Anaerobic redox cycling of iron by freshwater sediment microorganisms

Environmental Microbiology

Volumn 8, Issue 1, 2006, Pages 100-113

  Weber, Karrie A ^a,c   Urrutia, Matilde M ^a   Churchill, Perry F ^a   Kukkadapu, Ravi K ^b   Roden, Eric E ^a  

^a UNIVERSITY OF ALABAMA   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FRESH WATER; IRON; NITRATE; PRIMER DNA; RNA 16S;

ANAEROBIC BACTERIUM; ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; ELECTROPHORESIS; GENE LIBRARY; GENETICS; METABOLISM; MICROBIOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OXIDATION REDUCTION REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEDIMENT; TIME; X RAY DIFFRACTION;

BACTERIA, ANAEROBIC; BASE SEQUENCE; CLONING, MOLECULAR; DNA PRIMERS; ELECTROPHORESIS; FRESH WATER; GENE LIBRARY; GEOLOGIC SEDIMENTS; IRON; MOLECULAR SEQUENCE DATA; NITRATES; OXIDATION-REDUCTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TIME FACTORS; X-RAY DIFFRACTION;

DECHLOROMONAS; GEOBACTER; GEOBACTER SP.;

EID: 33644948280     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00873.x     Document Type: Article

References (76)

1. Achtnich C. Bak F. Conrad R. 1995 Competition for electron donors among nitrate reducers, ferric iron reducers, sulfate reducers, and methanogens in anoxic paddy soil Biol Fert Soils 19 65 72
2. Altschul SF. Madden TL. Schaffer AA. Zhang JH. Zhang Z. Miller W. Lipman DJ. 1997 Gapped blast and psi-blast: a new generation of protein database search programs Nucleic Acids Res 25 3389 3402
3. Benz M. Brune A. Schink B. 1998 Anaerobic and aerobic oxidation of ferrous iron at neutral pH by chemoheterotrophic nitrate-reducing bacteria Arch Microbiol 169 159 165
4. Brock TD. Gustafson J. 1972 Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature Arch Microbiol 84 54 68
5. Bruce RA. Achenback LA. Coates JD. 1999 Reduction of (per) chlorate by a novel organism isolated from paper mill waste Environ Microbiol 1 319 329
6. Bruggemann J. Stephen JR. Chang YJ. Macnaughton SJ. Kowalchuk GA. Kline E. White DC. 2000 Competitive PCR-DGGE analysis of bacterial mixtures: an internal standard and an appraisal of template enumeration accuracy J Microbiol Methods 40 111 123
7. Buchholz-Cleven BEE. Rattunde B. Straub KL. 1997 Screening for genetic diversity of isolates of anaerobic Fe(III) -oxidizing bacteria using DGGE and whole-cell hybridization Syst Appl Microbiol 20 301 309
8. Caldwell ME. Tanner RS. Suflita JM. 1999 Microbial metabolism of benzene and the oxidation of ferrous iron under anaerobic conditions: implications for bioremediation Anaerobe 5 595 603
9. Chapelle FH. 2001 Ground-water Microbiology and Geochemistry New York, NY, USA John Wiley & Sons.
10. Chaudhuri SK. Lack JG. Coates JD. 2001 Biogenic magnetite formation through anaerobic biooxidation of Fe(II) Appl Environ Microbiol 67 2844 2848
11. Coates JD. Phillips EJP. Lonergan DJ. Jenter H. Lovley DR. 1996 Isolation of Geobacter species from a variety of sedimentary environments Appl Environ Microbiol 62 1531 1536
12. Coates JD. Chakraborty R. Lack J. O'Connor SM. Cole KA. Bender KS. Achenbach LA. 2001 Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two novel organisms Nature 411 1039 1043
13. 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
14. Cooper DC. Picardal F. Rivera J. Talbot C. 2000 Zinc immobilization and magnetite formation via ferric oxide reduction by Shewanella putrefaciens 200 Environ Sci Technol 34 100 106
15. Cooper DA. Picardal FW. Schimmelmann A. Colby AJ. 2003 Chemical and biological interactions during nitrate and goethite reduction by Shewanella putrefaciens 200 Appl Environ Microbiol 69 3517 3525
16. Cornell RM. Schwertmann U. 1996 The Iron Oxides New York, NY, USA VCH.
17. Cummings DE., Jr, Spring S. Rosenzweig RF. 1999 Ferribacterium limneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments Arch Microbiol 171 183 188
18. Davison W. 1993 Iron and manganese in lakes Earth-Sci Rev 34 119 163
19. Davison W. Seed G. 1983 The kinetics of the oxidation of ferrous iron in synthetic and natural waters Geochim Cosmochim Acta 47 67 79
20. DiChristina TJ. 1992 Effects of nitrate on dissimilatory iron reduction by Shewanella putrefaciens 200 J Bacteriol 174 1891 1896
21. Emerson D. 2000 Microbial oxidation of Fe(II) and Mn(II) at circumneutral pH. In Environmental Metal-Microbe Interactions Lovley DR. (ed.). Washington, DC, USA American Society for Microbiology Press, pp. 31 52
22. Emerson D. Weiss JV. 2004 Bacterial iron oxidation in circumneutral freshwater habitats: findings from the field and the laboratory Geomicrobiol J 21 405 414
23. Finneran KT. Housewright ME. Lovley DR. 2002 Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments Environ Microbiol 4 510 516
24. Gillis M. Vandamme P. DeVos P. Swings J. Kersters K. 2001 Polyphasic taxonomy. In Bergey's Manual of Systematic Bacteriology Boone DR. Castenholz RW. (eds) New York, NY, USA Springer, pp. 43 48
25. Hansen HCB. Koch CB. Nancke-Krogh H. Borggaard OK. Sorensen J. 1996 Abiotic nitrate reduction to ammonium: key role of green rust Environ Sci Technol 30 2053 2056
26. Hansen HCB. Guldberg S. Erbs M. Koch CB. 2001 Kinetics of nitrate reduction by green rusts - effects of interlayer anion and Fe(II):Fe(III) ratio Appl Clay Sci 18 81 91
27. Hauck S. Benz M. Brune A. BS. 2001 Ferrous iron oxidation by denitrifying bacteria in profundal sediments of a deep lake (Lake Constance) FEMS Microbiol Ecol 37 127 134
28. Jackson CR. Harper JP. Willoughby D. Roden EE. Churchill PF. 1997 A simple, efficient method for the separation of humic substances and DNA from environmental samples Appl Environ Microbiol 63 4993 4995
29. Johnson DB. McGinness S. Ghauri MA. 1993 Biogeochemical cycling of iron and sulfur in leaching environments FEMS Microbiol Rev 11 63 70
30. Jones JG. Gardener S. Simon BB. 1983 Bacterial reduction of ferric iron in a stratified eutrophic lake J Gen Microbiol 129 131 139
31. Kemp PR. Lee S. Laroche J. 1993 Estimating the growth rate of slowly growing marine bacteria from RNA content Appl Environ Microbiol 59 2594 2601
32. Kluber HD. Conrad R. 1998 Effects of nitrate, nitrite, NO, and N2O on methanogenesis and other redox processes in anoxic rice soil FEMS Microbiol Ecol 25 301 318
33. Kukkadapu RK. Zachara JM. Smith SC. Fredrickson JK. Liu C. 2001 Dissimilatory bacterial reduction of Al-substituted goethite in subsurface sediments Geochim Cosmochim Acta 65 2913 2924
34. Kukkadapu RK. Zachara JM. Fredrickson JK. Kennedy DW. 2004 Biotransformation of two-line silica-ferrihydrite by a dissimilatory Fe(III)-reducing bacterium: formation of carbonate green rust in the presence of phosphate Geochim Cosmochim Acta 68 2799 2814
35. Lack JG. Chaudhuri SK. Kelly SD. Kemner KM. O'Connor SM. Coates JD. 2002 Immobilization of radionuclides and heavy metals through anaerobic bio-oxidation of Fe(II) Appl Environ Microbiol 68 2704 2710
36. Lovley DR. 1991 Dissimilatory Fe(III) and Mn (IV) reduction Microbiol Rev 55 259 287
37. Lovley DR. 2000 Fe(III) and Mn(IV) reduction. In Environmental Metal-Microbe Interactions Lovley DR. (ed.) Washington, DC, USA American Society for Microbiology Press, pp. 3 30
38. Lovley DR. 2002 Fe(III)- and Mn(IV)-reducing prokaryotes. In The Prokaryotes Stackebrandt E. (ed.) NY, USA Springer-Verlag [www document]. URL.
39. Lovley DR. Phillips EJP. 1988 Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese Appl Environ Microbiol 54 1472 1480
40. Lovley DR. Anderson RT. 2000 The influence of dissimilatory metal reduction on the fate of organic and metal contaminants in the subsurface J Hydrol 8 77 88
41. Mahne I. Tiedje J. 1995 Criteria and methodology for identifying respiratory denitrifiers Appl Environ Microbiol 61 1110 1115
42. Medlin L. Elwood HJ. Stickel S. Sogin ML. 1988 The characterization of enzymatically amplified eukaryotic 16S-like rRNA coding regions Gene 71 491 499
43. Millero FJ. Sotolongo S. Izaguirre M. 1987 The oxidation kinetics of Fe(II) in seawater Geochim Cosmochim Acta 51 793 801
44. Moran MA. Torsvik VL. Torsvik T. Hodson RE. 1993 Direct extraction and purification of rRNA for ecological studies Appl Environ Microbiol 59 915 918
45. Muyzer G. Ramsing NB. 1995 Molecular methods to study the organization of microbial communities Water Sci Technol 32 1 9
46. Muyzer G. Dewaal EC. Uitterlinden AG. 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
47. Muyzer G. Hottentrager S. Teske A. Wawer C. 1995 Denaturing gel electrophoresis of PCR-amplified 16S rDNA - a new molecular approach to analyse the genetic diversity of microbial communities. In Molecular Microbial Ecology Manual Akkermans DL. vanElsas JD. deBruijn FJ. (eds) Dordrecht, the Netherlands Kluwer, pp. 3.4.4.1 3 4.4.22
48. Nielsen JL. Nielsen PH. 1998a Microbial nitrate-dependent oxidation of ferrous iron in activated sludge Environ Sci Technol 32 3556 3561
49. Nielsen JL. Nielsen PH. 1998b Microbial Fe(II)-oxidation by nitrate in activated sludge Water Sci Technol 37 406 406
50. Obuekwe CO. Westlake DWS. Cook FD. 1981 Effect of nitrate on reduction of ferric iron by a bacterium isolated from crude oil Can J Microbiol 27 692 697
51. Ratering S. Schnell S. 2000 Nitrate-dependent iron (II) oxidation in paddy soil Environ Microbiol 3 100 109
52. 55Fe as a tracer of Fe(III) reduction in aquatic sediments Geomicrobiol J 11 49 56
53. Roden EE. Wetzel RG. 1996 Organic carbon oxidation and suppression of methane production by microbial Fe(III) oxide reduction in vegetated and unvegetated freshwater wetland sediments Limnol Oceanogr 41 1733 1748
54. Roden EE. Urrutia MM. 2002 Influence of biogenic Fe(II) on bacterial reduction of crystalline Fe(III) oxides Geomicrobiol J 19 209 251
55. Roden EE. Sobolev D. Glazer B. Luther GW. 2004 Potential for microscale bacterial Fe redox cycling at the aerobic-anaerobic interface Geomicrobiol J 21 379 391
56. Schwertmann U. Cornell RM. 1991 Iron Oxides in the Laboratory New York, NY, USA Weinheim.
57. Senko JM. Stolz JF. 2001 Evidence for iron-dependent nitrate respiration in the dissimilatory iron-reducing bacterium Geobacter metallireducens Appl Environ Microbiol 67 3750 3752
58. Senn DB. Hemond HF. 2002 Nitrate controls on iron and aresenic in an urban lake Science 296 2373 2376
59. Shelobolina ES. Gaw-VanPraagh C. Lovley DR. 2003 Use of ferric and ferrous iron containing minerals for respiration by Desulfitobacterium frappieri Geomicrobiol J 20 143 156
60. Singer PC. Stumm W. 1972 Acid mine drainage - the rate limiting step Science 167 1121 1123
61. Sorensen J. 1982 Reduction of ferric iron in anaerobic, marine sediment and interaction with reduction of nitrate and sulfate Appl Environ Microbiol 43 319 324
62. Stookey LL. 1970 Ferrozine - a new spectrophotometric reagent for iron Anal Chem 42 779 781
63. Straub KL. Benz M. Schink B. Widdel F. 1996 Anaerobic, nitrate-dependent microbial oxidation of ferrous iron Appl Environ Microbiol 62 1458 1460
64. Straub KL. Buchholz-Cleven BEE. 1998 Enumeration and detection of anaerobic ferrous-iron oxidizing, nitrate-reducing bacteria from diverse European sediments Appl Environ Microbiol 64 4846 4856
65. Straub KL. Benz M. Schink B. 2001 Iron metabolism in anoxic environments at near neutral pH FEMS Microbiol Ecol 34 181 186
66. Straub KL. Schonhuber WA. Buchholz-Cleven BEE. Schink B. 2004 Diversity of ferrous iron-oxidizing, nitrate-reducing bacteria and their involvement in oxygen-independent iron cycling Geomicrobiol J 21 371 378
67. Stumm W. Sulzberger B. 1992 The cycling of iron in natural environments: considerations based on laboratory studies of heterogeneous redox processes Geochim Cosmochim Acta 56 3233 3257
68. VanBreemen N. 1988 Long-term chemical, mineralogical and morphological effects of iron-redox processes in periodically flooded soils. In Iron in Soils and Clay Minerals Stucki JW. Goodman BA. Schwertmann U. (eds) Boston D. Reidel Publishing, pp. 811 823.
69. VonWintzingerode F. Goebel UB. Stackebrandt E. 1997 Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis FEMS Microbiol Rev 21 213 229
70. Wagner R. 1994 The regulation of ribosomal RNA synthesis and bacterial cell growth Arch Microbiol 161 100 109
71. Weber KA. 2002 Microbial coupling between nitrogen and iron cycles. Potential implications for nitrate and iron biogeochemistry and metal mobility in sedimentary environments PhD Dissertation. University of Alabama, Tuscaloosa, AL, USA
72. Weber KA. Picardal FW. Roden EE. 2001 Microbially-catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds Environ Sci Technol 35 1644 1650
73. Wetzel RG. Likens GE. 1991 Limnological Analyses New York, NY, USA Springer-Verlag
74. Woomer PL. 1994 Most probable number counts. In Methods of Soil Analysis Part 2 - Microbiological and Biochemical Properties Bigham JM. (ed.). Madison, WI, USA Soil Science Society of America, pp. 59 79
75. Zachara JM. Fredrickson JK. Smith SC. Gassman PL. 2001 Solubilization of Fe(III) oxide-bound trace metals by a dissimilatory Fe(III) reducing bacterium Geochim Cosmochim Acta 65 75 93
76. Zhou J. Bruns MA. Tiedje JM. 1996 DNA recovery from soils of diverse composition Appl Environ Microbiol 62 316 322