Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates

International Journal of Systematic and Evolutionary Microbiology

Volumn 55, Issue 4, 2005, Pages 1667-1674

  Nevin, Kelly P ^a   Holmes, Dawn E ^a   Woodard, Trevor L ^a   Hinlein, Erich S ^b   Ostendorf, David W ^b   Lovley, Derek R ^a  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b University of Massachusetts   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; ACETIC ACID DERIVATIVE; ALCOHOL; AROMATIC HYDROCARBON; BACTERIAL PROTEIN; BACTERIAL RNA; CITRIC ACID; FERRIC ION; FRESH WATER; FUMARIC ACID; GROUND WATER; IRON OXIDE; LACTIC ACID; MALIC ACID; PROTEIN NIFD; PYROPHOSPHORIC ACID DERIVATIVE; PYRUVIC ACID; RIBOSOME RNA; RNA 16S; SUCCINIC ACID; UNCLASSIFIED DRUG;

AQUIFER; ARTICLE; BACTERIAL FLAGELLUM; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; CULTURE MEDIUM; DELTAPROTEOBACTERIA; ELECTRON; GENETIC ANALYSIS; GENUS; GEOBACTER; GEOBACTER BEMIDJIENSIS; GEOBACTER PSYCHROPHILUS; GEOBACTERACEAE; GRAM NEGATIVE BACTERIUM; MOLECULAR PHYLOGENY; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION KINETICS; PHENOTYPE; PRIORITY JOURNAL; SPECIES DIFFERENCE; STRAIN DIFFERENCE; TEMPERATURE DEPENDENCE; UNITED STATES;

BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; COLD; DNA, BACTERIAL; DNA, RIBOSOMAL; FERRIC COMPOUNDS; FRESH WATER; GENES, RRNA; GEOBACTER; GEOLOGIC SEDIMENTS; MASSACHUSETTS; MINNESOTA; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; WATER SUPPLY;

DELTAPROTEOBACTERIA; GEOBACTER; GEOBACTER BEMIDJIENSIS; GEOBACTERACEAE; NEGIBACTERIA;

EID: 22544468862     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63417-0     Document Type: Article

References (64)

1. Achenbach, L. & Woese, C. (1995). 16S and 23S rRNA-like primers. In Archaea: a Laboratory Manual, pp. 201-203. Edited by F. T. Robb, A. R. Place, K. R. Sowers and others. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
3. Amann, R. I., Binder, B. J., Olson, R. J., Chisholm, S. W., Devereux, R. & Stahl, D. A. (1990). Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56, 1919-1925.
4. Anderson, R. T. & Lovley, D. R. (1999). Naphthalene and benzene degradation under Fe(III)-reducing conditions in petroleum-contaminated aquifers. Bioremediation J 3, 121-135.
5. Anderson, R. T. & Lovley, D. R. (2000). Anaerobic bioremediation of benzene under sulfate-reducing conditions in a petroleum-contaminated aquifer. Environ Sci Technol 34, 2261-2266.
6. Anderson, R. T., Vrionis, H. A., Ortiz-Bernad, I. & 10 other authors (2003). Stimulated in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl Environ Microbiol 69, 5884-5891.
7. 2-dependent growth and nitrogenase activity in the metal-metabolizing bacteria, Geobacter and Magnetospirillum species. Environ Microbiol 2, 266-273.
8. Bond, D. R. & Lovley, D. R. (2003). Electricity production by Geobacter sulfurreducens attached to electrodes. Appl Environ Microbiol 69, 1548-1555.
9. Bond, D. R., Holmes, D. E., Tender, L. M. & Lovley, D. R. (2002). Electrode-reducing microorganisms that harvest energy from marine sediments. Science 295, 483-485.
10. Bowman, J. P., McCammon, S. A., Nichols, D. S., Skerratt, J. H., Rea, S. M., Nichols, D. S. & McMeekin, T. A. (1997). Shewanella gelidimarina sp. nov. and Shewanella frigidimarina sp. nov., novel Antarctic species with the ability to produce eicosapentaenoic acid (20:5ω3) and grow anaerobically by dissimilatory Fe(III) reduction. Int J Syst Bacteriol 47, 1040-1047.
11. Bozal, N., Montes, M. J., Tudela, E., Jimenez, F. & Guinea, J. (2002). Shewanella frigidimarina and Shewanella livingstonensis sp. nov. isolated from Antarctic coastal areas. Int J Syst Evol Microbiol 52, 195-205.
12. Caccavo, F., Jr, Lonergan, D. J., Lovley, D. R., Davis, M., Stolz, J. F. & McInerney, M. J. (1994). Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60, 3752-3759.
13. Cashion, P., Holder-Franklin, M. A., McCully, J. & Franklin, M. (1977). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81, 461-466.
14. Childers, S. E., Ciufo, S. & Lovley, D. R. (2002). Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 416, 767-769.
15. Church, P., Armstrong, D., Granato, G., Stone, V., Smith, K. & Provencher, P. (1996). Effectiveness of highway-drainage systems in preventing contamination of ground water by road salt, Route 25, Southeastern Massachusetts - Description of study area, data collection programs, and methodology. US Geological Survey, Open-file report 96-317.
16. Coates, J. D., Phillips, E. J., Lonergan, D. J., Jenter, H. & Lovley, D. R. (1996). Isolation of Geobacter species from diverse sedimentary environments. Appl Environ Microbiol 62, 1531-1536.
17. Coates, J. D., Bhupathiraju, V. K., Achenbach, L. A., McInerney, M. J. & Lovley, D. R. (2001). Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int J Syst Evol Microbiol 51, 581-588.
18. Coppi, M. V., Leang, C., Sandler, S. J. & Lovley, D. R. (2001). Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 67, 3180-3187.
19. Cummings, D. E., Snoeyenbos-West, O. L., Newby, D. T., Niggemyer, A. M., Lovley, D. R., Achenbach, L. A. & Rosenzweig, R. F. (2003). Diversity of Geobacteraceae species inhabiting metal-polluted freshwater lake sediments ascertained by 16S rDNA analyses. Microb Ecol 46, 257-269.
20. De Ley, J., Cattoir, H. & Reynaerts, A. (1970). The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12, 133-142.
21. Eden, P. A., Schmidt, T. M., Blakemore, R. P. & Pace, N. R. (1991). Phylogenetic analysis of Aquaspirillum magnetotacticum using polymerase chain reaction-amplified 16S rRNA-specific DNA. Int J Syst Bacteriol 41, 324-325.
22. Finneran, K., Johnsen, C. V. & Lovley, D. R. (2003). Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III). Int J Syst Evol Microbiol 53, 669-673.
23. Helms, A. C., Martiny, A. C., Hofman-Bang, J., Ahring, B. K. & Kilstrup, M. (2004). Identification of bacterial cultures from archaeological wood using molecular biological techniques. Int Biodeterior Biodegrad 53, 79-88.
24. Holmes, D. E., Bond, D. R., O'Neil, R. A., Reimers, C. E., Tender, L. R. & Lovley, D. R. (2004a). Microbiol communities associated with electrodes harvesting electricity from a variety of aquatic sediments. Microb Ecol 48, 178-190.
25. Holmes, D. E., Nevin, K. P. & Lovley, D. R. (2004b). Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int J Syst Evol Microbiol 54, 1591-1599.
26. Holmes, D. E., Nicoll, J. S., Bond, D. R. & Lovley, D. R. (2004c). Potential role of a novel psychrotolerant member of the Geobacteraceae, Geopsychrobacter electrodiphilus gen. nov., sp. nov., in electricity production by the marine sediment fuel cell. Appl Environ Microbiol 70, 6023-6030.
27. Huß, V. A. R., Festl, H. & Schleifer, K. H. (1983). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4, 184-192.
28. Ikenaga, M., Asakawa, S., Muraoka, Y. & Kimura, M. (2003). Bacterial communities associated with nodal roots of rice plants along with the growth stages: estimation by PCR-DGGE and sequence analyses. Soil Sci Plant Nutr 49, 591-602.
29. Istok, J. D., Senko, J. M., Krumholz, L. R., Watson, D., Bogle, M. A., Peacock, A., Chang, Y.-J. & White, D. C. (2004). In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer. Environ Sci Technol 38, 468-475.
30. Kashefi, K. & Lovley, D. (2003). Extending the upper temperature limit for life. Science 301, 934.
31. Kashefi, K., Holmes, D. E., Lovley, D. R. & Tor, J. (2004). Potential importance of dissimilatory Fe(III)-reducing microorganisms in hot sedimentary environments. In The Subseafloor Biosphere at Mid-Ocean Ridges, Geophysical Monograph Series no. 144, pp. 199-211. Washington, DC: American Geophysical Union Press.
32. Knoblauch, C., Sahm, K. & Jorgensen, B. B. (1999). Psychrophilic sulfate-reducing bacteria isolated from permanently cold Arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov. Int J Syst Bacteriol 49, 1631-1643.
33. Leonardo, M. R., Moser, D. P., Barbieri, E., Brantner, C. A., MacGregor, B. J., Paster, B. J., Stackebrandt, E. & Nealson, K. H. (1999). Shewanella pealeana sp. nov., a member of the microbial community associated with the accessory nidamental gland of the squid Loligo pealei. Int J Syst Bacteriol 49, 1341-1351.
34. Lovley, D. R. (1991). Dissimilatory Fe(III) and Mn(IV) reduction. Microbiol Rev 55, 259-287.
35. Lovley, D. (2000). Fe(III) and Mn(IV)-reducing prokaryotes. In The Prokaryotes, 3rd edn. Edited by M. Dworkin, S. Falkow, E. Rosenberg, K. H. Schleifer & E. Stackebrandt. New York: Springer.
36. Lovley, D. (2005). Fe(III)- and Mn(IV)-reducing prokaryotes. In The Prokaryotes, 4th edn. Edited by M. Dworkin, S. Falkow, E. Rosenberg & M. Fletcher. New York: Springer (in press).
37. Lovley, D. R. & Chapelle, F. H. (1995). Deep subsurface microbial processes. Rev Geophys 33, 365-381.
38. Lovley, D. R. & Phillips, E. J. P. (1986). Availability of ferric iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River. Appl Environ Microbiol 52, 751-757.
39. Lovley, D. R. & Phillips, E. J. P. (1987). Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl Environ Microbiol 53, 1536-1540.
40. Lovley, D. R. & Phillips, E. J. P. (1988). Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 54, 1472-1480.
41. Lovley, D. R., Stolz, J. F., Nord, G. L. & Phillips, E. J. P. (1987). Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism. Nature 330, 252-254.
42. Lovley, D. R., Giovannoni, S. J., White, D. C., Champine, J. E., Phillips, E. J. P., Gorby, Y. A. & Goodwin, S. (1993). Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. Arch Microbiol 159, 336-344.
43. Lovley, D. R., Holmes, D. E. & Nevin, K. P. (2004). Dissimilatory Fe(III) and Mn(IV) reduction. Adv Microb Physiol 49, 219-286.
44. Maidak, B. L., Cole, J. R., Lilburn, T. G. & 7 other authors (2001). The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29, 173-174.
45. Methé, B. A., Nelson, K. E., Eisen, J. A. & 31 other authors (2003). Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 302, 1967-1969.
46. Nevin, K. P. & Lovley, D. R. (2000a). Lack of production of electron-shuttling compounds or solubilization of Fe(III) during reduction of insoluble Fe(III) oxide by Geobacter metallireducens. Appl Environ Microbiol 66, 2248-2251.
47. Nevin, K. P. & Lovley, D. R. (2000b). Potential for nonenzymatic reduction of Fe(III) via electron shuttling in subsurface sediments. Environ Sci Technol 34, 2472-2478.
48. Nevin, K. & Lovley, D. (2002a). Mechanisms for Fe(III) oxide reduction in sedimentary environments. Geomicrobiol J 19, 141-159.
49. Nevin, K. P. & Lovley, D. R. (2002b). Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans. Appl Environ Microbiol 68, 2294-2299.
50. Ostendorf, D. (1997-2004). Highway deicing agent impacts on soil and groundwater quality. Series of Monthly Progress Reports. Prepared under ISA and ISA 9775 for the Massachusetts Highway Department.
51. Pearson, W. R. (1990). Rapid and sensitive sequence comparison with FASTP and FASTA. Methods Enzymol 183, 63-98.
52. Petrie, L., North, N. N., Dollhopf, S. F., Balkwill, D. L. & Kostka, J. E. (2003). Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). Appl Environ Microbiol 69, 7467-7479.
53. Roling, W. F. M., van Breukelen, B. M., Braster, M., Lin, B. & van Verseveld, H. W. (2001). Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer. Appl Environ Microbiol 67, 4619-4629.
54. Rooney-Varga, J. N., Anderson, R. T., Fraga, J. L., Ringelberg, D. & Lovley, D. R. (1999). Microbiol communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl Environ Microbiol 65, 3056-3063.
55. Snoeyenbos-West, O. L., Nevin, K. P., Anderson, R. T. & Lovley, D. R. (2000). Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments. Microb Ecol 39, 153-167.
56. Stein, L. Y., La Duc, M. T., Grundl, T. J. & Nealson, K. H. (2001). Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. Environ Microbiol 3, 10-18.
57. Straub, K. L. & Buchholz-Cleven, B. E. E. (2001). Geobacter bremensis sp. nov. and Geobacter pelophilus sp. nov., two dissimilatory ferric-iron-reducing bacteria. Int J Syst Evol Microbiol 51, 1805-1808.
58. Straub, K. L., Hanzlik, M. & Buchholz-Cleven, B. E. E. (1998). The use of biologically produced ferrihydrite for the isolation of novel iron-reducing bacteria. Syst Appl Microbiol 21, 442-449.
59. Swofford, D. (1998). PAUP - Phylogenetic Analysis Using Parsimony (*and other methods), version 4. Sunderland, MA: Sinauer Associates.
60. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL_X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
61. 2-fixing bacteria associated with rice roots by molecular evolutionary analysis of a nifD library. Can J Microbiol 41, 235-240.
62. Vargas, M., Kashefi, K., Blunt-Harris, E. L. & Lovley, D. R. (1998). Microbiological evidence for Fe(III) reduction on early Earth. Nature 395, 65-67.
63. Vrionis, H. A., Anderson, R. T., Ortiz-Bernad, I., O'Neill, K. R., Resch, C. T., Long, P. E. & Lovley, D. R. (2005). Shifts in geochemistry and microbial community distributions in response to biostimulation in a uranium-contaminated aquifer. Appl Environ Microbiol (in press).
64. Wayne, L. G., Brenner, D. J., Colwell, R. R. & 9 other authors (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37, 463-464.