPARATIVE SEQUENCE ANALYSIS; FLUORESCENCE IN SITU HYBRIDIZATION; GENOME ORGANIZATION; IN-CELL; MAGNETOTACTIC BACTERIA; METAGENOMIC ANALYSIS; NITROSPIRAE;

FLUORESCENCE MICROSCOPY; RNA;

BACTERIOLOGY;

BACTERIAL DNA; FRESH WATER;

BACTERIUM; COMPARATIVE STUDY; FLUORESCENCE; FUNCTIONAL MORPHOLOGY; GENETIC ANALYSIS; GENETIC DIFFERENTIATION; GENOME; GENOMICS; HYBRIDIZATION; IDENTIFICATION METHOD;

ARTICLE; BACTERIUM; BIODIVERSITY; CHEMISTRY; CHINA; CLASSIFICATION; DNA SEQUENCE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE ORDER; GENETICS; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

BACTERIA; BIODIVERSITY; CHINA; DNA, BACTERIAL; FRESH WATER; GENE ORDER; IN SITU HYBRIDIZATION, FLUORESCENCE; METAGENOME; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA;

BEIJING [CHINA]; CHINA; MIYUN RESERVOIR;

CANDIDATUS MAGNETOBACTERIUM BAVARICUM; NITROSPIRAE;

EID: 79251646697     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01476-10     Document Type: Article

References (24)

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.
2. Amann, R., J. Peplies, and D. Schüler. 2006. Diversity and taxonomy of magnetotactic bacteria, p. 25-36. In D. Schüler (ed.), Magnetoreception and magnetosomes in bacteria. Springer, Berlin, Germany.
3. Bazylinski, D. A., and R. B. Frankel. 2004. Magnetosome formation in prokaryotes. Nat. Rev. Microbiol. 2:217-230.
4. Faivre, D., and D. Schüler. 2008. Magnetotactic bacteria and magnetosomes. Chem. Rev. 108:4875-4898.
5. 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.
6. 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.
7. Hobbs, M., and J. S. Mattick. 1993. Common components in the assembly of type 4 fimbriae, DNA transfer systems, filamentous phage and proteinsecretion apparatus: a general system for the formation of surface-associated protein complexes. Mol. Microbiol. 10:233-243.
8. Jogler, C., W. Lin, A. Meyerdierks, M. Kube, E. Katzmann, C. Flies, Y. Pan, R. Amann, R. Reinhardt, and D. Schüler. 2009. Towards cloning the magnetotactic metagenome: identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl. Environ. Microbiol. 75:3972-3979.
9. Jogler, C., M. Niebler, W. Lin, M. Kube, G. Wanner, S. Kolinko, P. Stief, A. Beck, D. DeBeer, N. Petersen, Y. Pan, R. Amann, R. Reinhardt, and D. Schüler. 19 April 2010. Cultivation-independent characterization of "Candidatus Magnetobacterium bavaricum" via ultrastructural, geochemical, ecological and metagenomic methods. Environ. Microbiol. doi:10.1111/j.1462-2920.2010.02220.x.
10. Jogler, C., and D. Schüler. 2009. Genomics, genetics, and cell biology of magnetosome formation. Annu. Rev. Microbiol. 63:501-521.
11. Jormakka, M., K. Yokoyama, T. Yano, M. Tamakoshi, S. Akimoto, T. Shimamura, P. Curmi, and S. Iwata. 2008. Molecular mechanism of energy conservation in polysulfide respiration. Nat. Struct. Mol. Biol. 15:730-737.
12. Lefèvre, C. T., F. Abreu, M. L. Schmidt, U. Lins, R. B. Frankel, B. P. Hedlund, and D. A. Bazylinski. 2010. Moderately thermophilic magnetotactic bacteria from hot springs in Nevada. Appl. Environ. Microbiol. 76:3740-3743.
13. Li, J., Y. Pan, Q. Liu, K. Yu-Zhang, N. Menguy, R. Che, H. Qin, W. Lin, W. Wu, and N. Petersen. 2010. Biomineralization, crystallography and magnetic properties of bullet-shaped magnetite magnetosomes in giant rod magnetotactic bacteria. Earth Planet. Sci. Lett. 293:368-376.
14. 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. 32:342-350.
15. Lin, W., and Y. Pan. 2010. Temporal variation of magnetotactic bacterial communities in two freshwater sediment microcosms. FEMS Microbiol. Lett. 302:85-92.
16. Lin, W., and Y. X. Pan. 2009. Specific primers for the detection of freshwater alphaproteobacterial magnetotactic cocci. Int. Microbiol. 12:237-242.
17. 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.
18. Murat, D., A. Quinlan, H. Vali, and A. Komeili. 2010. Comprehensive genetic dissection of the magnetosome gene island reveals the step-wise assembly of a prokaryotic organelle. Proc. Natl. Acad. Sci. U. S. A. 107:5593-5598.
19. 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.
20. Quaiser, A., T. Ochsenreiter, C. Lanz, S. C. Schuster, A. H. Treusch, J. Eck, and C. Schleper. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50:563-575.
21. Rocap, G., D. L. Distel, J. B. Waterbury, and S. W. Chisholm. 2002. Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences. Appl. Environ. Microbiol. 68:1180-1191.
22. Romero, H., Y. Zhang, V. N. Gladyshev, and G. Salinas. 2005. Evolution of selenium utilization traits. Genome Biol. 6:R66.
23. Simon, J., and M. Kern. 2008. Quinone-reactive proteins devoid of haem b form widespread membrane-bound electron transport modules in bacterial respiration. Biochem. Soc. Trans. 36:1011-1016.
24. 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.