Microbial Communities Associated with the Oxidation of Iron and Technetium in Bioreduced Sediments

REFERENCES

• Audic , S , Robert , C , Campagna , B , Parinello , H , Claverie , J-M , Raoult , D and Drancourt , M . 2007 . Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria . PLoS Genetics , 3 : 1454 – 1463 .
   Google Scholar
• Begg , J DC , Burke , I T , Charnock , J M and Morris , K . 2008 . Technetium reduction and reoxidation behaviour in Dounreay soils . RadiochimActa , 96 : 631 – 636 .
   Google Scholar
• Binsted , N. 1998 . CCLRC Daresbury Laboratory EXCURV98 Program , Warrington, , UK : CCLRC Daresbury Laboratory .
   Google Scholar
• Binsted , N , Strange , R W and Hasnain , S S . 1992 . Constrained and restrained refinement in EXAFS data analysis with curved wave theory . Biochemistry , 31 : 12117 – 12125 .
   PubMed Web of Science ®Google Scholar
• Blöthe , M and Roden , E E . 2009 . Composition and activity of an autotrophic Fe(II)-oxidizing nitrate-reducing enrichment culture . Appl Environ Microbiol , 75 : 6937 – 6940 .
   PubMed Web of Science ®Google Scholar
• Bondietti , E A and Francis , C W . 1979 . Geologic migration potentials of technetium-99 and neptunium-237 . Science , 203 : 1337 – 1340 .
   PubMed Web of Science ®Google Scholar
• Burke , I T , Boothman , C , Lloyd , J R , Livens , F R , Charnock , J M , McBeth , J M , Mortimer , R JG and Morris , K . 2006 . Reoxidation behavior of technetium, iron, and sulfur in estuarine sediments . Environ Sci Technol , 40 : 3529 – 3535 .
   PubMed Web of Science ®Google Scholar
• Burke , I T , Boothman , C , Lloyd , J R , Mortimer , R JG , Livens , F R and Morris , K . 2005 . Effects of progressive anoxia on the solubility of technetium in sediments . Environ Sci Technol , 39 : 4109 – 4116 .
   PubMed Web of Science ®Google Scholar
• Edwards , U , Rogall , T , Blocker , H , Emde , M and Bottger , E C . 1989 . Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA . Nucl Acids Res , 17 : 7843 – 7853 .
   PubMed Web of Science ®Google Scholar
• Finneran , K T , Housewright , M E and Lovley , D R . 2002 . Multiple influences of nitrate on uranium solubility during bioremediation of uranium-contaminated subsurface sediments . Environ Microbiol , 4 : 510 – 516 .
   PubMed Web of Science ®Google Scholar
• Fredrickson , J K , Zachara , JM , Kennedy , D W , Kukkadapu , R K , McKinley , J P , Heald , S M , Liu , C and Plymale , A E . 2004 . Reduction of TcO− 4 by sediment associated biogenic Fe(II) . Geochim Cosmochim Acta , 68 : 3171 – 3187 .
   Web of Science ®Google Scholar
• Fredrickson , J K , Zachara , J M , Plymale , A E , Heald , S M , McKinley , J P , Kennedy , D W , Liu , C and Nachimuthu , P . 2009 . Oxidative dissolution potential of biogenic and abiogenic TcO2 in subsurface sediments . Geochim Cosmochim Acta , 73 : 2299 – 2313 .
   Google Scholar
• Geissler , A. 2007 . “ Prokaryotic microorganisms in uranium mining waste piles and their interactions with uranium and other heavy metals ” . PhD thesis, TU Bergakademie Freiberg, Freiberg, Germany
   Google Scholar
• Goregues , C M , Michotey , V D and Bonin , P C . 2005 . Molecular, biochemical, and physiological approaches for understanding the ecology of denitrification . Microb Ecol , 49 : 198 – 208 .
   PubMed Web of Science ®Google Scholar
• Gurman , S J , Binsted , N and Ross , I . 1984 . A rapid, exact curved-wave theory for EXAFS calculations . J Phys C: Solid St Phys , 17 : 143 – 151 .
   Web of Science ®Google Scholar
• Hafenbradl , D , Keller , M , Dirmeier , R , Rachel , R , Rossnagel , P , Burggraf , S , Huber , H and Stetter , K O . 1996 . Ferroglobus placidus gen. nov., sp. nov., a novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions . Arch Microbiol , 166 : 308 – 314 .
   PubMed Web of Science ®Google Scholar
• Harris , S J and Mortimer , R JG . 2002 . Determination of nitrate in small water samples (100 μL) by the cadmium-copper reduction method: A manual technique with application to the interstitial waters of marine sediments . Int J Environ Anal Chem , 82 : 369 – 376 .
   Web of Science ®Google Scholar
• Istok , J D , Senko , J M , Krumholz , L R , Watson , D , Bogle , M A , Peacock , A , Chang , Y J and White , D C . 2004 . In situ bioreduction of technetium and uranium in a nitrate-contaminated aquifer . Environ Sci Technol , 38 : 468 – 475 .
   PubMed Web of Science ®Google Scholar
• Johnson , D B , McGinness , S and Ghauri , M A . 1993 . Biogeochemical cycling of iron and sulfur in leaching environments . FEMS Microbiol Rev , 11 : 63 – 70 .
   Web of Science ®Google Scholar
• Kincaid , C T , Bergeron , M P , Cole , C R , Freshley , M D , Johnson , V G , Kaplan , D I , Serne , R J , Streile , G P , Strenge , D L , Thorne , P D , Vail , L W , Whyatt , G A and Wurstner , S K . 2000 . “ Composite analysis for low-level waste disposal in the 200 area plateau of the Hanford site, southeast Washington ” . In Environmental Toxicology and Risk Assessment: Recent Achievements in Environmental Fate and Transport , Edited by: Price , F T , Brix , K V and Lane , N K . 104 – 117 . West Conshohocken: ASTM .
   Google Scholar
• Lack , J G , Chaudhuri , S K , Chakraborty , R , Achenbach , L A and Coates , J D . 2002 . Anaerobic biooxidation of Fe(II) by Dechlorosoma suillum . Microb Ecol , 43 : 424 – 431 .
   PubMed Web of Science ®Google Scholar
• Lane , DJ. 1991 . “ 16S/23S rRNA sequencing ” . In Nucleic acid techniques in bacterial systematics , Edited by: Stackebrandt , E and Goodfellow , M . 115 – 175 . New York : Wiley .
   Google Scholar
• Law , G TW , Geissler , A , Boothman , C , Burke , I T , Livens , F R , Lloyd , J R and Morris , K . 2010 . Role of nitrate in conditioning aquifer sediments for technetium bioreduction . Environ Sci Technol , 44 : 150 – 155 .
   PubMed Web of Science ®Google Scholar
• Li , X and Krumholz , L . 2008 . Influence of nitrate on microbial reduction of pertechnetate . Environ Sci Technol , 42 : 1910 – 1915 .
   PubMed Web of Science ®Google Scholar
• Lloyd , J R and Renshaw , J C . 2005 . Bioremediation of radioactive waste: Radionuclide-microbe interactions in laboratory and field-scale studies . Curr Opin Biotechnol , 16 : 254 – 260 .
   PubMed Web of Science ®Google Scholar
• Lloyd , J R , Sole , V A , Van Praagh , C VG and Lovley , D R . 2000 . Direct and Fe(II)-mediated reduction of technetium by Fe(III)-reducing bacteria . Appl Environ Microbiol , 66 : 3743 – 3749 .
   PubMed Web of Science ®Google Scholar
• Lovley , D R and Phillips , E JP . 1987 . Rapid assay for microbially reducible ferric iron in aquatic sediments . Appl Environ Microbiol , 53 : 1536 – 1540 .
   PubMed Web of Science ®Google Scholar
• Lukens , W W Jr. , Bucher , J J , Edelstein , N M and Shuh , D K . 2000 . Products of pertechnetate radiolysis in highly alkaline solution: Structure of TcO2-xH2O . Environ Sci Technol , 36 : 1124 – 1129 .
   Google Scholar
• Maes , A , Geraedts , K , Bruggeman , C , Vancluysen , J , Rossberg , A and Hennig , C . 2004 . Evidence for the interaction of technetium colloids with humic substances by X-ray absorption spectroscopy . Environ Sci Technol , 38 : 2044 – 2051 .
   PubMed Web of Science ®Google Scholar
• Maidak , B L , Cole , J R , Lilburn , T G , Parker , C T , Saxman , P R , Stredwick , J M , Garrity , G M , Li , B , Olsen , G J , Pramanik , S , Schmidt , T M and Tiedje , J M . 2000 . The RDP (Ribosomal Database Project) continues . Nucl Acids Res , 28 : 173 – 174 .
   PubMed Web of Science ®Google Scholar
• McBeth , J M , Lear , G , Lloyd , J R , Livens , F R , Morris , K and Burke , I T . 2007 . Technetium reduction and reoxidation in aquifer sediments . Geomicrobiol J , 24 : 189 – 197 .
   Web of Science ®Google Scholar
• Morris , K , Livens , F R , Charnock , J M , Burke , I T , McBeth , J M , Begg , J DC , Boothman , C and Lloyd , J R . 2008 . An X-ray absorption study of the fate of technetium in reduced and reoxidized sediments and mineral phases . Appl Geochem , 23 : 603 – 617 .
   Web of Science ®Google Scholar
• Osorio , H , Martínez , V , Nieto , P A , Holmes , D S and Quatrini , R . 2008 . Microbial iron management mechanisms in extremely acidic environments: comparative genomics evidence for diversity and versatility . BMC Microbiol , 8 : 203
   PubMedGoogle Scholar
• Probian , C , Wulfing , A and Harder , J . 2003 . Anaerobic mineralization of quaternary carbon atoms: Isolation of denitrifying bacteria on pivalic acid (2,2-dimethylpropionic acid) . Appl Environ Microbiol , 69 : 1866 – 1870 .
   PubMed Web of Science ®Google Scholar
• Ranjard , L , Poly , F , Combrisson , J , Richaume , A , Gourbiere , F , Thioulouse , J and Nazaret , S . 2000 . Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA) . Microb Ecol , 39 : 263 – 272 .
   PubMed Web of Science ®Google Scholar
• Senko , J M , Mohamed , Y , Dewers , T A and Krumholz , L . 2005 . Role for Fe(III) minerals in nitrate-dependent microbial U(IV) oxidation . Environ Sci Technol , 39 : 2529 – 2536 .
   PubMed Web of Science ®Google Scholar
• Singleton , M J , Woods , K N , Conrad , M E , DePaolo , D J and Dresel , P E . 2005 . Tracking sources of unsaturated zone and groundwater nitrate contamination using nitrogenand oxygen stable isotopes at the Hanford Site, WA . Environ Sci Technol , 39 : 3563 – 3570 .
   PubMed Web of Science ®Google Scholar
• Straub , K L , Benz , M , Schink , B and Widdel , F . 1996 . Anaerobic, nitrate-dependent microbial oxidation of ferrous iron . Appl Environ Microbiol , 62 : 1458 – 1460 .
   PubMed Web of Science ®Google Scholar
• Straub , K L and Buchholz-Cleven , B EE . 1998 . Enumeration and detection of anaerobic ferrous iron-oxidizing, nitrate-reducing bacteria from diverse european sediments . Appl Environ Microbiol , 64 : 4846 – 4856 .
   PubMed Web of Science ®Google Scholar
• Straub , K L , Schönhuber , W A , Buchholz-Cleven , B EE and Schink , B . 2004 . Diversity of ferrous iron-oxidizing, nitrate-reducing bacteria and their involvment in oxygen-independent iron cycling . Geomicrobiol J , 21 : 371 – 378 .
   Web of Science ®Google Scholar
• Tamura , K , Dudley , J , Nei , M and Kumar , S . 2007 . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0 . Mol Biol Evol , 24 : 1596 – 1599 .
   PubMed Web of Science ®Google Scholar
• Viollier , E , Inglett , P W , Hunter , K , Roychoudhury , P and van Cappellen , P . 2000 . The ferrozine method revisited: Fe(II)/Fe(III) determination in natural waters . Appl Geochem , 15 : 785 – 790 .
   Web of Science ®Google Scholar
• Weber , K A , Hedrick , D B , Peacock , A D , Thrash , J C , White , D C , Achenbach , L A and Coates , J D . 2009 . Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002 . Appl Micbiol Biotechnol , 83 : 555 – 565 .
   PubMed Web of Science ®Google Scholar
• Weber , K A , Picardal , F W and Roden , E E . 2001 . Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds . Environ Sci Technol , 35 : 1644 – 1650 .
   PubMed Web of Science ®Google Scholar
• Weber , K A , Pollock , J , Cole , K A , O’Connor , S M , Achenbach , L A and Coates , J D . 2006a . Anaerobic nitrate-dependent iron(II) bio-oxidation by a novel lithoautotrophic betaproteobacterium, strain 2002 . Appl Environ Microbiol , 72 : 686 – 694 .
   PubMed Web of Science ®Google Scholar
• Weber , K A , Urrutia , M M , Churchill , P F , Kukkkadapu , R K and Roden , E E . 2006b . Anaerobic redox cycling of iron by freshwater sediment microorganisms . Environ Microbiol , 8 : 100 – 113 .
   PubMed Web of Science ®Google Scholar
• Wharton , M J , Atkins , B , Charnock , J M , Livens , F R , Pattrick , R AD and Collison , D . 2000 . An X-ray absorption spectroscopy study of the coprecipitation of Tc and Re with mackinawite (FeS) . Appl Geochem , 15 : 347 – 354 .
   Web of Science ®Google Scholar
• Wildung , R E , Gorby , Y A , Krupka , K M , Hess , N J , Li , S W , Plymale , A E , McKinley , J E and Fredrickson , J K . 2000 . Effect of electron donor and solution chemistry on products of dissimilatory reduction of technetium by Shewanella putrefaciens . Appl Environ Microbiol , 66 : 2451 – 2460 .
   PubMed Web of Science ®Google Scholar
• Wildung , R E , Li , S W , Murray , C J , Krupka , K M , Xie , Y , Hess , N J and Roden , E E . 2004 . Technetium reduction in sediments of a shallow aquifer exhibiting dissimilatory iron reduction potential . FEMS Microbiol Ecol , 49 : 151 – 162 .
   PubMed Web of Science ®Google Scholar
• Zachara , J M , Heald , S M , Jeon , B-H , Kukkadapu , R K , Liu , C , McKinley , J P , Dohnalkova , A C and Moore , D A . 2007 . Reduction of pertechnetate [Tc(VII)] by aqueous Fe(II) and the nature of the solid phase redox products . Geochim Cosmochim Acta , 71 : 2137 – 2157 .
   Web of Science ®Google Scholar
• Zhang , Z , Schwartz , S , Wagner , L and Miller , W . 2000 . A greedy algorithm for aligning DNA sequences . J Comput Biol , 7 : 203 – 214 .
   PubMed Web of Science ®Google Scholar