The Microbial Community of a Black Shale Pyrite Biofilm and its Implications for Pyrite Weathering

REFERENCES

• Baker , B J and Banfield , J F . 2003 . Microbial communities in acid mine drainage . FEMS Microbiol Ecol , 44 : 139 – 152 .
   PubMed Web of Science ®Google Scholar
• Bond , P L and Banfield , J F . 2001 . Design and performance of rRNA targeted oligonucleotide probes for in situ detection and phylogenetic identification of microorganisms inhabiting acid mine drainage environments . Microbial Ecol , 41 : 149 – 161 .
   PubMed Web of Science ®Google Scholar
• Bond , P L , Smriga , S P and Banfield , J F . 2000 . Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site . Appl Environ Microbiol , 66 : 3842 – 3849 .
   PubMed Web of Science ®Google Scholar
• Boon , M. 2001 . The mechanism of “direct” and “indirect” bacterial oxidation of sulphide minerals . Hydrometallurgy , 62 : 67 – 70 .
   Google Scholar
• Bruneel , O , Duran , R , Casiot , C , Elbaz-Poulichet , F and Personné , J C . 2006 . Diversity of microorganisms in Fe-As-rich acid mine drainage waters of Carnoulès, France . Appl Environ Microbiol , 72 : 551 – 556 .
   PubMed Web of Science ®Google Scholar
• Chaudhuri , S K , Lack , J G and Coates , J D . 2001 . Biogenic magnetite formation through anaerobic biooxidation of Fe(II) . Appl Environ Microbiol , 67 : 2844 – 2848 .
   PubMed Web of Science ®Google Scholar
• Coates , J D , Ellis , D , Gaw , C and Lovley , D . 1999 . Geothrix fermentans gen. nov., sp. nov., a novel Fe(III)-reducing bacterium from a hydrocarbon-contaminated aquifer . Int J Syst Bacteriol , 49 : 1615 – 1622 .
   PubMedGoogle Scholar
• Cummings , D E , Caccavo , F Jr , Spring , S and Rosenzweig , R F . 1999 . Ferribacteriumlimneticum, gen. nov., sp. nov., an Fe(III)-reducing microorganism isolated from mining-impacted freshwater lake sediments . Arch Microbiol , 171 : 183 – 188 .
   Web of Science ®Google Scholar
• Devereux , R , Delaney , M , Widdel , F and Stahl , D A . 1989 . Natural relationships among sulfate-reducing eubacteria . J Bacteriol , 171 : 6689 – 6695 .
   PubMed Web of Science ®Google Scholar
• Edwards , KJ. 2004 . “ Formation and degradation of seafloor hydrothermal sulfide deposits ” . In Sulfur Biogeochemistry: Past and Present , Edited by: Amend , J P , Edwards , K J and Lyons , T W . 83 – 96 . Boulder, , Colorado : Geological Society of America .
   Google Scholar
• Edwards , K J , Bond , P L , Druschel , G K , McGuire , M M , Hamers , R J and Banfield , J F . 2000a . Geochemical and biological aspects of sulfide mineral dissolution: lessons from Iron Mountain, California . Chem Geol , 169 : 383 – 397 .
   Web of Science ®Google Scholar
• Edwards , K J , Bond , P L and Banfield , J F . 2000b . Characteristics of attachment and growth of Thiobacilluscaldus on sulphide minerals: a chemotactic response to sulphur minerals? . Environ Microbiol , 2 : 324 – 332 .
   PubMed Web of Science ®Google Scholar
• Edwards , K J , Goebel , B M , Rodgers , T M , Schrenk , M O , Gihring , T M , Cardona , M M , Hu , B , McGuire , M M , Hamers , R J and Pace , N R . 1999 . Geomicrobiology of pyrite (FeS2) dissolution: case study at iron mountain, California . Geomicrobiol J , 16 : 155 – 179 .
   Web of Science ®Google Scholar
• Edwards , K J , McCollom , T M , Konishi , H and Buseck , P R . 2003a . Seafloor bioalteration of sulfide minerals: results from in situ incubation studies . Geochim Cosmochim Acta , 67 : 2843 – 2856 .
   Web of Science ®Google Scholar
• Edwards , K J , Rogers , D R , Wirsen , C O and McCollom , T M . 2003b . Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrophic alpha- and gamma-Proteobacteria from the deep sea . Appl Environ Microbiol , 69 : 2906 – 2913 .
   PubMed Web of Science ®Google Scholar
• Ehrlich , HL. 2002 . “ Geomicrobiology of Iron ” . In Geomicrobiology , 4thed , Edited by: Ehrlich , H L . 345 – 408 . New York : Marcel Dekker, Inc. .
   Google Scholar
• Emerson , D and Moyer , CL . 1997 . Isolation and characterization of novel iron-oxidizing bacteria that grow at circumneutral pH . Appl Environ Microbiol , 63 : 4784 – 4792 .
   PubMed Web of Science ®Google Scholar
• Engel , A S , Porter , M L , Stern , L A , Quinlan , S and Bennett , P C . 2004 . Bacterial diversity and ecosystem function of filamentous microbial mats from a photic cave sulfidic springs dominated by chemolithoautotrophic “Epsilonproteobacteria” . FEMS Microbiol Ecol , 51 : 31 – 53 .
   PubMed Web of Science ®Google Scholar
• Ghiorse , WC. 1984 . Biology of iron-and manganese-depositing bacteria . Ann Rev Microbiol , 38 : 515 – 550 .
   PubMed Web of Science ®Google Scholar
• Hallberg , K B , Coupland , K , Kimura , S and Johnson , D B . 2006 . Macroscopic streamer growths in acidic, metal-rich mine waters in north wales consist of novel and remarkably simple bacterial communities . Appl Environ Microbiol , 72 : 2022 – 2030 .
   PubMed Web of Science ®Google Scholar
• Hao , C , Zhang , H , Haas , R , Bai , Z and Zhang , B . 2007 . A Novel Community of Acidophiles in an acid mine drainage sediment . World J Microb Biot , 23 : 15 – 21 .
   Google Scholar
• Harneit , K , Goksel , A , Kock , D , Klock , J H , Gehrke , T and Sand , W . 2006 . Adhesion to metal sulfide surfaces by cells of Acidithiobacillus ferrooxidans, Acidithiobacillus thiooxidans and Leptospirillum ferrooxidans . Hydrometallurgy , 83 : 245 – 254 .
   Web of Science ®Google Scholar
• Holmes , D E , Finneran , K T , O’Neil , R A and Lovley , D R . 2002 . Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments . Appl Environ Microbiol , 68 : 2300 – 2306 .
   PubMed Web of Science ®Google Scholar
• Jorgensen , B B and Nelson , D C . 2004 . “ Sulfide oxidation in marine sediments: Geochemistry meets microbiology ” . In Sulfur Biogeochemistry – Past and Present , Edited by: Amend , J P , Edwards , K J and Lyons , T W . 63 – 81 . Boulder, , Colorado : Geological Society of America .
   Google Scholar
• Kaçmaz , H and Nakoman , M E . 2009 . Hydrochemical characteristics of shallow groundwater in aquifer containing uranyl phosphate minerals, in the Köprübaşı Manisa area, Turkey . Environ Earth Sci , 59 : 449 – 457 .
   Google Scholar
• Kelly , W R , Holm , T R , Wilson , S D and Roadcap , G S . 2005 . Arsenic in glacial aquifers: Sources and geochemical controls . Ground Water , 43 : 500 – 510 .
   PubMedGoogle Scholar
• Kock , D and Schippers , A . 2008 . Quantitative microbial community analysis of three different sulfidic mine tailing dumps generating acid mine drainage . Appl Environ Microbiol , 74 : 5211 – 5219 .
   PubMed Web of Science ®Google Scholar
• Kodama , Y and Watanabe , K . 2003 . Isolation and characterization of a sulfur-oxidizing chemolithotroph growing on crude oil under anaerobic conditions . Appl Environ Microbiol , 69 : 107 – 112 .
   PubMed Web of Science ®Google Scholar
• Konhauser , K. 2006 . “ Microbial weathering ” . In Introduction to Geomicrobiology , Edited by: Konhauser , K . 192 – 234 . Oxford, UK : Wiley-Blackwell .
   Google Scholar
• Lacey , D T and Lawson , F . 1970 . “ Kinetics of the liquid phase oxidation of acid ferrous sulphate by the bacterium Thiobacillus ferrooxidans ” . Vol. 12 , 29 – 50 . Biotechnol Bioeng .
   Google Scholar
• Lack , J G , Chaudhuri , S K , Chakraborty , R , Achenbach , L A and Coates , J D . 2002 . Anaerobic biooxidation of Fe(II) by Dechlorosomasuillum . Microbial Ecol , 43 : 424 – 431 .
   PubMed Web of Science ®Google Scholar
• Lovley , DR. 1995 . Microbial reduction of iron, manganese, and other metals . Adv Agron , 54 : 175 – 231 .
   Web of Science ®Google Scholar
• Lovley , DR. 1997 . Microbial Fe(III) reduction in subsurface environments . FEMS Microbiol Rev , 20 : 305 – 313 .
   Web of Science ®Google Scholar
• Lovley , DR. 2001 . “ Reduction of iron and humics in subsurface environments ” . In Subsurface Microbiology and Biogeochemistry , Edited by: Fredrickson , J K and Fletcher , M . 193 – 217 . New York, NY : Wiley-Liss .
   Google Scholar
• Malik , A , Dastidar , M G and Roychoudhury , P K . 2001 . Biodesulphurization of coal: Mechanism and rate limiting factors . J Environ Sci Health A , 36 : 1113 – 1128 .
   Web of Science ®Google Scholar
• Malki , M , Gonzez-Toril , E , Sanz , J L , Gez , F , Rodruez , N and Amils , R . 2006 . Importance of the iron cycle in biohydrometallurgy . Hydrometallurgy , 83 : 223 – 228 .
   Web of Science ®Google Scholar
• McCollom , TM. 2000 . Geochemical constraints on primary productivity in submarine hydrothermal vent plumes . Deep-Sea Res Part I , 47 : 85 – 101 .
   Google Scholar
• Meyer , G , Waschkies , C and Huttl , R F . 1999 . Investigations on pyrite oxidation in mine spoils of the Lusatian lignite mining district . Plant Soil , 213 : 137 – 147 .
   Google Scholar
• Mikkelsen , D , Kappler , U , Webb , R I , Rasch , R , McEwan , A G and Sly , L I . 2007 . Visualization of pyrite leaching by selected thermophilicarchaea: Nature of microorganism-ore interactions during bioleaching . Hydrometallurgy , 88 : 143 – 153 .
   Google Scholar
• Petsch , S T , Edwards , K J and Eglinton , T I . 2005 . Microbial transformation of organic matter in black shales and implications for global biogeochemical cycles . Palaeogeogr Palaeocl , 219 : 157 – 170 .
   Web of Science ®Google Scholar
• Rhine , E D , Onesios , K M , Serfes , M E , Reinfelder , J R and Young , L Y . 2008 . Arsenictransformation and mobilization from minerals by the arsenite oxidizing strain WAO . Environ Sci Technol , 42 : 1423 – 1429 .
   PubMedGoogle Scholar
• Rodriguez , Y , Ballester , A , Blázquez , M L , González , F and Muñoz , J A . 2003a . New information on the pyrite bioleaching mechanism at low and high temperature . Hydrometallurgy , 71 : 37 – 46 .
   Web of Science ®Google Scholar
• Rodriguez , Y , Ballester , A , Blázquez , M L , González , F and Muñoz , J A . 2003b . Study of bacterial attachment during the bioleaching of pyrite, chalcopyrite, and sphalerite . Geomicrobiol J , 20 : 131 – 141 .
   Web of Science ®Google Scholar
• Sand , W and Gehrke , T . 2006 . Extracellular polymeric substances mediate bioleaching/biocorrosion via interfacial processes involving iron (III) ions and acidophilic bacteria . Res Microbiol , 157 : 49 – 56 .
   PubMed Web of Science ®Google Scholar
• Sand , W , Gerke , T , Hallmann , R and Schippers , A . 1995 . Sulfur chemistry, biofilm, and the (in)direct attack mechanism—a critical evaluation of bacterial leaching . Appl Microbiol Biot , 43 : 961 – 966 .
   Web of Science ®Google Scholar
• Schecher , W D and McAvoy , D C . 1992 . MINEQL+: a software environment for chemical equilibrium modeling . Comp Environ Urban Syst , 16 : 65 – 76 .
   Web of Science ®Google Scholar
• Schippers , A , Rohwerder , T and Sand , W . 1999 . Intermediary sulfur compounds in pyrite oxidation: implications for bioleaching and biodepyritization of coal . Appl Microbiol Biot , 52 : 104 – 110 .
   Web of Science ®Google Scholar
• Schippers , A and Sand , W . 1999 . Bacterial leaching of metal sulfides proceeds by two indirect mechanisms via thiosulfate or via polysulfides and sulfur . Appl Environ Microbiol , 65 : 319 – 321 .
   PubMed Web of Science ®Google Scholar
• Smedley , P L and Kinniburgh , D G . 2002 . A review of the source, behavior and distribution of arsenic in natural waters . Appl Geochem , 17 : 517 – 568 .
   Web of Science ®Google Scholar
• Toner , B M , Santelli , C M , Marcus , M A , Wirth , R , Chan , C S , McCollom , T , Bach , W and Edwards , K J . 2009 . Biogenic iron oxyhydroxide formation at mid-ocean ridge hydrothermal vents: Juan de Fuca Ridge . Geochim Cosmochim Acta , 73 : 388 – 403 .
   Web of Science ®Google Scholar
• Tributsch , H. 2001 . Direct versus indirect bioleaching . Hydrometallurgy , 59 : 177 – 185 .
   Web of Science ®Google Scholar
• Weber , K A , Achenbach , L A and Coates , J D . 2006a . Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction . Nat Rev Micro , 4 : 752 – 764 .
   PubMed Web of Science ®Google Scholar
• Weber , K A , Urrutia , M M , Churchill , P F , Kukkadapu , 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
• Yang , Y , Shi , W , Wan , M Z , Zou , L , Huang , J , Qiu , G and Liu , X . 2008 . Diversity of bacterial communities in acid mine drainage from the Shen-bu copper mine, Gansu province, China . Electron J Biot , 11 : 1
   Google Scholar
• Zhang , H , Bruns , M A and Logan , B E . 2002 . Perchlorate reduction by a novel chemolithoautotrophic, hydrogen-oxidizing bacterium . Environ Microbiol , 4 : 570 – 576 .
   PubMed Web of Science ®Google Scholar
• Zhu , W , Young , L Y , Yee , N , Serfes , M , Rhine , E D and Reinfelder , J R . 2008 . Sulfide-driven arsenic mobilization from arsenopyrite and black shale pyrite . Geochim Cosmochim Acta , 72 : 5243 – 5250 .
   Web of Science ®Google Scholar