Population dynamics of marine magnetotactic bacteria in a meromictic salt pond described with qPCR

Environmental Microbiology

Volumn 9, Issue 9, 2007, Pages 2162-2174

  Simmons, Sheri L ^a,d   Bazylinski, Dennis A ^b   Edwards, Katrina J ^c  

^a WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^b UNIVERSITY OF NEVADA   (United States)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; GREIGITE; IRON; MAGNETITE; RNA 16S; SEA WATER; SULFIDE; UNCLASSIFIED DRUG;

ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL COUNT; CLASSIFICATION; ECOSYSTEM; GAMMAPROTEOBACTERIA; GENETICS; GROWTH, DEVELOPMENT AND AGING; MAGNETISM; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; POPULATION DYNAMICS; SEASON; UNITED STATES; WETLAND;

ALPHAPROTEOBACTERIA; COLONY COUNT, MICROBIAL; DNA, BACTERIAL; ECOSYSTEM; FERROSOFERRIC OXIDE; GAMMAPROTEOBACTERIA; IRON; MAGNETICS; MASSACHUSETTS; POPULATION DYNAMICS; RNA, RIBOSOMAL, 16S; SEASONS; SEAWATER; SULFIDES; WETLANDS;

BACTERIA (MICROORGANISMS); GAMMAPROTEOBACTERIA; THIOMICROSPIRA PELOPHILA;

EID: 34547684292     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2007.01330.x     Document Type: Article

References (56)

1. Acinas, S.G., Marcelino, L.A., Klepac-Ceraj, V. Polz, M.F. (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186 : 2629 2635.
2. Bazylinski, D.A., Frankel, R.B., Heywood, B.R., Mann, S., King, J.W., Donaghay, P.L. Hanson, A.K. (1995) Controlled biomineralization of magnetite (Fe3O4) and gregite (Fe3S4) in a magnetotactic bacterium. Appl Environ Microbiol 61 : 3232 3239.
3. Bazylinski, D.A., Dean, A.J., Williams, T.J., Long, L.K., Middleton, S.L. Dubbels, B.L. (2004) Chemolithoautotrophy in the marine, magnetotactic bacterial strains MV-1 and MV-2. Arch Microbiol 182 : 373 387.
4. Canfield, D.E. Berner, R.A. (1987) Dissolution and pyritization of magnetite in anoxic marine sediments. Geochem Cosmochim Acta 51 : 645 659.
5. Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam, S.A., McGarrell, D.M., et al. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33 : D294 D296.
6. Cox, B.L., Popa, R., Bazylinski, D.A., Lanoil, B., Douglas, S., Belz, A., et al. (2002) Organization and elemental analysis of P-, S-, and Fe-rich inclusions in a population of freshwater magnetococci. Geomicrobiol J 19 : 387 406.
7. Daims, R., Bruhl, H., Amann, R., Schleifer, K.-H. Wagner, M. (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22 : 434 444.
8. DeLong, E.F., Frankel, R.B. Bazylinski, D.A. (1993) Multiple evolutionary origins of magnetotaxis in bacteria. Science 259 : 803 806.
9. Devouard, B., Posfai, M., Hua, X., Bazylinski, D.A., Frankel, R.B. Buseck, P.R. (1998) Magnetite from magnetotactic bacteria; size distributions and twinning. Am Mineral 83 : 1387 1398.
10. Flies, C.B., Jonkers, H.M., de Beer, D., Bosselmann, K., Bottcher, M.E. Schüler, D. (2005) Diversity and vertical distribution of magnetotactic bacteria along chemical gradients in freshwater microcosms. FEMS Microbiol Ecol 52 : 185 195.
11. Heyen, U. Schüler, D. (2003) Growth and magnetosome formation by microaerophilic Magnetospirillum strains in an oxygen-controlled fermentor. Appl Microbiol Biotechnol 61 : 536 544.
12. Heywood, B.R., Bazylinski, D.A., Garrett-Reed, A.J., Mann, S. Frankel, R.B. (1990) Controlled biosynthesis of greigite (Fe3S4) in magnetotactic bacteria. Naturwissenschaften 77 : 536 538.
13. Huu, N.B., Denner, E.B., Ha, D.T., Wanner, G. Stan-Lotter, H. (1999) Marinobacter aquaeolei sp. nov., a halophilic bacterium isolated from a Vietnamese oil-producing well. Intl J Syst Bacteriol 49 : 367 375.
14. Jørgensen, B.B., Kuenen, J.G. Cohen, Y. (1979) Microbial transformations of sulphur compounds in a stratified lake (Solar Lake, Sinai). Limnol Oceanogr 24 : 799 822.
15. Jørgensen, B.B., Fossing, H., Wirsen, C.O. Jannasch, H.W. (1991) Sulfide oxidation in the Black Sea chemocline. Deep Sea Res A 38 : S1083 S1103.
16. Karr, E.A., Sattley, W.M., Rice, M.R., Jung, D.O., Madigan, M.T. Achenbach, L.A. (2005) Diversity and distribution of sulfate-reducing bacteria in permanently Frozen Lake Fryxell, McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 71 : 6353 6359.
17. Kim, B.Y., Kodama, K.P. Moeller, R.E. (2005) Bacterial magnetite produced in water column dominates lake sediment mineral magnetism: Lake Ely, USA. Geophys J Int 163 : 26 37.
18. Klappenbach, J.A., Saxman, P.R., Cole, J.T. Schmidt, T.M. (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29 : 181 184.
19. Knittel, K., Boetius, A., Lemke, A., Eilers, H., Lochte, K., Pfannkuche, O., et al. (2003) Activity, distribution, and diversity of sulfate reducers and other bacteria in sediments above gas hydrate (Cascadia Margin, Oregon). Geomicrobiol J 20 : 269 294.
20. Lie, T.J., Clawson, M.L., Godchaux, W. Leadbetter, E.R. (1999) Sulfidogenesis from 2-aminoethanesulfonate (Taurine) fermentation by a morphologically unusual sulfate-reducing bacterium, Desulforhopalus singaporensis sp. nov. Appl Environ Microbiol 65 : 3328 3334.
21. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) arb: a software environment for sequence data. Nucleic Acids Res 32 : 1363 1371.
22. Manz, W., Amann, R., Ludwig, W., Wagner, M. Scheifer, K.-H. (1992) Phylogenetic oligodeoxynucleotide probes for the major subclasses of proteobacteria: problems and solutions. Syst Appl Microbiol 15 : 593 600.
23. Markowitz, V.M., Korzeniewski, F., Palaniappan, K., Szeto, E., Werner, G., Padki, A., et al. (2006) The integrated microbial genomes (IMG) system. Nucleic Acids Res 34 : D344 D348.
24. Mueller, R., Padmabandu, G. Taylor, R.H. (2004) Standardization of qPCR and RT-qPCR assays. In A-Z of Quantitative PCR. Bustin, S.A. (ed.). La Jolla, CA, USA : International University Line, pp. 578 590.
25. Muyzer, G., De Waal, E. Uitterlinden, A. (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rRNA. Appl Environ Microbiol 59 : 695 700.
26. Pernthaler, A., Pernthaler, J. Amann, R. (2002) Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl Environ Microbiol 68 : 3094 3101.
27. Pernthaler, J., Glöckner, F., Schönhuber, W. Amann, R. (2001) Flourescence in situ hybridization with rRNA-targeted oligonucleotide probes. In Methods in Microbiology. Paul, J. (ed.). San Diego, CA, USA : Academic Press, pp. 207 226.
28. Petermann, H. Bleil, U. (1993) Detection of live magnetotactic bacteria in deep-sea sediments. Earth Planet Sci Lett 117 : 223 228.
29. Pfaffl, M.W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29 : 2002 2007.
30. Pósfai, M., Buseck, P.R., Bazylinski, D.A. Frankel, R.B. (1998) Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers. Science 280 : 880 883.
31. Pósfai, M., Cziner, K., Marton, E., Marton, P., Buseck, P.R., Frankel, R.B. Bazylinski, D.A. (2001) Crystal-size distributions and possible biogenic origin of Fe sulfides. Eur J Mineral 13 : 691 703.
32. Ramsing, N., Fossing, H., Ferdelman, T., Andersen, F. Thamdrup, B. (1996) Distribution of bacterial populations in a stratified fjord (Mariager Fjord, Denmark) quantified by in situ hybridization and related to chemical gradients in the water column. Appl Environ Microbiol 62 : 1391 1404.
33. Roberts, A.P., Reynolds, R.L., Verosub, K.L. Adam, D.P. (1996) Environmental magnetic implications of greigite (Fe3S4) formation in a 3 my lake sediment record from Butte Valley, northern California. Geophys Res Lett 23 : 2859 2862.
34. Sakaguchi, T., Arakaki, A. Matsunaga, T. (2002) Desulfovibrio magneticus sp. nov., a novel sulfate-reducing bacterium that produces intracellular single-domain-sized magnetite particles. Intl J Syst Evol Microbiol 52 : 215 221.
35. Schramm, A., Fuchs, B.M., Nielsen, J.L., Tonolla, M. Stahl, D.A. (2002) Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries. Environ Microbiol 4 : 713 720.
36. Schwieger, F. Tebbe, C.C. (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64 : 4870 4876.
37. Simmons, S.L. Edwards, K.J. (2006) Unexpected diversity in populations of the many-celled magnetotactic prokaryote. Environ Microbiol 9 : 206 215.
38. Simmons, S.L., Sievert, S.M., Frankel, R.B., Bazylinski, D.A. Edwards, K.J. (2004) Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond. Appl Environ Microbiol 70 : 6230 6239.
39. Simmons, S.L., Bazylinski, D.A. Edwards, K.J. (2006) South-seeking magnetotactic bacteria in the Northern Hemisphere. Science 311 : 371 374.
40. Snowball, I.F., Sandgren, P. Petterson, G. (1999) The mineral magnetic properties of an annually laminated Holocene lake-sediment sequence in northern Sweden. Holocene 9 : 353 362.
41. Snowball, I.F., Zillen, L. Sandgren, P. (2002) Bacterial magnetite in Swedish varved lake-sediments: a potential bio-marker of environmental change. Quat Int 88 : 13 19.
42. Spring, S. Bazylinski, D. (2000) Magnetotactic Bacteria. [WWW document]. URL http://link.springer-ny.com/link/service/books/10125/.
43. Spring, S. Schleifer, K.H. (1995) Diversity of magnetotactic bacteria. Syst Appl Microbiol 18 : 147 153.
44. Spring, S., Amann, R., Ludwig, W., Schleifer, K.-H. Petersen, N. (1992) Phylogenetic diversity and identification of nonculturable magnetotactic bacteria. Syst Appl Microbiol 15 : 116 122.
45. Spring, S., Amann, R., Ludwig, W., Schleifer, K., van Gemerden, H. Petersen, N. (1993) Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment. Appl Environ Microbiol 59 : 2397 2403.
46. Spring, S., Amann, R., Ludwig, W., Schleifer, K.-H., Schüler, D., Poralla, K. Petersen, N. (1994) Phylogenetic analysis of uncultured magnetotactic bacteria from the alpha-subclass of Proteobacteria. Syst Appl Microbiol 17 : 501 508.
47. Spring, S., Lins, U., Amann, R., Schleifer, K.-H., Ferreira, L.C.S., Esquivel, D.M.S. Farina, M. (1998) Phylogenetic affiliation and ultrastructure of uncultured magnetic bacteria with unusually large magnetosomes. Arch Microbiol 169 : 136 147.
48. Suzuki, M.T., Taylor, L.T. DeLong, E.F. (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66 : 4605 4614.
49. Taylor, J.R. (1982) An Introduction to Error Analysis. Sausalito, CA, USA : University Science Books.
50. Teo, I.A., Choi, J.W., Morlese, J., Taylor, G. Shaunak, S. (2002) LightCycler qPCR optimisation for low copy number target DNA. J Immunol Methods 270 : 119 133.
51. Tortell, P.D., Maldonado, M.T. Price, N.M. (1996) The role of heterotrophic bacteria in iron-limited ocean ecosystems. Nature 383 : 330 332.
52. Viollier, E., Inglett, P.W., Hunter, K., Roychoudhury, A.N. Van Cappellen, P. (2000) The ferrozine method revisited: Fe(II)/Fe(III) determination in natural waters. Appl Geochem 15 : 785 790.
53. Wilkin, R.T. Barnes, H.L. (1997) Pyrite formation in an anoxic estuarine basin. Am J Sci 297 : 620 650.
54. Williams, T.J., Zhang, C.L., Scott, J.H. Bazylinski, D.A. (2006) Evidence for autotrophy via the reverse tricarboxylic acid cycle in the marine magnetotactic coccus strain MC-1. Appl Environ Microbiol 72 : 1322 1329.
55. Wilson, K. (2001) Preparation of genomic DNA from Bacteria. In Current Protocols in Molecular Biology. Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seidman, J.G., Smith, J.A. Struhl, K. (eds). New York, NY, USA : John Wiley & Sons, pp. 15.17.11 15. 17.18.
56. Zhu, F., Massana, R., Not, F., Marie, D. Vaulot, D. (2005) Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol 52 : 79 92.