The genetics of geochemistry

Annual Review of Genetics

Volumn 38, Issue , 2004, Pages 175-202

  Croal, Laura R ^a   Gralnick, Jeffrey A ^b   Malasarn, Davin ^a   Newman, Dianne K ^b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Arsenic; Biogeochemistry; Iron; Photosynthesis; Respiration

Indexed keywords

ARSENIC; BACTERIAL RNA; FERRIC ION; FERROUS ION; GENE PRODUCT; MENAQUINONE; METAL; MINERAL; PROTEIN CCTA; PROTEIN CYMA; PROTEIN OMCA; SIGNAL PEPTIDE; UNCLASSIFIED DRUG;

ACIDITHIOBACILLUS FERROOXIDANS; ANAEROBIC METABOLISM; BACTERIAL GENE; BACTERIAL GENETICS; BACTERIAL GROWTH; BACTERIAL METABOLISM; CYC2 GENE; ELECTRON TRANSPORT; ENERGY RESOURCE; ENVIRONMENTAL IMPACT; GENE CONTROL; GENE DISRUPTION; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYSIS; GEOCHEMISTRY; MOLECULAR CLONING; MTRA GENE; MTRB GENE; MUTAGENESIS; OMCB GENE; OPEN READING FRAME; OXIDATION; PHOTOSYNTHESIS; PHOTOTROPHIC BACTERIUM; PHYLOGENY; PPCA GENE; PRIORITY JOURNAL; PROMOTER REGION; REDUCTION; REVIEW; RUS GENE; SEDIMENT; SHEWANELLA; WATER QUALITY;

ACIDITHIOBACILLUS; ACIDITHIOBACILLUS FERROOXIDANS; BACTERIA (MICROORGANISMS); PHOTOBACTERIA; PROKARYOTA; SHEWANELLA;

EID: 10944259840     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.38.072902.091138     Document Type: Review

References (205)

1. Anderson GL, Williams J, Hille R. 1992. The purification and characterization of arsenite oxidase from Alcaligenes faecalis, a molybdenum-containing hydroxylase. J. Biol. Chem. 267:23674-82
2. Anderson RT, Vrionis HA, Ortiz-Bernad I, Resch CT, Long PE, et al. 2003. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl. Environ. Microbiol. 69:5884-91
3. Appia-Ayme C, Bengrine A, Cavazza C, Giudici-Orticoni MT, Bruschi M, et al. 1998. Characterization and expression of the co-transcribed cyc1 and cyc2 genes encoding the cytochrome c4 (c552) and a high-molecular-mass cytochrome c from Thiobacillus ferrooxidans ATCC 33020. FEMS Microbiol. Lett. 167:171-77
4. Appia-Ayme C, Guiliani N, Ratouchniak J, Bonnefoy V. 1999. Characterization of an operon encoding two c-type cytochromes, an aa(3)-type cytochrome oxidase, and rusticyanin in Thiobacillus ferrooxidans ATCC 33020. Appl. Environ. Microbiol. 65:4781-87
5. Armienta MA, Villasenor G, Rodriguez R, Ongley LK, Mango H. 2001. The role of arsenic-bearing rocks in groundwater pollution at Zimapan Valley, Mexico. Environ. Geol. 40:571-81
6. Beijerinck MW. 1901. Ueber oligonitrophile Mikroben. Zentralbl. Bakteriol. 7:561-82
7. Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, et al. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science 289:1902-6
8. Beliaev AS, Saffarini DA. 1998. Shewanella putrefaciens mtrB encodes an outer membrane protein required for Fe(III) and Mn(IV) reduction. J. Bacteriol. 180:6292-97
9. Beliaev AS, Saffarini DA, McLaughlin JL, Hunnicutt D. 2001. MtrC, an outer membrane decahaem c cytochrome required for metal reduction in Shewanella putrefaciens MR-1. Mol. Microbiol. 39:722-30
10. Beliaev AS, Thompson DK, Fields MW, Wu L, Lies DP, et al. 2002. Microarray transcription profiling of a Shewanella oneidensis etrA mutant. J. Bacteriol. 184:4612-16
11. Beliaev AS, Thompson DK, Khare T, Lim H, Brandt CC, et al. 2002. Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors. Omics 6:39-60
12. Bengrine A, Guiliani N, Appia-Ayme C, Jedlicki E, Holmes DS, et al. 1998. Sequence and expression of the rusticyanin structural gene from Thiobacillus ferrooxidans ATCC33020 strain. Biochim. Biophys. Acta 1443:99-112
13. Benz M, Brune A, Schink B. 1998. Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria. Arch. Microbiol. 169:159-65
14. Blake RC 2nd, Shute EA. 1994. Respiratory enzymes of Thiobacillus ferrooxidans. Kinetic properties of an acid stable iron:rusticyanin oxidoreductase. Biochemistry 33:9220-28
15. Blake RC 2nd, Shute EA, Waskovsky J, Harrison APJ. 1992. Respiratory components in acidophilic bacteria that respire iron. Geomicrobiol. J. 10:173-92
16. Blanchard L, Marion D, Pollock B, Voordouw G, Wall J, et al. 1993. Over-expression of Desulfovibrio vulgaris Hildenborough cytochrome c553 in Desulfovibrio desulfuricans G200. Evidence of conformational heterogeneity in the oxidized protein by NMR. Eur. J. Biochem. 218:293-301
17. Blankenship RE, Hartman H. 1998. The origin and evolution of oxygenic photosynthesis. Trends Biochem. Sci. 23:94-97
18. Bond DR, Lovley DR. 2003. Electricity production by Geobacter sulfurreducens attached to electrodes. Appl. Environ. Microbiol. 69:1548-55
19. Broer S, Ji G, Broer A, Silver S. 1993. Arsenic efflux governed by the arsenic resistance determinant of Staphylococcus aureus plasmid pI258. J. Bacteriol. 175:3480-85
20. 2+ oxidizing systems and multicopper oxidases: an overview of mechanisms and functions. Geomicrobiol. J. 17:1-24
21. Burnes BS, Mulberry MJ, DiChristina TJ. 1998. Design and application of two rapid screening techniques for isolation of Mn(IV) reduction-deficient mutants of Shewanella putrefaciens. Appl. Environ. Microbiol. 64:2716-20
22. Butcher BG, Deane SM, Rawlings DE. 2000. The chromosomal arsenic resistance genes of Thiobacillus ferrooxidans have an unusual arrangement and confer increased arsenic and antimony resistance to Escherichia coli. Appl. Environ. Microbiol. 66:1826-33
23. Caccavo F, Das A. 2002. Adhesion of dissimilatory Fe(III)-reducing bacteria to Fe(III) minerals. Geomicrobiol. J. 19:161-77
24. Chapelle FH, O'Neill K, Bradley PM, Methe BA, Ciufo SA, et al. 2002. A hydrogen-based subsurface microbial community dominated by methanogens. Nature 415:312-15
25. Chaudhuri SK, Lack JG, Coates JD. 2001. Biogenic magnetite formation through anaerobic biooxidation of Fe(II). Appl. Environ. Microbiol. 67:2844-48
26. Chiang SL, Rubin EJ. 2002. Construction of a mariner-based transposon for epitope-tagging and genomic targeting. Gene 296:179-85
27. Cloud P. 1973. Paleoecological significance of banded iron-formation. Econ. Geol. 68:1135-43
28. Coates JD, Phillips EJ, Lonergan DJ, Jenter H, Lovley DR. 1996. Isolation of Geobacter species from diverse sedimentary environments. Appl. Environ. Microbiol. 62:1531-36
29. 2+ and the preliminary characterization of rusticyanin a novel 'blue' copper protein. FEBS Lett. 60:29-33
30. Colmer AR, Temple KL, Hinkle ME. 1949. An iron-oxidizing bacterium from the drainage of some bituminous coal mines. J. Bacteriol. 59:317-28
31. Connon SA, Giovannoni SJ. 2002. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl. Environ. Microbiol. 68:3878-85
32. Conrads T, Hemann C, George GN, Pickering IJ, Prince RC, Hille R. 2002. The active site of arsenite oxidase from Alcaligenes faecalis. J. Am. Chem. Soc. 124:11276-77
33. Coppi MV, Leang C, Sandler SJ, Lovley DR. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl. Environ. Microbiol. 67:3180-87
34. Cox JC, Boxer DH. 1978. The purification and some properties of rusticyanin, a blue copper protein invloved in Fe(II) oxidation from Thiobacillus ferro-oxidans. Biochem. J. 174:497-502
35. Deleted in proof
36. Croal LR, Johnson CJ, Bread BL, Newman DK. 2004. Iron isotope fractionation by Fe(II)-oxidizing photoautotrophic bacteria. Geochim. Cosmochim. Acta 68:1227-42
37. Cullen WR, Reimer KJ. 1989. Arsenic speciation in the environment. Chem. Rev. 89:713-64
38. De Luca G, de Philip P, Dermoun Z, Rousset M, Vermeglio A. 2001. Reduction of technetium(VII) by Desulfovibrio fructosovorans is mediated by the nickel-iron hydrogenase. Appl. Environ. Microbiol. 67:4583-87
39. Dey S, Rosen BP. 1995. Dual mode of energy coupling by the oxyanion-translocating ArsB protein. J. Bacteriol. 177:385-89
40. 3+. J. Bacteriol. 176:1468-74
41. DiChristina TJ, Moore CM, Haller CA. 2002. Dissimilatory Fe(III) and Mn(IV) reduction by Shewanella putrefaciens requires ferE, a homolog of the pulE (gspE) type II protein secretion gene. J. Bacteriol. 184:142-51
42. Donohue TJ, Kaplan S. 1991. Genetic techniques in Rhodospirillaceae. Methods Enzymol. 204:459-85
43. Dowdle PR, Laverman AM, Oremland RS. 1996. Bacterial dissimilatory reduction of arsenic(V) to arsenic(III) in anoxic sediments. Appl. Environ. Microbiol. 62:1664-69
44. Dubiel M, Hsu CH, Chien CC, Mansfeld F, Newman DK. 2002. Microbial iron respiration can protect steel from corrosion. Appl. Environ. Microbiol. 68:1440-45
45. Edwards KJ, Bond PL, Gihring TM, Banfield JF. 2000. An archaeal iron-oxidizing extreme acidophile important in acid mine drainage. Science 287:1796-99
46. Edwards KJ, Rogers DR, Wirsen CO, McCollom TM. 2003. Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolitho-autotrophic alpha- and gamma-proteobacteria from the deep sea. Appl. Environ. Microbiol. 69:2906-13
47. Ehrenreich A, Widdel F. 1994. Anaerobic oxidation of ferrous iron by purple bacteria, a new type of phototrophic metabolism. Appl. Environ. Microbiol. 60:4517-26
48. Ehrlich HL. 1998. Geomicrobiology: its significance for geology. Earth Sci. Rev. 45:45-60
49. Ehrlich HL. 2002. Geomicrobiology of iron. In Geomicrobiology, HL Ehrlich, pp. 345-429. New York: Dekker.
50. Ehrlich HL. 2002. Geomicrobiology of iron. See Ref. 49, pp. 303-43
51. Ellis PJ, Conrads T, Hille R, Kuhn P. 2001. Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and 2.03 Å. Structure 9:125-32
52. Emerson D, Moyer C. 1997. Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH. Appl. Environ. Microbiol. 63:4784-92
53. Emerson D, Moyer CL. 2002. Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition. Appl. Environ. Microbiol. 68:3085-93
54. Emerson D, Weiss JV, Megonigal JP. 1999. Iron-oxidizing bacteria are associated with ferric hydroxide precipitates (Fe-plaque) on the roots of wetland plants. Appl. Environ. Microbiol. 65:2758-61
55. Field SJ, Dobbin PS, Cheesman MR, Watmough NJ, Thomson AJ, Richardson DJ. 2000. Purification and magneto-optical spectroscopic characterization of cytoplasmic membrane and outer membrane multiheme c-type cytochromes from Shewanella frigidimarina NCMIB400. J. Biol. Chem. 275:8515-22
56. Francesconi KA, Kuehnelt D. 2002. Arsenic compounds in the environment. See Ref. 56a, pp. 51-94
57. a. Frankenberger WT Jr, ed. 2002. Environmental Chemistry of Arsenic. New York/Basel: Marcel Dekker
58. Fukumori Y, Yano T, Sato A, Yamanaka T. 1988. Fe(H)-oxidizing enzyme purified from Thiobacillus ferrooxidans. FEMS Microbiol. Lett. 50:169-72
59. Ghiorse WC. 1984. Biology of iron- and manganese-depositing bacteria. Annu. Rev. Microbiol. 38:515-50
60. Gordon EH, Pike AD, Hill AE, Cuthbertson PM, Chapman SK, Reid GA. 2000. Identification and characterization of a novel cytochrome c(3) from Shewanella frigidimarina that is involved in Fe(III) respiration. Biochem. J. 349:153-58
61. Graber JR, Leadbetter JR, Breznak JA. 2004. Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the first spirochetes isolated from termite guts. Appl. Environ. Microbiol. 70:1315-20
62. Hall JF, Hasnain SS, Ingledew WJ. 1996. The structural gene for rusticyanin from Thiobacillus ferrooxidans: cloning and sequencing of the rusticyanin gene. FEMS Microbiol. Lett. 137:85-89
63. Harrington JM, Fendorf SE, Rosenzweig RF. 1998. Biotic generation of arsenic(III) in metal(loid)-contaminated freshwater lake sediments. Environ. Sci. Technol. 32:2425-30
64. Hartman H. 1984. The evolution of photosynthesis and microbial mats: a speculation on banded iron formations. In Microbial Mats: Stromatolites, ed. Y Cohen, RW Castenholz, HO Halvorson, pp. 451-53. New York: Liss
65. Harvey CF, Swartz CH, Badruzzaman AB, Keon-Blute N, Yu W, et al. 2002. Arsenic mobility and groundwater extraction in Bangladesh. Science 298:1602-6
66. Hauck S, Benz M, Brune A, Schink B. 2001. Ferrous iron oxidation by denitrifying bacteria in profundal sediments of a deep lake (Lake Constance). FEMS Microbiol. Ecol. 37:127-34
67. Hedges RW, Baumberg S. 1973. Resistance to arsenic compounds conferred by a plasmid transmissible between strains of Escherichia coli. J. Bacteriol. 115:459-60
68. Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, et al. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-23
69. Heising S, Richter L, Ludwig W, Schink B. 1999. Chlorobium ferrooxidans sp. nov., a phototrophic green sulfur bacterium that oxidizes ferrous iron in coculture with a "Geospirillum" sp. strain. Arch. Microbiol. 172:116-24
70. Heising S, Schink B. 1998. Phototrophic oxidation of ferrous iron by a Rhodomicrobium vannielii strain. Microbiology 144:2263-69
71. Deleted in proof
72. Hernandez ME, Newman DK. 2001. Extracellular electron transfer. Cell Mol. Life Sci. 58:1562-71
73. Holmes DE, Bond DR, Lovley DR. 2004. Electron transfer by Desulfobulbus propionicus to Fe(III) and graphite electrodes. Appl. Environ. Microbiol. 70:1234-37
74. Huber R, Sacher M, Vollmann A, Huber H, Rose D. 2000. Respiration of arsenate and selenate by hyperthermophilic archaea. Syst. Appl. Microbiol. 23:305-14
75. Ilyaletdinov AN, Abdrashitova SA. 1981. Autotrophic oxidation of arsenic by a culture of Pseudomonas arsenitoxidans. Microbiology 50:135-40
76. Ingledew WJ, Cobley JG. 1980. A potentiometric and kinetic study on the respiratory chain of ferrous-iron-grown Thiobacillus ferrooxidans. Biochim. Biophys. Acta 590:141-58
77. Ingledew WJ, Houston A. 1986. The organization of the respiratory chain of Thiobacillus ferrooxidans. Biotechnol. Appl. Biochem. 8:242-48
78. Ji G, Silver S. 1992. Reduction of arsenate to arsenite by the ArsC protein of the arsenic resistance operon of Staphylococcus aureus plasmid pI258. Proc. Natl. Acad. Sci. USA 89:9474-78
79. Deleted in proof
80. Johnson CM, Beard BL, Beukes NJ, Klein C, O'Leary JM. 2003. Ancient geochemical cycling in the Earth as inferred from Fe isotope studies of banded iron formations from the Transvaal Craton. Contrib. Mineral. Petrol. 144:523-47
81. Kashefi K, Lovley DR. 2003. Extending the upper temperature limit for life. Science 301:934
82. Kaur P, Rosen BP. 1992. Plasmid-encoded resistance to arsenic and antimony. Plasmid 27:29-40
83. Kiley PJ, Beinert H. 1998. Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster. FEMS Microbiol. Rev. 22:341-52
84. Klein C. 2002. Mineral Science. New York: Wiley
85. Kluyver AJ. 1924. Eenheid en verscheidenheid in de stofwisseling der microben. Chemisch. Weekbl. 21:266
86. Konhauser KO, Hamade T, Raiswell R, Morris RC, Ferris FG, et al. 2002. Could bacteria have formed the Precambrian banded iron formations? Geology 30:1079-82
87. Kusano T, Sugawara K, Inoue C, Takeshima T, Numata M, Shiratori T. 1992. Electrotransformation of Thiobacillus ferrooxidans with plasmids containing a mer determinant. J. Bacteriol. 174:6617-23
88. Kusano T, Takeshima T, Sugawara K, Inoue C, Shiratori T, et al. 1992. Molecular cloning of the gene encoding Thiobacillus ferrooxidans Fe(II) oxidase. High homology of the gene product with HiPIP. J. Biol. Chem. 267:11242-47
89. Lange M, Ahring BK. 2001. A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea. FEMS Microbiol. Rev. 25:553-71
90. Leang C, Coppi MV, Lovley DR. 2003. OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 185:2096-103
91. Leys D, Meyer TE, Tsapin AS, Nealson KH, Cusanovich MA, Van Beeumen JJ. 2002. Crystal structures at atomic resolution reveal the novel concept of "electron-harvesting" as a role for the small tetraheme cytochrome c. J. Biol. Chem. 277:35703-11
92. Lin WC, Coppi MV, Lovley DR. 2004. Geobacter sulfurreducens can grown with oxygen as a terminal electron acceptor. Appl. Environ. Microbiol. 70:2525-28
93. Liu Z, Guiliani N, Appia-Ayme C, Borne F, Ratouchniak J, Bonnefoy V. 2000. Construction and characterization of a recA mutant of Thiobacillus ferrooxidans by marker exchange mutagenesis. J. Bacteriol. 182:2269-76
94. Lloyd JR. 2003. Microbial reduction of metals and radionuclides. FEMS Microbiol. Rev. 27:411-25
95. Lloyd JR, Leang C, Hodges Myerson AL, Coppi MV, Cuifo S, et al. 2003. Biochemical and genetic characterization of PpcA, a periplasmic c-type cytochrome in Geobacter sulfurreducens. Biochem. J. 369:153-61
96. Lloyd JR, Lovley DR, Macaskie LE. 2003. Biotechnological application of metal-reducing microorganisms. Adv. Appl. Microbiol. 53:85-128
97. Lovley DR. 1993. Dissimilatory metal reduction. Annu. Rev. Microbiol. 47:263-90
98. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJ, et al. 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. 159:336-44
99. Luo Y, Wasserfallen A. 2001. Gene transfer systems and their applications in Archaea. Syst. Appl. Microbiol. 24:15-25
100. Mackenzie C, Simmons AE, Kaplan S. 1999. Multiple chromosomes in bacteria. The yin and yang of trp gene localization in Rhodobactersphaeroides 2.4.1. Genetics 153:525-38
101. Macy JM, Nunan K, Hagen KD, Dixon DR, Harbour PJ, et al. 1996. Chrysiogenes arsenatis gen nov, sp nov; a new arsenate-respiring bacterium isolated from gold mine wastewater. Int. J. Sys. Bacteriol. 46:1153-57
102. Maier TM, Myers CR. 2001. Isolation and characterization of a Shewanella putrefaciens MR-1 electron transport regulator etrA mutant: reassessment of the role of EtrA. J. Bacteriol. 183:4918-26
103. Deleted in proof
104. Deleted in proof
105. McNellis L, Anderson GL. 1998. Redoxstate dependent chemical inactivation of arsenite oxidase. J. Inorg. Biochem. 69:253-57
106. Merrick MJ, Edwards RA. 1995. Nitrogen control in bacteria. Microbiol. Rev. 59:604-22
107. Metcalf WW, Wolfe RS. 1998. Molecular genetic analysis of phosphite and hypophosphite oxidation by Pseudomonas stutzeri WM88. J. Bacteriol. 180:5547-58
108. Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, et al. 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 302:1967-69
109. Meuer J, Kuettner HC, Zhang JK, Hedderich R, Metcalf WW. 2002. Genetic analysis of the archaeon Methanosarcina barkeri Fusaro reveals a central role for Ech hydrogenase and ferredoxin in methanogenesis and carbon fixation. Proc. Natl. Acad. Sci. USA 99:5632-37
110. Mobley HL, Chen CM, Silver S, Rosen BP. 1983. Cloning and expression of R-factor mediated arsenate resistance in Escherichia coli. Mol. Gen. Genet. 191:421-26
111. Muller D, Lievremont D, Simeonova DD, Hubert JC, Lett MC. 2003. Arsenite oxidase aox genes from a metal-resistant beta-proteobacterium. J. Bacteriol. 185:135-41
112. Myers CR, Myers JM. 1993. Ferric reductase is associated with the membranes of anaerobically grown Shewanella putrefaciens MR-1. FEMS Microbiol. Lett. 108:15-22
113. Myers CR, Myers JM. 1993. Role of menaquinone in the reduction of fumarate, nitrate, iron(III) and manganese(IV) by Shewanella putrefaciens MR-1. FEMS Microbiol. Lett 114:215-22
114. Myers CR, Myers JM. 1997. Cloning and sequence of cymA, a gene encoding a tetraheme cytochrome c required for reduction of iron(III), fumarate, and nitrate by Shewanella putrefaciens MR-1. J. Bacteriol. 179:1143-52
115. Myers CR, Myers JM. 1997. Outer membrane cytochromes of Shewanella putrefaciens MR-1: spectral analysis, and purification of the 83-kDa c-type cytochrome. Biochim. Biophys. Acta 1326:307-18
116. Myers CR, Myers JM. 2002. MtrB is required for proper incorporation of the cytochromes OmcA and OmcB into the outer membrane of Shewanella putrefaciens MR-1. Appl. Environ. Microbiol. 68:5585-94
117. Myers CR, Myers JM. 2003. Cell surface exposure of the outer membrane cytochromes of Shewanella oneidensis MR-1. Lett. Appl. Microbiol. 37:254-58
118. Myers JM, Myers CR. 1998. Isolation and sequence of omcA, a gene encoding a decaheme outer membrane cytochrome c of Shewanella putrefaciens MR-1, and detection of omcA homologs in other strains of S. putrefaciens. Biochim. Biophys. Acta 1373:237-51
119. Myers JM, Myers CR. 2000. Role of the tetraheme cytochrome CymA in anaerobic electron transport in cells of Shewanella putrefaciens MR-1 with normal levels of menaquinone. J. Bacteriol. 182:67-75
120. Myers JM, Myers CR. 2001. Role for outer membrane cytochromes OmcA and OmcB of Shewanella putrefaciens MR-1 in reduction of manganese dioxide. Appl. Environ. Microbiol. 67:260-69
121. Myers JM, Myers CR. 2003. Overlapping role of the outer membrane cytochromes of Shewanella oneidensis MR-1 in the reduction of manganese(IV) oxide. Lett. Appl. Microbiol. 37:21-25
122. Nealson KH. 1983. The microbial iron cycle. In Microbial Geochemistry, ed. WE Krumbein, pp. 159-89. Boston: Blackwell Sci.
123. Nealson KH, Belz A, McKee B. 2002. Breathing metals as a way of life: geobiology in action. Antonie Van Leeuwenhoek J. Microbiol. Serol. 81:215-22
124. Nealson KH, Saffarini D. 1994. Iron and manganese in anaerobic respiration: environmental significance, physiology, and regulation. Annu. Rev. Microbiol. 48:311-43
125. Nevin KP, Lovley DR. 2002. Mechanisms for accessing insoluble Fe(III) oxide during dissimilatory Fe(III) reduction by Geothrix fermentans. Appl. Environ. Microbiol. 68:2294-99
126. Newman DK, Ahmann D, Morel FMM. 1998. A brief review of microbial arsenate respiration. Geomicrobiology 15:255-68
127. Newman DK, Banfield JF. 2002. Geomicrobiology: How molecular-scale interactions underpin biogeochemical systems. Science 296:1071-77
128. Newman DK, Kolter R. 2000. A role for excreted quinones in extracellular electron transfer. Nature 405:94-97
129. Neyt C, Iriarte M, Thi VH, Cornelis GR. 1997. Virulence and arsenic resistance in Yersiniae. J. Bacteriol. 179:612-19
130. Nickson R, McArthur J, Burgess W, Ahmed KM, Ravenscroft P, Rahman M. 1998. Arsenic poisoning of Bangladesh groundwater. Nature 395:338
131. Nriagu J. 2002. Arsenic poisoning through the ages. See Ref. 56a, pp. 1-26
132. Oremland RS, Dowdle PR, Hoeft SE, Sharp JO, Schaefer JK, et al. 2000. Bacterial dissimilatory reduction of arsenate and sulfate in meromictic Mono Lake, California. Geochim. Cosmochim. Acta 64:3073-84
133. Oremland RS, Hoeft SE, Santini JA, Bano N, Hollibaugh RA, Hollibaugh JT. 2002. Anaerobic oxidation of arsenite in Mono Lake water and by facultative, arsenite-oxidizing chemoautotroph, strain MLHE-1. Appl. Environ. Microbiol. 68:4795-802
134. Oremland RS, Stolz JF. 2003. The ecology of arsenic. Science 300:939-44
135. Page MD, Sockett RE. 1999. Molecular genetic methods in Paracoccus and Rhodobacter with particular reference to the analysis of respiration and photosynthesis. In Methods in Microbiology, ed. MCM Smith, RE Sockett, pp. 427-66. San Diego: Academic
136. Pawellek T, Aigner T. 2003. Stratigraphic architecture and gamma ray logs of deeper ramp carbonates (Upper Jurassic, SW Germany). Sediment. Geol. 159:203-40
137. Peng JB, Yan WM, Bao XZ. 1994. Plasmid and transposon transfer to Thiobacillus ferrooxidans. J. Bacteriol. 176:2892-97
138. Deleted in proof
139. Pitts KE, Dobbin PS, Reyes-Ramirez F, Thomson AJ, Richardson DJ, Seward HE. 2003. Characterization of the Shewanella oneidensis MR-1 decaheme cytochrome MtrA: Expression in Escherichia coli confers the ability to reduce soluble Fe(III) chelates. J. Biol. Chem. 278:27758-65
140. Priscu JC, Fritsen CH, Adams EE, Giovannoni SJ, Paerl HW, et al. 1998. Perennial Antarctic lake ice: an oasis for life in a polar desert. Science 280:2095-98
141. Rae AJ, Cooke D, Phillips M, Zaide-Delfin M. 2004. The nature of magmatism at Palinpinon geothermal field, Negros Island, Philippines: implications for geothermal activity and regional tectonics. J. Volcanol. Geotherm. Res. 129:321-42
142. Rawlings DE. 1994. Molecular genetics of Thiobacillus ferrooxidans. Microbiol. Rev. 58:39-55
143. Rawlings DE. 2001. The molecular genetics of Thiobacillus ferrooxidans and other mesophilic, acidophilic, chemolithotrophic, iron- or sulfur-oxidizing bacteria. Hydrometallurgy 59:187-201
144. Robertson LA, Gijs Kuenen J. 2002. The genus Thiobacillus. In The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community. Release 3.9, ed. M Dworkin. New York: Springer-Verlag. http://141.150.157.117: 8080/prok.PUB/index.htm
145. Rondon MR, Goodman RM, Handelsman J. 1999. The Earth's bounty: assessing and accessing soil microbial diversity. Trends Biotechnol. 17:403-9
146. Rooney-Varga JN, Anderson RT, Fraga JL, Ringelberg D, Lovley DR. 1999. Microbial communities associated with anaerobic benzene degradation in a petroleum-contaminated aquifer. Appl. Environ. Microbiol. 65:3056-63
147. Rosen BP. 2002. Transport and detoxification systems for transition metals, heavy metals and metalloids in eukaryotic and prokaryotic microbes. Comp. Biochem. Physiol. A Mol. Integr. Physiol. 133:689-93
148. Saffarini DA, Blumerman SL, Mansoorabadi KJ. 2002. Role of menaquinones in Fe(III) reduction by membrane fractions of Shewanella putrefaciens. J. Bacteriol. 184:846-48
149. Saffarini DA, Schultz R, Beliaev A. 2003. Involvement of cyclic AMP (cAMP) and cAMP receptor protein in anaerobic respiration of Shewanella oneidensis. J. Bacteriol. 185:3668-71
150. Salmassi TM, Venkateswaran K, Satomi M, Nealson KH, Newman DK, Hering JG. 2002. Oxidation of arsenite by Agrobacterium albertimagni, AOL 15, sp nov., isolated from Hot Creek, California. Geomicrobiol. J. 19:53-66
151. Saltikov CW, Cifuentes A, Venkateswaran K, Newman DK. 2003. The ars detoxification system is advantageous but not required for As(V) respiration by the genetically tractable Shewanella species strain ANA-3. Appl. Environ. Microbiol. 69:2800-9
152. Deleted in proof
153. Saltikov CW, Newman DK. 2003. Genetic identification of a respiratory arsenate reductase. Proc. Natl. Acad. Sci. USA 100:10983-88
154. Sanders OI, Rensing C, Kuroda M, Mitra B, Rosen BP. 1997. Antimonite is accumulated by the glycerol facilitator GlpF in Escherichia coli. J. Bacteriol. 179:3365-67
155. Sandkvist M. 2001. Biology of type II secretion. Mol. Microbiol. 40:271-83
156. Santini JM, Sly LI, Schnagl RD, Macy JM. 2000. A new chemolithoautotrophic arsenite-oxidizing bacterium isolated from a gold mine: phylogenetic, physiological, and preliminary biochemical studies. Appl. Environ. Microbiol. 66:92-97
157. Santini JM, vanden Hoven RN. 2004. Molybdenum-containing arsenite oxidase of the chemolithoautotrophic arsenite oxidizer NT-26. J. Bacteriol. 186:1614-19
158. Sato T, Kobayashi Y. 1998. The ars operon in the skin element of Bacillus subtilis confers resistance to arsenate and arsenite. J. Bacteriol. 180:1655-61
159. Schrader JA, Holmes DS. 1988. Phenotypic switching of Thiobacillus ferrooxidans. J. Bacteriol. 170:3915-23
160. Schwalb C, Chapman SK, Reid GA. 2002. The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella. Biochem. Soc. Trans. 30:658-62
161. Schwalb C, Chapman SK, Reid GA. 2003. The tetraheme cytochrome CymA is required for anaerobic respiration with dimethyl sulfoxide and nitrite in Shewanella oneidensis. Biochemistry 42:9491-97
162. Senn DB, Hemond HF. 2002. Nitrate controls on iron and arsenic in an urban lake. Science 296:2373-76
163. Shi J, Vlamis-Gardikas A, Aslund F, Holmgren A, Rosen BP. 1999. Reactivity of glutaredoxins 1, 2, and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction. J. Biol. Chem. 274:36039-42
164. Shyu JB, Lies DP, Newman DK. 2002. Protective role of tolC in efflux of the electron shuttle anthraquinone-2,6-disulfonate. J. Bacteriol. 184:1806-10
165. Silver S, Budd K, Leahy KM, Shaw WV, Hammond D, et al. 1981. Inducible plasmid-determined resistance to arsenate, arsenite, and antimony (III) in Escherichia coli and Staphylococcus aureus. J. Bacteriol. 146:983-96
166. Silver S, Phung LT, Rosen BP. 2002. Arsenic metabolism: resistance, reduction, and oxidation. See Ref. 56a, pp. 247-72
167. Snoeyenbos-West OL, Nevin KP, Anderson RT, Lovley DR. 2000. Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments. Microb. Ecol. 39:153-67
168. Sobolev D, Roden EE. 2001. Suboxic deposition of ferric iron by bacteria in opposing gradients of Fe(II) and oxygen at circumneutral pH. Appl. Environ. Microbiol. 67:1328-34
169. Sofia HJ, Burland V, Daniels DL, Plunkett G, Blattner FR. 1994. Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 minutes to 81.5 minutes. Nucleic Acids Res. 22:2576-86
170. Spliethoff HM, Hemond HF. 1996. History of toxic metal discharge to surface waters of the Aberjona Watershed. Environ. Sci. Technol. 30:121-28
171. Straub KL, Benz M, Schink B. 2001. Iron metabolism in anoxic environments at near neutral pH. FEMS Microbiol. Ecol. 34:181-86
172. Straub KL, Benz M, Schink B, Widdel F. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl. Environ. Microbiol. 62:1458-60
173. Straub KL, Buchholz-Cleven BE. 1998. Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse European sediments. Appl. Environ. Microbiol. 64:4846-56
174. Straub KL, Rainey FA, Widdel F. 1999. Rhodovulum iodosum sp. nov. and Rhodovulum robiginosum sp. nov., two new marine phototrophic ferrous-iron-oxidizing purple bacteria. Int. J. Syst. Bacteriol. 49:729-35
175. Tebo BM, Ghiorse WC, vanWaasbergen LG, Siering PL, Caspi R. 1997. Bacterially mediated mineral formation: Insights into manganese(II) oxidation from molecular genetic and biochemical studies. Rev. Mineral. 35:225-66
176. Temple KL, Colmer AR. 1951. The autotrophic oxidation of iron by a new bacterium, Thiobacillus ferrooxidans. J. Bacteriol. 62:605-11
177. Thompson DK, Beliaev AS, Giometti CS, Tollaksen SL, Khare T, et al. 2002. Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress. Appl. Environ. Microbiol. 68:881-92
178. Tisa LS, Rosen BP. 1990. Molecular characterization of an anion pump. The ArsB protein is the membrane anchor for the ArsA protein. J. Biol. Chem. 265:190-94
179. Tsapin AI, Nealson KH, Meyers T, Cusanovich MA, Van Beuumen J, et al. 1996. Purification and properties of a low-redox-potential tetraheme cytochrome c3 from Shewanella putrefaciens. J. Bacteriol. 178:6386-88
180. Tsapin AI, Vandenberghe I, Nealson KH, Scott JH, Meyer TE, et al. 2001. Identification of a small tetraheme cytochrome c and a flavocytochrome c as two of the principal soluble cytochromes c in Shewanella oneidensis strain MR1. Appl. Environ. Microbiol. 67:3236-44
181. Tumbula DL, Whitman WB. 1999. Genetics of Methanococcus: possibilities for functional genomics in Archaea. Mol. Microbiol. 33:1-7
182. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, et al. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37-43
183. 2+ oxidation from Thiobacillus ferrooxidans. FEMS Microbiol. Lett. 121:61-69
184. Vargas M, Kashefi K, Blunt-Harris EL, Lovley DR. 1998. Microbiological evidence for Fe(III) reduction on early Earth. Nature 395:65-67
185. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, et al. 1999. Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int. J. Syst. Bacteriol. 49(Part 2):705-24
186. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
187. Vernon LP, Mangum JH, Beck JV, Shafia FM. 1960. Studies on a ferrousion-oxidizing bacterium. II. Cytochrome composition. Arch. Biochem. Biophys. 88:227-31
188. Weeger W, Lievremont D, Perret M, Lagarde F, Hubert JC, et al. 1999. Oxidation of arsenite to arsenate by a bacterium isolated from an aquatic environment. Biometals 12:141-49
189. Widdel F, Schnell S, Heising S, Ehrenreich A, Assmus B, Schink B. 1993. Ferrous iron oxidation by anoxygenic phototrophic bacteria. Nature 362:834-36
190. Wilkie JA, Hering JG. 1998. Rapid oxidation of geothermal arsenic(III) in stream-waters of the eastern Sierra Nevada. Environ. Sci. Technol. 32:657-62
191. Willsky GR, Malamy MH. 1980. Characterization of two genetically separable inorganic phosphate transport systems in Escherichia coli. J. Bacteriol. 144:356-65
192. Winogradsky S. 1889. Recherches physiologiques sur les sulfobacteries. Ann. Inst. Pasteur 3:49-60
193. Woods DR, Rawlings DE, Barros ME, Pretorius I, Ramesar R. 1986. Molecular genetic studies of Thiobacillus ferrooxidans: the development of genetic systems and the expression of cloned genes. Biotechnol. Appl. Biochem. 8:231-41
194. World Health Organization. 2001. Fact sheet, No. 210: Arsenic in drinking water
195. Deleted in proof
196. Wu J, Rosen BP. 1991. The ArsR protein is a trans-acting regulatory protein. Mol. Microbiol. 5:1331-36
197. Wu J, Rosen BP. 1993. The arsD gene encodes a second trans-acting regulatory protein of the plasmid-encoded arsenical resistance operon. Mol. Microbiol. 8:615-23
198. Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE. 2000. Molecular evidence for the early evolution of photosynthesis. Science 289:1724-30
199. Xu C, Shi W, Rosen BP. 1996. The chromosomal arsR gene of Escherichia coli encodes a trans-acting metalloregulatory protein. J. Biol. Chem. 271:2427-32
200. Yamanaka T, Fukumori Y. 1995. Molecular aspects of the electron transfer system which participates in the oxidation of ferrous ion by Thiobacillus ferrooxidans. FEMS Microbiol. Rev. 17:401-13
201. Yamanaka T, Yano T, Kai M, Tamegai H, Sato A, Fukumori Y. 1991. The electron transfer system in an acidophilic iron-oxidizing bacterium. In New Era of Bioenergetics, ed. Y Mukohata, pp. 223-46. Tokyo: Academic
202. Yarzabal A, Brasseur G, Ratouchniak J, Lund K, Lemesle-Meunier D, et al. 2002. The high-molecular-weight cytochrome c Cyc2 of Acidithiobacillus ferrooxidans is an outer membrane protein. J. Bacteriol. 184:313-17
203. Yarzabal A, Duquesne K, Bonnefoy V. 2003. Rusticyanin gene expression of Acidithiobacillus ferrooxidans ATCC 33020 in sulfur- and in ferrous iron media. Hydrometallurgy 71:107-14
204. Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, et al. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:15681-86
205. Zobrist J, Dowdle PR, Davis JA, Oremland RS. 2000. Mobilization of arsenite by dissimilatory reduction of adsorbed arsenate. Environ. Sci. Technol. 34:4747-53