Design of Shewanella-specific 16S rRNA primers and application to analysis of Shewanella in a minerotrophic wetland

Environmental Microbiology

Volumn 8, Issue 3, 2006, Pages 426-432

  Todorova, Svetoslava G ^a   Costello, Andria M ^a  

^a Syracuse University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; PRIMER DNA; RIBOSOME DNA; RNA 16S;

ARTICLE; CHEMISTRY; DNA FINGERPRINTING; DNA SEQUENCE; ECOSYSTEM; GENETICS; ISOLATION AND PURIFICATION; METHODOLOGY; MOLECULAR GENETICS; PHYLOGENY; POLYMERASE CHAIN REACTION; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SHEWANELLA;

DNA FINGERPRINTING; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SHEWANELLA;

SHEWANELLA; SHEWANELLA ONEIDENSIS;

EID: 33644949413     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00908.x     Document Type: Article

References (25)

1. Bowman JP. McCammon SA. Nichols DS. Skerratt JH. Rea SM. Nichols PD. Mcmeekin TA. 1997 Shewanella gelidimarina sp. nov. & Shewanella fridigimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (10: 5ω3) and grow anaerobically by dissimilatory Fe(III) reduction Intl J Syst Bacteriol 47 1040 1047
2. Chapelle FH. Lovley DR. 1992 Competitive exclusion of sulfate reduction by Fe(III)-reducing bacteria: a mechanism for producing discrete zones of high-iron ground water Ground Water 30 29 36
3. Cole JR. Chai B. Marsh TL. Farris RJ. Wang Q. Kulam SA. et al. 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
4. Costello AM. Lidstrom ME. 1999 Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments Appl Environ Microbiol 65 5066 5074
5. Cummings DE. March AW. Bostick B. Spring S. Caccavo F. Fendorf S. Rosenzweig RF. 2000 Evidence for microbial Fe(III) reduction in anoxic, mining impacted lake sediments (Lake Coeur d'Alene, Idaho) Appl Environ Microbiol 66 154 162
6. DiChristina TJ. DeLong EF. 1993 Design and application of rRNA-targeted oligonucleotide probes for dissimilatory iron- and manganese-reducing bacterium Shewanella putrefaciens Appl Environ Microbiol 59 4152 4160
7. Drexler JZ. Bedford BL. DeGaetano AT. Siegel DI. 1999 Quantification of the water budget and nutrient loading in a small peatland J Amer Water Res Assoc 35 753 769
8. Felsenstein J. 1993 PHYLIP - Phylogeny Interface Package, Version 3.5c. [3.5c]. URL
9. Galand PE. Saarnio S. Fritze H. Yrjälä K. 2002 Depth related diversity of methanogen archaea in Finnish oligotrophic fen FEMS Microbiol Ecol 42 441 449
10. Good IJ. 1953 The population frequencies of species and the estimation of population parameters Biometrika 40 237 264
11. Hall BG. 2001 Phylogenetic Trees Made Easy: A How-to Manual for Molecular Biologists Sunderland, MA, USA Sinauer Assiciates.
12. Jacobsen R. Postma D. 1999 Redox zoning, rates of sulfate reduction and interactions with Fe-reduction and methanogenesis in shallow sandy aquifer, Romo, Denmark Geochem Cosmochim Acta 63 137 151
13. Kostka JE. Dalton DD. Skelton H. Dollhopf S. Stucki JW. 2002 Growth of iron(III)-reducing bacteria on clay minerals as the sole electron acceptor and comparison of growth yields on a variety of oxidized iron forms Appl Environ Microbiol 68 6256 6262
14. Lane DJ. 1991 16S/23S rRNA Sequencing. In Nucleic Acid Techniques in Bacterial Systematics Stackebrandt E. Goodfellow M. (eds) Chichester, UK John Wiley & Sons, pp. 115 175
15. Lovley DR. Phillips EJP. 1986 Organic matter mineralization with reduction of ferric iron in anaerobic sediments Appl Environ Microbiol 51 683 689
16. Lovley DR. Phillips EJP. 1988 Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron and manganese Appl Environ Microbiol 54 1472 1480
17. McLeod ES. MacDonald R. Brözel VS. 2002 Distribution of Shewanella putrefaciens and Desulfovibrio vulgaris in sulfidogenic biofilms of industrial cooling water systems determined by fluorescent in situ hybridization Water SA 28 123 128
18. Myers CR. Nealson KH. 1988 Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor Science 240 1319 1321
19. Nealson KH. Myers CR. 1992 Microbial reduction of manganese and iron: new approaches to carbon cycling Appl Environ Microbiol 58 439 443
20. Page RDM. 1996 TreeView: an application to display phylogenetic trees on personal computers Comput Applic Biosci 12 357 358
21. Ratering S. Schnell S. 2000 Localization of iron-reducing activity in paddy soil by profile studies Biogeochem 48 341 365
22. Roden EE. Wetzel RG. 1996 Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxidized reduction in vegetated and unvegetated freshwater wetland sediments Limnol Ocean 41 1733 1748
23. Thompson JD. Gibson TJ. Plewniak F. Jeanmougin F. Higgins DG. 1997 The ClustalX Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 24 4876 4882
24. Todorova SG. Siegel DI. Costello AM. 2005 Microbial Fe(III) reduction in a minerotrophic wetland - geochemical controls and involvement in organic matter decomposition Appl Geochem 20 1120 1130
25. Venkateswaran K. Moser DP. Dollhopf ME. Lies DP. Saffarini DA. MacGregor BJ. et al. 1999 Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov Intl J Syst Bacteriol 49 705 724