1887

Chapter 7 : Microorganisms and Processes Linked to Uranium Reduction and Immobilization

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Microorganisms and Processes Linked to Uranium Reduction and Immobilization, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817190/9781555815363_Chap07-1.gif /docserver/preview/fulltext/10.1128/9781555817190/9781555815363_Chap07-2.gif

Abstract:

This chapter focuses on the microorganisms and electron transfer processes that are likely to impact the reductive immobilization of U(VI) in the contaminated terrestrial subsurface. It offers a perspective on how microbial eukaryotes may play a role in U(VI) biotransformation, and ends with a discussion of the nonreductive immobilization of U(VI) through microbially facilitated precipitation with phosphate. The mobility of uranium in porous media is mainly controlled by complexation and redox reactions. Extensive microbial community characterization has revealed a diverse assemblage of microbes encompassing all phyla within the domain in the subsurface of the Oak Ridge Integrated Field Research Challenge (ORIFRC). Recent work shows that the subsurface clade exhibits a remarkable genotypic and phenotypic plasticity and the 16S rRNA marker is not diagnostic for this plasticity. Field studies indicate that microbially mediated, reductive immobilization is a promising strategy for the remediation of U(VI) contamination in subsurface environments. To direct the function of subsurface microbial communities, and to achieve the aims of bioremediation and natural attenuation, genome-enabled studies are needed to directly link the phylogenetic structure with the metabolic activity of U(VI)-transforming microbial groups in situ. Expanded sequencing efforts will no doubt provide a clearer view of subsurface microbial community structure, but pure-culture studies are required for development of techniques to evaluate in situ function through quantification of gene expression patterns.

Citation: Kostka J, Green S. 2011. Microorganisms and Processes Linked to Uranium Reduction and Immobilization, p 117-138. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch7

Key Concept Ranking

Microbial Ecology
1.294047
Chemicals
0.6412152
Biogeochemical Cycle
0.47118333
Microbial Habitats
0.46882245
16s rRNA Sequencing
0.46717042
1.294047
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

Schematic summarizing the predominant biogeochemical reactions and processes impacting U(VI) mobility in the contaminated subsurface. U(IV) in the solid phase is represented by uraninite (UO), but other mineral forms may be present. 10.1128/9781555817190.ch7.f1

Citation: Kostka J, Green S. 2011. Microorganisms and Processes Linked to Uranium Reduction and Immobilization, p 117-138. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Phylogenetic tree of U(VI)-reducing microorganisms. Bootstrapped neighbor-joining trees were generated using partial and full-length 16S rRNA gene sequences obtained from the National Center for Biotechnology Information and from the DOE’s Joint Genome Institute. Sequences were aligned using the software package Greengenes ( ) and analyzed within the phylogenetic software package MEGA ( ). Bootstrap values greater than 50% are indicated at each node, and polytomies indicate branching points that were not consistently supported by bootstrap analyses. Organisms for which genome sequences are available are highlighted in grey, with all the 16S rRNA genes present in the genome compressed into a single cluster. The number of 16S rRNA genes present in the genome is indicated in brackets adjacent to the accession number. Relevant references are indicated for each organism. Species shown to conserve energy using U(VI) as a sole electron acceptor are indicated with a black box. The scale bar represents 0.05 substitutions per nucleotide position. Missing from the tree are the short gene sequences from the genome of ATCC 482 (NZ_ABTJ00000000), as well as several organisms for which no sequences were available, including ATCC 13867, sp. CRB5, and (formerly ). 10.1128/9781555817190.ch7.f2

Citation: Kostka J, Green S. 2011. Microorganisms and Processes Linked to Uranium Reduction and Immobilization, p 117-138. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817190.ch07
1. Akob, D. M.,, H. J. Mills,, T. M. Gihring,, L. Kerkhof,, J. W. Stucki,, A. S. Anastacio,, K. J. Chin,, K. Kusel,, A. V. Palumbo,, D. B. Watson, and, J. E. Kostka. 2008. Functional diversity and electron donor dependence of microbial populations capable of U(VI) reduction in radionuclide-contaminated subsurface sediments. Appl. Environ. Microbiol. 74:31593170.
2. Akob, D. M.,, H. J. Mills, and, J. E. Kostka. 2007. Metabolically active microbial communities in uranium-contaminated subsurface sediments. FEMS Microbiol. Ecol. 59:95107.
3. Anderson, R. T. 2006. DOE genomics: applications to in situ subsurface bioremediation. Remediat. J. 17:2338.
4. Anderson, R. T.,, H. A. Vrionis,, I. Ortiz-Bernad,, C. T. Resch,, P. E. Long,, R. Dayvault,, K. Karp,, S. Marutzky,, D. R. Metzler,, A. Peacock,, D. C. White,, M. Lowe, and, D. R. Lovley. 2003. Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer. Appl. Environ. Microbiol. 69:58845891.
5. Bärlocher, F.,, L. G. Nikolcheva,, K. P. Wilson, and, D. D. Williams. 2006. Fungi in the Hyporheic Zone of a Springbrook. Microb. Ecol. 52:708715.
6. Baronofsky, J. J.,, W. J. A. Schreurs, and, E. R. Kashket. 1984. Uncoupling by acetic-acid limits growth of and acetogenesis by Clostridium-Thermoaceticum. Appl. Environ. Microbiol. 48:11341139.
7. Beazley, M. J. 2009. Non-reductive biomineralization of Uranium(VI) as a result of microbial phosphatase activity. Ph.D. thesis. Georgia Institute of Technology, Atlanta.
8. Beazley, M. J.,, R. J. Martinez,, P. A. Sobecky,, S. M. Webb, and, M. Taillefert. 2007. Uranium biomineralization as a result of bacterial phosphatase activity: insights from bacterial isolates from a contaminated subsurface. Environ. Sci. Technol. 41:57015707.
9. Beazley, M. J.,, R. J. Martinez,, P. A. Sobecky,, S. M. Webb, and, M. Taillefert. 2009. Non-reductive biomineralization of uranium(VI) phosphate via microbial phosphatase activity in anaerobic conditions. Geomicrobiol. J. 26:431441.
10. Beller, H. R. 2005. Anaerobic, nitrate-dependent oxidation of U(IV) oxide minerals by the chemolithoautotrophic bacterium Thiobacillus denitrificans. Appl. Environ. Microbiol. 71:21702174.
11. Blakeney, M. D.,, T. Moulaei, and, T. J. Di-Christina. 2000. Fe(III) reduction activity and cytochrome content of Shewanella putrefaciens grown on ten compounds as sole terminal electron acceptor. Microbiol. Res. 155:8794.
12. Borden, R. C. 2007. Concurrent bioremediation of perchlorate and 1,1,1-trichloroethane in an emulsified oil barrier. J. Contam. Hydrol. 94:1333.
13. Brad, T.,, M. Braster,, B. M. van Breukelen,, N. M. van Straalen, and, W. F. M. Roling. 2008. Eukaryotic diversity in an anaerobic aquifer polluted with landfill leachate. Appl. Environ. Microbiol. 74:39593968.
14. Brooks, S. C. 2001. Waste Characteristics of the Former S-3 Ponds and Outline of Uranium Chemistry Relevant to NABIR Field Research Center Studies. NABIR Field Research Center, Oak Ridge, TN.
15. Brooks, S. C.,, J. K. Fredrickson,, S. L. Carroll,, D. W. Kennedy,, J. M. Zachara,, A. E. Plymale,, S. D. Kelly,, K. M. Kemner, and, S. Fendorf. 2003. Inhibition of bacterial U(VI) reduction by calcium. Environ. Sci. Technol. 37:18501858.
16. Canfield, D. E.,, B. Thamdrup, and, E. Kristensen. 2005. Aquatic Geomicrobiology. Elsevier Academic Press, San Diego, CA.
17. Cardenas, E.,, W. M. Wu,, M. B. Leigh,, J. Carley,, S. Carroll,, T. Gentry,, J. Luo,, D. Watson,, B. Gu,, M. Ginder-Vogel,, P. K. Kitanidis,, P. M. Jardine,, J. Zhou,, C. S. Criddle,, T. L. Marsh, and, J. A. Tiedje. 2008. Microbial communities in contaminated sediments, associated with bioremediation of uranium to submicromolar levels. Appl. Environ. Microbiol. 74:37183729.
18. Catalano, J. G.,, and G. E. Brown. 2005. Uranyl adsorption onto montmorillonite: evaluation of binding sites and carbonate complexation. Geochim. Cosmochim. Acta 69:29953005.
19. Chang, Y. J.,, P. E. Long,, R. Geyer,, A. D. Peacock,, C. T. Resch,, K. Sublette,, S. Pfiffner,, A. Smithgall,, R. T. Anderson,, H. A. Vrionis,, J. R. Stephen,, R. Dayvault,, I. Ortiz-Bernad,, D. R. Lovley, and, D. C. White. 2005. Microbial incorporation of C-13-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI). Environ. Sci. Technol. 39:90399048.
20. Chang, Y. J.,, A. D. Peacock,, P. E. Long,, J. R. Stephen,, J. P. McKinley,, S. J. Macnaughton,, A. K. M. A. Hussain,, A. M. Saxton, and, D. C. White. 2001. Diversity and characterization of sulfate-reducing bacteria in groundwater at a uranium mill tailings site. Appl. Environ. Microbiol. 67:31493160.
21. Chapelle, F. H. 2000. The significance of microbial processes in hydrogeology and geochemistry. Hydrogeol. J. 8:4146.
22. Childers, S. E.,, S. Ciufo, and, D. R. Lovley. 2002. Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 416:767769.
23. Coates, J. D.,, V. K. Bhupathiraju,, L. A. Achenbach,, M. J. McInerney, and, D. R. Lovley. 2001. Geobacter hydrogenophilus, Geobacter chapellei and Geobacter grbiciae, three new, strictly anaerobic, dissimilatory Fe(III)-reducers. Int. J. Syst. Evol. Microbiol. 51:581588.
24. Cole, J. R.,, B. Chai,, R. J. Farris,, Q. Wang,, A. S. Kulam-Syed-Mohideen,, D. M. McGarrell,, A. M. Bandela,, E. Cardenas,, G. M. Garrity, and, J. M. Tiedje. 2007. The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. Nucleic Acids Res. 35:D169D172.
25. Dadachova, E.,, R. A. Bryan,, X. Huang,, T. Moadel,, A. D. Schweitzer,, P. Aisen,, J. D. Nosanchuk, and, A. Casadevall. 2007. Ionizing radiation changes the electronic properties of melanin and enhances the growth of melanized fungi. PLoS ONE 2:e457.
26. DeSantis, T. Z.,, P. Hugenholtz,, K. Keller,, E. L. Brodie,, N. Larsen,, Y. M. Piceno,, R. Phan, and, G. L. Andersen. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34:W394W399.
27. DiChristina, T. J.,, J. K. Fredrickson, and, J. M. Zachara. 2005. Enzymology of electron transport: energy generation with geochemical consequences. Rev. Mineral. Geochem. 59:2752.
28. Duff, M. C.,, J. U. Coughlin, and, D. B. Hunter. 2002. Uranium co-precipitation with iron oxide minerals. Geochim. Cosmochim. Acta 66:35333547.
29. Edwards, L.,, K. Kusel,, H. Drake, and, J. E. Kostka. 2007. Electron flow in acidic subsurface sediments co-contaminated with nitrate and uranium. Geochim. Cosmochim. Acta 71:643654.
30. Elias, D. A.,, L. R. Krumholz,, D. Wong,, P. E. Long, and, J. M. Suflita. 2003. Characterization of microbial activities and U reduction in a shallow aquifer contaminated by uranium mill tailings. Microb. Ecol. 46:8391.
31. Fields, M. W.,, T. F. Yan,, S. K. Rhee,, S. L. Carroll,, P. M. Jardine,, D. B. Watson,, C. S. Criddle, and, J. Z. Zhou. 2005. Impacts on microbial communities and cultivable isolates from groundwater contaminated with high levels of nitric aciduranium waste. FEMS Microbiol. Ecol. 53:417428.
32. Finneran, K. T.,, M. E. Housewright, and, D. R. Lovley. 2002. Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments. Environ. Microbiol. 4:510516.
33. Fomina, M.,, S. Charnock,, S. Hillier,, R. Alvarez,, F. Livens, and, G. M. Gadd. 2008. Role of fungi in the biogeochemical fate of depleted uranium. Curr. Biol. 18:R375R377.
34. Francis, A. J.,, C. J. Dodge,, F. L. Lu,, G. P. Halada, and, C. R. Clayton. 1994. XPS and XANES studies of uranium reduction by Clostridium sp. Environ. Sci. Technol. 28:636639.
35. Fredrickson, J. K.,, H. M. Kostandarithes,, S. W. Li,, A. E. Plymale, and, M. J. Daly. 2000. Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1. Appl. Environ. Microbiol. 66:20062011.
36. Fredrickson, J. K.,, and J. M. Zachara. 2008. Electron transfer at the microbe-mineral interface: a grand challenge in biogeochemistry. Geobiology 6:245253.
37. Fuller, C. C.,, J. R. Bargar,, J. A. Davis, and, M. J. Piana. 2002. Mechanisms of uranium interactions with hydroxyapatite: implications for groundwater remediation. Environ. Sci. Technol. 36:158165.
38. Gadd, G. M. 2007. Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation. Mycol. Res. 111:349.
39. Gao, W. M.,, and A. J. Francis. 2008. Reduction of uranium(VI) to uranium(IV) by clostridia. Appl. Environ. Microbiol. 74:45804584.
40. Giovannoni, S. J.,, R. A. Foster,, M. S. Rappe, and, S. Epstein. 2007. New cultivation strategies bring more microbial plankton species into the laboratory. Oceanography 20:6269.
41. Griebler, C.,, and T. Lueders. 2009. Microbial biodiversity in groundwater ecosystems. Freshw. Biol. 54:649677.
42. Hayatsu, M.,, K. Tago, and, M. Saito. 2008. Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci. Plant Nutr. 54:3345.
43. Holmes, D. E.,, D. R. Bond, and, D. R. Lovley. 2004. Electron transfer by Desulfobulbus propionicus to Fe(III) and graphite electrodes. Appl. Environ. Microbiol. 70:12341237.
44. Holmes, D. E.,, R. A. O’Neil,, H. A. Vrionis,, L. A. N’Guessan,, I. Ortiz-Bernad,, M. J. Larrahondo,, L. A. Adams,, J. A. Ward,, J. S. Nicoll,, K. P. Nevin,, M. A. Chavan,, J. P. Johnson,, P. E. Long, and, D. R. Lovley. 2007. Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments. ISME J. 1:663677.
45. Hua, B.,, H. F. Xu,, J. Terry, and, B. L. Deng. 2006. Kinetics of uranium(VI) reduction by hydrogen sulfide in anoxic aqueous systems. Sci. Technol. 40:46664671.
46. Hwang, C. C.,, W. M. Wu,, T. J. Gentry,, J. Carley,, G. A. Corbin,, S. L. Carroll,, D. B. Watson,, P. M. Jardine,, J. Z. Zhou,, C. S. Criddle, and, M. W. Fields. 2009. Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths. ISME J. 3:4764.
47. Ilton, E. S.,, N. P. Qafoku,, C. X. Liu,, D. A. Moore, and, J. M. Zachara. 2008. Advective removal of intraparticle uranium from contaminated Vadose zone sediments, Hanford, US. Environ. Sci. Technol. 42:15651571.
48. Istok, J. D.,, J. M. Senko,, L. R. Krumholz,, D. Watson,, M. A. Bogle,, A. Peacock,, Y. J. Chang, and, D. C. White. 2004. In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer. Environ. Sci. Technol. 38:468475.
49. Jakobsen, R.,, and D. Postma. 1999. Redox zoning, rates of sulfate reduction and interactions with Fe-reduction and methanogenesis in a shallow sandy aquifer, Romo, Denmark. Geochim. Cosmochim. Acta 63:137151.
50. Janssen, P. H. 2008. New cultivation strategies for terrestrial microorganisms, p. 173–192. In K. Zengler (ed.), Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back. ASM Press, Washington, DC.
51. Jeon, B. H.,, S. D. Kelly,, K. M. Kemner,, M. O. Barnett,, W. D. Burgos,, B. A. Dempsey, and, E. E. Roden. 2004. Microbial reduction of U(VI) at the solid-water interface. Sci. Technol. 38:56495655.
52. Kashefi, K.,, and D. R. Lovley. 2000. Reduction of Fe(III), Mn(IV), and toxic metals at 100°C by Pyrobaculum islandicum. Appl. Environ. Microbiol. 66:10501056.
53. Kelly, S. D.,, K. M. Kemner,, J. Carley,, C. Criddle,, P. M. Jardine,, T. L. Marsh,, D. Phillips,, D. Watson, and, W. M. Wu. 2008. Speciation of uranium in sediments before and after in situ biostimulation. Environ. Sci. Technol. 42:15581564.
54. Khijniak, T. V.,, A. I. Slobodkin,, V. Coker,, J. C. Renshaw,, F. R. Livens,, E. A. Bonch-Osmolovskaya,, N. K. Birkeland,, N. N. Medvedeva-Lyalikova, and, J. R. Lloyd. 2005. Reduction of uranium(VI) phosphate during growth of the thermophilic bacterium Thermoterrabacterium ferrireducens. Appl. Environ. Microbiol. 71:64236426.
55. Kieft, T. L.,, J. K. Fredrickson,, T. C. Onstott,, Y. A. Gorby,, H. M. Kostandarithes,, T. J. Bailey,, D. W. Kennedy,, S. W. Li,, A. E. Plymale,, C. M. Spadoni, and, M. S. Gray. 1999. Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate. Appl. Environ. Microbiol. 65:12141221.
56. Kumar, S.,, M. Nei,, J. Dudley, and, K. Tamura. 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinformat. 9:299306.
57. Kunapuli, U.,, M. K. Jahn,, T. Lueders,, R. Geyer,, H. J. Heipieper, and, R. U. Meckenstock. 2009. Anaerobic degradation of monoaromatic hydrocarbons by two novel iron-reducing bacteria: description of Desulfitobacterium aromaticivorans sp. nov., and Geobacter toluoenoxydans sp. nov. Int. J. Syst. Evol. Microbiol. doi:10.1099/ijs.0. 003525-0.
58. Laughlin, R. J.,, and R. J. Stevens. 2002. Evidence for fungal dominance of denitrification and code-nitrification in a grassland soil. Soil Sci. Soc. Am. J. 66:15401548.
59. Liger, E.,, L. Charlet, and, P. Van Cappellen. 1999. Surface catalysis of uranium(VI) reduction by iron(II). Geochim. Cosmochim. Acta 63:29392955.
60. Lin, B.,, H. V. Westerhoff, and, W. F. M. Roling. 2009. How Geobacteraceae may dominate subsurface biodegradation: physiology of Geobacter metallireducens in slow-growth habitat-simulating retentostats. Environ. Microbiol. 11:24252433.
61. Liu, C. X.,, B. H. Jeon,, J. M. Zachara,, Z. M. Wang,, A. Dohnalkova, and, J. K. Fredrickson. 2006. Kinetics of microbial reduction of solid phase U(VI). Environ. Sci. Technol. 40:62906296.
62. Liu, C. X.,, J. M. Zachara,, O. Qafoku,, J. P. McKinley,, S. M. Heald, and, Z. M. Wang. 2004. Dissolution of uranyl microprecipitates in subsurface sediments at Hanford site, USA. Geochim. Cosmochim. Acta 68:45194537.
63. Lloyd, J. R.,, and L. E. Macaskie. 2000. Bioremediation of radioactive metals, p. 277–327. In D. R. Lovley (ed.), Environmental Microbe-Metal Interactions. ASM Press, Washington, DC.
64. Loffler, F. E.,, and E. A. Edwards. 2006. Harnessing microbial activities for environmental cleanup. Curr. Opin. Biotechnol. 17:274284.
65. Lovley, D. R.,, D. E. Holmes, and, K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:219286.
66. Lovley, D. R.,, R. Mahadevan, and, K. P. Nevin. 2008. Systems biology approach to bioremediation with extracellular electron transfer, p. 71–96. In E. Diaz (ed.), Microbial Biodegradation: Genomics and Molecular Biology. Horizon Scientific Press, Norwich, United Kingdom.
67. Lovley, D. R.,, and E. J. P. Phillips. 1992. Bioremediation of uranium contamination with enzymatic uranium reduction. Environ. Sci. Technol. 26:22282234.
68. Lovley, D. R.,, E. J. P. Phillips,, Y. A. Gorby, and, E. R. Landa. 1991. Microbial reduction of uranium. Nature 350:413416.
69. Lovley, D. R.,, E. E. Roden,, E. J. P. Philips, and, J. C. Woodward. 1993. Enzymatic iron and uranium reduction by sulfate-reducing bacteria. Mar. Geol. 113:4153.
70. Luo, W. S.,, S. D. Kelly,, K. M. Kemner,, D. Watson,, J. Z. Zhou,, P. M. Jardine, and, B. H. Gu. 2009. Sequestering uranium and technetium through co-precipitation with aluminum in a contaminated acidic environment. Environ. Sci. Technol. 43:75167522.
71. Madden, A. S.,, A. C. Smith,, D. L. Balkwill,, L. A. Fagan, and, T. J. Phelps. 2007. Microbial uranium immobilization independent of nitrate reduction. Environ. Microbiol. 9:23212330.
72. Marietou, A.,, L. Griffiths, and, J. Cole. 2009. Preferential reduction of the thermodynamically less favorable electron acceptor, sulfate, by a nitrate-reducing strain of the sulfate-reducing bacterium Desulfovibrio desulfuricans 27774. J. Bacteriol. 191:882889.
73. Markich, S. J. 2002. Uranium speciation and bioavailability in aquatic systems: an overview. Sci. World J. 2:707729.
74. Martinez, R. J.,, M. J. Beazley,, M. Taillefert,, A. K. Arakaki,, J. Skolnick, and, P. A. Sobecky. 2007. Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide-and metal-contaminated subsurface soils. Environ. Microbiol. 9:31223133.
75. Mckelvie, I. D.,, B. T. Hart,, T. J. Cardwell, and, R. W. Cattrall. 1995. Use of immobilized 3-phytase and flow-injection for the determination of phosphorus species in natural-waters. Anal. Chim. Acta 316:277289.
76. Mohagheghi, A.,, D. M. Updegraff, and, M. B. Goldhaber. 1985. The role of sulfate-reducing bacteria in the deposition of sedimentary uranium ores. Geomicrobiol. J. 4:153173.
77. Moon, J.,, Y. Roh,, T. J. Phelps,, D. H. Philips,, D. B. Watson,, Y.-J. Kim, and, S. C. Brooks. 2005. Physicochemical and mineralogical characterization of soil-saprolite cores from a field research site, Tennessee. J. Environ. Qual. 35:17311741.
78. Murphy, W. M.,, and E. L. Shock. 1999. Environmental aqueous geochemistry of actinides, p. 221–253. In P. C. Burns and, R. Finch (ed.), Uranium: Mineralogy, Geochemistry and the Environment, vol. 38. Mineralogical Society of America, Washington, DC.
79. Muyzer, G.,, and A. J. M. Stams. 2008. The ecology and biotechnology of sulphate-reducing bacteria. Nat. Rev. Microbiol. 6:441454.
80. Nash, K. L.,, M. P. Jensen, and, M. A. Schmidt. 1998. Actinide immobilization in the subsurface environment by in-situ treatment with a hydrolytically unstable organophosphorus complexant: uranyl uptake by calcium phytate. J. Alloys Compd. 271:257261.
81. National Research Council. 1993. In Situ Bioremediation: When Does It Work? National Academy Press, Washington, DC.
82. Natural and Accelerated Bioremediation Research (NABIR). 2003. Bioremediation of Metals and Radionuclides: What It Is and How It Works. Lawrence Berkeley National Laboratory, Berkeley, CA.
83. Nealson, K. H.,, A. Belz, and, B. McKee. 2002. Breathing metals as a way of life: geobiology in action. Antonie Van Leeuwenhoek 81:215222.
84. N’Guessan, A. L.,, H. A. Vrionis,, C. T. Resch,, P. E. Long, and, D. R. Lovley. 2008. Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction. Environ. Sci. Technol. 42:29993004.
85. North, N. N.,, S. L. Dollhopf,, L. Petrie,, J. D. Istok,, D. L. Balkwill, and, J. E. Kostka. 2004. Change in bacterial community structure during in situ biostimulation of subsurface sediment cocontaminated with uranium and nitrate. Appl. Environ. Microbiol. 70:49114920.
86. Payne, R. B.,, D. A. Gentry,, B. J. Rapp-Giles,, L. Casalot, and, J. D. Wall. 2002. Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c3 mutant. Appl. Environ. Microbiol. 68:31293132.
87. Peacock, A. D.,, Y. J. Chang,, J. D. Istok,, L. Krumholz,, R. Geyer,, B. Kinsall,, D. Watson,, K. L. Sublette, and, D. C. White. 2004. Utilization of microbial biofilms as monitors of bioremediation. Microb. Ecol. 47:284292.
88. Petrie, L.,, N. N. North,, S. L. Dollhopf,, D. L. Balkwill, and, J. E. Kostka. 2003. Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI). Appl. Environ. Microbiol. 69:74677479.
89. Pietzsch, K.,, and W. Babel. 2003. A sulfate-reducing bacterium that can detoxify U(VI) and obtain energy via nitrate reduction. J. Basic Microbiol. 43:348361.
90. Prakash, O.,, T. M. Gihring,, D. D. Dalton,, K.-J. Chin,, S. J. Green,, D. M. Akob,, G. Wanger, and, J. E. Kostka. 2010. Geobacter daltonii sp. nov., an iron(III)-and uranium(VI)-reducing bacterium isolated from the shallow subsurface exposed to mixed heavy metal and hydrocarbon contamination. Int. J. Syst. Evol. Microbiol. 60:546553. doi:10.1099/ijs.0.010843-0.
91. Raicevic, S.,, J. V. Wright,, V. Veljkovic, and, J. L. Conca. 2006. Theoretical stability assessment of uranyl phosphates and apatites: selection of amendments for in situ remediation of uranium. Sci. Total Environ. 355:1324.
92. Read, D.,, T. A. Lawless,, R. J. Sims, and, K. R. Butter. 1993. Uranium migration through intact sandstone cores. J. Contam. Hydrol. 13:277289.
93. Riley, R. G.,, and J. M. Zachara. 1992. Chemical Contaminants on DOE Lands and Selection of Contaminant Mixtures for Subsurface Research, vol. DOE/ER-0547T. U.S. Department of Energy, Washington, DC.
94. Roh, Y.,, S. V. Liu,, G. S. Li,, H. S. Huang,, T. J. Phelps, and, J. Z. Zhou. 2002. Isolation and characterization of metal-reducing Thermoanaerobacter strains from deep subsurface environments of the Piceance Basin, Colorado. Appl. Environ. Microbiol. 68:60136020.
95. Sanford, R. A.,, Q. Wu,, Y. Sung,, S. H. Thomas,, B. K. Amos,, E. K. Prince, and, F. E. Loffler. 2007. Hexavalent uranium supports growth of Anaeromyxobacter dehalogenans and Geobacter spp. with lower than predicted biomass yields. Environ. Microbiol. 9:28852893.
96. Sani, R. K.,, B. M. Peyton,, J. E. Amonette, and, G. G. Geesey. 2004. Reduction of uranium(VI) under sulfate-reducing conditions in the presence of Fe(III)-(hydr)oxides. Geochim. Cosmochim. Acta 68:26392648.
97. Sani, R. K.,, B. M. Peyton,, W. A. Smith,, W. A. Apel, and, J. N. Petersen. 2002. Dissimilatory reduction of Cr(VI), Fe(III), and U(VI) by Cellulomonas isolates. Appl. Microbiol. Biotechnol. 60:192199.
98. Schmidt, S. K.,, K. L. Wilson,, A. F. Meyer,, C. W. Schadt,, T. M. Porter, and, J. M. Moncalvo. 2008. The missing fungi: new insights from culture-independent molecular studies of soil, p. 55–66. In K. Zengler (ed.), Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back. ASM Press, Washington, DC.
99. Scott, T. B.,, G. C. Allen,, P. J. Heard, and, M. G. Randell. 2005. Reduction of U(VI) to U(IV) on the surface of magnetite. Geochim. Cosmochim. Acta 69:56395646.
100. Seaman, J. C.,, J. M. Hutchison,, B. P. Jackson, and, V. M. Vulava. 2003. In situ treatment of metals in contaminated soils with phytate. J. Environ. Qual. 32:153161.
101. Senko, J. M.,, J. D. Istok,, J. M. Suflita, and, L. R. Krumholz. 2002. In-situ evidence for uranium immobilization and remobilization. Environ. Sci. Technol. 36:14911496.
102. Senko, J. M.,, Y. Mohamed,, T. A. Dewers, and, L. R. Krumholz. 2005. Role for Fe(III) minerals in nitrate-dependent microbial U(IV) oxidation. Environ. Sci. Technol. 39:25292536.
103. Shan, Y.,, I. D. Mckelvie, and, B. T. Hart. 1993. Characterization of immobilized Escherichia coli alkaline-phosphatase reactors in flow-injection analysis. Anal. Chem. 65:30533060.
104. Shelobolina, E. S.,, H. Konishi,, H. Xu, and, E. E. Roden. 2009. U(VI) Sequestration in hydroxyapatite produced by microbial glycerol 3-phosphate metabolism. Appl. Environ. Microbiol. 75:57735778.
105. Shelobolina, E. S.,, K. P. Nevin,, J. D. Blakeney-Hayward,, C. V. Johnsen,, T. W. Plaia,, P. Krader,, T. Woodard,, D. E. Holmes,, C. G. VanPraagh, and, D. R. Lovley. 2007. Geobacter pickeringii sp nov., Geobacter argillaceus sp nov and Pelosinus fermentans gen. nov., sp nov., isolated from subsurface kaolin lenses. Int. J. Syst. Evol. Microbiol. 57:126135.
106. Shelobolina, E. S.,, S. A. Sullivan,, K. R. O’Neill,, K. P. Nevin, and, D. R. Lovley. 2004. Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant bacterium from low-pH, nitrate-and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp nov. Appl. Environ. Microbiol. 70:29592965.
107. Shelobolina, E. S.,, C. G. Vanpraagh, and, D. R. Lovley. 2003. Use of ferric and ferrous iron containing minerals for respiration by Desulfitobacterium frappieri. Geomicrobiol. J. 20:143156.
108. Shelobolina, E. S.,, H. A. Vrionis,, R. H. Findlay, and, D. R. Lovley. 2008. Geobacter uraniireducens sp nov., isolated from subsurface sediment undergoing uranium bioremediation. Int. J. Syst. Evol. Microbiol. 58:10751078.
109. Shoun, H.,, D.-H. Kim,, H. Uchiyama, and, J. Sugiyama. 1992. Denitrification by fungi. FEMS Microbiol. Lett. 94:281.
110. Singer, D. M.,, J. M. Zachara, and, G. E. Brown. 2009. Uranium speciation as a function of depth in contaminated hanford sediments—a micro-XRF, micro-XRD, and micro-and bulk-XAFS study. Environ. Sci. Technol. 43:630636.
111. Sowder, A. G.,, S. B. Clark, and, R. A. Fjeld. 2001. The impact of mineralogy in the U(VI)-Ca-PO4 system on the environmental availability of uranium. J. Radioanal. Nucl. Chem. 248:517524.
112. Spain, A. M.,, A. D. Peacock,, J. D. Istok,, M. S. Elshahed,, F. Z. Najar,, B. A. Roe,, D. C. White, and, L. R. Krumholz. 2007. Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate-and uranium-contaminated aquifer. Appl. Environ. Microbiol. 73:48924904.
113. Suzuki, Y.,, S. D. Kelly,, K. M. Kemner, and, J. F. Banfield. 2004. Enzymatic U(VI) reduction by Desulfosporosinus species. Radiochim. Acta 92:1116.
114. Suzuki, Y.,, and T. Suko. 2006. Geomicrobiological factors that control uranium mobility in the environment: update on recent advances in the bioremediation of uranium-contaminated sites. J. Mineral. Petrol. Sci. 101:299307.
115. Tebo, B. M.,, and A. Y. Obraztsova. 1998. Sulfate-reducing bacterium grows with Cr(VI), U(VI), Mn(IV), and Fe(III) as electron acceptors. FEMS Microbiol. Lett. 162:193198.
116. Thomas, S. H.,, E. Padilla-Crespo,, P. M. Jar-dine,, R. A. Sanford, and, F. E. Loffler. 2009. Diversity and distribution of Anaeromyxobacter strains in a uranium-contaminated subsurface environment with a nonuniform groundwater flow. Appl. Environ. Microbiol. 75:36793687.
117. Truex, M. J.,, B. M. Peyton,, N. B. Valentine, and, Y. A. Gorby. 1997. Kinetics of U(VI) reduction by a dissimilatory Fe(III)-reducing bacterium under non-growth conditions. Biotechnol. Bioeng. 55:490496.
118. Turner, B. L.,, M. J. Paphazy,, P. M. Haygarth, and, I. D. McKelvie. 2002. Inositol phosphates in the environment. Philos. Trans. R. Soc. Lond. Ser. B 357:449469.
119. Ullah, A. H. J.,, and D. M. Gibson. 1987. Extracellular phytase (EC 3.1.3.8) from Aspergillus ficuum Nrrl 3135—purification and characterization. Prep. Biochem. 17:6391.
120. Vrionis, H. A.,, R. T. Anderson,, I. Ortiz-Bernad,, K. R. O’Neill,, C. T. Resch,, A. D. Peacock,, R. Dayvault,, D. C. White,, P. E. Long, and, D. R. Lovley. 2005. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71:63086318.
121. Wall, J. D.,, and L. R. Krumholz. 2006. Uranium reduction. Annu. Rev. Microbiol. 60:149166.
122. Wan, J. M.,, T. K. Tokunaga,, E. Brodie,, Z. M. Wang,, Z. P. Zheng,, D. Herman,, T. C. Hazen,, M. K. Firestone, and, S. R. Sutton. 2005. Reoxidation of bioreduced uranium under reducing conditions. Environ. Sci. Technol. 39:61626169.
123. Wang, Z. M.,, J. M. Zachara,, P. L. Gassman,, C. X. Liu,, O. Qafoku,, W. Yantasee, and, J. G. Catalan. 2005. Fluorescence spectroscopy of U(VI)-silicates and U(VI)-contaminated Hanford sediment. Geochim. Cosmochim. Acta 69:13911403.
124. Wellman, D. M.,, K. M. Gunderson,, J. P. Icenhower,, S. W. Forrester, and, S. W. Forrester. 2007. Dissolution kinetics of synthetic and natural meta-autunite minerals, X-3-n((n)+) [(UO2)(PO4)](2) • xH(2)O, under acidic conditions. Geochem. Geophys. Geosyst. doi:10.1029/2007GC001695.
125. Wellman, D. M.,, E. M. Pierce,, D. H. Bacon,, M. Oostrom,, K. M. Gunderson,, S. M. Webb,, C. C. Bovaird,, E. A. Cordova,, E. T. Clayton,, K. E. Parker,, R. M. Ermi,, S. R. Baum,, V. R. Vermeul, and, J. S. Fruchter. 2008a. 300 Area treatability test: laboratory development of polyphosphate remediation technology for in situ treatment of uranium contamination in the vadose zone and capillary fringe, vol. PNNL-17818, Contract DE-AC05-76RL01830. U.S. Department of Energy, Pacific Northwest National Laboratory, Richland, WA.
126. Wellman, D. M.,, E. M. Pierce,, V. R. Vermeul,, S. V. Mattigod,, E. L. Richards,, M. D. Williams,, J. S. Fruchter, and, J. P. Icenhower. 2008b. In situ uranium stabilization through polyphosphate remediation: development and demonstration at the Hanford Site 300 Area, Washington State, p. 25–104. In T. V. Golush (ed.), Waste Management Research Trends. Nova Science Publishers, Inc., New York, NY.
127. Wilkins, M. J.,, F. R. Livens,, D. J. Vaughan, and, J. R. Lloyd. 2006. The impact of Fe(III)-reducing bacteria on uranium mobility. Biogeochemistry 78:125150.
128. Wu, Q.,, R. A. Sanford, and, F. E. Loffler. 2006a. Uranium(VI) reduction by Anaeromyxobacter dehalogenans strain 2CP-C. Appl. Environ. Microbiol. 72:36083614.
129. Wu, W. M.,, J. Carley,, M. Fienen,, T. Mehlhorn,, K. Lowe,, J. Nyman,, J. Luo,, M. E. Gentile,, R. Rajan,, D. Wagner,, R. F. Hickey,, B. H. Gu,, D. Watson,, O. A. Cirpka,, P. K. Kitanidis,, P. M. Jardine, and, C. S. Criddle. 2006b. Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 1. Conditioning of a treatment zone. Environ. Sci. Technol. 40:39783985.
130. Wu, W. M.,, J. Carley,, T. Gentry,, M. A. Ginder-Vogel,, M. Fienen,, T. Mehlhorn,, H. Yan,, S. Caroll,, M. N. Pace,, J. Nyman,, J. Luo,, M. E. Gentile,, M. W. Fields,, R. F. Hickey,, B. H. Gu,, D. Watson,, O. A. Cirpka,, J. Z. Zhou,, S. Fendorf,, P. K. Kitanidis,, P. M. Jardine, and, C. S. Criddle. 2006c Pilot-scale in situ bioremediation of uranium in a highly contaminated aquifer. 2. Reduction of U(VI) and geochemical control of U(VI) bioavailability. Environ. Sci. Technol. 40:39863995.
131. Wu, W. M.,, J. Carley,, J. Luo,, M. A. Ginder-Vogel,, E. Cardenas,, M. B. Leigh,, C. C. Hwang,, S. D. Kelly,, C. M. Ruan,, L. Y. Wu,, J. Van Nostrand,, T. Gentry,, K. Lowe,, T. Mehlhorn,, S. Carroll,, W. S. Luo,, M. W. Fields,, B. H. Gu,, D. Watson,, K. M. Kemner,, T. Marsh,, J. Tiedje,, J. Z. Zhou,, S. Fendorf,, P. K. Kitanidis,, P. M. Jardine, and, C. S. Criddle. 2007. In situ bioreduction of uranium (VI) to submicromolar levels and reoxidation by dissolved oxygen. Environ. Sci. Technol. 41:57165723.
132. Yan, T. F.,, M. W. Fields,, L. Y. Wu,, Y. G. Zu,, J. M. Tiedje, and, J. Z. Zhou. 2003. Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate-and uranium-contaminated groundwater. Environ. Microbiol. 5:1324.
133. Zengler, K. 2008. Accessing Uncultivated Microorganisms: from the Environment to Organisms and Genomes and Back. ASM Press, Washington, DC.
134. Zengler, K.,, G. Toledo,, M. Rappe,, J. Elkins,, E. J. Mathur,, J. M. Short, and, M. Keller. 2002. Cultivating the uncultured. Proc. Natl. Acad. Sci. USA 99:1568115686.

Tables

Generic image for table
TABLE 1

Taxonomic profiling of small-subunit rRNA gene sequences recovered from cultivation-independent analyses of uranium-contaminated environments

Citation: Kostka J, Green S. 2011. Microorganisms and Processes Linked to Uranium Reduction and Immobilization, p 117-138. In Stolz J, Oremland R (ed), Microbial Metal and Metalloid Metabolism. ASM Press, Washington, DC. doi: 10.1128/9781555817190.ch7

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error